Index (Anchor - merged Javadoc across key repositories. This documentation is a work-in-progress. 1.0.0-SNAPSHOT API)

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

A

absolute() - Method in class org.anchoranalysis.spatial.point.Tuple3d: Convert each dimension's component into its absolute value.
AbsoluteValue<T> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic: A feature that calculates the absolute value of another feature's result.
AbsoluteValue() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.AbsoluteValue
accept(int) - Method in interface org.anchoranalysis.core.functional.checked.CheckedIntConsumer: Like IntConsumer.accept(int) but throws an exception.
accept(int, int) - Method in interface org.anchoranalysis.math.histogram.Histogram.BinConsumer: Accepts a particular bin and corresponding count.
accept(int, int) - Method in interface org.anchoranalysis.spatial.point.consumer.ScalarTwoDimensionalConsumer: Accepts a point like with a Consumer in general.
accept(int, int, int) - Method in interface org.anchoranalysis.spatial.point.consumer.OffsettedScalarTwoDimensionalConsumer: Accepts a point
accept(int, int, int) - Method in interface org.anchoranalysis.spatial.point.consumer.ScalarThreeDimensionalConsumer: Accepts a point like with a Consumer in general.
accept(BinaryVoxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.image.voxel.object.morphological.predicate.AcceptIterationList
accept(BinaryVoxels<UnsignedByteBuffer>) - Method in interface org.anchoranalysis.image.voxel.object.morphological.predicate.AcceptIterationPredicate: Whether a particular voxels fulfills the condition or not.
accept(ObjectMask) - Method in class org.anchoranalysis.plugin.image.object.merge.condition.AndCondition
accept(ObjectMask) - Method in class org.anchoranalysis.plugin.image.object.merge.condition.NeighborhoodCondition
accept(ObjectMask) - Method in interface org.anchoranalysis.plugin.image.object.merge.condition.UpdatableBeforeCondition: Checks if the destination object should be merged with the previously set source object.
accept(ObjectMask) - Method in class org.anchoranalysis.plugin.image.object.merge.condition.WrapAsUpdatable
accept(ObjectMask, ObjectMask, Optional<UnitConverter>) - Method in interface org.anchoranalysis.plugin.image.object.merge.condition.BeforeCondition: Checks if the source and destination objects satisfy the condition for merging.
accept(ObjectMask, ObjectMask, Optional<UnitConverter>) - Method in class org.anchoranalysis.plugin.image.object.merge.condition.DistanceCondition
accept(ObjectMask, ObjectMask, ObjectMask) - Method in interface org.anchoranalysis.plugin.image.object.merge.condition.AfterCondition: Checks if the merged object satisfies the condition.
accept(ObjectMask, ObjectMask, ObjectMask) - Method in class org.anchoranalysis.plugin.image.object.merge.condition.IncreaseFeatureCondition
accept(ParsedFilePathBag) - Method in class org.anchoranalysis.plugin.io.bean.file.group.check.AtLeastZSlices
accept(ParsedFilePathBag) - Method in class org.anchoranalysis.plugin.io.bean.file.group.check.CheckParsedFilePathBag
accept(Point2i) - Method in interface org.anchoranalysis.spatial.point.consumer.PointTwoDimensionalConsumer: Accepts a point like with a Consumer in general.
accept(Point2i, int) - Method in interface org.anchoranalysis.spatial.point.consumer.OffsettedPointTwoDimensionalConsumer: Accepts a point like with a Consumer in general.
accept(S) - Method in interface org.anchoranalysis.core.functional.checked.CheckedConsumer: Like Consumer.accept(T) but throws an exception.
accept(S, T) - Method in interface org.anchoranalysis.core.functional.checked.CheckedBiConsumer: Calls the function.
accepted() - Method in interface org.anchoranalysis.annotation.mark.DualMarks: The accepted marks.
AcceptIterationList - Class in org.anchoranalysis.image.voxel.object.morphological.predicate: The condition is accepted if any one of a list of AcceptIterationPredicate fulfills the condition.
AcceptIterationList() - Constructor for class org.anchoranalysis.image.voxel.object.morphological.predicate.AcceptIterationList
AcceptIterationPredicate - Interface in org.anchoranalysis.image.voxel.object.morphological.predicate: A condition that must be fulfilled for a particular iteration of a morphological operation to be accepted.
accepts(Class<?>) - Method in class org.anchoranalysis.bean.initializable.property.AssignerMatchClass
accepts(Class<?>) - Method in interface org.anchoranalysis.bean.initializable.property.InitializationParameterAssigner: Whether a particular type of initialization parameters is accepted?
AccessObjectMask<T> - Interface in org.anchoranalysis.image.core.object.scale: Provides functions to provide access and creation to/from the object-mask representation of a generic type.
AccessObjectMaskSimple - Class in org.anchoranalysis.image.core.object.scale: Provides access to the simple-case of a list of ObjectMasks.
AccessObjectMaskSimple() - Constructor for class org.anchoranalysis.image.core.object.scale.AccessObjectMaskSimple
AcquisitionDateReader - Class in org.anchoranalysis.io.bioformats.metadata: Reads the image acquisition-date. from EXIF metadata, if specified in an image-file.
activateDebugMode(String) - Method in class org.anchoranalysis.experiment.arguments.ExecutionArguments: Activates debug-mode.
add(double) - Method in class org.anchoranalysis.math.arithmetic.RunningSumExtrema: Adds a value to the running-sum, also remembering if value is the minimum or maximum of calls to this method.
add(double) - Method in class org.anchoranalysis.math.statistics.VarianceCalculatorDouble: Adds a value to the running sum.
add(double) - Method in class org.anchoranalysis.mpp.feature.energy.EnergyTotal: Adds a value to the total energy.
add(double, double) - Method in class org.anchoranalysis.spatial.point.Point2d: Arithmetically adds two double values, to the X- and Y- dimensions.
add(double, double, double) - Method in class org.anchoranalysis.spatial.point.Tuple3d: Arithmetically adds values to each dimension's component.
add(double, double, T) - Method in class org.anchoranalysis.spatial.rtree.IntervalRTree: Adds a bounding-box with a corresponding index.
add(int) - Method in class org.anchoranalysis.math.statistics.VarianceCalculatorLong: Adds a value to the running sum.
add(int, int) - Method in class org.anchoranalysis.math.statistics.VarianceCalculatorLong: Adds a multiple instances of a value to the running sum.
add(int, int) - Method in class org.anchoranalysis.spatial.point.Point2d: Arithmetically adds two int values, to the X- and Y- dimensions.
add(int, int, int) - Method in class org.anchoranalysis.spatial.box.PointRange: Adds a new point to be considered in the range.
add(int, String) - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetChannel
add(int, RGBColor) - Method in class org.anchoranalysis.core.color.ColorList: Inserts a Color into the list, at a particular index.
add(Rectangle, T) - Method in class org.anchoranalysis.spatial.rtree.RTree: Adds a Rectangle with a corresponding payload.
add(Color) - Method in class org.anchoranalysis.core.color.ColorList: Appends a Color to the list.
add(Class<? extends InputFromManager>) - Method in class org.anchoranalysis.experiment.task.InputTypesExpected: Appends an input-type class to the existing list.
add(Double) - Method in class org.anchoranalysis.bean.primitive.DoubleList
add(Double) - Method in class org.anchoranalysis.bean.primitive.DoubleSet
add(Integer) - Method in class org.anchoranalysis.bean.primitive.IntegerList
add(Integer) - Method in class org.anchoranalysis.bean.primitive.IntegerSet
add(String) - Method in class org.anchoranalysis.bean.primitive.StringList
add(String) - Method in class org.anchoranalysis.bean.primitive.StringSet
add(String) - Method in class org.anchoranalysis.core.collection.StringSetTrie: Adds an string to the set.
add(String) - Method in class org.anchoranalysis.feature.name.FeatureNameList: Adds a feature-name.
add(String) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNode: Adds an error message to this node.
add(String) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeNull
add(String, boolean) - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputs: Adds a new output-name to the set of recorded names.
add(String, int) - Method in class org.anchoranalysis.feature.name.FeatureNameMapToIndex: Adds a new featureName and index
add(String, StoreSupplier<Stack>) - Method in class org.anchoranalysis.image.core.stack.named.NamedStacks
add(String, StoreSupplier<TimeSeries>) - Method in class org.anchoranalysis.image.io.stack.time.ExtractFrameStore
add(String, StoreSupplier<TimeSeries>) - Method in class org.anchoranalysis.mpp.io.input.StackWithMap
add(String, StoreSupplier<T>) - Method in class org.anchoranalysis.core.identifier.provider.store.EagerEvaluationStore
add(String, StoreSupplier<T>) - Method in class org.anchoranalysis.core.identifier.provider.store.LazyEvaluationStore
add(String, StoreSupplier<T>) - Method in interface org.anchoranalysis.core.identifier.provider.store.NamedProviderStore: Adds an element to the store.
add(String, StoreSupplier<T>) - Method in interface org.anchoranalysis.mpp.io.input.MultiInputSubMap: Adds an entry to the map.
add(String, StoreSupplier<T>) - Method in class org.anchoranalysis.mpp.io.input.OperationMap
add(String, Feature<T>) - Method in class org.anchoranalysis.feature.store.NamedFeatureStore: Adds a named-feature to the store.
add(String, Channel) - Method in class org.anchoranalysis.plugin.image.task.channel.aggregator.NamedChannels: Adds a Channel with a name.
add(String, Stack) - Method in class org.anchoranalysis.image.core.stack.named.NamedStacks: Add a stack.
add(String, Stack) - Method in class org.anchoranalysis.image.core.stack.named.NamedStacksUniformSize: Adds an element to the store.
add(String, EnergyScheme) - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergySchemeSet: Adds a new EnergyScheme to the set with the given name.
add(String, T) - Method in class org.anchoranalysis.core.identifier.provider.NameValueMap: Adds an element.
add(Path) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.path.ExtensionCount
add(Path) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.path.FilePathPattern
add(Path) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.path.FileSizeStatistics
add(Optional<String>, List<Pair<String, S>>) - Method in class org.anchoranalysis.plugin.image.task.grouped.GroupMapByName: Adds an item with a non-group identifier, and also optionally a group identifier.
add(NamedBean<?>) - Method in class org.anchoranalysis.bean.define.Define: Adds a named-bean to our definitions, using the {#link GroupingRoot} annotation to determine a group where definitions are stored.
add(RGBColor) - Method in class org.anchoranalysis.core.color.ColorList: Like ColorList.add(Color) but adds a RGBColor.
add(CheckedSupplier<LabelledResultsVector, OperationFailedException>, CheckedSupplier<Optional<DisplayStack>, OperationFailedException>) - Method in class org.anchoranalysis.plugin.image.task.feature.FeatureResultsAndThumbnails: Adds results, together with a thumbnail.
add(NameValue<T>) - Method in class org.anchoranalysis.core.identifier.provider.NameValueMap: Adds an element.
add(SubmittedJob) - Method in class org.anchoranalysis.experiment.task.processor.ConcurrentJobMonitor: Adds a job to be considered in the aggregate view.
add(Feature<? extends T>) - Method in class org.anchoranalysis.feature.bean.list.FeatureList: Adds a feature to the current list.
add(LabelledResultsVector) - Method in class org.anchoranalysis.feature.io.csv.results.LabelledResultsCSVWriter: Adds a results-element to be written.
add(LabelledResultsVector) - Method in interface org.anchoranalysis.feature.io.results.LabelledResultsCollector: Adds a results-element to be written.
add(ResultsVector) - Method in class org.anchoranalysis.feature.results.ResultsVectorList: Add a ResultsVector to the list in the final position.
add(CacheTransferSource<? extends FeatureInput>) - Method in class org.anchoranalysis.feature.session.cache.finder.CacheTransferSourceCollection: Adds a source.
add(BoundingBoxEnclosed) - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.StackArrangement: Adds a new BoundingBoxEnclosed to the arrangement.
add(ObjectWithProperties) - Method in class org.anchoranalysis.image.core.object.properties.ObjectCollectionWithProperties: Add an ObjectWithProperties to the collection.
add(IndexedChannel) - Method in class org.anchoranalysis.image.io.channel.input.ChannelMap: Adds a IndexedChannel into the map.
add(ImageMetadataInput) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.image.ImageSize
add(ImageMetadataInput) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.image.SummarizerImageMetadataSimple
add(AcceptIterationPredicate) - Method in class org.anchoranalysis.image.voxel.object.morphological.predicate.AcceptIterationList: Adds an item to the list of predicates.
add(ObjectMask) - Method in class org.anchoranalysis.image.core.object.properties.ObjectCollectionWithProperties: Add an ObjectMask to the collection, assigning empty properties to it.
add(VoxelStatistics) - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsCombined: Adds an element.
add(RunningSum) - Method in class org.anchoranalysis.math.arithmetic.RunningSum: Adds the values of another RunningSum to the current values.
add(EnergyTotal) - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedIndividual: Adds a new energy total to the list and updates the total energy.
add(EnergySavedIndividual, VoxelizedMarkMemo, EnergyStackWithoutParameters, EnergySchemeWithSharedFeatures) - Method in class org.anchoranalysis.mpp.feature.mark.EnergyMemoList: Adds a new mark to the list and calculates its energy.
add(EnergyMemoList, VoxelizedMarkMemo, EnergyStackWithoutParameters) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown: Adds a new mark to the collection and updates energies.
add(IndexByRegion<T>) - Method in class org.anchoranalysis.mpp.index.IndexByChannel: Adds an IndexByRegion to the channel index.
add(Mark) - Method in class org.anchoranalysis.mpp.mark.MarkCollection: Adds a mark to the collection.
add(Mark, Color) - Method in class org.anchoranalysis.mpp.mark.ColoredMarks: Adds a mark with an associated color.
add(Mark, RGBColor) - Method in class org.anchoranalysis.mpp.mark.ColoredMarks: Adds a mark with an associated RGBColor.
add(MemoForIndex, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
add(MemoForIndex, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedPairs
add(MemoForIndex, VoxelizedMarkMemo) - Method in interface org.anchoranalysis.mpp.mark.UpdatableMarks: Adds a new mark to the existing set of marks.
add(VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy: Adds a voxelized mark to the collection.
add(VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.mark.MemoList: Appends the specified element to the end of this list.
add(Overlay) - Method in class org.anchoranalysis.overlay.collection.OverlayCollection: Append an overlay to the end of the list.
add(Overlay, RGBColor) - Method in class org.anchoranalysis.overlay.collection.ColoredOverlayCollection: Append an overlay and its respective color to the end of the list..
add(ImageCounter<T>) - Method in class org.anchoranalysis.plugin.annotation.counter.ImageCounterList: Adds an ImageCounter to the list.
add(LevelResult) - Method in class org.anchoranalysis.plugin.image.intensity.level.LevelResultCollection: Adds a LevelResult to the collection.
add(FileDetails) - Method in class org.anchoranalysis.plugin.io.multifile.ParsedFilePathBag: Adds a FileDetails object to the collection.
add(BoundingBox) - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.StackArrangement: Adds a new BoundingBox to the arrangement, with no padding.
add(BoundingBox, T) - Method in class org.anchoranalysis.spatial.rtree.BoundingBoxRTree: Adds a bounding-box with a corresponding payload.
add(Point2d) - Method in class org.anchoranalysis.spatial.point.Point2d: Arithmetically adds a Point2d's values across each dimension.
add(Point2i) - Method in class org.anchoranalysis.spatial.point.Point2d: Arithmetically adds a Point2i's values across each dimension.
add(Point2i) - Method in class org.anchoranalysis.spatial.point.Point2i: Adds values from a Point2i across each corresponding dimension.
add(ReadableTuple3i) - Method in class org.anchoranalysis.image.voxel.object.DeriveObjectFromPoints: Adds a point to the object.
add(ReadableTuple3i) - Method in class org.anchoranalysis.spatial.box.PointRange: Adds a new point to be considered in the range.
add(ReadableTuple3i) - Method in class org.anchoranalysis.spatial.point.Tuple3d: Arithmetically adds a ReadableTuple3i's values across each dimension.
add(ReadableTuple3i) - Method in class org.anchoranalysis.spatial.point.Tuple3i: Arithmetically adds a ReadableTuple3i's values across each dimension.
add(Tuple3d) - Method in class org.anchoranalysis.spatial.point.Tuple3d: Arithmetically adds a Tuple3d's values across each dimension.
add(S, T) - Method in interface org.anchoranalysis.plugin.image.task.grouped.AddToAggregateItem: Adds an individual item to an aggregate item.
add(T) - Method in interface org.anchoranalysis.bean.primitive.PrimitiveBeanCollection: Add an element to the collection.
add(T) - Method in class org.anchoranalysis.io.generator.sequence.OutputSequenceIncrementing: Outputs an additional element in the sequence.
add(T) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.input.SummarizerInputFromManager
add(T) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.Summarizer: Adds a element to the summary.
add(T) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerAggregate
add(T) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerCount
add(T) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerListMultiline
add(T) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerSplitMoreThan
add(T, String) - Method in class org.anchoranalysis.plugin.image.task.labeller.FileLabelMap: Adds a new file identifier and label pair to the map.
add(T, Optional<S>) - Method in class org.anchoranalysis.io.generator.sequence.OutputSequenceIndexed: Outputs an additional element in the sequence.
add(T, S) - Method in class org.anchoranalysis.io.generator.sequence.OutputSequenceIndexed: Outputs an additional element in the sequence.
addAdditionalOptions(Options) - Method in class org.anchoranalysis.launcher.config.LauncherConfig: Adds additional options to the command-line parser.
addAdditionalOptions(Options) - Static method in class org.anchoranalysis.launcher.options.CommandLineOptions: Adds additional options to the Options object.
addAll(Collection<S>) - Method in class org.anchoranalysis.plugin.annotation.counter.ImageCounterList: Adds a collection of ImageCounters to the list.
addAll(Collection<T>) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.Summarizer: Adds the elements to the summary.
addAll(List<NamedBean<T>>) - Method in class org.anchoranalysis.bean.define.Define: Adds all the named-beans from source to the current map.
addAll(Define) - Method in class org.anchoranalysis.bean.define.Define: Adds all the named-beans from source to the current map.
addAll(ColorList) - Method in class org.anchoranalysis.core.color.ColorList: Appends Colors to the list.
addAll(FeatureList<? extends T>) - Method in class org.anchoranalysis.feature.bean.list.FeatureList: Add all the features in other to the current list.
addAll(ColoredMarks) - Method in class org.anchoranalysis.mpp.mark.ColoredMarks: Adds all marks and colors from another ColoredMarks instance.
addAll(MarkCollection) - Method in class org.anchoranalysis.mpp.mark.MarkCollection: Adds all marks from another collection to this collection.
addAll(MarkCollection, RGBColor) - Method in class org.anchoranalysis.mpp.mark.ColoredMarks: Adds all marks from a MarkCollection with the same color.
addAll(MemoForIndex) - Method in class org.anchoranalysis.mpp.feature.mark.MemoList: Adds all elements from another MemoForIndex to this list.
addAllOutputNamesTo(OutputEnabledMutable) - Method in class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputter: Adds all possible output-names to a OutputEnabledMutable.
addAnnotatedImage(T) - Method in interface org.anchoranalysis.plugin.annotation.counter.ImageCounter: Add an image that had an associated annotation.
addAnnotatedImage(T) - Method in class org.anchoranalysis.plugin.annotation.counter.ImageCounterList
addAsSeparateChannels(NamedProviderStore<TimeSeries>, int, Logger) - Method in class org.anchoranalysis.image.io.channel.map.NamedChannelsConcatenate
addAsSeparateChannels(NamedProviderStore<TimeSeries>, int, Logger) - Method in interface org.anchoranalysis.image.io.channel.map.NamedChannelsMap: Adds each Channel as a separate TimeSeries in a NamedProviderStore.
addAsSeparateChannels(NamedProviderStore<TimeSeries>, int, Logger) - Method in class org.anchoranalysis.image.io.channel.map.OpenedNamedChannels
addAsSeparateChannels(NamedStacks, int, Logger) - Method in class org.anchoranalysis.image.io.channel.map.NamedChannelsConcatenate
addAsSeparateChannels(NamedStacks, int, Logger) - Method in interface org.anchoranalysis.image.io.channel.map.NamedChannelsMap: Adds each Channel as a separate Stack in a NamedStacks.
addAsSeparateChannels(NamedStacks, int, Logger) - Method in class org.anchoranalysis.image.io.channel.map.OpenedNamedChannels
addAssignedPair(ObjectMask, ObjectMask, double) - Method in class org.anchoranalysis.annotation.io.assignment.OverlappingObjects: Adds an assigned pair of objects with a particular overlap-ratio.
addAsynchronously(T) - Method in class org.anchoranalysis.io.generator.sequence.OutputSequenceIncrementing: Like OutputSequenceIncrementing.add(Object) but does not immediately execute the underlying add operation, instead returning an operation that can be called later.
addBasicOptions(Options) - Static method in class org.anchoranalysis.launcher.options.CommandLineOptions: Adds basic options to the Options object.
addBlankChannel() - Method in class org.anchoranalysis.image.core.stack.Stack: Adds a new empty Channel in the final-most position in the list.
addChangeID(Mark, Color) - Method in class org.anchoranalysis.mpp.mark.ColoredMarks: Adds a mark, changes its ID, and associates it with a color.
addChangeID(Mark, RGBColor) - Method in class org.anchoranalysis.mpp.mark.ColoredMarks: Adds a mark, changes its ID, and associates it with an RGBColor.
addChannel(Channel) - Method in class org.anchoranalysis.image.core.stack.Stack: Appends a channel to the stack, as the new final-most channel position-wise.
addChannel(Channel) - Method in class org.anchoranalysis.image.core.stack.StackNotUniformSized: Appends a channel to the stack, as the new final-most channel position-wise.
addChannel(Channel, Logger) - Method in class org.anchoranalysis.image.bean.channel.ChannelAggregator: Adds a Channel to the aggregation.
addChannelAfterCheck(Channel) - Method in class org.anchoranalysis.image.bean.channel.ChannelAggregator: Adds a Channel to the aggregation - after checking channel has acceptable dimensions.
addChannelAfterCheck(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.aggregator.ProjectableBufferAggregator
addChannelsFrom(Stack) - Method in class org.anchoranalysis.image.core.stack.Stack: Add the channels from another instance into this instance.
AddConstant - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic: Adds a constant value to each voxel in a channel.
AddConstant() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.AddConstant
AddConstantTo<T> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic: A feature that adds a constant value to the result of another feature.
AddConstantTo() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.AddConstantTo
AddCriteria<T> - Interface in org.anchoranalysis.mpp.feature.addcriteria: Criteria for adding edges between marks in a graph-based model.
AddCriteriaEnergyPair - Class in org.anchoranalysis.mpp.feature.addcriteria: Implements AddCriteria for energy pairs, combining energy calculations with additional criteria.
AddCriteriaEnergyPair(FeatureList<FeatureInputPairMemo>, AddCriteriaPair) - Constructor for class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaEnergyPair: Creates an AddCriteriaEnergyPair with specified energy pairs and add criteria.
AddCriteriaNever<T> - Class in org.anchoranalysis.mpp.feature.addcriteria: An implementation of AddCriteria that never adds an edge between marks.
AddCriteriaNever() - Constructor for class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaNever
AddCriteriaOr - Class in org.anchoranalysis.mpp.feature.addcriteria: An AddCriteriaPair that combines multiple criteria using a logical OR operation.
AddCriteriaOr() - Constructor for class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaOr
AddCriteriaPair - Class in org.anchoranalysis.mpp.feature.addcriteria: Abstract base class for criteria used to determine if a pair of marks should be included.
AddCriteriaPair() - Constructor for class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaPair
addDefaultOutputs(OutputEnabledMutable) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.AnnotationComparisonAssigner: Adds any default outputs that should occur from the assigner.
addDefaultOutputs(OutputEnabledMutable) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner
addDefaultOutputs(OutputEnabledMutable) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.MaskIntersectionAssigner
addDictionary(String, Dictionary) - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitialization: Adds a Dictionary to the corresponding named-collection of dictionaries.
addDouble(String, double) - Method in class org.anchoranalysis.annotation.io.comparer.StatisticsToExport: Adds a statistic that is a double.
addEdge(V, V) - Method in class org.anchoranalysis.core.graph.GraphWithoutPayload: Add an edge between two vertices.
addEdge(V, V, P) - Method in class org.anchoranalysis.core.graph.GraphWithPayload: Add an edge between two vertices.
AddEdgeFilters - Class in org.anchoranalysis.plugin.imagej.bean.define: Adds edge filters and their gradients to a Define object.
AddEdgeFilters() - Constructor for class org.anchoranalysis.plugin.imagej.bean.define.AddEdgeFilters
addEdges(V, Collection<V>) - Method in class org.anchoranalysis.core.graph.GraphWithoutPayload: Adds edge(s) from the vertex from to each element in toCollection.
addEnabledOutputFirst(String...) - Method in class org.anchoranalysis.io.output.enabled.OutputEnabledMutable: Adds enabled first-level outputs.
addEnabledOutputs(OutputEnabledMutable) - Method in class org.anchoranalysis.io.output.enabled.OutputEnabledMutable: Adds enabled outputs from another OutputEnabledMutable.
addEnabledOutputSecond(String, String...) - Method in class org.anchoranalysis.io.output.enabled.OutputEnabledMutable: Adds enabled second-level outputs.
addErrorLevel(String) - Method in class org.anchoranalysis.mpp.proposer.ProposerContext: Creates a new ProposerContext with an additional error level.
addExtension(String, String) - Static method in class org.anchoranalysis.test.image.stackwriter.ExtensionAdder: Adds a file extension to a filename.
addForSlice(int, int) - Method in interface org.anchoranalysis.mpp.index.VoxelPartition: Adds a value to the voxel partition for a specific slice.
addForSlice(int, int) - Method in class org.anchoranalysis.mpp.index.VoxelPartitionHistogram
addFrom(List<? extends NameValue<?>>) - Method in class org.anchoranalysis.bean.BeanInstanceMap: Populates from a list of NamedBean.
addFrom(BeanInstanceMap) - Method in class org.anchoranalysis.bean.BeanInstanceMap: Populates the entries from another BeanInstanceMap
addFrom(NamedProvider<Stack>) - Method in class org.anchoranalysis.image.core.stack.named.NamedStacks: Adds a Stack from a NamedProvider.
addFrom(CommandLineExtracter, InputArguments) - Static method in class org.anchoranalysis.launcher.options.process.AddInputOptions: Adds options to change the inputs from the command-line.
addFrom(CommandLineExtracter, OutputArguments) - Static method in class org.anchoranalysis.launcher.options.process.AddOutputOptions: Adds options to add/remove change the outputs the inputs from the command-line.
addFromList(FeatureList<FeatureInput>) - Method in class org.anchoranalysis.feature.shared.SharedFeatures: Add features from a feature-list.
addFromProviders(NamedProvider<FeatureList<FeatureInput>>) - Method in class org.anchoranalysis.feature.shared.SharedFeatures: Add features from a NamedProvider of feature-lists.
addFromWithPrefix(NamedProvider<Stack>, String) - Method in class org.anchoranalysis.image.core.stack.named.NamedStacks: Like NamedStacks.addFrom(NamedProvider) but additionally adds a prefix to the name when adding.
addFromXmlFile(Path) - Method in class org.anchoranalysis.plugin.io.input.path.RootPathMap: Adds root-paths contained in a list of XML Beans in an xml file
addHistogram(Histogram) - Method in class org.anchoranalysis.math.histogram.Histogram: Adds the counts from another histogram to the current object.
addIndexToRetain(int) - Method in class org.anchoranalysis.image.inference.segment.ReductionOutcome: Adds an index to be retained after reduction.
addInputOptions(Options) - Static method in class org.anchoranalysis.launcher.options.CommandLineOptions: Adds input-related options to the Options object.
AddInputOptions - Class in org.anchoranalysis.launcher.options.process: Adds options relating to inputting from the command-line.
addInt(String, int) - Method in class org.anchoranalysis.annotation.io.comparer.StatisticsToExport: Adds a statistic that is an int.
additionalLabelsFor(ImageMetadataInput) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromImageMetadata
additionalLabelsFor(ProvidesStackInput) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromImage
additionalLabelsFor(FileInput) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromHistogram
additionalLabelsFor(T) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.SingleRowPerInput: Additional labels for an input to include (after the identifier, and before any group labels).
addMeanExtrema(String, double, double, double) - Method in class org.anchoranalysis.annotation.io.comparer.StatisticsToExport: Adds three statistics a mean, min and max.
addMeanExtrema(String, RunningSumExtrema) - Method in class org.anchoranalysis.annotation.io.comparer.StatisticsToExport: Like StatisticsToExport.addMeanExtrema(String, double, double, double) but determines the statistics from a RunningSumExtrema.
addMultiple(RGBColor, int) - Method in class org.anchoranalysis.core.color.ColorList: Append multiple entries for the same color to the end of the list.
addNewlyAdded(T) - Method in class org.anchoranalysis.image.inference.segment.ReductionOutcome: Adds a newly-added element, that didn't exist in the input list for reduction, but should exist in the output list.
addObjectsFrom(NamedProvider<ObjectCollection>) - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitialization: Adds all the ObjectCollections available in a NamedProvider using the corresponding identifiers.
addObjectsNoBoundingBoxChange(Collection<T>) - Method in class org.anchoranalysis.spatial.box.BoundedList: Adds elements without changing the bounding-box
addObjectsToGraph(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.object.merge.MergeGraph: Adds objects to the graph.
addObjectsWithColor(ObjectCollectionProvider, RGBColor) - Method in class org.anchoranalysis.plugin.image.object.ColoredObjectCollection: Adds objects from a ObjectCollectionProvider all with one specific color
addOptionsFromCommandLine() - Method in class org.anchoranalysis.launcher.options.process.AddInputOptions
addOptionsFromCommandLine() - Method in class org.anchoranalysis.launcher.options.process.AddOptionsFromCommandLine: Maybe add options to the arguments from the command-line.
addOptionsFromCommandLine() - Method in class org.anchoranalysis.launcher.options.process.AddOutputOptions
AddOptionsFromCommandLine<T> - Class in org.anchoranalysis.launcher.options.process: Base class for adding options from command-line arguments.
AddOptionsFromCommandLine(CommandLineExtracter, T) - Constructor for class org.anchoranalysis.launcher.options.process.AddOptionsFromCommandLine: Creates a new AddOptionsFromCommandLine instance.
AddOutputOptions - Class in org.anchoranalysis.launcher.options.process: Adds options relating to outputting from the command-line.
addResultsFor(LabelledResultsVector) - Method in class org.anchoranalysis.feature.io.results.group.GroupedResults: Adds a result to the group-writer, but doesn't write yet.
addRow(List<TypedValue>) - Method in class org.anchoranalysis.feature.io.csv.FeatureCSVWriter: Directly adds a row in the form of typed-values.
addRow(LabelledResultsVector) - Method in class org.anchoranalysis.feature.io.csv.FeatureCSVWriter: Directly adds a row of feature-values.
addSharedObjectsDictionary(Optional<SharedObjects>, Optional<Dictionary>) - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitialization: Adds stacks and object-collections from a SharedObjects using the respective identifiers, and also adds a Dictionary.
addStack(String, Stack) - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitialization: Adds a Stack to the corresponding named-collection of stacks.
addStack(Provider<Stack>) - Method in class org.anchoranalysis.image.bean.provider.stack.Arrange: Adds a stack to the existing list of stack-providers.
addStacksFrom(NamedProvider<Stack>) - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitialization: Adds all the Stacks available in a NamedProvider using the corresponding identifiers.
addString(String, String) - Method in class org.anchoranalysis.annotation.io.comparer.StatisticsToExport: Adds a statistic that is a String.
addTimestamp(long) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster.ClusterIdentifier: Adds a timestamp to the cluster.
addTo(Define) - Method in class org.anchoranalysis.bean.define.adder.Concatenate
addTo(Define) - Method in interface org.anchoranalysis.bean.define.adder.DefineAdder: Adds items to define.
addTo(Define) - Method in class org.anchoranalysis.bean.define.adder.FromXMLList
addTo(Define) - Method in class org.anchoranalysis.plugin.imagej.bean.define.AddEdgeFilters
addTo(Define) - Method in class org.anchoranalysis.plugin.mpp.bean.define.VisualizeOnBackground
addTo(ObjectMask, int) - Method in interface org.anchoranalysis.image.voxel.arithmetic.VoxelsArithmetic: Adds a constant-value to each voxel but only for voxels inside an object-mask.
AddToAggregateItem<S,T> - Interface in org.anchoranalysis.plugin.image.task.grouped: Adds an individual-item to an aggregate-item.
AddToDefaults - Class in org.anchoranalysis.io.output.bean.rules: Adds additional outputs-names to be enabled to the defaults.
AddToDefaults() - Constructor for class org.anchoranalysis.io.output.bean.rules.AddToDefaults
addToErrorNode(ErrorNode) - Method in exception class org.anchoranalysis.mpp.proposer.error.ErrorNodeException: Adds the error message associated with this exception to an ErrorNode.
addToRow(List<TypedValue>) - Method in class org.anchoranalysis.feature.io.csv.metadata.RowLabels: Adds the identifiers to a row to be outputted in a features CSV.
addToStore(NamedProviderStore<TimeSeries>, int, Logger) - Method in class org.anchoranalysis.mpp.io.input.StackWithMap: Adds the main stack and other stacks to the store.
addToStore(NamedProviderStore<TimeSeries>, Logger) - Method in class org.anchoranalysis.mpp.io.input.StackWithMap
addToStore(NamedProviderStore<T>, Logger) - Method in interface org.anchoranalysis.mpp.io.input.MultiInputSubMap: Copies all the existing entries into a NamedProviderStore.
addToStore(NamedProviderStore<T>, Logger) - Method in class org.anchoranalysis.mpp.io.input.OperationMap
addToStoreInferNames(NamedProviderStore<Stack>, Logger) - Method in interface org.anchoranalysis.image.io.stack.input.ProvidesStackInput: Adds the current object to a named-store of stacks (using the default series).
addToStoreInferNames(NamedProviderStore<TimeSeries>, int, Logger) - Method in class org.anchoranalysis.image.io.channel.input.NamedChannelsInput
addToStoreInferNames(NamedProviderStore<TimeSeries>, int, Logger) - Method in interface org.anchoranalysis.image.io.stack.input.ProvidesStackInput: Adds any stacks exposed by the current element to a named-store of stacks - inferring the names of the Stacks.
addToStoreInferNames(NamedProviderStore<TimeSeries>, int, Logger) - Method in class org.anchoranalysis.mpp.io.input.MultiInput
addToStoreInferNames(NamedProviderStore<TimeSeries>, int, Logger) - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertNamedChannelsInputToStack
addToStoreWithName(String, NamedProviderStore<TimeSeries>, int, Logger) - Method in class org.anchoranalysis.image.io.channel.input.NamedChannelsInput
addToStoreWithName(String, NamedProviderStore<TimeSeries>, int, Logger) - Method in interface org.anchoranalysis.image.io.stack.input.ProvidesStackInput: Adds any stacks exposed by the current element to a named-store of stacks - with a particular name.
addToStoreWithName(String, NamedProviderStore<TimeSeries>, int, Logger) - Method in class org.anchoranalysis.mpp.io.input.MultiInput
addToStoreWithName(String, NamedProviderStore<TimeSeries>, int, Logger) - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertNamedChannelsInputToStack
addToVoxelList(int, int, int) - Method in class org.anchoranalysis.mpp.index.IndexByRegion: Adds a value to the voxel list for a specific region and slice.
addTypedValuesTo(Collection<TypedValue>, int) - Method in class org.anchoranalysis.feature.results.ResultsVector: Adds TypedValue representations of the results to a Collection.
addUnannotatedImage() - Method in interface org.anchoranalysis.plugin.annotation.counter.ImageCounter: Add an image that did not have an associated annotation.
addUnannotatedImage() - Method in class org.anchoranalysis.plugin.annotation.counter.ImageCounterList
addUnassignedLeft(ObjectCollection) - Method in class org.anchoranalysis.annotation.io.assignment.OverlappingObjects: Add unassigned objects to the left set.
addUnassignedLeft(ObjectMask) - Method in class org.anchoranalysis.annotation.io.assignment.OverlappingObjects: Add an unassigned object to the left set.
addUnassignedRight(ObjectCollection) - Method in class org.anchoranalysis.annotation.io.assignment.OverlappingObjects: Add unassigned objects to the right set.
addUnassignedRight(ObjectMask) - Method in class org.anchoranalysis.annotation.io.assignment.OverlappingObjects: Add an unassigned object to the right set.
addUnused(Histogram) - Method in class org.anchoranalysis.mpp.index.factory.VoxelPartitonFactoryHistogram: Adds an unused histogram to the factory.
addUnused(T) - Method in interface org.anchoranalysis.mpp.index.factory.VoxelPartitionFactory: Adds an unused part to the factory.
addVertex(V) - Method in class org.anchoranalysis.core.graph.GraphWithoutPayload: Adds a vertex.
addVertex(V) - Method in class org.anchoranalysis.core.graph.GraphWithPayload: Adds a vertex.
addVoxelBuffer(VoxelBuffer<T>) - Method in interface org.anchoranalysis.image.voxel.buffer.ProjectableBuffer: Adds a VoxelBuffer to the projection, as a single entity.
addVoxelBuffer(VoxelBuffer<T>) - Method in class org.anchoranalysis.image.voxel.projection.CountedProjectableBuffer
addVoxelBufferInternal(VoxelBuffer<T>, int) - Method in class org.anchoranalysis.image.voxel.projection.CountedProjectableBuffer: Adds a VoxelBuffer without incrementing the count.
addVoxels(Voxels<T>) - Method in interface org.anchoranalysis.image.voxel.buffer.ProjectableBuffer: Adds a Voxels to the projection, as a single entity.
addVoxels(Voxels<T>) - Method in class org.anchoranalysis.image.voxel.projection.CountedProjectableBuffer
addWithName(Define, String, AnchorBean<?>) - Method in class org.anchoranalysis.bean.define.adder.DefineAdderWithPrefixBean: Add an item to define with a name being added.
adjacentVerticesOutgoing(ObjectForReduction) - Method in class org.anchoranalysis.image.inference.bean.reduce.ReduceObjectsGraph: The vertices that are connected to a particular vertex by an outgoing edge.
adjacentVerticesOutgoing(V) - Method in class org.anchoranalysis.core.graph.GraphWithoutPayload: The vertices that are connected to a particular vertex by an outgoing edge.
adjacentVerticesOutgoing(V) - Method in class org.anchoranalysis.core.graph.GraphWithPayload: The vertices that are connected to a particular vertex by an outgoing edge.
adjacentVerticesOutgoingStream(ObjectForReduction) - Method in class org.anchoranalysis.image.inference.bean.reduce.ReduceObjectsGraph: Like ReduceObjectsGraph.adjacentVerticesOutgoing(org.anchoranalysis.image.inference.bean.reduce.ObjectForReduction) but returns a Stream instead of a Set.
adjacentVerticesOutgoingStream(V) - Method in class org.anchoranalysis.core.graph.GraphWithoutPayload: Like GraphWithoutPayload.adjacentVerticesOutgoing(V) but returns a Stream instead of a Set.
adjacentVerticesOutgoingStream(V) - Method in class org.anchoranalysis.core.graph.GraphWithPayload: Like GraphWithPayload.adjacentVerticesOutgoing(V) but returns a Stream instead of a Set.
afterAllJobsAreExecuted(NoSharedState, InputOutputContext) - Method in class org.anchoranalysis.experiment.bean.task.TaskWithoutSharedState
afterAllJobsAreExecuted(NoSharedState, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat
afterAllJobsAreExecuted(CSVWriter, InputOutputContext) - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
afterAllJobsAreExecuted(AggregateSharedState, InputOutputContext) - Method in class org.anchoranalysis.plugin.annotation.bean.aggregate.AggregateAnnotations
afterAllJobsAreExecuted(ComparisonSharedState<T>, InputOutputContext) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
afterAllJobsAreExecuted(FeatureExporter<S>, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures
afterAllJobsAreExecuted(GroupedSharedState<S, T>, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase
afterAllJobsAreExecuted(SharedStateFilteredImageOutput<T>, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageAssignLabel
afterAllJobsAreExecuted(SharedStateSegmentInstance<T>, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel
afterAllJobsAreExecuted(MontageSharedState, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage
afterAllJobsAreExecuted(SharedStateSelectedSlice, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice
afterAllJobsAreExecuted(Summarizer<S>, InputOutputContext) - Method in class org.anchoranalysis.plugin.io.bean.task.SummarizeBase
afterAllJobsAreExecuted(RecordingCounter<T>, InputOutputContext) - Method in class org.anchoranalysis.plugin.io.bean.task.CopyFiles
afterAllJobsAreExecuted(SharedStateRememberConverted<U, S>, InputOutputContext) - Method in class org.anchoranalysis.plugin.mpp.bean.convert.ConvertNamedChannels
afterAllJobsAreExecuted(S, InputOutputContext) - Method in class org.anchoranalysis.experiment.bean.task.Task: Called once after all calls to Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>).
afterAllJobsAreExecuted(S, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage
AfterCondition - Interface in org.anchoranalysis.plugin.image.object.merge.condition: A condition to be checked after merging two ObjectMasks.
AggregateAnnotations<S> - Class in org.anchoranalysis.plugin.annotation.bean.aggregate: Aggregates many per-image annotations together in form of a CSV file.
AggregateAnnotations() - Constructor for class org.anchoranalysis.plugin.annotation.bean.aggregate.AggregateAnnotations
AggregateChannelTask - Class in org.anchoranalysis.plugin.image.task.bean.combine: Creates a an aggregated-image for each group, where each voxel-value is aggregated across each channel in each image in the group.
AggregateChannelTask() - Constructor for class org.anchoranalysis.plugin.image.task.bean.combine.AggregateChannelTask
aggregatedChannel() - Method in class org.anchoranalysis.image.bean.channel.ChannelAggregator: Retrieve or create a Channel with containing the aggregated values.
aggregateResults(List<Double>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjectsSingleElement: Aggregates the results from individual intersecting object calculations.
aggregateResults(List<Double>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.MaxFeatureIntersectingObjects
aggregateResults(List<Double>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.MinFeatureIntersectingObjectsAboveThreshold
aggregateResults(List<Double>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.NumberIntersectingObjectsAboveThreshold
align(int, int, int) - Method in enum class org.anchoranalysis.image.bean.nonbean.spatial.align.AlignmentOnDimension: Determine the minimum value after alignment.
align(BoundingBox, BoundingBox) - Method in class org.anchoranalysis.image.bean.spatial.arrange.align.BoxAligner: Determines a BoundingBox to use for smaller BoundingBox so that it fits inside larger BoundingBox.
align(Extent, BoundingBox) - Method in class org.anchoranalysis.image.bean.spatial.arrange.align.BoxAligner: Determines a BoundingBox to use for a smaller Extent so that it fits inside larger BoundingBox.
align(Extent, Extent) - Method in class org.anchoranalysis.image.bean.spatial.arrange.align.BoxAligner: Determines a BoundingBox to use for a smaller Extent so that it fits inside larger Extent.
Align - Class in org.anchoranalysis.image.bean.spatial.arrange.align: Align the bounding-box to the larger without resizing.
Align() - Constructor for class org.anchoranalysis.image.bean.spatial.arrange.align.Align
Align(String, String, String) - Constructor for class org.anchoranalysis.image.bean.spatial.arrange.align.Align: Creates with alignment text for each axis.
alignAfterCheck(BoundingBox, BoundingBox) - Method in class org.anchoranalysis.image.bean.spatial.arrange.align.Align
alignAfterCheck(BoundingBox, BoundingBox) - Method in class org.anchoranalysis.image.bean.spatial.arrange.align.BoxAligner: Determines a BoundingBox to use for smaller BoundingBox so that it fits inside larger BoundingBox.
alignAfterCheck(BoundingBox, BoundingBox) - Method in class org.anchoranalysis.image.bean.spatial.arrange.align.Grow
alignAfterCheck(Extent, BoundingBox) - Method in class org.anchoranalysis.image.bean.spatial.arrange.align.Align
alignAfterCheck(Extent, BoundingBox) - Method in class org.anchoranalysis.image.bean.spatial.arrange.align.BoxAligner: Determines a BoundingBox to use for smaller Extent so that it fits inside larger BoundingBox.
alignAfterCheck(Extent, BoundingBox) - Method in class org.anchoranalysis.image.bean.spatial.arrange.align.Grow
alignAfterCheck(Extent, Extent) - Method in class org.anchoranalysis.image.bean.spatial.arrange.align.Align
alignAfterCheck(Extent, Extent) - Method in class org.anchoranalysis.image.bean.spatial.arrange.align.BoxAligner: Determines a BoundingBox to use for smaller Extent so that it fits inside larger Extent.
alignAfterCheck(Extent, Extent) - Method in class org.anchoranalysis.image.bean.spatial.arrange.align.Grow
alignCorner(BoundingBox, Extent) - Method in class org.anchoranalysis.image.bean.spatial.arrange.align.Align: The minimum corner at which the entity should be locate after alignment, ignoring the space to the left.
alignmentForDimension(String, String) - Method in class org.anchoranalysis.image.bean.nonbean.spatial.align.PositionChoices: Calculates how to align a particular axis.
AlignmentOnDimension - Enum Class in org.anchoranalysis.image.bean.nonbean.spatial.align: How the alignment will occur for a particular dimension.
alignX(String) - Static method in class org.anchoranalysis.image.bean.nonbean.spatial.align.PositionChoicesConstants: How to align on the X-axis.
alignY(String) - Static method in class org.anchoranalysis.image.bean.nonbean.spatial.align.PositionChoicesConstants: How to align on the Y-axis.
alignZ(String) - Static method in class org.anchoranalysis.image.bean.nonbean.spatial.align.PositionChoicesConstants: How to align on the Z-axis.
All - Class in org.anchoranalysis.io.output.bean.enabled: All outputs are allowed irrespective of outputName.
All - Class in org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels: Selects all possible channels from all possible stacks
All() - Constructor for class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.All
ALL_SUPPORTED_VOXEL_TYPES - Static variable in class org.anchoranalysis.test.image.stackwriter.PNGTestBase: All possible voxel types that can be supported.
ALL_SUPPORTED_VOXEL_TYPES - Static variable in class org.anchoranalysis.test.image.stackwriter.StackWriterTestBase: All possible voxel types that can be supported.
allAssociatedPaths() - Method in interface org.anchoranalysis.io.input.InputFromManager: A path to all files associated with the input, including InputFromManager.pathForBinding().
allChannelsAsStack(int, Logger) - Method in class org.anchoranalysis.image.io.channel.map.NamedChannelsConcatenate
allChannelsAsStack(int, Logger) - Method in interface org.anchoranalysis.image.io.channel.map.NamedChannelsMap: Combines all channels as a single Stack at a particular time-frame.
allChannelsAsStack(int, Logger) - Method in class org.anchoranalysis.image.io.channel.map.OpenedNamedChannels
allChannelsEightBit() - Method in class org.anchoranalysis.image.io.stack.output.StackWriteAttributes: Mark the attributes to indicate that channels are no longer guaranteed to be 8-bit.
allChannelsHaveIdenticalType() - Method in class org.anchoranalysis.image.core.stack.Stack: Determines if all channels have an identical voxel data-type.
allChannelsHaveType(VoxelDataType) - Method in class org.anchoranalysis.image.core.stack.RGBStack: Determines if all channels have a specific data-type.
allChannelsHaveType(VoxelDataType) - Method in class org.anchoranalysis.image.core.stack.Stack: Determines if all channels have a specific data-type.
allChannelsHaveType(VoxelDataType) - Method in class org.anchoranalysis.image.io.stack.time.TimeSeries: Whether all Channels in all frames in the times-series have a particular voxel-data type?
allExtensions() - Method in enum class org.anchoranalysis.core.format.ImageFileFormat: All extensions associated with a file-format.
allHeaders() - Method in class org.anchoranalysis.feature.io.csv.metadata.LabelHeaders: The non-group and group headers combined (in this order respectively)
allImageExtensions() - Static method in class org.anchoranalysis.core.format.FormatExtensions: The extensions of all image file formats as enumerated in ImageFileFormat.
allLabels(NoSharedState) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.BinaryOutcomeImageLabeller
allLabels(ImageCSVLabellerInitialization) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageCSVLabeller
allLabels(ImageLabellerStringMapInitialization<T>) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageLabellerStringMap
allLabels(T) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageLabeller: Returns a set of identifiers for all groups that can be outputted by the labeller.
allMatchIntensity(ObjectMask, Voxels<T>, IntPredicate) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsObjectMask: Do all points on an object-mask match a predicate on the point's voxel-intensity?
allocate(int) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer: Allocates a new buffer of unsigned-bytes.
allocate(int) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer: Allocates a new (direct) buffer of unsigned-ints.
allocate(int) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer: Allocates a new (direct) buffer of unsigned-shorts.
allocateFloat(int) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferFactory: Allocates a new float voxel-buffers of given size.
allocateFloatArray(int) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferFactory: Creates an array of float voxel-buffers of given size.
allocateUnsignedByte(int) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferFactory: Allocates a new unsigned byte voxel-buffer of given size.
allocateUnsignedByteArray(int) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferFactory: Creates an array of unsigned byte voxel-buffers of given size.
allocateUnsignedInt(int) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferFactory: Allocates a new unsigned int voxel-buffers of given size.
allocateUnsignedIntArray(int) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferFactory: Creates an array of unsigned int voxel-buffers of given size.
allocateUnsignedShort(int) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferFactory: Allocates a new unsigned short voxel-buffers of given size.
allocateUnsignedShortArray(int) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferFactory: Creates an array of unsigned short voxel-buffers of given size.
AllowEmpty - Annotation Interface in org.anchoranalysis.bean.annotation: Indicates that a String is allowed be empty, otherwise by default it must be non-empty.
allSuccessful() - Method in class org.anchoranalysis.experiment.task.TaskStatistics: Did all jobs execute and completely successfully?
AllValuesOff - Class in org.anchoranalysis.plugin.image.bean.mask.provider: Creates a new mask of particular dimensionality where all values are off.
AllValuesOff() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.AllValuesOff
AllValuesOn - Class in org.anchoranalysis.plugin.image.bean.mask.provider: Creates a new mask of particular dimensionality where all values are on.
AllValuesOn() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.AllValuesOn
ALPHA - Static variable in class org.anchoranalysis.image.core.stack.RGBChannelNames: Name for the alpha channel.
Always - Class in org.anchoranalysis.plugin.image.bean.object.match: Specifies a single object that will always be the "match" for whatever source object.
Always() - Constructor for class org.anchoranalysis.plugin.image.bean.object.match.Always
ALWAYS_NEW - Enum constant in enum class org.anchoranalysis.image.core.channel.convert.ConversionPolicy: Always make a new channel.
always2D() - Static method in class org.anchoranalysis.image.io.stack.output.OutputSequenceStackFactory: The stacks that are outputted are guaranteed to be two-dimensional.
always2D(boolean) - Method in class org.anchoranalysis.image.io.stack.output.StackWriteAttributes: Derives a StackWriteAttributes that will always be 2D, but is otherwise unchanged.
AlwaysAllowed - Class in org.anchoranalysis.io.output.writer: Allows every output, irrespective of whether the OutputterChecked allows the output-name.
AlwaysAllowed(ElementOutputter, Optional<WriterExecuteBeforeEveryOperation>) - Constructor for class org.anchoranalysis.io.output.writer.AlwaysAllowed: Creates a new AlwaysAllowed instance.
alwaysExecuteBeforeCallingLibrary() - Static method in class org.anchoranalysis.plugin.opencv.CVInit: This routine must always be executed at least once before calling any routines in the OpenCV library
AlwaysNew<T> - Class in org.anchoranalysis.feature.session.replace: Always create a new SessionInputSequential with no reuse or caching between calls.
AlwaysNew(CacheCreator) - Constructor for class org.anchoranalysis.feature.session.replace.AlwaysNew: Constructor with default means of creating a FeatureCalculationInput.
AlwaysNew(CacheCreator, ChildCacheFinder) - Constructor for class org.anchoranalysis.feature.session.replace.AlwaysNew
AlwaysReject - Class in org.anchoranalysis.plugin.io.bean.metadata.reader: A special ImageMetadataReader that will always throw an exception and reject a file.
AlwaysReject() - Constructor for class org.anchoranalysis.plugin.io.bean.metadata.reader.AlwaysReject
AnchorBean<F> - Class in org.anchoranalysis.bean: The base class of all beans used in Anchor.
AnchorBean() - Constructor for class org.anchoranalysis.bean.AnchorBean
AnchorBeanFactory - Class in org.anchoranalysis.bean.xml.factory: Base class for all Anchor-specific bean factories.
AnchorBeanFactory() - Constructor for class org.anchoranalysis.bean.xml.factory.AnchorBeanFactory
AnchorCheckedException - Exception Class in org.anchoranalysis.core.exception: A base class for all checked exceptions used on the Anchor platform.
AnchorCheckedException() - Constructor for exception class org.anchoranalysis.core.exception.AnchorCheckedException: Creates without message or cause.
AnchorCheckedException(String) - Constructor for exception class org.anchoranalysis.core.exception.AnchorCheckedException: Creates with only a message.
AnchorCheckedException(String, Throwable) - Constructor for exception class org.anchoranalysis.core.exception.AnchorCheckedException: Creates with message and cause.
AnchorCheckedException(Throwable) - Constructor for exception class org.anchoranalysis.core.exception.AnchorCheckedException: Creates with only a cause.
AnchorCombinableException - Exception Class in org.anchoranalysis.core.exception.combinable: An exception that can be combined with similar exceptions and summarized.
AnchorCombinableException(String, Throwable) - Constructor for exception class org.anchoranalysis.core.exception.combinable.AnchorCombinableException: Creates with a description and a cause.
AnchorDefaultBeanFactory - Class in org.anchoranalysis.bean.xml.factory: The default bean factory used for initializing AnchorBeans.
AnchorDefaultBeanFactory(BeanInstanceMap) - Constructor for class org.anchoranalysis.bean.xml.factory.AnchorDefaultBeanFactory: Creates a new AnchorDefaultBeanFactory instance.
AnchorFriendlyCheckedException - Exception Class in org.anchoranalysis.core.exception.friendly: A base class for particular checked-exceptions which are guaranteed to provide a user-friendly error description.
AnchorFriendlyCheckedException(String) - Constructor for exception class org.anchoranalysis.core.exception.friendly.AnchorFriendlyCheckedException: A user-friendly error message WITHOUT a cause.
AnchorFriendlyCheckedException(String, Throwable) - Constructor for exception class org.anchoranalysis.core.exception.friendly.AnchorFriendlyCheckedException: A user-friendly error message and its cause.
AnchorFriendlyCheckedException(Throwable) - Constructor for exception class org.anchoranalysis.core.exception.friendly.AnchorFriendlyCheckedException: A wrapped exception.
AnchorFriendlyRuntimeException - Exception Class in org.anchoranalysis.core.exception.friendly: A base class for particular runtime-exceptions which are guaranteed to provide a user-friendly error description.
AnchorFriendlyRuntimeException(String) - Constructor for exception class org.anchoranalysis.core.exception.friendly.AnchorFriendlyRuntimeException: A user-friendly error message without a cause.
AnchorFriendlyRuntimeException(String, Throwable) - Constructor for exception class org.anchoranalysis.core.exception.friendly.AnchorFriendlyRuntimeException: A user-friendly error message and its cause.
AnchorFriendlyRuntimeException(Throwable) - Constructor for exception class org.anchoranalysis.core.exception.friendly.AnchorFriendlyRuntimeException: A wrapped exception.
AnchorImpossibleSituationException - Exception Class in org.anchoranalysis.core.exception.friendly: A run-time exception to throw in situations which should never logically occur by design.
AnchorImpossibleSituationException() - Constructor for exception class org.anchoranalysis.core.exception.friendly.AnchorImpossibleSituationException: Default constructor.
AnchorImpossibleSituationException(String) - Constructor for exception class org.anchoranalysis.core.exception.friendly.AnchorImpossibleSituationException: Creates with a specific message explaining the exception.
AnchorNeverOccursException - Exception Class in org.anchoranalysis.core.exception: This is an exception that should never be thrown, but can be used for type-safety where an exception is needed.
AnchorNeverOccursException() - Constructor for exception class org.anchoranalysis.core.exception.AnchorNeverOccursException
AnchorRuntimeException - Exception Class in org.anchoranalysis.core.exception: A base class for all unchecked (runtime) exceptions used on the Anchor platform.
AnchorRuntimeException() - Constructor for exception class org.anchoranalysis.core.exception.AnchorRuntimeException: Creates without message or cause.
AnchorRuntimeException(String) - Constructor for exception class org.anchoranalysis.core.exception.AnchorRuntimeException: Creates with only a message.
AnchorRuntimeException(String, Throwable) - Constructor for exception class org.anchoranalysis.core.exception.AnchorRuntimeException: Creates with message and cause.
AnchorRuntimeException(Throwable) - Constructor for exception class org.anchoranalysis.core.exception.AnchorRuntimeException: Creates with only a cause.
AnchorWebsiteLinks - Class in org.anchoranalysis.launcher: A centralized location for hyperlinks to the Anchor website.
and(StackWriteAttributes) - Method in class org.anchoranalysis.image.io.stack.output.StackWriteAttributes: Combines with another StackWriteAttributes by performing a logical and on each field.
And - Class in org.anchoranalysis.plugin.image.bean.mask.provider.combine: Outputs the logical operation and voxelwise on both masks, modifying {mask} with the result.
And - Class in org.anchoranalysis.plugin.image.bean.object.filter.combine: Applies multiples filter with logical AND i.e. an object must pass all objects in the list to remain.
And() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.combine.And
And() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.combine.And
AndCondition - Class in org.anchoranalysis.plugin.image.object.merge.condition: Combines two UpdatableBeforeConditions as LOGICAL ANDs
AndCondition(UpdatableBeforeCondition, UpdatableBeforeCondition) - Constructor for class org.anchoranalysis.plugin.image.object.merge.condition.AndCondition
AndKernel - Class in org.anchoranalysis.image.voxel.kernel: Combines two BinaryKernels so that they only a true value exists only at a point where both kernels return true.
AndKernel(BinaryKernel, BinaryKernel) - Constructor for class org.anchoranalysis.image.voxel.kernel.AndKernel: Create for the two kernels.
AndObjectsWithMasks - Class in org.anchoranalysis.plugin.image.bean.object.provider.mask: Reduce the size of individual objects (if neccessary, and minimally) to fit within a binary-mask.
AndObjectsWithMasks() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.mask.AndObjectsWithMasks
AnisotropicDiffusion - Class in org.anchoranalysis.plugin.fiji.bean.channel.provider: Performs Perona-Malik Anisotropic Diffusion.
AnisotropicDiffusion() - Constructor for class org.anchoranalysis.plugin.fiji.bean.channel.provider.AnisotropicDiffusion
Annotation - Interface in org.anchoranalysis.annotation: Base class for types of image annotations.
AnnotationAggregateCSVGenerator - Class in org.anchoranalysis.plugin.annotation.bean.aggregate: Generates a CSV file containing aggregated annotation data.
AnnotationAggregateCSVGenerator() - Constructor for class org.anchoranalysis.plugin.annotation.bean.aggregate.AnnotationAggregateCSVGenerator: Constructs an AnnotationAggregateCSVGenerator with predefined column headers.
AnnotationBackground - Class in org.anchoranalysis.annotation.io.bean: How to display one or more Stacks as background during an annotation process.
AnnotationBackground() - Constructor for class org.anchoranalysis.annotation.io.bean.AnnotationBackground
AnnotationComparisonAssigner<T> - Class in org.anchoranalysis.plugin.annotation.bean.comparison.assigner: Compares similar object-sets produced from two different sources.
AnnotationComparisonAssigner() - Constructor for class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.AnnotationComparisonAssigner
AnnotationComparisonInput<T> - Class in org.anchoranalysis.plugin.annotation.comparison: Input for annotation comparison, containing sources to compare and associated metadata.
AnnotationComparisonInput(T, Tuple2<ComparableSource, ComparableSource>, Tuple2<String, String>, StackReader) - Constructor for class org.anchoranalysis.plugin.annotation.comparison.AnnotationComparisonInput: Creates an annotation comparison input.
AnnotationComparisonInputManager<T> - Class in org.anchoranalysis.plugin.annotation.bean.comparison: An input manager for annotation comparison that extends InputManagerWithStackReader.
AnnotationComparisonInputManager() - Constructor for class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager
AnnotationDeleter - Interface in org.anchoranalysis.annotation.io: Allows an annotation to be deleted from the file-system.
AnnotationInputManager<T,S> - Class in org.anchoranalysis.annotation.io.bean: An InputManager that provides annotations corresponding to images.
AnnotationInputManager() - Constructor for class org.anchoranalysis.annotation.io.bean.AnnotationInputManager
AnnotationLabel - Class in org.anchoranalysis.plugin.annotation.bean.label: Represents a label used for annotation, with associated metadata.
AnnotationLabel() - Constructor for class org.anchoranalysis.plugin.annotation.bean.label.AnnotationLabel
annotationLabelFor(ProvidesStackInput, OperationContext) - Method in class org.anchoranalysis.annotation.io.bean.AnnotatorStrategy: A human-friendly textual description of the annotation, or Optional.empty() if no label is available.
annotationLabelFor(ProvidesStackInput, OperationContext) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.ImageLabelStrategy
annotationLabelFor(ProvidesStackInput, OperationContext) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy
AnnotationReader<T> - Interface in org.anchoranalysis.annotation.io: Allows an annotation to be read from the file-system.
AnnotationWithMarks - Interface in org.anchoranalysis.annotation.mark: An image-annotation that involves a mark-collection.
AnnotationWithStrategy<T> - Class in org.anchoranalysis.annotation.io: One particular annotation, associated with its strategy.
AnnotationWithStrategy(ProvidesStackInput, T) - Constructor for class org.anchoranalysis.annotation.io.AnnotationWithStrategy: Creates for a particular input and associated annotation strategy.
AnnotationWriter<T> - Interface in org.anchoranalysis.annotation.io: Allows an annotation to be written to the file-system.
AnnotatorStrategy - Class in org.anchoranalysis.annotation.io.bean: How an input is associated with annotations on the file-system, and how this is presented visually.
AnnotatorStrategy() - Constructor for class org.anchoranalysis.annotation.io.bean.AnnotatorStrategy
Anonymize - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming: Copies files to a number 001, 002 etc. in the same order they are inputted.
Anonymize() - Constructor for class org.anchoranalysis.plugin.io.bean.file.copy.naming.Anonymize
AnonymizeSharedState - Class in org.anchoranalysis.plugin.io.shared
AnonymizeSharedState(NumberToStringConverter, Map<Integer, Integer>) - Constructor for class org.anchoranalysis.plugin.io.shared.AnonymizeSharedState
any() - Method in class org.anchoranalysis.image.voxel.VoxelsUntyped: Exposes without any specific buffer type.
anyDimensionIsLargerThan(Extent) - Method in class org.anchoranalysis.spatial.box.Extent: Returns true if any dimension in this extent is larger than the corresponding dimension in other extent.
anyExists() - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateAtCorner
anyExists() - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateImplementation
anyExists() - Method in interface org.anchoranalysis.image.voxel.extracter.predicate.VoxelsPredicate: Does at least one value satisfy the predicate - across all voxels?
anyMatch(Predicate<ObjectMask>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream: Does the predicate evaluate to true on any object in the collection?
anyPredicateMatch(Voxels<T>, Predicate<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll: Tries to apply a predicate to all the remaining buffer locations, returning true if the predicate matches.
append(Optional<FeatureList<T>>) - Method in class org.anchoranalysis.feature.bean.list.FeatureList: Appends the features one or more (optional) feature-lists to the existing list.
append(StatisticsToExport) - Method in class org.anchoranalysis.annotation.io.comparer.StatisticsToExport: Appends the names and values from another AnnotationComparison to the existing.
appendExtension(String, Optional<String>) - Static method in class org.anchoranalysis.core.system.path.ExtensionUtilities: Appends an (optional) extension to a string, adding in the leading period if the extension is defined.
appendExtension(Path, Optional<String>) - Static method in class org.anchoranalysis.core.system.path.ExtensionUtilities: Like ExtensionUtilities.appendExtension(String, Optional) but accepts and returns a Path.
apply(int) - Method in interface org.anchoranalysis.core.functional.checked.CheckedIntFunction: Calls the function
apply(int) - Method in interface org.anchoranalysis.core.functional.unchecked.UnaryIntOperator: Apply the operator.
apply(Throwable, Writer, String, int, boolean) - Static method in class org.anchoranalysis.core.exception.friendly.RecursivelyDescribeExceptionStack: Incrementally adds a line to a string builder with the message of each exception moving onto the next nested exception until there are no more
apply(BiFunction<T, T, R>) - Method in class org.anchoranalysis.image.inference.segment.DualScale: Apply a BiFunction to both elements.
apply(IFormatReader, ReadOptions, int) - Method in class org.anchoranalysis.io.bioformats.DimensionsCreator: Infers the dimensions from an image file.
apply(Mask, Mask) - Static method in class org.anchoranalysis.image.core.mask.combine.MaskAnd: Performs a logical and operation on each voxel in two masks, writing the result onto the second mask.
apply(Mask, Mask) - Static method in class org.anchoranalysis.image.core.mask.combine.MaskOr: Performs a logical or operation on each voxel in two masks, writing the result onto the first mask.
apply(Mask, Mask) - Static method in class org.anchoranalysis.image.core.mask.combine.MaskXor: Performs a logical xor (exclusive or) operation on each voxel in two masks, writing the result onto the first mask.
apply(BinaryVoxels<UnsignedByteBuffer>, BinaryVoxels<UnsignedByteBuffer>) - Static method in class org.anchoranalysis.image.core.mask.combine.MaskXor: Performs a logical xor (exclusive or) operation on each voxel in two Voxels (considered to be masks), writing the result onto the second mask.
apply(BinaryKernel, BinaryVoxels<UnsignedByteBuffer>, KernelApplicationParameters) - Static method in class org.anchoranalysis.image.voxel.kernel.ApplyKernel: Apply the kernel to BinaryVoxels<UnsignedByteBuffer> using the same binary-values as voxels to calculate a value for each voxel.
apply(Voxels<UnsignedByteBuffer>, Voxels<UnsignedByteBuffer>, BinaryValuesByte, BinaryValuesByte) - Static method in class org.anchoranalysis.image.core.mask.combine.MaskAnd: Performs a logical and operation on each voxel in two Voxels (considered to be masks), writing the result onto the second mask.
apply(S) - Method in interface org.anchoranalysis.core.functional.checked.CheckedFunction: Calls the function.
apply(S, int) - Method in interface org.anchoranalysis.core.functional.checked.CheckedFunctionWithInt: Calls the function.
apply(S, int) - Method in interface org.anchoranalysis.core.functional.unchecked.FunctionWithInt: Calls the function.
apply(S, T) - Method in interface org.anchoranalysis.core.functional.checked.CheckedBiFunction: Calls the function.
apply(T) - Method in interface org.anchoranalysis.core.functional.checked.CheckedUnaryOperator: Applies the operation.
applyAsDouble(T) - Method in interface org.anchoranalysis.core.functional.checked.CheckedToDoubleFunction: Applies this function to the given arguments.
applyAsDouble(T, U) - Method in interface org.anchoranalysis.core.functional.checked.CheckedToDoubleBiFunction: Applies this function to the given arguments.
applyAsFloat(int) - Method in interface org.anchoranalysis.core.functional.unchecked.IntToFloatFunction: Applies this function to the given argument.
applyAsInt(S) - Method in interface org.anchoranalysis.core.functional.checked.CheckedToIntFunction: Calls the function.
applyCoefficientsToMark(DoubleMatrix2D, Mark, Dimensions) - Method in class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresViaNormalEquationBase: Applies the calculated coefficients to the mark.
applyDelta(MultiLevelOutputEnabled) - Method in class org.anchoranalysis.io.output.recorded.OutputEnabledDelta: Applies the changes to enable or disable additional outputs, if they are defined.
applyFitResultToMark(Ellipsoid, Dimensions, double) - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult: Applies the fit result to an Ellipsoid mark.
applyForCount(BinaryKernel, BinaryVoxels<UnsignedByteBuffer>, KernelApplicationParameters) - Static method in class org.anchoranalysis.image.voxel.kernel.ApplyKernel: Applies a BinaryKernel to voxels and counts how many true values occur en aggregate.
applyForCount(CountKernel, BinaryVoxels<UnsignedByteBuffer>, KernelApplicationParameters) - Static method in class org.anchoranalysis.image.voxel.kernel.ApplyKernel: Applies the kernel to voxels and sums the returned value.
applyForCount(CountKernel, BinaryVoxels<UnsignedByteBuffer>, BoundingBox, KernelApplicationParameters) - Static method in class org.anchoranalysis.image.voxel.kernel.ApplyKernel: Applies the kernel to voxels and sums the returned value.
ApplyImageJMorphologicalOperation - Class in org.anchoranalysis.plugin.imagej.mask: Applies an ImageJ (2D) morphological operation to voxels.
applyInitializationIfPossibleTo(Object, Object, Logger) - Method in class org.anchoranalysis.bean.initializable.property.BeanInitializer: Applies the initialization to a bean if possible.
ApplyKernel - Class in org.anchoranalysis.image.voxel.kernel: Applies various kinds of Kernel to BinaryVoxels.
applyMorphologicalOperation(Mask, boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Dilate
applyMorphologicalOperation(Mask, boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Erode
applyMorphologicalOperation(Mask, boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.MorphologicalOperatorBase: Applies the morphological operation to the source mask.
applyMorphologicalOperation(ObjectMask, Optional<Extent>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Dilate
applyMorphologicalOperation(ObjectMask, Optional<Extent>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Erode
applyMorphologicalOperation(ObjectMask, Optional<Extent>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.ObjectCollectionProviderMorphological: Applies the morphological operation to a single ObjectMask.
applyOperation(UnaryOperator<Stack>, Optional<Dimensions>) - Method in class org.anchoranalysis.image.core.stack.named.NamedStacks: Applies an operation on each Stack in the collection and returns a new derived collection.
applyOperation(BinaryVoxels<UnsignedByteBuffer>, String, int) - Static method in class org.anchoranalysis.plugin.imagej.mask.ApplyImageJMorphologicalOperation: Applies a specified morphological operation to the given binary voxels.
applyOperation(ObjectMask, Extent, boolean) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateIncrementalOperationMap: Applies the incremental operation to the input object.
applyOperation(ObjectMask, Extent, boolean) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateDilationMap
applyOperation(ObjectMask, Extent, boolean) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateErosionMap
applyRadiiSubtractScale(double, double) - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult: Applies a subtraction and scaling to the radii of the ellipsoid.
applyRankFilter(Channel, int, int) - Static method in class org.anchoranalysis.plugin.imagej.channel.provider.FilterHelper: Applies a 2D rank-filter to each slice independently of a Channel.
applyUntilPositive(CountKernel, BinaryVoxels<UnsignedByteBuffer>, BoundingBox, KernelApplicationParameters) - Static method in class org.anchoranalysis.image.voxel.kernel.ApplyKernel: Applies the kernel to voxels until a positive value is returned, then exits with true.
arbitraryElement() - Method in class org.anchoranalysis.spatial.rtree.RTree: Any arbitrary element from the tree.
ArbitraryInsidePoint - Class in org.anchoranalysis.plugin.image.feature.bean.object.single: Calculates deterministically a point that is definitely inside the object-mask and outputs a selected axis value.
ArbitraryInsidePoint() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.ArbitraryInsidePoint
ArbitraryInsidePoint(String) - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.ArbitraryInsidePoint: Creates an ArbitraryInsidePoint with a specified axis.
ArbitraryPointCommon - Class in org.anchoranalysis.mpp.feature.addcriteria: If one arbitrarily point overlaps between two MarkPointList then true, otherwise false
ArbitraryPointCommon() - Constructor for class org.anchoranalysis.mpp.feature.addcriteria.ArbitraryPointCommon
Area<T> - Class in org.anchoranalysis.plugin.image.feature.bean.dimensions: Area of the stack (XY dimensions only, Z dimension is not considered).
Area() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.dimensions.Area
areAllPointsInBigNeighborhood(List<Point3i>) - Static method in class org.anchoranalysis.spatial.point.PointsNeighborChecker: Are all points in a list neighboring the next point in the list?
AreaPhysical - Class in org.anchoranalysis.image.bean.unitvalue.extent.area: Area expressed in square meters, or units thereof.
AreaPhysical() - Constructor for class org.anchoranalysis.image.bean.unitvalue.extent.area.AreaPhysical
AreaPixels - Class in org.anchoranalysis.image.bean.unitvalue.extent.area: Area expressed in pixels.
AreaPixels() - Constructor for class org.anchoranalysis.image.bean.unitvalue.extent.area.AreaPixels
AreaPixels(double) - Constructor for class org.anchoranalysis.image.bean.unitvalue.extent.area.AreaPixels: Creates with a particular area value.
areaXY() - Method in class org.anchoranalysis.image.core.dimensions.Dimensions: Size in X multiplied by size in Y.
areaXY() - Method in class org.anchoranalysis.spatial.box.Extent: Size in X multiplied by size in Y.
areCSVFilesEqual(Path, Path, PrintStream) - Method in class org.anchoranalysis.test.image.csv.CSVComparer: Are two CSV files equal?
areDocumentsEqual(Document, Document) - Static method in class org.anchoranalysis.test.CompareXML: Are two XML-documents equal in content, ignoring whitespace and comments?
areEqual(double, double) - Static method in class org.anchoranalysis.math.arithmetic.DoubleUtilities: Are the two numbers equal, within a tolerance?
areEqual(float, float) - Static method in class org.anchoranalysis.math.arithmetic.FloatUtilities: Are the two numbers equal?
arePointsNeighbors(Point3i, Point3i) - Static method in class org.anchoranalysis.spatial.point.PointsNeighborChecker: Do two points have a big neighbor relationship to each other?
ArgumentConverter - Class in org.anchoranalysis.launcher.executor.selectparam.path.convert: Converts string passed as arguments.
arithmetic() - Method in class org.anchoranalysis.image.core.channel.Channel: Interface that allows manipulation of voxel intensities via arithmetic operations.
arithmetic() - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: Interface that allows manipulation of voxel intensities via arithmetic operations.
arithmetic() - Method in class org.anchoranalysis.image.voxel.Voxels: Interface that allows manipulation of voxel intensities via arithmetic operations.
arithmetic() - Method in class org.anchoranalysis.image.voxel.VoxelsUntyped: Interface that allows manipulation of voxel intensities via arithmetic operations.
ArithmeticWithConstantBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic: Base-class for operations that perform a binary arithmetic operation with each voxel-value and a constant.
ArithmeticWithConstantBase() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.ArithmeticWithConstantBase
ArithmeticWithConstantConditionallyWriteBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic: Base class for arithmetic operations that conditionally overwrite voxel values with a constant.
ArithmeticWithConstantConditionallyWriteBase() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.ArithmeticWithConstantConditionallyWriteBase
Arrange - Class in org.anchoranalysis.image.bean.provider.stack: Creates a stack that combines other stacks.
Arrange() - Constructor for class org.anchoranalysis.image.bean.provider.stack.Arrange
Arrange(boolean, boolean) - Constructor for class org.anchoranalysis.image.bean.provider.stack.Arrange: Shortcut to create with some explicit parameters.
ArrangeStackException - Exception Class in org.anchoranalysis.image.bean.nonbean.spatial.arrange: When the position of a particular RGBStack cannot be determined, when combined with others onto a single plane.
ArrangeStackException(Exception) - Constructor for exception class org.anchoranalysis.image.bean.nonbean.spatial.arrange.ArrangeStackException: Create with a cause.
ArrangeStackException(String) - Constructor for exception class org.anchoranalysis.image.bean.nonbean.spatial.arrange.ArrangeStackException: Create with a message.
ArrangeStackException(String, Exception) - Constructor for exception class org.anchoranalysis.image.bean.nonbean.spatial.arrange.ArrangeStackException: Create with a message and cause.
arrangeStacks(Iterator<Extent>, OperationContext) - Method in class org.anchoranalysis.image.bean.spatial.arrange.fill.Fill
arrangeStacks(Iterator<Extent>, OperationContext) - Method in class org.anchoranalysis.image.bean.spatial.arrange.overlay.Overlay
arrangeStacks(Iterator<Extent>, OperationContext) - Method in class org.anchoranalysis.image.bean.spatial.arrange.Single
arrangeStacks(Iterator<Extent>, OperationContext) - Method in class org.anchoranalysis.image.bean.spatial.arrange.StackArranger: Arranges stacks to that they fit together in a single raster.
arrangeStacks(Iterator<Extent>, OperationContext) - Method in class org.anchoranalysis.image.bean.spatial.arrange.tile.Tile
array() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer: The array of the buffer ala ByteBuffer.array().
array() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer: The array of the buffer ala IntBuffer.array().
array() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer: The array of the buffer ala ShortBuffer.array().
as(boolean) - Static method in enum class org.anchoranalysis.image.voxel.kernel.OutsideKernelPolicy: Multiplexes between OutsideKernelPolicy.AS_ON and OutsideKernelPolicy.AS_OFF.
AS_OFF - Enum constant in enum class org.anchoranalysis.image.voxel.kernel.OutsideKernelPolicy: Pretend any parts of the neighborhood that lie outside the scene are being off-valued.
AS_ON - Enum constant in enum class org.anchoranalysis.image.voxel.kernel.OutsideKernelPolicy: Pretend any parts of the neighborhood that lie outside the scene are being on-valued.
asArray(boolean) - Static method in class org.anchoranalysis.image.core.stack.RGBChannelNames: Creates an array with all channel-names in R-G-B order.
asByte() - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValuesInt: Derives a BinaryValuesByte representation from the current values.
asByte() - Method in class org.anchoranalysis.image.voxel.VoxelsUntyped: Casts to use a UnsignedByteBuffer if the voxels contain this data-type, otherwise throws a IncorrectVoxelTypeException.
asByte(ImageProcessor) - Static method in class org.anchoranalysis.io.imagej.convert.ConvertToVoxelBuffer: Convert a ImageProcessor to VoxelBuffer<UnsignedByteBuffer>
asCollectionOrderNotPreserved() - Method in class org.anchoranalysis.image.core.object.scale.ScaledElements: Returns the scaled-elements as a collection but without preserving the original element order.
asExtent() - Method in class org.anchoranalysis.image.bean.spatial.SizeXY: Creates an extent with identical width and height and depth (z-extent) of 1.
asExtent(int) - Method in class org.anchoranalysis.image.bean.spatial.SizeXY: Creates an extent with identical width and height and a specific depth (z-extent).
asFile() - Method in interface org.anchoranalysis.io.input.InputFromManager: Expresses the input as a file with a name (the unique identifier).
asFloat() - Method in class org.anchoranalysis.image.voxel.VoxelsUntyped: Casts to use a FloatBuffer if the voxels contain this data-type, otherwise throws a IncorrectVoxelTypeException.
asFloat(ImageProcessor) - Static method in class org.anchoranalysis.io.imagej.convert.ConvertToVoxelBuffer: Convert a ImageProcessor to VoxelBuffer<FloatBuffer>
asGraph() - Method in class org.anchoranalysis.image.voxel.object.IntersectingObjects: Constructs a graph where each vertex is an element and an edge exists between any elements that intersect.
asInt() - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte: Derives a BinaryValuesInt representation from the current values.
asInt() - Method in class org.anchoranalysis.image.voxel.VoxelsUntyped: Casts to use a UnsignedIntBuffer if the voxels contain this data-type, otherwise throws a IncorrectVoxelTypeException.
asList() - Method in class org.anchoranalysis.bean.primitive.StringList: Exposes the underlying list of values.
asList() - Method in class org.anchoranalysis.core.color.ColorList: Exposes the underlying List in the data-structure.
asList() - Method in class org.anchoranalysis.feature.bean.list.FeatureList: Exposes the underlying list of features in this data-structure.
asList() - Method in class org.anchoranalysis.feature.name.FeatureNameList: Exposes the underlying list of names.
asList() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection: Exposes the underlying objects as a ArrayList.
asList(boolean) - Static method in class org.anchoranalysis.image.core.stack.RGBChannelNames: Creates a list with all channel-names in R-G-B order.
asListChannels() - Method in class org.anchoranalysis.image.core.stack.Stack: Derives a List of Channels from those in the Stack, preserving order.
asListOrderPreserved(List<T>) - Method in class org.anchoranalysis.image.core.object.scale.ScaledElements: Returns a list of scaled-elements corresponding to a list of unscaled-elements.
asMap() - Method in class org.anchoranalysis.image.core.object.scale.ScaledElements: The underlying map used to map an unscaled object to its scaled counterpart.
asMarks() - Method in class org.anchoranalysis.mpp.feature.mark.EnergyMemoList: Converts the energy memo list to a collection of marks.
asNamedStacks() - Method in class org.anchoranalysis.image.core.stack.named.NamedStacksUniformSize: Exposes the stacks as a NamedStacks.
asObjectMask() - Method in class org.anchoranalysis.image.core.object.properties.ObjectWithProperties: Exposes the underlying ObjectMask ignoring any properties.
AsObjectMask - Class in org.anchoranalysis.plugin.image.feature.bean.stack.object: Treats a channel as an object-mask, assuming binary values of 0 and 255 and calls an object-mask feature
AsObjectMask() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.stack.object.AsObjectMask
asOperationFailedException() - Method in exception class org.anchoranalysis.core.index.GetOperationFailedException: Converts to a OperationFailedException using an identical message.
asPath() - Method in class org.anchoranalysis.bean.shared.path.RootPath: Exposes the path field as a Path.
asPath(boolean) - Method in class org.anchoranalysis.io.output.path.prefixer.DirectoryWithPrefix: A path that combines the directory and fileNamePrefix and delimiter.
aspectRatioInverted() - Method in class org.anchoranalysis.image.bean.spatial.arrange.fill.ExtentToArrange: Returns the ratio of *image height to width*.
aspectRatioXY() - Method in class org.anchoranalysis.spatial.box.Extent: Derives an aspect-ratio, by dividing the X-dimension by the Y-dimension value.
asPoint() - Method in class org.anchoranalysis.image.bean.spatial.Padding: Exposes the padding as a Point3i.
asPredicateDouble() - Method in class org.anchoranalysis.bean.shared.relation.threshold.RelationToThreshold: Expresses the relation as a predicate on values, where only values that fulfill the relation to threshold are true.
asPredicateInt() - Method in class org.anchoranalysis.bean.shared.relation.threshold.RelationToThreshold: Like RelationToThreshold.asPredicateDouble() but expresses the relationship for an integer.
asScaleFactor() - Method in class org.anchoranalysis.spatial.scale.ScaleFactorInt: Converts to a ScaleFactor that accepts floating-point values.
assertCalc(ResultsVector, Object...) - Static method in class org.anchoranalysis.test.feature.plugins.ResultsVectorTestUtilities: Asserts that a ResultsVector matches the expected values within a small epsilon.
assertDoubleResult(String, Feature<T>, T, double) - Static method in class org.anchoranalysis.test.feature.plugins.FeatureTestCalculator: Asserts that a feature calculation results in an expected double value.
assertDoubleResult(String, Feature<T>, T, Optional<SharedObjects>, double) - Static method in class org.anchoranalysis.test.feature.plugins.FeatureTestCalculator: Asserts that a feature calculation results in an expected double value, with shared objects.
assertDoubleResult(String, Feature<T>, T, T, double, double) - Static method in class org.anchoranalysis.test.feature.plugins.FeatureTestCalculatorDuo: Asserts that a feature calculation results in expected double values for both positive and negative inputs.
assertExpectedTaskOutputs(List<T>, V, Path, String, Iterable<String>) - Method in class org.anchoranalysis.test.experiment.task.ExecuteTaskHelper: Executes a task on a multiple inputs and asserts expected outputs - with task arguments.
assertExpectedTaskOutputs(T, V, Path, String, Iterable<String>) - Method in class org.anchoranalysis.test.experiment.task.ExecuteTaskHelper: Executes a task on a single-input.
assertIdentical(String, String, Path) - Method in interface org.anchoranalysis.test.image.rasterwriter.comparison.ImageComparer: Asserts that two image-files being compared are identical as images.
assertIntResult(String, Feature<T>, T, int) - Static method in class org.anchoranalysis.test.feature.plugins.FeatureTestCalculator: Asserts that a feature calculation results in an expected integer value.
assertIntResult(String, Feature<T>, T, Optional<SharedObjects>, int) - Static method in class org.anchoranalysis.test.feature.plugins.FeatureTestCalculator: Asserts that a feature calculation results in an expected integer value, with shared objects.
assertIntResult(String, Feature<T>, T, T, int, int) - Static method in class org.anchoranalysis.test.feature.plugins.FeatureTestCalculatorDuo: Asserts that a feature calculation results in expected integer values for both positive and negative inputs.
assertValid() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown: Asserts that the energy calculations are valid.
assertValid() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedIndividual: Asserts that the total energy is valid (not NaN).
assertValid() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedPairs: Asserts that the total energy is valid (not NaN).
asSet() - Method in class org.anchoranalysis.spatial.rtree.RTree: All elements contained within the tree, as a Set.
asSet(boolean) - Static method in class org.anchoranalysis.image.core.stack.RGBChannelNames: Creates a set of the channel names.
asSet(Logger) - Method in interface org.anchoranalysis.image.io.stack.input.ProvidesStackInput: Exposes the input as a set of named stacks (inferring the names).
asShort() - Method in class org.anchoranalysis.image.voxel.VoxelsUntyped: Casts to use a UnsignedShortBuffer if the voxels contain this data-type, otherwise throws a IncorrectVoxelTypeException.
asShort(ImageProcessor) - Static method in class org.anchoranalysis.io.imagej.convert.ConvertToVoxelBuffer: Convert a ImageProcessor to VoxelBuffer<UnsignedShortBuffer>
assignAccepted(DualMarks) - Method in class org.anchoranalysis.annotation.mark.DualMarksAnnotation: Assigns marks with an overall accepted state.
assignAllVoxels(RGBColor) - Method in class org.anchoranalysis.image.core.stack.RGBStack: Assigns a RGBColor to all voxels in the respective channels.
assignBoundingBox(BoundingBox) - Method in class org.anchoranalysis.spatial.box.BoundedList: Assigns a new containing bounding-box.
assignBoundingBoxAndMap(BoundingBox, UnaryOperator<T>) - Method in class org.anchoranalysis.spatial.box.BoundedList: Assigns a new containing bounding-box and maps each individual element.
assignCallUponDirectoryCreation(Consumer<Path>) - Method in class org.anchoranalysis.experiment.arguments.InputArguments: Indicates that consumer will be called when an output directory is first created.
assignCopyNonInputs() - Method in class org.anchoranalysis.experiment.arguments.InputArguments: Activates a toggle where any files in the input directory that are unused as inputs, are copied to the output directory.
assignEachMatchingPoint(Voxels<?>, IntPredicate, int) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll: Assigns a value to any voxel whose intensity matches a predicate, reading and writing the buffer as an int.
AssignerMatchClass - Class in org.anchoranalysis.bean.initializable.property: Allows assignment of parameters if they are are of type paramTypeMatch or subclass of it.
AssignerMatchClass(Class<?>) - Constructor for class org.anchoranalysis.bean.initializable.property.AssignerMatchClass
assignExtent(Extent) - Method in class org.anchoranalysis.plugin.image.task.size.SizeMapping: Replace the existing Extent with a new value.
AssignFeatureNameUtilities - Class in org.anchoranalysis.feature.name: Utilities for assigning a name to a feature.
assignFilterGlob(String) - Method in class org.anchoranalysis.io.input.InputContextParameters: Assigns a glob that can be used by beans to filter input.
assignFixedLimit(int) - Method in class org.anchoranalysis.io.input.InputContextParameters: Assigns a fixed upper limit of number of inputs.
assignFrom(Mark) - Method in class org.anchoranalysis.mpp.mark.voxelized.memo.VoxelizedMarkMemo: Assigns a new mark to replace the existing mark.
AssignFromChannel - Class in org.anchoranalysis.plugin.image.bean.channel.provider.assign: Copies the pixels from channelAssignFrom to channel (possibly masking).
AssignFromChannel() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromChannel
AssignFromDictionary - Class in org.anchoranalysis.plugin.image.bean.channel.provider.assign: Assigns a value from a dictionary to all voxels in a channel.
AssignFromDictionary() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromDictionary
AssignFromIntersectingObjects - Class in org.anchoranalysis.plugin.image.bean.channel.provider.assign: Matches source-objects to target objects, based upon intersection, and assigns the value in the respective source object to the target object
AssignFromIntersectingObjects() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromIntersectingObjects
assignGroup(String) - Method in class org.anchoranalysis.experiment.arguments.TaskArguments: Assigns an index-range to use to form groups, by subsetting components from each input's identifier.
assignIdentifierSubrange(IndexRangeNegative) - Method in class org.anchoranalysis.io.input.InputContextParameters: If defined, this indicates and specifies only a subset of the elements of the identifier to use.
assignInitializationToProperties(Object, Object, Object, Logger) - Method in class org.anchoranalysis.bean.initializable.property.AssignerMatchClass
assignInitializationToProperties(Object, Object, Object, Logger) - Method in interface org.anchoranalysis.bean.initializable.property.InitializationParameterAssigner: Assigns the parameter to the bean.
assignInputDirectory(Optional<Path>) - Method in class org.anchoranalysis.io.input.InputContextParameters: Sets an input-directory.
assignInputFilterExtensions(StringSetTrie) - Method in class org.anchoranalysis.io.input.InputContextParameters: Assigns extensions that can be used filter inputs, but irrespective of whether extensions have already been set.
assignInputFilterExtensionsIfMissing(Supplier<Optional<StringSetTrie>>) - Method in class org.anchoranalysis.io.input.InputContextParameters: Assigns extensions that can be used filter inputs, but only when no extensions have already been set.
assignLogger(Logger) - Method in class org.anchoranalysis.io.output.outputter.OutputterChecked: Assigns a logger to the outputter, which is used to output warnings or messages when outputting.
assignMaxNumberProcessors(String) - Method in class org.anchoranalysis.experiment.arguments.TaskArguments: Assigns a suggested maximum number of processors (CPUs) for a task.
Assignment<T> - Interface in org.anchoranalysis.annotation.io.assignment: A one-to-one pairing between items in two respective sets.
AssignmentColorPool - Class in org.anchoranalysis.annotation.io.assignment.generator: Different ColorSchemes that can be used to select colors for paired and unpaired objects.
AssignmentColorPool(int, ColorScheme) - Constructor for class org.anchoranalysis.annotation.io.assignment.generator.AssignmentColorPool: Creates with a number and colors for the paired objects, and defaults colors for unpaired.
AssignmentColorPool(int, ColorScheme, ColorScheme, boolean) - Constructor for class org.anchoranalysis.annotation.io.assignment.generator.AssignmentColorPool: Creates a new AssignmentColorPool instance.
AssignmentGenerator - Class in org.anchoranalysis.annotation.io.assignment.generator: Outputs a raster showing an Assignment on a background.
AssignmentGenerator(DrawColoredObjects, IntFunction<AssignmentColorPool>, Tuple2<String, String>, boolean) - Constructor for class org.anchoranalysis.annotation.io.assignment.generator.AssignmentGenerator: Creates a new AssignmentGenerator instance.
assignModelDirectory(Path) - Method in class org.anchoranalysis.experiment.arguments.InputArguments: Assigns a directory indicating where models can be located.
assignName(String) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster.ClusterIdentifier: Assigns a name for the cluster.
assignOff() - Method in class org.anchoranalysis.image.core.mask.Mask: Interface that allows assignment of an off state to all or subsets of the voxels.
assignOff() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels: Creates an assigner that may set the off state in subsequently specified regions of the voxels.
assignOff() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Assigns the off value to voxels, expecting global coordinates.
assignOn() - Method in class org.anchoranalysis.image.core.mask.Mask: Interface that allows assignment of an on state to all or subsets of the voxels.
assignOn() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels: Creates an assigner that may set the on state in subsequently specified regions of the voxels.
assignOn() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Assigns the on value to voxels, expecting global coordinates.
assignOutputDirectory(Path) - Method in class org.anchoranalysis.io.output.path.prefixer.OutputPrefixerSettings: Assigns a directory indicating where inputs can be located.
AssignOverlappingObjects - Class in org.anchoranalysis.annotation.io.assignment: Creates a one-to-one assignment between two sets of ObjectMasks.
AssignOverlappingObjects(FeatureEvaluator<FeatureInputPairObjects>, boolean) - Constructor for class org.anchoranalysis.annotation.io.assignment.AssignOverlappingObjects: Creates a new AssignOverlappingObjects instance.
assignPaths(List<Path>) - Method in class org.anchoranalysis.io.input.InputContextParameters: Assigns a specific list of paths that are used for the inputs.
assignPaused(DualMarks) - Method in class org.anchoranalysis.annotation.mark.DualMarksAnnotation: Assigns marks with an overall paused state.
AssignPermutationException - Exception Class in org.anchoranalysis.bean.permute.assign: When the assignment of a permuted value to a property cannot succeed.
AssignPermutationException(String) - Constructor for exception class org.anchoranalysis.bean.permute.assign.AssignPermutationException: Create with an error message.
assignPriority(ObjectVertex, ObjectVertex, GraphLogger) - Method in class org.anchoranalysis.plugin.image.object.merge.priority.AssignPriority: Assigns a priority to a potential merge between two objects.
AssignPriority - Class in org.anchoranalysis.plugin.image.object.merge.priority: Abstract class for assigning priorities to potential object merges.
AssignPriority() - Constructor for class org.anchoranalysis.plugin.image.object.merge.priority.AssignPriority
AssignPriorityFromImprovement - Class in org.anchoranalysis.plugin.image.object.merge.priority: Allows merges if there is an increase in the payload i.e.
AssignPriorityFromImprovement(PayloadCalculator) - Constructor for class org.anchoranalysis.plugin.image.object.merge.priority.AssignPriorityFromImprovement
AssignPriorityFromPair - Class in org.anchoranalysis.plugin.image.object.merge.priority: Calculates pair-feature on each potential merge, and this value determines priority..
AssignPriorityFromPair(FeatureCalculatorSingle<FeatureInputPairObjects>, double, DoubleBiPredicate) - Constructor for class org.anchoranalysis.plugin.image.object.merge.priority.AssignPriorityFromPair
assignPriorityToEdge(ObjectVertex, ObjectVertex, ObjectMask, ErrorReporter) - Method in class org.anchoranalysis.plugin.image.object.merge.priority.AssignPriority: Assigns a priority to an edge between two objects.
assignPriorityToEdge(ObjectVertex, ObjectVertex, ObjectMask, ErrorReporter) - Method in class org.anchoranalysis.plugin.image.object.merge.priority.AssignPriorityFromImprovement
assignPriorityToEdge(ObjectVertex, ObjectVertex, ObjectMask, ErrorReporter) - Method in class org.anchoranalysis.plugin.image.object.merge.priority.AssignPriorityFromPair
assignRatioLimit(double) - Method in class org.anchoranalysis.io.input.InputContextParameters: Assigns a fixed upper limit that is a ratio of the number of inputs allowed.
assignRejected(DualMarks, T) - Method in class org.anchoranalysis.annotation.mark.DualMarksAnnotation: Assigns marks with an overall rejected state.
assignRelativeForIdentifier() - Method in class org.anchoranalysis.io.input.InputContextParameters: Specify that the entire filename or relative path (excluding extension) is used to determine a unique identifier.
assignResolution(Optional<Resolution>) - Method in class org.anchoranalysis.image.core.channel.Channel: Assigns a new resolution.
assignResolution(Resolution) - Method in class org.anchoranalysis.image.core.stack.Stack: Assigns a new resolution.
assignShuffle() - Method in class org.anchoranalysis.io.input.InputContextParameters: Indicates that the order of the inputs should be shuffled (randomized).
assignSize(String) - Method in class org.anchoranalysis.experiment.arguments.TaskArguments: Assign dimensions or scaling factor or size for an image, as may be used by a task.
assignSuggestedImageOutputFormat(ImageFileFormat) - Method in class org.anchoranalysis.experiment.arguments.OutputArguments: Assigns a suggestion for a preferred image-output format.
assignSuggestedImageOutputFormat(ImageFileFormat) - Method in class org.anchoranalysis.io.output.path.prefixer.OutputPrefixerSettings: Assigns a suggestion for a preferred image-output format.
assignTaskName(Optional<String>) - Method in class org.anchoranalysis.experiment.arguments.TaskArguments: Assigns a name for the task.
assignTo(Feature<FeatureInput>) - Method in class org.anchoranalysis.feature.bean.Feature: Copies fields in this (base) class to target.
assignTo(ConicFitterBase) - Method in class org.anchoranalysis.plugin.points.bean.fitter.ConicFitterBase: Copies fields in this (base) class to target.
assignValue(int) - Method in class org.anchoranalysis.image.core.channel.Channel: Interface that allows assignment of a particular value to all or subsets of the voxels.
assignValue(int) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: Assigns a value to a bounded-voxels accepting global coordinates for objects, boxes etc.
assignValue(int) - Method in class org.anchoranalysis.image.voxel.Voxels: Interface that allows assignment of a particular value to all or subsets of the voxels.
assignValue(int) - Method in class org.anchoranalysis.image.voxel.VoxelsFloat
assignValue(int) - Method in class org.anchoranalysis.image.voxel.VoxelsUnsignedByte
assignValue(int) - Method in class org.anchoranalysis.image.voxel.VoxelsUnsignedInt
assignValue(int) - Method in class org.anchoranalysis.image.voxel.VoxelsUnsignedShort
assignValue(int) - Method in class org.anchoranalysis.image.voxel.VoxelsUntyped: Interface that allows assignment of a particular value to all or subsets of the voxels.
assignValue(AnchorBean<?>, Object) - Method in interface org.anchoranalysis.bean.permute.assign.PermutationAssigner: Assigns value to one or more properties in bean.
AssignValue - Class in org.anchoranalysis.plugin.image.bean.channel.provider.assign: Assigns a constant (scalar) value to the portion of the image covered by a mask
AssignValue() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignValue
assignVoxel(Point3i, RGBColor) - Method in class org.anchoranalysis.image.core.stack.RGBStack: Assigns a RGBColor to a single voxel in the respective channels.
assignWithPrefix(Feature<? extends FeatureInput>, String, String) - Static method in class org.anchoranalysis.feature.name.AssignFeatureNameUtilities: Assigns a new custom-name to a feature, by combining an existing-name with a prefix.
AsSingle - Class in org.anchoranalysis.mpp.feature.bean.energy.element: Extracts one of the memos from the pair, and processes as a FeatureSingleMemo
AsSingle() - Constructor for class org.anchoranalysis.mpp.feature.bean.energy.element.AsSingle
associated - Variable in class org.anchoranalysis.launcher.options.process.AddOptionsFromCommandLine: An associated entity which consumers accept.
associatedFile() - Method in class org.anchoranalysis.annotation.io.AnnotationWithStrategy: The file associated with the annotation, if such a file exists.
AssociatedIndex - Interface in org.anchoranalysis.core.index: Associated an index with the object.
associateFileWithCluster(File, long, ClusterIdentifier) - Method in class org.anchoranalysis.plugin.io.file.copy.ClusterMembership: Indicates a particular file is a member of a particular cluster.
associateXML(XMLConfiguration) - Method in interface org.anchoranalysis.bean.xml.AssociateXMLUponLoad: Associated an XML configuration with an object.
associateXML(XMLConfiguration) - Method in class org.anchoranalysis.experiment.bean.Experiment
AssociateXMLUponLoad - Interface in org.anchoranalysis.bean.xml: For classes that wish to have a XmlConfiguration associated with them.
asStack() - Method in class org.anchoranalysis.feature.energy.EnergyStack: Derive a Stack representation containing the identical channels to the current instance.
asStack() - Method in class org.anchoranalysis.feature.energy.EnergyStackWithoutParameters: Derive a Stack representation containing the identical channels to the current instance.
asStack() - Method in class org.anchoranalysis.image.core.stack.RGBStack: Exposes the underlying stack, storing the three RGB channels in respective order.
asStack(Logger) - Method in interface org.anchoranalysis.image.io.stack.input.ProvidesStackInput: Exposes the input as a single Stack throw an error if more than one exists.
asTuple() - Method in class org.anchoranalysis.spatial.box.Extent: Exposes the extent as a tuple.
asVector3d() - Method in class org.anchoranalysis.spatial.orientation.DirectionVector: Converts to a Vector3d representation.
at(int, int, int, int) - Static method in class org.anchoranalysis.spatial.box.BoundingBoxFactory: Short-hand factory method for creating a 2D bounding-box.
at(int, int, int, int, int, int) - Static method in class org.anchoranalysis.spatial.box.BoundingBoxFactory: Short-hand factory method for creating a 3D bounding-box.
atanHandlingNan(double) - Static method in class org.anchoranalysis.plugin.points.bean.fitter.EllipseStandardFormConverter: Calculates the arctangent, handling NaN values.
atBorder(Extent) - Method in class org.anchoranalysis.spatial.box.BoundingBox: Does the bounding-box have an edge at the border of an image of size extent?
AtBorderBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.border: Base class for features that check if an object is at the border of an image.
AtBorderBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.border.AtBorderBase
atBorderXY(Extent) - Method in class org.anchoranalysis.spatial.box.BoundingBox: Like BoundingBox.atBorder(Extent) but considers only the X- and Y- dimensions.
AtBorderXY - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.border: Checks if an object's bounding box is at the border of the image in the XY plane.
AtBorderXY() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.border.AtBorderXY
atBorderZ(Extent) - Method in class org.anchoranalysis.spatial.box.BoundingBox: Like BoundingBox.atBorder(Extent) but considers only the Z-dimension.
AtBorderZ - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.border: Checks if an object's bounding box is at the border of the image in the Z dimension.
AtBorderZ() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.border.AtBorderZ
atCorner(ReadableTuple3i, VoxelsExtracter<T>) - Static method in class org.anchoranalysis.image.voxel.extracter.VoxelsExtracterFactory: Projects a VoxelsExtracter to a corner in a larger global space.
AtIndex - Class in org.anchoranalysis.plugin.image.bean.object.provider: Extract a single ObjectMask into a new collection.
AtIndex() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.AtIndex
atInputScale() - Method in class org.anchoranalysis.image.inference.segment.DualScale: The element scaled to match the size of the input-image.
atInputScale() - Method in class org.anchoranalysis.image.inference.segment.SegmentedBackground: The background scaled to match the size of the input-image.
atLeastOne(String, String, boolean, boolean) - Static method in class org.anchoranalysis.bean.initializable.CheckMisconfigured: Checks that one of two properties is defined, or both.
AtLeastZSlices - Class in org.anchoranalysis.plugin.io.bean.file.group.check
AtLeastZSlices() - Constructor for class org.anchoranalysis.plugin.io.bean.file.group.check.AtLeastZSlices
atModelScale() - Method in class org.anchoranalysis.image.inference.segment.DualScale: The element scaled to match the size of the input for model inference.
atModelScale() - Method in class org.anchoranalysis.image.inference.segment.SegmentedBackground: The background scaled to match the size of the input for model inference.
AtScale - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel: Perform a segmentation at a different scale, and then fit the results back to the original scale.
AtScale() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.channel.AtScale
attachObject(Channel) - Method in class org.anchoranalysis.image.core.channel.convert.attached.channel.QuantileIntensity
attachObject(Channel) - Method in class org.anchoranalysis.image.core.channel.convert.attached.channel.UpperLowerQuantileIntensity
attachObject(Channel) - Method in class org.anchoranalysis.image.core.channel.convert.attached.channel.IntensityRange
attachObject(Channel) - Method in class org.anchoranalysis.image.core.channel.convert.attached.channel.MaxIntensity
attachObject(Histogram) - Method in class org.anchoranalysis.image.core.channel.convert.attached.histogram.MaxIntensityFromHistogram
attachObject(Histogram) - Method in class org.anchoranalysis.image.core.channel.convert.attached.histogram.QuantileIntensityFromHistogram
attachObject(Histogram) - Method in class org.anchoranalysis.image.core.channel.convert.attached.histogram.UpperLowerQuantileIntensityFromHistogram
attachObject(S) - Method in interface org.anchoranalysis.image.core.channel.convert.attached.ChannelConverterAttached: Associate the convert with a particular object.
AutoLocalThreshold - Class in org.anchoranalysis.plugin.fiji.bean.mask.provider: Applies local thresholding algorithm using Fiji's {link Auto_Local_Threshold} plugin
AutoLocalThreshold() - Constructor for class org.anchoranalysis.plugin.fiji.bean.mask.provider.AutoLocalThreshold
Autoname - Class in org.anchoranalysis.plugin.io.bean.channel.map: Names of the channels from the metadata if it exists, or after RGB, or by index.
Autoname() - Constructor for class org.anchoranalysis.plugin.io.bean.channel.map.Autoname
Axis - Enum Class in org.anchoranalysis.spatial.axis: Identifies axis in a Cartesian coordinate system.
AxisAlignedUnitVector - Class in org.anchoranalysis.image.bean.spatial.direction: Creates a DirectionVector that is a unit-vector along a particular image-axis.
AxisAlignedUnitVector() - Constructor for class org.anchoranalysis.image.bean.spatial.direction.AxisAlignedUnitVector
AxisConversionException - Exception Class in org.anchoranalysis.spatial.axis: When converting another type to a corresponding Axis fails.
AxisConversionException(String) - Constructor for exception class org.anchoranalysis.spatial.axis.AxisConversionException: Create with a messsage, without an underlying cause.
AxisConverter - Class in org.anchoranalysis.spatial.axis: Converts to/from Axis to a String and int representations, checking for invalid input.
AxisRatioEllipsoid - Class in org.anchoranalysis.plugin.points.bean.feature: Calculates the axis ratio of an Ellipsoid.
AxisRatioEllipsoid() - Constructor for class org.anchoranalysis.plugin.points.bean.feature.AxisRatioEllipsoid

B

background() - Method in class org.anchoranalysis.image.inference.segment.SegmentedObjectsAtScale: The background image associated with this particular scale.
BackgroundCreator - Class in org.anchoranalysis.mpp.io.output: Utility class for creating background DisplayStacks.
backgroundDisplayStack() - Method in class org.anchoranalysis.image.inference.segment.SegmentedObjectsAtScale: Like SegmentedObjectsAtScale.background() but instead creates a DisplayStack.
BackgroundSubtractor - Class in org.anchoranalysis.plugin.imagej.bean.channel.provider: Subtracts background from a channel using ImageJ's BackgroundSubtracter.
BackgroundSubtractor() - Constructor for class org.anchoranalysis.plugin.imagej.bean.channel.provider.BackgroundSubtractor
BASE - Enum constant in enum class org.anchoranalysis.image.core.dimensions.SpatialUnits.UnitSuffix: A unit amount.
BeanCreator - Class in org.anchoranalysis.bean.xml.creator: Creates a single AnchorBean from XML.
BeanDuplicateException - Exception Class in org.anchoranalysis.bean.exception: An exception occurs when the duplication of a bean fails.
BeanDuplicateException(String) - Constructor for exception class org.anchoranalysis.bean.exception.BeanDuplicateException: Creates with a message only.
BeanDuplicateException(String, Throwable) - Constructor for exception class org.anchoranalysis.bean.exception.BeanDuplicateException: Creates with a message and cause.
BeanDuplicateException(Throwable) - Constructor for exception class org.anchoranalysis.bean.exception.BeanDuplicateException: Creates with a cause only.
BeanField - Annotation Interface in org.anchoranalysis.bean.annotation: Indicates that a field in an Anchor Bean class is to be treated as a bean-field.
BeanInitialization - Interface in org.anchoranalysis.bean.initializable.parameters: Parent class for all state used to initialise beans in InitializableBean.
BeanInitializer - Class in org.anchoranalysis.bean.initializable.property: Tries to initialize a bean and it's children with particular parameters, if possible.
BeanInitializer(Class<?>) - Constructor for class org.anchoranalysis.bean.initializable.property.BeanInitializer: Simpler case where only the current-parameters can be initialized, but for no further property-types.
BeanInitializer(Class<?>, List<ExtractDerivedParameter<P, ?>>) - Constructor for class org.anchoranalysis.bean.initializable.property.BeanInitializer: More complex-case where both current-parameters and other extracted property-types can be initialized.
BeanInstanceMap - Class in org.anchoranalysis.bean: Maps a AnchorBean family-type to a bean that belongs to the family.
BeanInstanceMap() - Constructor for class org.anchoranalysis.bean.BeanInstanceMap
BeanInstanceMapFixture - Class in org.anchoranalysis.test.image.io: Creates a BeanInstanceMap with useful entries for testing, and associates it with bean creation.
BeanListCreator - Class in org.anchoranalysis.bean.xml.creator: Like BeanCreator but creates a list of beans.
BeanMisconfiguredException - Exception Class in org.anchoranalysis.bean.exception: If a Bean is misconfigured.
BeanMisconfiguredException(String) - Constructor for exception class org.anchoranalysis.bean.exception.BeanMisconfiguredException: Creates with a message only.
BeanMisconfiguredException(String, Throwable) - Constructor for exception class org.anchoranalysis.bean.exception.BeanMisconfiguredException: Creates with a message and a cause.
BeanMisconfiguredXMLException - Exception Class in org.anchoranalysis.bean.xml.exception: A bean's XML is thrown when a bean has misconfigured XML.
BeanMisconfiguredXMLException(String, Throwable) - Constructor for exception class org.anchoranalysis.bean.xml.exception.BeanMisconfiguredXMLException: Constructor
BeanMisconfiguredXMLException(Throwable) - Constructor for exception class org.anchoranalysis.bean.xml.exception.BeanMisconfiguredXMLException: Constructor
BeanPathCalculator - Class in org.anchoranalysis.bean.xml.factory: Calculates file-system paths involving an AnchorBean.
BeanProviderAsStackBase<T,S> - Class in org.anchoranalysis.image.bean.provider: A provider base-class that as well as providing type S, also provides a Stack.
BeanProviderAsStackBase() - Constructor for class org.anchoranalysis.image.bean.provider.BeanProviderAsStackBase
BeanStrangeException - Exception Class in org.anchoranalysis.bean.exception: When something quite strange happens that we don't usually want to catch.
BeanStrangeException(String) - Constructor for exception class org.anchoranalysis.bean.exception.BeanStrangeException: Creates with a message only.
BeanStrangeException(String, Throwable) - Constructor for exception class org.anchoranalysis.bean.exception.BeanStrangeException: Creates with a message and cause.
BeanTestChecker - Class in org.anchoranalysis.test.experiment: Checks to see if a bean has been misconfigured, when created manually in tests (thereby skipping the usual checks during the BeanXML loading process).
BeanXMLException - Exception Class in org.anchoranalysis.bean.xml.exception: An exception that occurs when one cannot process BeanXML for some reason.
BeanXMLException(String) - Constructor for exception class org.anchoranalysis.bean.xml.exception.BeanXMLException: Creates with a message only.
BeanXMLException(String, Throwable) - Constructor for exception class org.anchoranalysis.bean.xml.exception.BeanXMLException: Creates with a message and cause.
BeanXMLException(Throwable) - Constructor for exception class org.anchoranalysis.bean.xml.exception.BeanXMLException: Creates with a cause only.
BeanXMLLoader - Class in org.anchoranalysis.bean.xml: Creates beans based on XML specifying their properties (including nested children).
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<AnnotationWithStrategy<S>>, ParametersExperiment) - Method in class org.anchoranalysis.plugin.annotation.bean.aggregate.AggregateAnnotations
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<NamedChannelsInput>, ParametersExperiment) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<NamedChannelsInput>, ParametersExperiment) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<ProvidesStackInput>, ParametersExperiment) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<ProvidesStackInput>, ParametersExperiment) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageAssignLabel
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<StackSequenceInput>, ParametersExperiment) - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<StackSequenceInput>, ParametersExperiment) - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImageCommonSize
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<StackSequenceInput>, ParametersExperiment) - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImageIndependently
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<StackSequenceInput>, ParametersExperiment) - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<FileInput>, ParametersExperiment) - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<FileWithDirectoryInput>, ParametersExperiment) - Method in class org.anchoranalysis.plugin.io.bean.task.CopyFiles
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<AnnotationComparisonInput<ProvidesStackInput>>, ParametersExperiment) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<T>, ParametersExperiment) - Method in class org.anchoranalysis.experiment.bean.task.Task: Called once before all calls to Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>).
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<T>, ParametersExperiment) - Method in class org.anchoranalysis.experiment.bean.task.TaskWithoutSharedState
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<T>, ParametersExperiment) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<T>, ParametersExperiment) - Method in class org.anchoranalysis.plugin.io.bean.task.SummarizeBase
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<T>, ParametersExperiment) - Method in class org.anchoranalysis.plugin.mpp.bean.convert.ConvertNamedChannels
beforeCalc(FeatureInitialization) - Method in class org.anchoranalysis.feature.bean.Feature: Dummy method, that children can optionally override.
beforeCalc(FeatureInitialization) - Method in class org.anchoranalysis.image.feature.bean.physical.ConvertToPhysicalDistance: Initializes the direction vector before calculation.
beforeCalc(FeatureInitialization) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjects
beforeCalc(FeatureInitialization) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.PairedWithMask
beforeCalc(FeatureInitialization) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.FeatureSingleObjectFromShared
beforeCalc(FeatureInitialization) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.ParamFromCollection
beforeCalc(FeatureInitialization) - Method in class org.anchoranalysis.plugin.operator.feature.bean.FromDictionary
beforeCalcSetup(Histogram, int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevel
beforeCalcSetup(Histogram, int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevelBase: Performs setup operations before calculation.
beforeCalcSetup(Histogram, int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.DifferenceCalculateLevelStandardDeviation
beforeCalcWithInitialization(ImageInitialization) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.FeatureSingleObjectFromShared: Performs initialization before calculation with image-specific initialization.
beforeCalcWithInitialization(ImageInitialization) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.MaskAsSingleObject
beforeCalcWithInitialization(ImageInitialization) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.ObjectAggregationBase
BeforeCondition - Interface in org.anchoranalysis.plugin.image.object.merge.condition: A condition to be checked before merging two ObjectMasks.
beforeCopying(Path, List<FileWithDirectoryInput>) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.Anonymize
beforeCopying(Path, List<FileWithDirectoryInput>) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster.ClusterByTimestamp
beforeCopying(Path, List<FileWithDirectoryInput>) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.CopyFilesNaming: To be called once before any calls to CopyFilesNaming.destinationPath(File, DirectoryWithPrefix, int, CopyContext).
beforeCopying(Path, List<FileWithDirectoryInput>) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.CopyFilesNamingOne
beforeCopying(Path, List<FileWithDirectoryInput>) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.CopyFilesNamingWithoutSharedState
beforeCopying(Path, List<FileWithDirectoryInput>) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.PreserveName
BiFloatPredicate - Interface in org.anchoranalysis.core.functional.unchecked: Tests two arguments of type float as a predicate.
BiIntPredicate - Interface in org.anchoranalysis.core.functional.unchecked: Tests two arguments of type int as a predicate.
BiLongPredicate - Interface in org.anchoranalysis.core.functional.unchecked: Tests two arguments of type long as a predicate.
binary - Variable in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage: Iff true the image to be scaled is treated as a binary-mask, and interpolation during scaling ensures only two binary-values are outputted.
binaryChannel(boolean) - Static method in class org.anchoranalysis.image.io.stack.output.StackWriteAttributesFactory: A StackWriteAttributes which is always a binary-channel, and depending on a flag, may be guaranteed to be 2D.
BinaryClassifierImageLabeller - Class in org.anchoranalysis.plugin.image.task.bean.labeller: Labels images using a binary classifier.
BinaryClassifierImageLabeller() - Constructor for class org.anchoranalysis.plugin.image.task.bean.labeller.BinaryClassifierImageLabeller
BinaryKernel - Class in org.anchoranalysis.image.voxel.kernel: Base class for kernels that return a boolean for every voxel.
BinaryKernel(int) - Constructor for class org.anchoranalysis.image.voxel.kernel.BinaryKernel: Creates with a specific kernel-size.
BinaryKernelMorphological - Class in org.anchoranalysis.image.voxel.kernel.morphological: A parent class for any BinaryKernel that implements a morphological operation.
BinaryKernelMorphological(boolean, boolean, boolean) - Constructor for class org.anchoranalysis.image.voxel.kernel.morphological.BinaryKernelMorphological: Creates with a flag for big-neighborhood, and boolean outcomes for certain cases.
BinaryNotOffVoxels - Class in org.anchoranalysis.image.bean.threshold.relation: Selects voxels that are not off voxels.
BinaryNotOffVoxels() - Constructor for class org.anchoranalysis.image.bean.threshold.relation.BinaryNotOffVoxels
BinaryNotOnVoxels - Class in org.anchoranalysis.image.bean.threshold.relation: Selects voxels that are not on voxels.
BinaryNotOnVoxels() - Constructor for class org.anchoranalysis.image.bean.threshold.relation.BinaryNotOnVoxels
BinaryOffVoxels - Class in org.anchoranalysis.image.bean.threshold.relation: Selects only the off voxels.
BinaryOffVoxels() - Constructor for class org.anchoranalysis.image.bean.threshold.relation.BinaryOffVoxels
BinaryOnOffSetter - Interface in org.anchoranalysis.image.voxel.binary: Getters and setters for reading and assigning binary state to voxels.
BinaryOnVoxels - Class in org.anchoranalysis.image.bean.threshold.relation: Selects only the on pixels.
BinaryOnVoxels() - Constructor for class org.anchoranalysis.image.bean.threshold.relation.BinaryOnVoxels
binaryOperation(Voxels<UnsignedByteBuffer>, Voxels<UnsignedByteBuffer>, Voxels<UnsignedByteBuffer>, IntBinaryOperator) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll: Iterate over each voxel in a bounding-box - applying a binary operation with values from two input Voxels<UnsignedByteBuffer> for each slice and writing it into an output Voxels<UnsignedByteBuffer>.
BinaryOutcomeImageLabeller - Class in org.anchoranalysis.plugin.image.task.bean.labeller: Abstract base class for image labellers that produce binary outcomes (positive or negative).
BinaryOutcomeImageLabeller() - Constructor for class org.anchoranalysis.plugin.image.task.bean.labeller.BinaryOutcomeImageLabeller
binaryResizer(int) - Method in class org.anchoranalysis.image.voxel.resizer.VoxelsResizerFactory: A VoxelsResizer that is suitable for resizing a binary raster-image, restricted to two possible intensity values only.
BinarySegmentation - Class in org.anchoranalysis.image.bean.segment.binary: Performs a segmentation on voxels so that each voxel has an on or off state after the operation.
BinarySegmentation() - Constructor for class org.anchoranalysis.image.bean.segment.binary.BinarySegmentation
BinarySegmentationParameters - Class in org.anchoranalysis.image.bean.nonbean.segment: Parameters that are passed during a BinarySegmentation.
BinarySegmentationParameters() - Constructor for class org.anchoranalysis.image.bean.nonbean.segment.BinarySegmentationParameters: Creates with no intensity-histogram or resolution.
BinarySegmentationParameters(Optional<Resolution>) - Constructor for class org.anchoranalysis.image.bean.nonbean.segment.BinarySegmentationParameters: Creates with a specific resolution, but no intensity-histogram.
BinarySegmentationParameters(Optional<Histogram>, Optional<Resolution>) - Constructor for class org.anchoranalysis.image.bean.nonbean.segment.BinarySegmentationParameters: Creates a new BinarySegmentationParameters instance.
BinarySegmentationParameters(Resolution, Optional<Histogram>) - Constructor for class org.anchoranalysis.image.bean.nonbean.segment.BinarySegmentationParameters: Creates with a specific resolution and intensity-histogram.
BinarySegmentationReference - Class in org.anchoranalysis.image.bean.segment.binary: Uses an existing BinarySegmentation that is located by a unique identifier.
BinarySegmentationReference() - Constructor for class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationReference
binarySegmentations() - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitialization: A collection of BinarySegmentations, indexed by name.
BinarySegmentationThreshold - Class in org.anchoranalysis.image.bean.segment.binary: Implementation of BinarySegmentation that performs global thresholding.
BinarySegmentationThreshold() - Constructor for class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationThreshold
BinarySegmentationUnary - Class in org.anchoranalysis.image.bean.segment.binary: An implementation of BinarySegmentation that delegates to one other BinarySegmentation.
BinarySegmentationUnary() - Constructor for class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationUnary
BinarySegmentByObject - Class in org.anchoranalysis.plugin.image.bean.object.provider.segment: Performs a binary-segmentation using the upstream objects as masks.
BinarySegmentByObject() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.segment.BinarySegmentByObject
binaryValues() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels: Which two intensity values represent off and on states.
binaryValues() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: What values constitute an on and off state in voxels - as ints.
binaryValuesByte() - Method in class org.anchoranalysis.image.core.mask.Mask: The two states which are permitted to be assigned to the voxels, stored as bytes.
binaryValuesByte() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: What values constitute an on and off state in voxels - as bytes.
BinaryValuesByte - Class in org.anchoranalysis.image.voxel.binary.values: Two values representing byte binary states in an UnsignedByteBuffer.
BinaryValuesByte(byte, byte) - Constructor for class org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte: Creates a new BinaryValuesByte instance.
BinaryValuesByte(int, int) - Constructor for class org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte: Create with int values for off and on states.
binaryValuesInt() - Method in class org.anchoranalysis.image.core.mask.Mask: The two states which are permitted to be assigned to the voxels, stored as unsigned ints.
BinaryValuesInt - Class in org.anchoranalysis.image.voxel.binary.values: Two values representing int binary states in an unsigned-byte buffer.
BinaryValuesInt(int, int) - Constructor for class org.anchoranalysis.image.voxel.binary.values.BinaryValuesInt: Creates a new BinaryValuesInt instance.
binaryVoxels() - Method in class org.anchoranalysis.image.core.mask.Mask: The underlying voxels in the mask, exposed as BinaryVoxels.
binaryVoxels() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: The underlying voxel memory buffers for the object-mask, exposed via a BinaryVoxels.
BinaryVoxels<T> - Class in org.anchoranalysis.image.voxel.binary: Like Voxels but should only contain two distinct intensity-values representing on and off. states.
BinaryVoxels(Voxels<T>, BinaryValuesInt) - Constructor for class org.anchoranalysis.image.voxel.binary.BinaryVoxels: Creates a new BinaryVoxels instance.
BinaryVoxelsBase - Class in org.anchoranalysis.image.bean.threshold.relation: A base class for implementations of RelationToThreshold where the threshold is derived from a BinaryValuesInt.
BinaryVoxelsBase() - Constructor for class org.anchoranalysis.image.bean.threshold.relation.BinaryVoxelsBase
BinaryVoxelsFactory - Class in org.anchoranalysis.image.voxel.binary: Creates BinaryVoxels parameterized by size and initial state.
binaryVoxelsFor(Voxels<T>, BinaryValuesInt) - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels: Creates a BinaryVoxels corresponding to a particular voxels and BinaryValuesInt.
BindFailedException - Exception Class in org.anchoranalysis.io.output.outputter: When an outputter cannot be successfully bound to an output directory.
BindFailedException(String) - Constructor for exception class org.anchoranalysis.io.output.outputter.BindFailedException: Create from message.
BindFailedException(Throwable) - Constructor for exception class org.anchoranalysis.io.output.outputter.BindFailedException: Create from cause.
BioformatsReader - Class in org.anchoranalysis.io.bioformats.bean: Reads a stack using the Bioformats library.
BioformatsReader() - Constructor for class org.anchoranalysis.io.bioformats.bean.BioformatsReader
BioformatsReader(ReadOptions) - Constructor for class org.anchoranalysis.io.bioformats.bean.BioformatsReader: Create with particular options.
BioformatsWriter - Class in org.anchoranalysis.io.bioformats.bean.writer: Base class for writing a stack to the filesystem using the Bioformats library.
BioformatsWriter(boolean) - Constructor for class org.anchoranalysis.io.bioformats.bean.writer.BioformatsWriter: Creates a new BioformatsWriter instance.
BiShortPredicate - Interface in org.anchoranalysis.core.functional.unchecked: Tests two arguments of type short as a predicate.
BIT_DEPTH - Static variable in class org.anchoranalysis.image.voxel.datatype.FloatVoxelType: How many bits to represent this voxel-type.
BIT_DEPTH - Static variable in class org.anchoranalysis.image.voxel.datatype.SignedShortVoxelType: How many bits to represent this voxel-type.
BIT_DEPTH - Static variable in class org.anchoranalysis.image.voxel.datatype.UnsignedByteVoxelType: How many bits to represent this voxel-type.
BIT_DEPTH - Static variable in class org.anchoranalysis.image.voxel.datatype.UnsignedIntVoxelType: How many bits to represent this voxel-type.
BIT_DEPTH - Static variable in class org.anchoranalysis.image.voxel.datatype.UnsignedShortVoxelType: How many bits to represent this voxel-type.
bitDepth() - Method in class org.anchoranalysis.image.voxel.datatype.VoxelDataType: The number of bits required to represent a voxel.
bitDepth(Logger) - Method in class org.anchoranalysis.image.io.channel.input.NamedChannelsInput: Bit-depth of image.
bitDepth(Logger) - Method in interface org.anchoranalysis.image.io.stack.input.OpenedImageFile: The bit-depth of the image voxels e.g. 8 for 8-bit, 16 for 16-bit etc.
bitDepth(Logger) - Method in class org.anchoranalysis.plugin.io.multifile.OpenedMultiFile
BitDepth - Class in org.anchoranalysis.plugin.io.bean.summarizer.image
BitDepth() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.image.BitDepth
BitDepthPerChannel - Class in org.anchoranalysis.plugin.image.feature.bean.metadata: The bit-depth of the image per channel.
BitDepthPerChannel() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.metadata.BitDepthPerChannel
blockUntilLoaded() - Static method in class org.anchoranalysis.plugin.opencv.CVInit: Blocks a thread until the initialization has completed.
blue() - Method in class org.anchoranalysis.image.core.stack.RGBStack: The blue channel.
BLUE - Static variable in class org.anchoranalysis.image.core.stack.RGBChannelNames: Name for the blue channel.
blur(VoxelsUntyped, Dimensions, MessageLogger) - Method in class org.anchoranalysis.plugin.image.bean.blur.BlurGaussian3D
blur(VoxelsUntyped, Dimensions, MessageLogger) - Method in class org.anchoranalysis.plugin.image.bean.blur.BlurGaussianEachSlice2D
blur(VoxelsUntyped, Dimensions, MessageLogger) - Method in class org.anchoranalysis.plugin.image.bean.blur.BlurStrategy: Applies the blur operation to the given voxels.
Blur - Class in org.anchoranalysis.plugin.image.bean.channel.provider.intensity: Blurs an image using a particular strategy (defaults to a gaussian blur in each slice)
Blur() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.Blur
BlurGaussian3D - Class in org.anchoranalysis.plugin.image.bean.blur: Performs a Gaussian Blur in 3D
BlurGaussian3D() - Constructor for class org.anchoranalysis.plugin.image.bean.blur.BlurGaussian3D
BlurGaussianEachSlice2D - Class in org.anchoranalysis.plugin.image.bean.blur: Performs a Gaussian-blur in 2D on each slice independently
BlurGaussianEachSlice2D() - Constructor for class org.anchoranalysis.plugin.image.bean.blur.BlurGaussianEachSlice2D
BlurStrategy - Class in org.anchoranalysis.plugin.image.bean.blur: A method for applying blurring to an image.
BlurStrategy() - Constructor for class org.anchoranalysis.plugin.image.bean.blur.BlurStrategy
BMP - Class in org.anchoranalysis.plugin.io.bean.metadata.header: The headers found in a BMP file.
BMP - Enum constant in enum class org.anchoranalysis.core.format.ImageFileFormat: Windows Bitmap - note that this comes in many variants.
BMP() - Constructor for class org.anchoranalysis.plugin.io.bean.metadata.header.BMP
bothNameAndParameters() - Static method in class org.anchoranalysis.feature.store.NamedFeatureStoreFactory: The custom-names of the features are derived from both their name and their parameters.
BOTTOM - Static variable in class org.anchoranalysis.image.bean.nonbean.spatial.align.PositionChoicesConstants: Align to the bottom in the Y-dimension.
Bound - Class in org.anchoranalysis.mpp.bean.bound: An abstract class representing an upper and lower bound.
Bound() - Constructor for class org.anchoranalysis.mpp.bean.bound.Bound
boundaryMax(FeatureCalculationInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.CompareWithRangeFeature
boundaryMax(FeatureCalculationInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareBase: Defines the maximum accepted value in the range.
boundaryMax(FeatureCalculationInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareFromScalars
boundaryMin(FeatureCalculationInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.CompareWithRangeFeature
boundaryMin(FeatureCalculationInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareBase: Defines the minimum accepted value in the range.
boundaryMin(FeatureCalculationInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareFromScalars
BoundDegrees - Class in org.anchoranalysis.mpp.bean.bound: Represents an upper and lower bound in degrees which is converted to radians when resolved.
BoundDegrees() - Constructor for class org.anchoranalysis.mpp.bean.bound.BoundDegrees: Creates a new instance with default bounds of 0 to 360 degrees.
BoundDegrees(BoundDegrees) - Constructor for class org.anchoranalysis.mpp.bean.bound.BoundDegrees: Creates a new instance by copying an existing BoundDegrees.
BoundedList<T> - Class in org.anchoranalysis.spatial.box: One or more elements, each with an individual bounding-box, and collectively with a bounding-box that fully contains them all.
boundedVoxels() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: The underlying voxel memory buffers for the object-mask, exposed via BoundedVoxels.
BoundedVoxels<T> - Class in org.anchoranalysis.image.voxel: Voxels that exist within a particular bounding-box in an image.
BoundedVoxels(BoundedVoxels<T>) - Constructor for class org.anchoranalysis.image.voxel.BoundedVoxels: Copy constructor.
BoundedVoxels(Voxels<T>) - Constructor for class org.anchoranalysis.image.voxel.BoundedVoxels: Creates voxels bounded to match the entire voxel-data at the origin.
BoundedVoxels(BoundingBox, Voxels<T>) - Constructor for class org.anchoranalysis.image.voxel.BoundedVoxels: Creates voxels with a corresponding bounding box.
boundingBox() - Method in class org.anchoranalysis.image.core.object.properties.ObjectWithProperties: The bounding-box which gives a location for the object-mask on an image.
boundingBox() - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: A bounding-box that associates voxels to a particular part of an image.
boundingBox() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: The bounding-box which gives a location for the object-mask on an image.
boundingBox() - Method in interface org.anchoranalysis.mpp.mark.voxelized.VoxelizedMark: Gets the bounding-box enclosing the voxelized representation of the mark.
boundingBox() - Method in class org.anchoranalysis.spatial.box.BoundedList: A bounding-box that must contain all elements in the collection
BoundingBox - Class in org.anchoranalysis.spatial.box: A bounding-box in two or three dimensions.
BoundingBox(Extent) - Constructor for class org.anchoranalysis.spatial.box.BoundingBox: Constructs a bounding-box to cover the entirety of a certain extent.
BoundingBoxAlongAxisBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox: Base class for features that calculate a value along a specific axis of an object's bounding box.
BoundingBoxAlongAxisBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxAlongAxisBase
BoundingBoxCalculator - Class in org.anchoranalysis.mpp.mark.conic: Functions to calculate a bounding-box for a point surrounded by some form of radius.
BoundingBoxContains - Class in org.anchoranalysis.spatial.box: Does a bounding box contain other objects?
BoundingBoxContains(BoundingBox) - Constructor for class org.anchoranalysis.spatial.box.BoundingBoxContains: Create with the BoundingBox that is queried.
BoundingBoxDistance - Class in org.anchoranalysis.spatial.box: Calculates distance between two bounding boxes.
BoundingBoxEnclosed - Class in org.anchoranalysis.image.bean.nonbean.spatial.arrange: Describes a BoundingBox that is optionally enclosed by a larger containing BoundingBox to given padding.
BoundingBoxEnclosed(BoundingBox) - Constructor for class org.anchoranalysis.image.bean.nonbean.spatial.arrange.BoundingBoxEnclosed: Create with a box that has no padding.
BoundingBoxEnclosed(BoundingBox, BoundingBox) - Constructor for class org.anchoranalysis.image.bean.nonbean.spatial.arrange.BoundingBoxEnclosed: Creates a new BoundingBoxEnclosed instance.
BoundingBoxExtentAlongAxis - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox: Calculates the extent of an object's bounding box along a specified axis.
BoundingBoxExtentAlongAxis() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxExtentAlongAxis
BoundingBoxFactory - Class in org.anchoranalysis.spatial.box: Utility methods to create a BoundingBox.
boundingBoxFlattened() - Method in interface org.anchoranalysis.mpp.mark.voxelized.VoxelizedMark: Gets the bounding-box flattened in z dimension.
boundingBoxFor(T) - Method in interface org.anchoranalysis.image.core.object.scale.AccessObjectMask: A bounding-box for a given element.
BoundingBoxFromPoints - Class in org.anchoranalysis.image.core.points: Creates a bounding-box from one or more points.
BoundingBoxIntersection - Class in org.anchoranalysis.mpp.feature.addcriteria: An AddCriteriaPair that includes marks if their bounding boxes intersect.
BoundingBoxIntersection - Class in org.anchoranalysis.spatial.box: Methods for checking intersection between a particular bounding-box and others.
BoundingBoxIntersection() - Constructor for class org.anchoranalysis.mpp.feature.addcriteria.BoundingBoxIntersection
BoundingBoxIntersection(BoundingBox) - Constructor for class org.anchoranalysis.spatial.box.BoundingBoxIntersection
BoundingBoxMaximumAlongAxis - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox: Calculates the maximum coordinate of an object's bounding box along a specified axis.
BoundingBoxMaximumAlongAxis() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxMaximumAlongAxis
BoundingBoxMerger - Class in org.anchoranalysis.spatial.box: Merges one or more BoundingBox together, to create a single BoundingBox that spans them all.
BoundingBoxMinimumAlongAxis - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox: Calculates the minimum coordinate of an object's bounding box along a specified axis.
BoundingBoxMinimumAlongAxis() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxMinimumAlongAxis
BoundingBoxNumberVoxels - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox: Calculates the number of voxels in the bounding box of an object.
BoundingBoxNumberVoxels() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxNumberVoxels
BoundingBoxRTree<T> - Class in org.anchoranalysis.spatial.rtree: An R-Tree that contains items, each with an associated bounding-box in three dimensions.
BoundingBoxRTree() - Constructor for class org.anchoranalysis.spatial.rtree.BoundingBoxRTree: Creates an empty R-Tree.
BoundingBoxRTree(int) - Constructor for class org.anchoranalysis.spatial.rtree.BoundingBoxRTree: Creates an empty R-Tree with a specified number of children.
boundingBoxThatSpansInput(FeatureInputPairObjects) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
boundingBoxThatSpansInput(FeatureInputSingleObject) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.EachObjectIndependently
boundingBoxThatSpansInput(T) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.CombineObjectsForFeatures: Creates a bounding-box that tightly fits the input to a particular table row (could be for one or more objects).
BoundingBoxUnion - Class in org.anchoranalysis.spatial.box: Performs union of a bounding-box with other entities
BoundingBoxUnion(BoundingBox) - Constructor for class org.anchoranalysis.spatial.box.BoundingBoxUnion
BoundMinMax - Class in org.anchoranalysis.mpp.bean.bound: An abstract class representing a bound with minimum and maximum values.
BoundMinMax() - Constructor for class org.anchoranalysis.mpp.bean.bound.BoundMinMax: Creates a new instance with default minimum and maximum values.
BoundMinMax(double, double) - Constructor for class org.anchoranalysis.mpp.bean.bound.BoundMinMax: Creates a new instance with specified minimum and maximum values.
BoundMinMax(BoundMinMax) - Constructor for class org.anchoranalysis.mpp.bean.bound.BoundMinMax: Creates a new instance by copying another BoundMinMax.
BoundOutputter<T> - Class in org.anchoranalysis.io.generator.sequence: An outputter bound together with OutputPattern and a generator.
BoundOutputter(OutputterChecked, OutputPattern, Generator<T>) - Constructor for class org.anchoranalysis.io.generator.sequence.BoundOutputter: Creates a new BoundOutputter instance.
BoundPhysicalExtent - Class in org.anchoranalysis.mpp.bean.bound: A bound representing physical extents, which can be resolved based on image resolution.
BoundPhysicalExtent() - Constructor for class org.anchoranalysis.mpp.bean.bound.BoundPhysicalExtent
BoundPhysicalExtent(double, double) - Constructor for class org.anchoranalysis.mpp.bean.bound.BoundPhysicalExtent: Creates a new instance with specified minimum and maximum values.
BoundPhysicalExtent(BoundPhysicalExtent) - Constructor for class org.anchoranalysis.mpp.bean.bound.BoundPhysicalExtent: Creates a new instance by copying another BoundPhysicalExtent.
BoundReplaceStrategy<T,S> - Class in org.anchoranalysis.feature.session.replace: Attaches a replacement-strategy to a session lazily.
BoundReplaceStrategy(Function<CacheCreator, S>) - Constructor for class org.anchoranalysis.feature.session.replace.BoundReplaceStrategy: Creates a new BoundReplaceStrategy instance.
BoundRotation - Class in org.anchoranalysis.mpp.bean.bound.rotation: Abstract base class for defining bounds on rotations.
BoundRotation() - Constructor for class org.anchoranalysis.mpp.bean.bound.rotation.BoundRotation
BoundRotation2D - Class in org.anchoranalysis.mpp.bean.bound.rotation: Creates a randomly-generated orientation in 2D by uniformally sampling a scalar rotation angle
BoundRotation2D() - Constructor for class org.anchoranalysis.mpp.bean.bound.rotation.BoundRotation2D
BoundRotation3D - Class in org.anchoranalysis.mpp.bean.bound.rotation: Creates a randomly-generated orientation in 3D based upon Euler Angles
BoundRotation3D() - Constructor for class org.anchoranalysis.mpp.bean.bound.rotation.BoundRotation3D
BoundUnitless - Class in org.anchoranalysis.mpp.bean.bound: A bound representing unitless values, where the minimum and maximum are not affected by resolution.
BoundUnitless() - Constructor for class org.anchoranalysis.mpp.bean.bound.BoundUnitless: Creates a new instance with default minimum and maximum values.
BoundUnitless(double, double) - Constructor for class org.anchoranalysis.mpp.bean.bound.BoundUnitless: Creates a new instance with specified minimum and maximum values.
BoundUnitless(BoundUnitless) - Constructor for class org.anchoranalysis.mpp.bean.bound.BoundUnitless: Creates a new instance by copying another BoundUnitless.
box() - Method in class org.anchoranalysis.mpp.mark.points.PointListBase: Creates a bounding box from the min and max points.
box(Dimensions, int) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
box(Dimensions, int) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
box(Dimensions, int) - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
box(Dimensions, int) - Method in class org.anchoranalysis.mpp.mark.Mark: Calculates the bounding box for a specific region of the mark.
box(Dimensions, int) - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
box(Dimensions, int) - Method in class org.anchoranalysis.mpp.mark.points.PointListBase
box(Dimensions, int) - Method in class org.anchoranalysis.mpp.mark.points.RotatableBoundingBox
box(DrawOverlay, Dimensions) - Method in class org.anchoranalysis.mpp.overlay.OverlayMark
box(DrawOverlay, Dimensions) - Method in class org.anchoranalysis.overlay.object.OverlayObjectMask
box(DrawOverlay, Dimensions) - Method in class org.anchoranalysis.overlay.Overlay: A bounding-box around the overlay.
box(BoundingBox) - Method in class org.anchoranalysis.spatial.box.BoundingBoxContains: Is this other bounding-box fully contained within this bounding box?
Box - Class in org.anchoranalysis.plugin.image.bean.mask.provider.morphological: Creates a Mask where all pixels are on within a box region.
Box() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Box
BoxAligner - Class in org.anchoranalysis.image.bean.spatial.arrange.align: Aligns a smaller BoundingBox to fit inside a larger BoundingBox.
BoxAligner() - Constructor for class org.anchoranalysis.image.bean.spatial.arrange.align.BoxAligner
boxAllRegions(Dimensions) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
boxAllRegions(Dimensions) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
boxAllRegions(Dimensions) - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
boxAllRegions(Dimensions) - Method in class org.anchoranalysis.mpp.mark.Mark: Calculates the bounding box for all regions of the mark.
boxAllRegions(Dimensions) - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
boxAllRegions(Dimensions) - Method in class org.anchoranalysis.mpp.mark.points.PointList
boxAllRegions(Dimensions) - Method in class org.anchoranalysis.mpp.mark.points.Polygon
boxAllRegions(Dimensions) - Method in class org.anchoranalysis.mpp.mark.points.PolygonCurve
boxAllRegions(Dimensions) - Method in class org.anchoranalysis.mpp.mark.points.RotatableBoundingBox
boxCopyTo(BoundingBox, Voxels<T>, BoundingBox) - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter: Copies a bounding-box area to another Voxels.
boxes() - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.StackArrangement: Where to locate a respective image on a larger image.
boxFromBounds(Point3d, double, boolean, Dimensions) - Static method in class org.anchoranalysis.mpp.mark.conic.BoundingBoxCalculator: Calculates a bounding box for a point with a scalar radius in all dimensions.
boxFromBounds(Point3d, DoubleMatrix1D, boolean, Dimensions) - Static method in class org.anchoranalysis.mpp.mark.conic.BoundingBoxCalculator: Calculates a bounding box for a point with varying radii in each dimension (that have already been resolved into a matrix)
boxList(Dimensions, int) - Method in class org.anchoranalysis.mpp.mark.MarkCollection: Creates a list of bounding boxes for all marks in the collection.
BranchChannels - Class in org.anchoranalysis.plugin.io.bean.stack.writer: Uses different raster-writers depending on the number/type of channels.
BranchChannels() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.writer.BranchChannels
BranchExtension - Class in org.anchoranalysis.plugin.io.bean.stack.reader: If the extension(s) of a path matches a particular value, then use a particular reader, otherwise a fallback.
BranchExtension() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.reader.BranchExtension
BranchIfDebug<T> - Class in org.anchoranalysis.plugin.io.bean.input: Uses one input-manager normally, but a different one if in debug mode.
BranchIfDebug() - Constructor for class org.anchoranalysis.plugin.io.bean.input.BranchIfDebug
BranchStack - Class in org.anchoranalysis.plugin.io.bean.stack.writer: Uses different raster-writers depending on whether it is always 2D (not a z-stack) or possibly 3D.
BranchStack() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.writer.BranchStack
BranchSuggestedFormat - Class in org.anchoranalysis.plugin.io.bean.stack.writer: Selects particular writers based on if particular suggested image formats are present.
BranchSuggestedFormat() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.writer.BranchSuggestedFormat
Bridge - Class in org.anchoranalysis.plugin.image.bean.object.match: Matches to another object, and then uses that object to bridge to another
Bridge() - Constructor for class org.anchoranalysis.plugin.image.bean.object.match.Bridge
buffer() - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer: The associated buffer for storing the voxels.
buffer() - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferUnsigned
BufferedImageFromStack - Class in org.anchoranalysis.image.core.bufferedimage: Converts a Stack or similar data-objects into an AWT BufferedImage.
BufferedImageFromVoxels - Class in org.anchoranalysis.image.voxel.convert.bufferedimage: Converts a Voxels instance into an AWT BufferedImage.
bufferRelative(int) - Method in class org.anchoranalysis.image.voxel.buffer.SlidingBuffer: Returns the corresponding buffer at a relative z-slice index to the current focused z-slice.
BufferRetriever - Interface in org.anchoranalysis.image.voxel.kernel: Retrieves a buffer corresponding to a relative index in the z-dimension.
buildPath(String) - Method in interface org.anchoranalysis.core.format.FileFormat: Builds a path which has an existing path but missing an extension.
buildPath(String, String) - Method in interface org.anchoranalysis.core.format.FileFormat: Builds a path with a directory and filename component.
buildPath(Path) - Method in interface org.anchoranalysis.core.format.FileFormat: Builds a path which has an existing path but missing an extension.
buildPath(Path, String) - Method in interface org.anchoranalysis.core.format.FileFormat: Builds a path with a directory and filename component.
bySymbol() - Method in interface org.anchoranalysis.feature.calculate.FeatureCalculationInput: Calculates a feature if only an symbol (ID/name) is known, which refers to another feature.
bySymbol() - Method in class org.anchoranalysis.feature.session.SessionInputSequential
ByteRepresentationForChannel - Interface in org.anchoranalysis.io.bioformats.bean.writer: Creates or retrieves a byte representation of the voxels for a particular slice.
bytesForSlice(int) - Method in interface org.anchoranalysis.io.bioformats.bean.writer.ByteRepresentationForChannel: The byte-representation of the voxels for a particular slice.
bytesPerVoxel() - Method in class org.anchoranalysis.io.bioformats.copyconvert.ConvertTo: The number bytes to describe each source-voxel.
bytesPerVoxel() - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromFloat
bytesPerVoxel() - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedByte
bytesPerVoxel() - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedByteNoInterleavingScale
bytesPerVoxel() - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedInt
bytesPerVoxel() - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedShort
bytesPerVoxel() - Method in class org.anchoranalysis.io.bioformats.copyconvert.tofloat.FloatFromUnsignedByte
bytesPerVoxel() - Method in class org.anchoranalysis.io.bioformats.copyconvert.tofloat.FloatFromUnsignedInt
bytesPerVoxel() - Method in class org.anchoranalysis.io.bioformats.copyconvert.toint.UnsignedIntFromUnsignedInt
bytesPerVoxel() - Method in class org.anchoranalysis.io.bioformats.copyconvert.toshort.ToUnsignedShort
Bytewise - Class in org.anchoranalysis.plugin.io.bean.file.copy.method: Makes a simple bytewise copy of a file, where no byte is changed.
Bytewise() - Constructor for class org.anchoranalysis.plugin.io.bean.file.copy.method.Bytewise

C

cache(Supplier<T>) - Static method in class org.anchoranalysis.core.cache.CachedSupplier: Creates a cached-version of a Supplier.
cache(StoreSupplier<T>) - Static method in interface org.anchoranalysis.core.identifier.provider.store.StoreSupplier: Memoizes (caches) the supplied object, and returning it with an identical interface.
cache(FeatureCalculatorMulti<T>) - Static method in class org.anchoranalysis.feature.session.calculator.FeatureCalculatorCache: Creates a cached version of a FeatureCalculatorMulti with a default cache-size.
cache(FeatureCalculatorMulti<T>, int) - Static method in class org.anchoranalysis.feature.session.calculator.FeatureCalculatorCache: Creates a cached version of a FeatureCalculatorMulti with a particular cache-size.
cache(FeatureCalculatorSingle<T>) - Static method in class org.anchoranalysis.feature.session.calculator.FeatureCalculatorCache: Creates a cached version of a FeatureCalculatorSingle with a default cache-size.
cache(FeatureCalculatorSingle<T>, int) - Static method in class org.anchoranalysis.feature.session.calculator.FeatureCalculatorCache: Creates a cached version of a FeatureCalculatorSingle with a particular cache-size.
cache(NamedStacksSupplier) - Static method in interface org.anchoranalysis.image.core.stack.named.NamedStacksSupplier: Caches a NamedStacksSupplier so that its value will be remembered after first execution.
CACHE_NAME_FIRST - Static variable in class org.anchoranalysis.image.feature.bean.object.pair.FeatureDeriveFromPair: Cache name for the first object in the pair.
CACHE_NAME_MERGED - Static variable in class org.anchoranalysis.image.feature.bean.object.pair.FeatureDeriveFromPair: Cache name for the merged object from the pair.
CACHE_NAME_SECOND - Static variable in class org.anchoranalysis.image.feature.bean.object.pair.FeatureDeriveFromPair: Cache name for the second object in the pair.
CacheAndReuseStrategy<T> - Class in org.anchoranalysis.feature.session.replace: Reuse an existing FeatureCalculationInput, as stored in a least-recently used cache, and without invalidating it.
CacheAndReuseStrategy(CacheCreator) - Constructor for class org.anchoranalysis.feature.session.replace.CacheAndReuseStrategy: Create with a particular CacheCreator.
cacheChecked(CheckedSupplier<T, E>) - Static method in class org.anchoranalysis.core.cache.CachedSupplier: Creates a cached-version of a CheckedSupplier.
CacheCreator - Interface in org.anchoranalysis.feature.calculate.cache: Creates a FeatureCalculationCache that accepts a particular input type.
CachedSupplier<T,E> - Class in org.anchoranalysis.core.cache: Memoizes (caches) a CheckedSupplier.
CachedSupplierBase<T> - Class in org.anchoranalysis.core.cache: Base class for functions that memoize (cache) a call to an interface.
CachedSupplierBase() - Constructor for class org.anchoranalysis.core.cache.CachedSupplierBase
cacheName() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.DerivedObject: Provides a unique name for caching the derived object.
cacheName() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.Erode: Provides a unique name for caching the eroded object.
cacheName() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.Shell
cacheResettable(StoreSupplier<T>) - Static method in interface org.anchoranalysis.core.identifier.provider.store.StoreSupplier: Memoizes (caches) the supplied object, and returning it with a CachedSupplier interface
cachesToAvoidInvalidating() - Method in class org.anchoranalysis.feature.session.cache.finder.CheckCacheForSpecificChildren
cachesToAvoidInvalidating() - Method in interface org.anchoranalysis.feature.session.cache.finder.ChildCacheFinder: If set, these particular-caches are exceptionally not invalidated during the typical invalidation operation on their parent.
cachesToAvoidInvalidating() - Method in class org.anchoranalysis.feature.session.cache.finder.DefaultChildCacheFinder
CacheSupplier<T,E> - Interface in org.anchoranalysis.feature.session.cache.finder: Supplies a LRUCache that maps a feature input-type to a corresponding to FeatureCalculationInput.
CacheTransferSource<T> - Class in org.anchoranalysis.feature.session.cache.finder: An existing cache that can be used as a source for child-caches elsewhere.
CacheTransferSource(CacheSupplier<T, OperationFailedException>, Set<ChildCacheName>) - Constructor for class org.anchoranalysis.feature.session.cache.finder.CacheTransferSource: Creates a new CacheTransferSource instance.
CacheTransferSourceCollection - Class in org.anchoranalysis.feature.session.cache.finder: A collection of existing caches that can collectively be used as sources for child-caches elsewhere.
CacheTransferSourceCollection() - Constructor for class org.anchoranalysis.feature.session.cache.finder.CacheTransferSourceCollection
calc(CalculateForChild<T>, Feature<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.FeatureSingleObjectFromShared: Calculates the feature value for a single object.
calc(CalculateForChild<T>, Feature<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.MaskAsSingleObject
calc(CalculateForChild<T>, Feature<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.ObjectAggregationBase
calc(FeatureCalculationInput<T>, CalculationPart<U, T>, Function<ResolvedPart<U, T>, CalculateInputFromDelegateOption<S, T, U>>, Feature<S>, ChildCacheName, double) - Static method in class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegateOption: Calculates a feature using a cached-calculation as delegate.
calc(EnergyMemoList, EnergySchemeWithSharedFeatures, EnergyStackWithoutParameters) - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedAll: Calculates the total energy for all items using the provided energy scheme and stack.
calculate(int) - Method in interface org.anchoranalysis.math.optimization.SearchClosestValueMonoticallyIncreasing.ValueFunction: Calculate the output value, for a particular input-value.
calculate(int[]) - Method in class org.anchoranalysis.image.feature.bean.VoxelScore: Calculates a score for a set of voxel intensities.
calculate(int[]) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Difference
calculate(int[]) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Identity
calculate(int[]) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram
calculate(int[]) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.OutsideRange
calculate(int[]) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.RejectIfIntensityLessThan
calculate(int[]) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.SingleChannel
calculate(Optional<Dimensions>, Optional<ImageSizeSuggestion>) - Method in class org.anchoranalysis.image.bean.spatial.ScaleCalculator: Calculates a scaling-factor for a source image/entity of particular dimensions.
calculate(Optional<Dimensions>, Optional<ImageSizeSuggestion>) - Method in class org.anchoranalysis.plugin.image.bean.scale.ConstantScaleFactor
calculate(Optional<Dimensions>, Optional<ImageSizeSuggestion>) - Method in class org.anchoranalysis.plugin.image.bean.scale.FitTo
calculate(Optional<Dimensions>, Optional<ImageSizeSuggestion>) - Method in class org.anchoranalysis.plugin.image.bean.scale.Invert
calculate(Optional<Dimensions>, Optional<ImageSizeSuggestion>) - Method in class org.anchoranalysis.plugin.image.bean.scale.MinimumXYResolution
calculate(Optional<Dimensions>, Optional<ImageSizeSuggestion>) - Method in class org.anchoranalysis.plugin.image.bean.scale.ToDimensions
calculate(Optional<Dimensions>, Optional<ImageSizeSuggestion>) - Method in class org.anchoranalysis.plugin.image.bean.scale.ToSuggested
calculate(Feature<S>, CalculationPart<S, T>, ChildCacheName) - Method in interface org.anchoranalysis.feature.calculate.cache.CalculateForChild: Calculates a feature in a child-cache using a new input created from a CalculationPart.
calculate(Feature<S>, S, ChildCacheName) - Method in interface org.anchoranalysis.feature.calculate.cache.CalculateForChild: Calculates a feature in a child-cache.
calculate(Feature<T>) - Method in interface org.anchoranalysis.feature.calculate.FeatureCalculationInput: Calculates the result of a feature using this input.
calculate(Feature<T>) - Method in class org.anchoranalysis.feature.session.SessionInputSequential
calculate(Feature<T>, FeatureCalculationInput<T>) - Method in interface org.anchoranalysis.feature.calculate.FeatureCalculator: Calculate the result of feature with a particular input.
calculate(FeatureList<T>) - Method in interface org.anchoranalysis.feature.calculate.FeatureCalculationInput: Calculates the results of several features using this input.
calculate(FeatureList<T>) - Method in class org.anchoranalysis.feature.session.SessionInputSequential
calculate(FeatureList<T>, FeatureCalculationInput<T>) - Method in interface org.anchoranalysis.feature.calculate.FeatureCalculator: Calculates results for a list of features with a particular input, throwing an exception if a calculation fails.
calculate(ChildCacheName, S, Function<CalculationPartResolver<S>, ResolvedPart<U, S>>) - Method in interface org.anchoranalysis.feature.calculate.cache.CalculateForChild: Calculates a CalculationPart in a child-cache.
calculate(ResolvedPart<S, T>) - Method in interface org.anchoranalysis.feature.calculate.FeatureCalculationInput: Calculates a resolved Feature-calculation.
calculate(ResolvedPart<S, T>) - Method in class org.anchoranalysis.feature.session.SessionInputSequential
calculate(FeatureCalculationInput<FeatureInput>) - Method in class org.anchoranalysis.test.feature.plugins.mockfeature.MockFeatureWithCalculation
calculate(FeatureCalculationInput<FeatureInputResults>) - Method in class org.anchoranalysis.feature.bean.results.FeatureResults
calculate(FeatureCalculationInput<FeatureInputHistogram>) - Method in class org.anchoranalysis.image.feature.bean.histogram.FeatureHistogramStatistic
calculate(FeatureCalculationInput<FeatureInputHistogram>) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.LevelFromHistogram
calculate(FeatureCalculationInput<FeatureInputHistogram>) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.ThresholdHistogram
calculate(FeatureCalculationInput<FeatureInputImageMetadata>) - Method in class org.anchoranalysis.image.feature.bean.FeatureImageMetadata
calculate(FeatureCalculationInput<FeatureInputObjectCollection>) - Method in class org.anchoranalysis.image.feature.bean.object.collection.FeatureObjectCollection
calculate(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.image.feature.bean.object.pair.First
calculate(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.image.feature.bean.object.pair.Merged
calculate(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.image.feature.bean.object.pair.Minimum
calculate(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.image.feature.bean.object.pair.RatioFirstToSecond
calculate(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.image.feature.bean.object.pair.Second
calculate(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.image.feature.bean.object.pair.SubtractSecondFromFirst
calculate(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.Intersection
calculate(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.CostOverlapWithinMidpointDistance
calculate(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.OverlapRelative
calculate(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.TouchingVoxels
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.image.feature.bean.object.single.CenterOfGravity
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.image.feature.bean.object.single.NumberVoxels
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.ArbitraryInsidePoint
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.border.AtBorderBase
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxAlongAxisBase
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxNumberVoxels
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.SpecificEnergyChannelBase
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.FeatureEnergyChannel
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.GradientMagnitude
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.GradientMeanForAxis
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.ImageMomentsBase
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.DerivedObject
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.NumberRemovedVoxelsAfterClosing
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.OutlineKernelBase
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shape.ObjectRadiusStandardDeviation
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shape.ShapeRegularityCenterSlice
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shape.ShapeRegularityMaximumIntensityProjection
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjects
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.PairedWithMask
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.slice.MaximumNumberContourVoxelsOnSlice
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.slice.MaximumNumberVoxelsOnSlice
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.surface.SurfaceNumberVoxelsBase
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.points.bean.feature.EllipsoidBase
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.points.bean.feature.Ellipticity
calculate(FeatureCalculationInput<FeatureInputStack>) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.intensity.Intensity
calculate(FeatureCalculationInput<FeatureInputStack>) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.intensity.NumberChannels
calculate(FeatureCalculationInput<FeatureInputStack>) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.AsObjectMask
calculate(FeatureCalculationInput<FeatureInputStack>) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.QuantileAcrossConnectedComponents
calculate(FeatureCalculationInput<FeatureInputStack>) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGFeature
calculate(FeatureCalculationInput<FeatureInputPairMemo>) - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.AsSingle
calculate(FeatureCalculationInput<FeatureInputSingleMemo>) - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.FeatureSingleMemo
calculate(FeatureCalculationInput<T>) - Method in class org.anchoranalysis.feature.bean.Feature: Calculates a value for some input.
calculate(FeatureCalculationInput<T>) - Method in class org.anchoranalysis.feature.bean.operator.Constant
calculate(FeatureCalculationInput<T>) - Method in class org.anchoranalysis.feature.bean.operator.Reference
calculate(FeatureCalculationInput<T>) - Method in class org.anchoranalysis.feature.bean.operator.Sum
calculate(FeatureCalculationInput<T>) - Method in class org.anchoranalysis.image.feature.bean.physical.WithResolutionBase: Calculates the feature value, handling cases where resolution might be missing.
calculate(FeatureCalculationInput<T>) - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.FromDimensionsBase
calculate(FeatureCalculationInput<T>) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.FeatureSingleObjectFromShared
calculate(FeatureCalculationInput<T>) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.ParamFromCollection
calculate(FeatureCalculationInput<T>) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.intensity.DataTypeMaxIntensity
calculate(FeatureCalculationInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.AbsoluteValue
calculate(FeatureCalculationInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.Divide
calculate(FeatureCalculationInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.InvertedMax
calculate(FeatureCalculationInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.Multiply
calculate(FeatureCalculationInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.conditional.IfCondition
calculate(FeatureCalculationInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.FromDictionary
calculate(FeatureCalculationInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.list.Maximum
calculate(FeatureCalculationInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.list.Mean
calculate(FeatureCalculationInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.list.MeanGeometric
calculate(FeatureCalculationInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.list.Minimum
calculate(FeatureCalculationInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.NormalizedRange
calculate(FeatureCalculationInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.Range
calculate(FeatureCalculationInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareBase
calculate(FeatureCalculationInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.statistics.StatisticalBase
calculate(FeatureCalculationInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.WithValueBase
calculate(FeatureCalculationInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.physical.ConvertUnits
calculate(CalculationPart<S, T>) - Method in interface org.anchoranalysis.feature.calculate.FeatureCalculationInput: Calculates a feature-calculation after resolving it against the main cache.
calculate(CalculationPart<S, T>) - Method in class org.anchoranalysis.feature.session.SessionInputSequential
calculate(FeatureInputResults) - Method in class org.anchoranalysis.feature.bean.results.Count
calculate(FeatureInputResults) - Method in class org.anchoranalysis.feature.bean.results.FeatureResults: Calculates the feature-result given a FeatureInputResults.
calculate(FeatureInputResults) - Method in class org.anchoranalysis.feature.bean.results.FeatureResultsStatistic
calculate(ImageMetadata) - Method in class org.anchoranalysis.image.feature.bean.FeatureImageMetadata: Calculates the feature-value for a given ImageMetadata.
calculate(ImageMetadata) - Method in class org.anchoranalysis.plugin.image.feature.bean.metadata.BitDepthPerChannel
calculate(ImageMetadata) - Method in class org.anchoranalysis.plugin.image.feature.bean.metadata.NumberChannels
calculate(ImageMetadata) - Method in class org.anchoranalysis.plugin.image.feature.bean.metadata.NumberFrames
calculate(ImageMetadata) - Method in class org.anchoranalysis.plugin.image.feature.bean.metadata.NumberResolutionLevels
calculate(ImageMetadata) - Method in class org.anchoranalysis.plugin.image.feature.bean.metadata.NumberSeries
calculate(FeatureInputObjectCollection) - Method in class org.anchoranalysis.image.feature.bean.object.collection.FeatureObjectCollection: Calculates the feature-value for a given FeatureInputObjectCollection.
calculate(FeatureInputObjectCollection) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.collection.NumberObjects
calculate(FeatureInputPairObjects) - Method in class org.anchoranalysis.image.feature.calculator.merged.PairsTableCalculator
calculate(FeatureInputPairObjects, FeatureList<FeatureInputPairObjects>) - Method in class org.anchoranalysis.image.feature.calculator.merged.PairsTableCalculator
calculate(FeatureInputSingleObject) - Method in class org.anchoranalysis.image.feature.calculator.SingleTableCalculator
calculate(FeatureInputSingleObject, FeatureList<FeatureInputSingleObject>) - Method in class org.anchoranalysis.image.feature.calculator.SingleTableCalculator
calculate(ObjectMask) - Method in interface org.anchoranalysis.plugin.image.object.merge.PayloadCalculator: Calculates the payload value for a given object mask.
calculate(T) - Method in interface org.anchoranalysis.feature.calculate.bound.FeatureCalculatorMulti: Calculate the results of the features with a particular input.
calculate(T) - Method in class org.anchoranalysis.feature.calculate.bound.FeatureCalculatorMultiChangeInput
calculate(T) - Method in interface org.anchoranalysis.feature.calculate.bound.FeatureCalculatorSingle: Calculate the results of the feature with a particular input.
calculate(T) - Method in class org.anchoranalysis.feature.calculate.bound.FeatureCalculatorSingleChangeInput
calculate(T) - Method in class org.anchoranalysis.feature.calculate.bound.FeatureCalculatorSingleFromMulti
calculate(T) - Method in class org.anchoranalysis.feature.session.SequentialSession
calculate(T, ErrorReporter, boolean) - Method in interface org.anchoranalysis.feature.calculate.bound.FeatureCalculatorMulti: Calculates the results for an input, either calling FeatureCalculatorMulti.calculate(T) or FeatureCalculatorMulti.calculateSuppressErrors(T, org.anchoranalysis.core.log.error.ErrorReporter) depending on a flag.
calculate(T, FeatureList<T>) - Method in interface org.anchoranalysis.feature.calculate.bound.FeatureCalculatorMulti: Calculates the results of a subset of the features with a particular input.
calculate(T, FeatureList<T>) - Method in class org.anchoranalysis.feature.calculate.bound.FeatureCalculatorMultiChangeInput
calculate(T, FeatureList<T>) - Method in class org.anchoranalysis.feature.session.SequentialSession
calculateAndOutput(T, FeatureCalculationContext<FeatureList<S>>) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.SingleRowPerInput
calculateAndOutput(T, FeatureCalculationContext<S>) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FeatureSource: Processes one input to calculate feature-results and output them to the file-system.
calculateAreaXYAsDouble() - Method in class org.anchoranalysis.spatial.box.Extent: Calculates the area freshly by multiplying the x-size with y-size, as doubles.
calculateAt(KernelPointCursor) - Method in class org.anchoranalysis.image.voxel.kernel.AndKernel
calculateAt(KernelPointCursor) - Method in class org.anchoranalysis.image.voxel.kernel.BinaryKernel: Calculates the boolean at a particular point.
calculateAt(KernelPointCursor) - Method in class org.anchoranalysis.image.voxel.kernel.ConditionalKernel
calculateAt(KernelPointCursor) - Method in class org.anchoranalysis.image.voxel.kernel.count.CountKernel: Calculates the count at a particular point.
calculateAt(KernelPointCursor) - Method in class org.anchoranalysis.image.voxel.kernel.morphological.BinaryKernelMorphological
calculateCheckInitialized(FeatureCalculationInput<T>) - Method in class org.anchoranalysis.feature.bean.Feature: Calculates the result of a feature and throws an exception if the feature has not been initialized.
calculateConnectedComponentID(Point3i, int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels: Calculates the connected component ID for a given point and initial chain code.
calculateCornerMaxExclusive() - Method in class org.anchoranalysis.spatial.box.BoundingBox: The maximum (right-most) point just outside the box.
calculateCornerMaxInclusive() - Method in class org.anchoranalysis.spatial.box.BoundingBox: The maximum (right-most) point inside the box.
calculateDenominator(FeatureInputPairObjects) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.OverlapRelative: Calculates the denominator for the overlap ratio.
calculateDenominator(FeatureInputPairObjects) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.OverlapRelativeToFirst
calculateDenominator(FeatureInputPairObjects) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.OverlapRelativeToMaxVolume
calculateDenominator(FeatureInputPairObjects) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.OverlapRelativeToMerged
calculateDenominator(FeatureInputPairObjects) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.OverlapRelativeToSecond
CalculateDeriveObjectInput - Class in org.anchoranalysis.plugin.image.feature.bean.stack.object: Derives a FeatureInputSingleObject from a FeatureInputStack by extracting an object mask from a specific energy channel.
CalculateDeriveObjectInput(int) - Constructor for class org.anchoranalysis.plugin.image.feature.bean.stack.object.CalculateDeriveObjectInput: Creates a new CalculateDeriveObjectInput instance.
CalculateDeriveSingleMemoFromPair - Class in org.anchoranalysis.mpp.feature.bean.energy.element: Derives a FeatureInputSingleMemo from a FeatureInputPairMemo.
CalculateDeriveSingleMemoFromPair(boolean) - Constructor for class org.anchoranalysis.mpp.feature.bean.energy.element.CalculateDeriveSingleMemoFromPair: Creates a new CalculateDeriveSingleMemoFromPair instance.
CalculateDilation - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological: Calculates the dilation of an ObjectMask.
CalculateDilationMap - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological: Calculates a map of dilated ObjectMasks for different iteration counts.
CalculateDilationMap(boolean) - Constructor for class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateDilationMap: Creates a new CalculateDilationMap.
CalculateDilationMap(CalculateIncrementalOperationMap) - Constructor for class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateDilationMap: Copy constructor for CalculateDilationMap.
calculateEccentricity(double, double) - Static method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.PrincipalAxisEccentricity: Calculates the eccentricity from two eigenvalues.
CalculateEllipseLeastSquares - Class in org.anchoranalysis.plugin.points.calculate.ellipse: Calculates the best-fit ellipse for an ObjectMask using linear least squares.
CalculateEllipseLeastSquares() - Constructor for class org.anchoranalysis.plugin.points.calculate.ellipse.CalculateEllipseLeastSquares: Creates a new instance of CalculateEllipseLeastSquares.
CalculateEllipsoidLeastSquares - Class in org.anchoranalysis.plugin.points.calculate.ellipsoid: Calculates the best-fit Ellipsoid for an object using linear least squares.
CalculateErosion - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological: Calculates the erosion of an ObjectMask.
CalculateErosionMap - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological: Calculates a map of eroded ObjectMasks for different iteration counts.
CalculateErosionMap(boolean) - Constructor for class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateErosionMap: Creates a new CalculateErosionMap.
CalculateErosionMap(CalculateIncrementalOperationMap) - Constructor for class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateErosionMap: Copy constructor for CalculateErosionMap.
calculateFeatureByIdentifier(String, FeatureCalculationInput<T>) - Method in interface org.anchoranalysis.feature.calculate.cache.FeatureSymbolCalculator: Searches for a feature that matches a particular identifier.
CalculateFeaturesForObjects<T> - Class in org.anchoranalysis.plugin.image.task.feature.calculator: Calculates features for objects and stores the results.
CalculateFeaturesForObjects(CombineObjectsForFeatures<T>, InitializationWithEnergyStack, boolean, FeatureCalculationContext<FeatureTableCalculator<T>>) - Constructor for class org.anchoranalysis.plugin.image.task.feature.calculator.CalculateFeaturesForObjects: Creates a new CalculateFeaturesForObjects.
calculateForAxis(Dimensions, Axis) - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.Extent
calculateForAxis(Dimensions, Axis) - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.ForSpecificAxis: Calculates a feature value for a specific axis of the given dimensions.
calculateForAxis(Dimensions, Axis) - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.VoxelPhysicalSize
calculateForChannel(FeatureCalculationInput<FeatureInputSingleObject>, Channel) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.FeatureEnergyChannel: Calculates the feature value for a specific channel in the energy stack.
calculateForChannel(FeatureCalculationInput<FeatureInputSingleObject>, Channel) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.Intensity
calculateForChannel(FeatureCalculationInput<FeatureInputSingleObject>, Channel) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanMaxSlice: Calculates the maximum mean intensity across all slices of the object in the given channel.
calculateForChannel(FeatureCalculationInput<FeatureInputSingleObject>, Channel) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase
calculateForChannel(FeatureCalculationInput<FeatureInputSingleObject>, Channel) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.TextureScore
CalculateForChild<T> - Interface in org.anchoranalysis.feature.calculate.cache: Performs calculations using child-caches instead of the main cache
calculateForObjects(ObjectCollectionProvider, LabelsForInput) - Method in class org.anchoranalysis.plugin.image.task.feature.calculator.CalculateFeaturesForObjects: Calculates features for objects provided by a ObjectCollectionProvider.
calculateForObjects(ObjectCollection, EnergyStack, LabelsForInput) - Method in class org.anchoranalysis.plugin.image.task.feature.calculator.CalculateFeaturesForObjects: Calculates the feature-results for objects, and stores the results.
calculateForShell(ObjectMask, Channel) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShell
calculateForShell(ObjectMask, Channel) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase: Calculates the feature value for the given shell and channel.
calculateForShell(ObjectMask, Channel) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellMaxSlice
calculateForVoxel(int, int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevel
calculateForVoxel(int, int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevelBase: Calculates a score for a single voxel based on its intensity and the threshold level.
calculateForVoxel(int, int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.DifferenceCalculateLevelStandardDeviation
calculateFromAllMoments(ImageMoments) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.ImageMomentsBase: Calculates the feature value from the ImageMoments.
calculateFromAllMoments(ImageMoments) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.PrincipalAxisEccentricity
calculateFromAllMoments(ImageMoments) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.RatioPrincipalAxisLength
calculateFromAllMoments(ImageMoments) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.SpecificAxisBase
calculateFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.Area
calculateFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.ForSpecificAxis
calculateFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.FromDimensionsBase: Calculates a feature value from the given dimensions.
calculateFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.Volume
calculateFromSpecificMoment(EigenvalueAndVector) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.PrincipalAxisLength
calculateFromSpecificMoment(EigenvalueAndVector) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.PrincipalAxisOrientation
calculateFromSpecificMoment(EigenvalueAndVector) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.SpecificAxisBase: Calculates the result for the specific moment identified by index.
CalculateHistogram - Class in org.anchoranalysis.plugin.image.feature.stack.calculation: Calculates a Histogram from a specific channel in a FeatureInputStack.
CalculateHistogram(int) - Constructor for class org.anchoranalysis.plugin.image.feature.stack.calculation.CalculateHistogram: Creates a new CalculateHistogram instance.
CalculateHistogramMasked - Class in org.anchoranalysis.plugin.image.feature.stack.calculation: Calculated a histogram for a specific region on a channel, as identified by a mask in another channel
CalculateHistogramMasked(int, int) - Constructor for class org.anchoranalysis.plugin.image.feature.stack.calculation.CalculateHistogramMasked: Creates a new CalculateHistogramMasked instance.
CalculateIncrementalOperationMap - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single: Calculates incremental operations on ObjectMasks and stores the results in a map.
CalculateIncrementalOperationMap(boolean) - Constructor for class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateIncrementalOperationMap: Creates a new instance with the specified 3D flag.
CalculateIncrementalOperationMap(CalculateIncrementalOperationMap) - Constructor for class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateIncrementalOperationMap: Copy constructor.
CalculateInputFromDelegate<S,T,U> - Class in org.anchoranalysis.plugin.image.feature.object.calculation.delegate: A base class for CalculationParts that derive from an existing "delegate" calculation.
CalculateInputFromDelegate(ResolvedPart<U, T>) - Constructor for class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegate: Creates a new CalculateInputFromDelegate instance.
CalculateInputFromDelegate(CalculationPart<U, T>, CalculationPartResolver<T>) - Constructor for class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegate: Creates a new CalculateInputFromDelegate.
CalculateInputFromDelegateOption<S,T,U> - Class in org.anchoranalysis.plugin.image.feature.object.calculation.delegate: Like CalculateInputFromDelegate except assumes optional return value and no parameters.
CalculateInputFromDelegateOption(ResolvedPart<U, T>) - Constructor for class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegateOption: Creates with a delegate.
CalculateInputFromPair - Class in org.anchoranalysis.image.feature.calculation: Calculates a single-input from a pair of objects.
CalculateInputFromPair(CalculateInputFromPair.Extract) - Constructor for class org.anchoranalysis.image.feature.calculation.CalculateInputFromPair: Creates a new CalculateInputFromPair instance.
CalculateInputFromPair.Extract - Enum Class in org.anchoranalysis.image.feature.calculation: Defines the extraction mode for the calculation.
CalculateIntersecting - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting: Calculates a FeatureInputPairObjects from a FeatureInputSingleObject and an intersecting ObjectCollection.
CalculateIntersecting(ResolvedPart<ObjectCollection, FeatureInputSingleObject>, int) - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.CalculateIntersecting: Creates a new CalculateIntersecting instance.
calculateLevel(Histogram) - Method in class org.anchoranalysis.image.bean.threshold.CalculateLevel: Determines a voxel intensity that can be used for thresholding.
calculateLevel(Histogram) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelRelativeToThreshold
calculateLevel(Histogram) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.ClampHistogramMax
calculateLevel(Histogram) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Constant
calculateLevel(Histogram) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.EmptyHistogramConstant
calculateLevel(Histogram) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Maximum
calculateLevel(Histogram) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Minimum
calculateLevel(Histogram) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Otsu
calculateLevel(Histogram) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.OtsuWeighted
calculateLevel(Histogram) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Quantile
CalculateLevel - Class in org.anchoranalysis.image.bean.threshold: Calculates a threshold-level from a histogram.
CalculateLevel - Class in org.anchoranalysis.plugin.image.feature.bean.score: Calculates a level score based on voxel intensity and a given threshold.
CalculateLevel() - Constructor for class org.anchoranalysis.image.bean.threshold.CalculateLevel
CalculateLevel() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevel
CalculateLevelBase - Class in org.anchoranalysis.plugin.image.feature.bean.score: Base class for calculating a score based on a threshold level derived from a histogram.
CalculateLevelBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevelBase
calculateLevelFromDelegate(Histogram) - Method in class org.anchoranalysis.image.bean.threshold.CalculateLevelUnary: Determines a voxel intensity that can be used for thresholding from the delegate calculateLevel.
CalculateLevelListBase - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold: Base class for CalculateLevel implementations that operate on a list of other CalculateLevel objects.
CalculateLevelListBase() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelListBase
CalculateLevelRelativeToThreshold - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold: A CalculateLevelUnary that calculates a level relative to a threshold, with an alternative calculation method.
CalculateLevelRelativeToThreshold() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelRelativeToThreshold
CalculateLevelUnary - Class in org.anchoranalysis.image.bean.threshold: Implementation of CalculateLevel that calls a single delegate CalculateLevel.
CalculateLevelUnary() - Constructor for class org.anchoranalysis.image.bean.threshold.CalculateLevelUnary
calculateMaximum() - Method in class org.anchoranalysis.math.histogram.Histogram: Calculates the maximum value with non zero-count among the histogram values.
calculateMaybeSuppressErrors(FeatureInputPairObjects, ErrorReporter) - Method in class org.anchoranalysis.image.feature.calculator.merged.PairsTableCalculator: Calculates features for the input, optionally suppressing errors.
calculateMeanIntensityObject(Channel, ObjectMask) - Static method in class org.anchoranalysis.plugin.image.intensity.IntensityMeanCalculator: Calculates the mean intensity of an object in a channel.
calculateMeanIntensityObject(Channel, ObjectMask, boolean) - Static method in class org.anchoranalysis.plugin.image.intensity.IntensityMeanCalculator: Calculates the mean intensity of an object in a channel, with an option to exclude zero values.
calculateMinimum() - Method in class org.anchoranalysis.math.histogram.Histogram: Calculates the minimum value with non zero-count among the histogram values.
calculateMinMax(Optional<Resolution>, boolean) - Method in class org.anchoranalysis.mpp.bean.bound.MarkBounds: Calculates the resolved minimum and maximum values as a ResolvedBound.
calculateMode() - Method in class org.anchoranalysis.math.histogram.Histogram: Calculates the mode of the histogram values.
CalculateNumberVoxels - Class in org.anchoranalysis.image.feature.calculation: Calculates the number of voxels in a single object, optionally flattening in the Z-dimension.
CalculateNumberVoxels(boolean) - Constructor for class org.anchoranalysis.image.feature.calculation.CalculateNumberVoxels: Creates a new CalculateNumberVoxels instance.
CalculateObjectMask - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single: Calculates an ObjectMask based on a specified number of iterations.
CalculateObjectMask(int, ResolvedPartMap<ObjectMask, FeatureInputSingleObject, Integer>) - Constructor for class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateObjectMask: Creates a new CalculateObjectMask instance.
CalculateObjectMask(CalculateObjectMask) - Constructor for class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateObjectMask: Copy constructor.
calculateOrientationChange(Logger) - Method in interface org.anchoranalysis.image.io.stack.CalculateOrientationChange: Calculates any needed orientation change.
CalculateOrientationChange - Interface in org.anchoranalysis.image.io.stack: Calculates any needed orientation change.
calculateResultsForInput(ImageMetadataInput, FeatureCalculationContext<FeatureList<FeatureInputImageMetadata>>) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromImageMetadata
calculateResultsForInput(ProvidesStackInput, FeatureCalculationContext<FeatureList<FeatureInputStack>>) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromImage
calculateResultsForInput(FileInput, FeatureCalculationContext<FeatureList<FeatureInputHistogram>>) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromHistogram
calculateResultsForInput(T, FeatureCalculationContext<FeatureList<S>>) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.SingleRowPerInput: Calculates feature-results for a particular input.
calculateRunningSum(Mask, Voxels<UnsignedByteBuffer>) - Static method in class org.anchoranalysis.image.core.mask.IterateVoxelsMask: Calculates the sum and count across voxels intensity that correspond to on voxels on a mask
calculateScaleFactor(Optional<Extent>) - Method in interface org.anchoranalysis.image.core.dimensions.size.suggestion.ImageSizeSuggestion: Calculates the scaling factor.
CalculateShellObjectMask - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single: Calculates a shell ObjectMask by performing dilation and erosion operations.
CalculateShellObjectMask(ResolvedPart<ObjectMask, FeatureInputSingleObject>, ResolvedPart<ObjectMask, FeatureInputSingleObject>, int, boolean, boolean) - Constructor for class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateShellObjectMask: Creates a new CalculateShellObjectMask instance.
calculateSigma(Dimensions, MessageLogger) - Method in class org.anchoranalysis.plugin.image.bean.blur.BlurStrategy: Calculates the sigma value to use for blurring, considering the dimensions and whether sigma is in meters.
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.image.feature.bean.histogram.FeatureHistogramStatistic: Calculates the statistic from the histogram, that is subsequently returned as the feature-value.
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.image.feature.bean.histogram.Mean
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.CoefficientOfVariation
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Count
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Kurtosis
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Maximum
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.MeanRaisedToPower
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Median
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Minimum
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Mode
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.NumberDistinctValues
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Quantile
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Range
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.RatioNonMode
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Skewness
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.StandardDeviation
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Sum
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.TotalCount
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Variance
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.RatioThreshold
calculateSum() - Method in class org.anchoranalysis.math.histogram.Histogram: Calculates the sum of all values in the distribution considering their counts.
calculateSumCubes() - Method in class org.anchoranalysis.math.histogram.Histogram: Calculates the cube of the squares of all values in the distribution considering their counts.
calculateSumSquares() - Method in class org.anchoranalysis.math.histogram.Histogram: Calculates the sum of the squares of all values in the distribution considering their counts.
calculateSuppressErrors(FeatureInputPairObjects, ErrorReporter) - Method in class org.anchoranalysis.image.feature.calculator.merged.PairsTableCalculator
calculateSuppressErrors(FeatureInputSingleObject, ErrorReporter) - Method in class org.anchoranalysis.image.feature.calculator.SingleTableCalculator
calculateSuppressErrors(T, ErrorReporter) - Method in interface org.anchoranalysis.feature.calculate.bound.FeatureCalculatorMulti: Calculates the results for an input recording the error to an ErrorReporter if anything goes wrong, but throwing no exception.
calculateSuppressErrors(T, ErrorReporter) - Method in class org.anchoranalysis.feature.calculate.bound.FeatureCalculatorMultiChangeInput
calculateSuppressErrors(T, ErrorReporter) - Method in interface org.anchoranalysis.feature.calculate.bound.FeatureCalculatorSingle: Calculates the result for an input recording the error to an ErrorReporter if anything goes wrong, but throwing no exception.
calculateSuppressErrors(T, ErrorReporter) - Method in class org.anchoranalysis.feature.calculate.bound.FeatureCalculatorSingleChangeInput
calculateSuppressErrors(T, ErrorReporter) - Method in class org.anchoranalysis.feature.calculate.bound.FeatureCalculatorSingleFromMulti
calculateSuppressErrors(T, ErrorReporter) - Method in class org.anchoranalysis.feature.session.SequentialSession: Calculates the results for the next input in the session, reporting any exceptions into an ErrorReporter.
calculateVolume() - Method in class org.anchoranalysis.image.core.dimensions.Dimensions: Calculates the volume of the Extent when considered as a box.
calculateVolume() - Method in class org.anchoranalysis.spatial.box.Extent: Calculates the volume of the Extent when considered as a box.
calculateVolumeAsInt() - Method in class org.anchoranalysis.spatial.box.Extent: Like Extent.calculateVolume() but uses an int to calculate the volume.
calculateWith(Feature<T>, T, Logger) - Static method in class org.anchoranalysis.feature.session.FeatureSession: Starts a feature-session for a single feature - and performs a calculation.
calculateWithChannel(ObjectMask, Channel) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.CountEqual: Calculates the number of voxels in the object that have the specified intensity value in the channel.
calculateWithChannel(ObjectMask, Channel) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.SpecificEnergyChannelBase: Calculates the feature value for a specific object and channel.
calculateWithEllipsoid(FeatureInputSingleObject, Ellipsoid) - Method in class org.anchoranalysis.plugin.points.bean.feature.AxisRatioEllipsoid
calculateWithEllipsoid(FeatureInputSingleObject, Ellipsoid) - Method in class org.anchoranalysis.plugin.points.bean.feature.EllipsoidBase: Calculates a feature value based on the fitted Ellipsoid.
calculateWithEllipsoid(FeatureInputSingleObject, Ellipsoid) - Method in class org.anchoranalysis.plugin.points.bean.feature.Ellipsoidicity
calculateWithIntersection(ObjectMask, ObjectMask, BoundingBox) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.HasTouchingVoxels
calculateWithIntersection(ObjectMask, ObjectMask, BoundingBox) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.NumberTouchingVoxelFaces
calculateWithIntersection(ObjectMask, ObjectMask, BoundingBox) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.NumberTouchingVoxels
calculateWithIntersection(ObjectMask, ObjectMask, BoundingBox) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.TouchingVoxels: Calculates the feature value for the intersection of two objects.
calculateWithParameters(ObjectMask, KernelApplicationParameters, CheckedSupplier<EnergyStack, FeatureCalculationException>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.border.NumberVoxelsAtBorder
calculateWithParameters(ObjectMask, KernelApplicationParameters, CheckedSupplier<EnergyStack, FeatureCalculationException>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.NumberNeighboringVoxels
calculateWithParameters(ObjectMask, KernelApplicationParameters, CheckedSupplier<EnergyStack, FeatureCalculationException>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.OutlineKernelBase: Calculates the feature value using the specified parameters.
calculateWithResolution(double, Resolution) - Method in class org.anchoranalysis.image.feature.bean.physical.FeatureConvertUnits: Calculates the feature value with resolution information.
calculateWithResolution(double, Resolution) - Method in class org.anchoranalysis.image.feature.bean.physical.WithResolutionBase: Calculates the feature value using the provided value and resolution.
calculateWithResolution(double, Resolution) - Method in class org.anchoranalysis.plugin.image.feature.bean.physical.UnitsWithinRange
calculateZScore(double, double, double) - Static method in class org.anchoranalysis.math.statistics.ZScoreCalculator: Calculates a Z-Score for a particular value and parameterization.
CalculationPart<S,T> - Class in org.anchoranalysis.feature.calculate.part: A sub-part of the calculation of a feature, that can be cached, and reused by other features.
CalculationPart() - Constructor for class org.anchoranalysis.feature.calculate.part.CalculationPart
CalculationPartMap<S,T,U,E> - Class in org.anchoranalysis.feature.calculate.part: Similar to a CalculationPart but stores several evaluation results, differentiated by a key.
CalculationPartMap(int) - Constructor for class org.anchoranalysis.feature.calculate.part.CalculationPartMap: Creates for a particular cache-size.
CalculationPartResolver<T> - Interface in org.anchoranalysis.feature.calculate.part: Searches a cache to reuses a CalculationPart if it already exists.
calculationResultsNeeded(MultiLevelOutputEnabled) - Method in class org.anchoranalysis.feature.io.results.FeatureOutputNames: If any output is enabled that requires calculation of feature results?
calculator() - Method in interface org.anchoranalysis.feature.calculate.cache.FeatureCalculationCache: A means of calculating feature values using this cache.
calculatorForAll(FeatureList<T>) - Method in class org.anchoranalysis.plugin.image.task.feature.calculator.FeatureCalculatorFromProvider: Calculates all image-features in the feature-store.
calculatorSingleFromProvider(FeatureListProvider<T>, String) - Method in class org.anchoranalysis.plugin.image.task.feature.calculator.FeatureCalculatorFromProvider: Calculates a single-feature that comes from a provider (but can reference the other features from the store).
call() - Method in class org.anchoranalysis.experiment.task.processor.CallableJob
call(CheckedSupplier<T, E>) - Method in class org.anchoranalysis.core.cache.CachedSupplierBase: Gets the value supplied by supplier via the cache if it exists, or otherwise via the supplier.
CallableJob<T,S> - Class in org.anchoranalysis.experiment.task.processor: A job derived from a Task that can be placed on different threads
CallableJob(Task<T, S>, ParametersUnbound<T, S>, JobStateMonitor, JobDescription, ConcurrentJobMonitor, Optional<MessageLogger>, int) - Constructor for class org.anchoranalysis.experiment.task.processor.CallableJob: Constructor.
callEachPointInNeighborhood(Point3i, Neighborhood, boolean, ProcessVoxelNeighbor<T>, int, int) - Static method in class org.anchoranalysis.image.voxel.iterator.neighbor.IterateVoxelsNeighbors: Iterate over each point in the neighborhood of an existing point.
canEqual(Object) - Method in class org.anchoranalysis.bean.primitive.DoubleList
canEqual(Object) - Method in class org.anchoranalysis.bean.primitive.DoubleSet
canEqual(Object) - Method in class org.anchoranalysis.bean.primitive.IntegerList
canEqual(Object) - Method in class org.anchoranalysis.bean.primitive.IntegerSet
canEqual(Object) - Method in class org.anchoranalysis.bean.primitive.StringList
canEqual(Object) - Method in class org.anchoranalysis.bean.primitive.StringSet
canEqual(Object) - Method in class org.anchoranalysis.bean.shared.path.RootPath
canEqual(Object) - Method in class org.anchoranalysis.bean.shared.relation.EqualToBean
canEqual(Object) - Method in class org.anchoranalysis.bean.shared.relation.GreaterThanBean
canEqual(Object) - Method in class org.anchoranalysis.bean.shared.relation.GreaterThanEqualToBean
canEqual(Object) - Method in class org.anchoranalysis.bean.shared.relation.LessThanBean
canEqual(Object) - Method in class org.anchoranalysis.bean.shared.relation.LessThanEqualToBean
canEqual(Object) - Method in class org.anchoranalysis.bean.shared.relation.RelationBean
canEqual(Object) - Method in class org.anchoranalysis.bean.shared.relation.threshold.RelationToConstant
canEqual(Object) - Method in class org.anchoranalysis.core.index.Indexable
canEqual(Object) - Method in class org.anchoranalysis.feature.calculate.cache.ChildCacheName
canEqual(Object) - Method in class org.anchoranalysis.feature.input.FeatureInputDimensions
canEqual(Object) - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy
canEqual(Object) - Method in class org.anchoranalysis.feature.input.FeatureInputNull
canEqual(Object) - Method in class org.anchoranalysis.feature.io.name.SimpleName
canEqual(Object) - Method in class org.anchoranalysis.image.bean.spatial.SizeXY
canEqual(Object) - Method in class org.anchoranalysis.image.bean.threshold.CalculateLevelUnary
canEqual(Object) - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryNotOffVoxels
canEqual(Object) - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryNotOnVoxels
canEqual(Object) - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryOffVoxels
canEqual(Object) - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryOnVoxels
canEqual(Object) - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryVoxelsBase
canEqual(Object) - Method in class org.anchoranalysis.image.feature.calculation.CalculateInputFromPair
canEqual(Object) - Method in class org.anchoranalysis.image.feature.calculation.CalculateNumberVoxels
canEqual(Object) - Method in class org.anchoranalysis.image.feature.input.FeatureInputImageMetadata
canEqual(Object) - Method in class org.anchoranalysis.image.feature.input.FeatureInputObjectCollection
canEqual(Object) - Method in class org.anchoranalysis.image.feature.input.FeatureInputPairObjects
canEqual(Object) - Method in class org.anchoranalysis.image.feature.input.FeatureInputSingleObject
canEqual(Object) - Method in class org.anchoranalysis.image.feature.input.FeatureInputStack
canEqual(Object) - Method in class org.anchoranalysis.image.inference.segment.LabelledWithConfidence
canEqual(Object) - Method in class org.anchoranalysis.image.inference.segment.WithConfidence
canEqual(Object) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer
canEqual(Object) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBufferAsInt
canEqual(Object) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
canEqual(Object) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer
canEqual(Object) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
canEqual(Object) - Method in class org.anchoranalysis.inference.concurrency.WithPriority
canEqual(Object) - Method in class org.anchoranalysis.math.equation.QuadraticEquationSolver.QuadraticRoots
canEqual(Object) - Method in class org.anchoranalysis.math.statistics.MeanScale
canEqual(Object) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMap
canEqual(Object) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
canEqual(Object) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipWithFlags
canEqual(Object) - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.CalculateDeriveSingleMemoFromPair
canEqual(Object) - Method in class org.anchoranalysis.mpp.feature.bean.mark.FeatureInputMark
canEqual(Object) - Method in class org.anchoranalysis.mpp.feature.energy.IndexableMarksWithEnergy
canEqual(Object) - Method in class org.anchoranalysis.mpp.feature.input.FeatureInputAllMemo
canEqual(Object) - Method in class org.anchoranalysis.mpp.feature.input.FeatureInputPairMemo
canEqual(Object) - Method in class org.anchoranalysis.mpp.feature.input.FeatureInputSingleMemo
canEqual(Object) - Method in class org.anchoranalysis.mpp.feature.mark.MemoList
canEqual(Object) - Method in class org.anchoranalysis.mpp.overlay.OverlayMark
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelListBase
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelRelativeToThreshold
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.ClampHistogramMax
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Constant
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.EmptyHistogramConstant
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.IfGreaterThan
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.IfLessThan
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Maximum
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Minimum
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Otsu
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.OtsuWeighted
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Quantile
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.CalculateIntersecting
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.CalculateDeriveObjectInput
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegate
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegateOption
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateIncrementalOperationMap
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateObjectMask
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateShellObjectMask
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateDilation
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateDilationMap
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateErosion
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateErosionMap
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.stack.calculation.CalculateHistogram
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.stack.calculation.CalculateHistogramMasked
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ChangeableOutputSequence
canEqual(Object) - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetChannel
canEqual(Object) - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetSlice
canEqual(Object) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters
canEqual(Object) - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult
canEqual(Object) - Method in class org.anchoranalysis.plugin.points.calculate.ellipse.CalculateEllipseLeastSquares
canEqual(Object) - Method in class org.anchoranalysis.plugin.points.calculate.ellipsoid.CalculateEllipsoidLeastSquares
canEqual(Object) - Method in class org.anchoranalysis.spatial.orientation.Orientation2D
canEqual(Object) - Method in class org.anchoranalysis.spatial.orientation.Orientation3DEulerAngles
canEqual(Object) - Method in class org.anchoranalysis.spatial.orientation.OrientationAxisAngle
canEqual(Object) - Method in class org.anchoranalysis.spatial.orientation.OrientationRotationMatrix
canEqual(Object) - Method in class org.anchoranalysis.spatial.point.Point3d
canEqual(Object) - Method in class org.anchoranalysis.spatial.point.Point3f
canEqual(Object) - Method in class org.anchoranalysis.spatial.point.Point3i
canEqual(Object) - Method in class org.anchoranalysis.spatial.point.Tuple3d
canEqual(Object) - Method in class org.anchoranalysis.spatial.point.Tuple3f
canEqual(Object) - Method in class org.anchoranalysis.spatial.point.Tuple3i
canEqual(Object) - Method in class org.anchoranalysis.spatial.point.Vector3d
canExceptionBeCombined(Throwable) - Method in exception class org.anchoranalysis.bean.xml.exception.BeanMisconfiguredXMLException
canExceptionBeCombined(Throwable) - Method in exception class org.anchoranalysis.bean.xml.exception.LocalisedBeanException
canExceptionBeCombined(Throwable) - Method in exception class org.anchoranalysis.core.exception.combinable.AnchorCombinableException: Can another exception be combined with this exception?
canExceptionBeCombined(Throwable) - Method in exception class org.anchoranalysis.core.identifier.provider.NamedProviderGetException
canExceptionBeSkipped(Throwable) - Method in exception class org.anchoranalysis.bean.xml.exception.BeanMisconfiguredXMLException
canExceptionBeSkipped(Throwable) - Method in exception class org.anchoranalysis.bean.xml.exception.LocalisedBeanException
canExceptionBeSkipped(Throwable) - Method in exception class org.anchoranalysis.core.exception.combinable.AnchorCombinableException: Can another exception be skipped, when we combine with the current exception?
canExceptionBeSkipped(Throwable) - Method in exception class org.anchoranalysis.core.identifier.provider.NamedProviderGetException
canMatchSubdirectories() - Method in class org.anchoranalysis.io.input.bean.path.matcher.FilePathMatcher: Determines if it possible to match a file in a subdirectory.
canMatchSubdirectories() - Method in class org.anchoranalysis.io.input.bean.path.matcher.MatchExtensions
canMatchSubdirectories() - Method in class org.anchoranalysis.io.input.bean.path.matcher.MatchGlob
canMatchSubdirectories() - Method in class org.anchoranalysis.io.input.bean.path.matcher.MatchRegularExpression
canValueRangeChange() - Method in class org.anchoranalysis.image.voxel.resizer.Lanczos
canValueRangeChange() - Method in class org.anchoranalysis.image.voxel.resizer.Linear
canValueRangeChange() - Method in class org.anchoranalysis.image.voxel.resizer.NearestNeighbor
canValueRangeChange() - Method in class org.anchoranalysis.image.voxel.resizer.VoxelsResizer: Returns true if it's possible for values to be created after interpolation that aren't found in the input-image.
canValueRangeChange() - Method in class org.anchoranalysis.image.voxel.resizer.VoxelsResizerExecutionTime
canValueRangeChange() - Method in class org.anchoranalysis.image.voxel.resizer.VoxelsResizerNone
canValueRangeChange() - Method in class org.anchoranalysis.io.imagej.resizer.VoxelsResizerImageJ
canValueRangeChange() - Method in class org.anchoranalysis.plugin.opencv.resizer.VoxelsResizerOpenCV
capacity() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer: The capacity of the buffer ala Buffer.capacity.
capacity() - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer: The capacity (i.e. size) of the buffer.
capacity() - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferUnsigned
carGrayscale16Bit() - Method in class org.anchoranalysis.test.image.load.CarImageLoader: Loads and returns the 16-bit grayscale image of a car.
carGrayscale16BitAsEnergy() - Method in class org.anchoranalysis.test.image.load.CarImageLoader: Loads the 16-bit grayscale image of a car and wraps it in an EnergyStackWithoutParameters.
carGrayscale8Bit() - Method in class org.anchoranalysis.test.image.load.CarImageLoader: Loads and returns the 8-bit grayscale image of a car.
carGrayscale8BitAsEnergy() - Method in class org.anchoranalysis.test.image.load.CarImageLoader: Loads the 8-bit grayscale image of a car and wraps it in an EnergyStackWithoutParameters.
CarImageLoader - Class in org.anchoranalysis.test.image.load: Loads some images of a car.
CarImageLoader() - Constructor for class org.anchoranalysis.test.image.load.CarImageLoader
carRGB() - Method in class org.anchoranalysis.test.image.load.CarImageLoader: Loads and returns the RGB image of a car.
carRGBAsEnergy() - Method in class org.anchoranalysis.test.image.load.CarImageLoader: Loads the RGB image of a car and wraps it in an EnergyStackWithoutParameters.
castAs() - Method in class org.anchoranalysis.feature.bean.Feature: Casts the feature to having a different input-type.
Cell - Class in org.anchoranalysis.image.bean.spatial.arrange.tile: Indicates how to arrange one or more RGBStacks in a cell in a table.
Cell() - Constructor for class org.anchoranalysis.image.bean.spatial.arrange.tile.Cell
Cell(StackArranger, int, int) - Constructor for class org.anchoranalysis.image.bean.spatial.arrange.tile.Cell: Creates a new Cell instance.
CENTER - Enum constant in enum class org.anchoranalysis.image.bean.nonbean.spatial.align.AlignmentOnDimension: Aligns to the center position along the axis.
CENTER - Static variable in class org.anchoranalysis.image.bean.nonbean.spatial.align.PositionChoicesConstants: Align to the center (middle) in the respective dimension.
centerOfGravity() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Calculates center-of-gravity across all axes.
centerOfGravity() - Method in class org.anchoranalysis.spatial.box.BoundingBox: A mid-point in the bounding-box, corresponding to the mean of all points inside the box.
centerOfGravity(Axis) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Calculates center-of-gravity for one specific axis only.
CenterOfGravity - Class in org.anchoranalysis.image.feature.bean.object.single: Calculates the center of gravity of a single object along a specified axis.
CenterOfGravity() - Constructor for class org.anchoranalysis.image.feature.bean.object.single.CenterOfGravity
CenterOfGravity(Axis) - Constructor for class org.anchoranalysis.image.feature.bean.object.single.CenterOfGravity: Creates a CenterOfGravity feature for a specific axis.
centerPoint() - Method in class org.anchoranalysis.mpp.mark.Mark: Returns the center point of the mark.
centerPoint() - Method in class org.anchoranalysis.mpp.mark.MarkWithPosition
centerPoint() - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
centerPoint() - Method in class org.anchoranalysis.mpp.mark.points.PointList
centerPoint() - Method in class org.anchoranalysis.mpp.mark.points.Polygon
centerPoint() - Method in class org.anchoranalysis.mpp.mark.points.PolygonCurve
centerPoint() - Method in class org.anchoranalysis.plugin.points.bean.fitter.EllipseStandardFormConverter: Gets the center point of the ellipse.
chainCode(int, int, int) - Static method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.ChainCodesDirection: Encodes a direction into a chain code.
chainCodes(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.WatershedEncoding: Decodes a chain-code into a point.
ChainCodesDirection - Class in org.anchoranalysis.plugin.image.segment.watershed.encoding: Maps directions to chain codes and vice versa.
CHANGE_EXISTING_CHANNEL - Enum constant in enum class org.anchoranalysis.image.core.channel.convert.ConversionPolicy: The old channel is converted into the new type if needed.
ChangeableOutputSequence<T,S> - Class in org.anchoranalysis.plugin.image.task.bean.format: A wrapper class that allows changing the output sequence for a given type.
ChangeableOutputSequence() - Constructor for class org.anchoranalysis.plugin.image.task.bean.format.ChangeableOutputSequence
changedOffset(int, int) - Method in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsoluteWithSlidingBuffer: Calculates the offset in the buffer for a voxel, indicated by its relative-change in position.
changeExtension(Path, NonImageFileFormat, FileFormat) - Static method in class org.anchoranalysis.core.format.FormatExtensions: Change the extension in a path.
changeExtent(UnaryOperator<Extent>) - Method in class org.anchoranalysis.spatial.box.BoundingBox: Creates a copied BoundingBox but with a different extent.
changeExtent(Extent) - Method in class org.anchoranalysis.spatial.box.BoundingBox: Creates a copied BoundingBox but with a different extent.
changeExtentZ(int) - Method in class org.anchoranalysis.spatial.box.BoundingBox: Creates a copied BoundingBox but with a different extent in the Z-dimension.
changeInput(U) - Method in class org.anchoranalysis.experiment.task.InputBound: Copies the current instance but changes the input.
changeInputAndSharedState(U, V) - Method in class org.anchoranalysis.experiment.task.InputBound: Copies the current instance but changes both the input and shared-state.
changeIntensity(Voxels<?>, IntUnaryOperator) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll: Changes each voxel, reading and writing the buffer as an int.
changePrefix(DirectoryWithPrefix) - Method in class org.anchoranalysis.io.output.outputter.directory.OutputterTarget: Creates a new OutputterTarget with a changed prefix.
changePrefix(DirectoryWithPrefix) - Method in class org.anchoranalysis.io.output.outputter.OutputterChecked: Creates a OutputterChecked with a changed prefix.
changeZ(int, int) - Method in class org.anchoranalysis.spatial.box.BoundingBox: Creates a copied BoundingBox but with a different corner and extent in the Z-dimension.
channel() - Method in class org.anchoranalysis.image.core.mask.Mask: The underlying channel which contains the binary-values.
channel(String) - Static method in class org.anchoranalysis.plugin.image.provider.ReferenceFactory: Creates a reference to a channel.
Channel - Class in org.anchoranalysis.image.core.channel: A channel from an image.
Channel(Voxels<?>, Optional<Resolution>) - Constructor for class org.anchoranalysis.image.core.channel.Channel: Creates for particular voxels and resolution.
CHANNEL_TO_SKIP_WHEN_TWO - Static variable in class org.anchoranalysis.image.core.stack.DisplayStack: Index of channel to leave blank when there are only two channels. 0=first, 1=second, 2=third.
ChannelAggregator - Class in org.anchoranalysis.image.bean.channel: A method of aggregating the voxels from many identically-sized Channels into one.
ChannelAggregator() - Constructor for class org.anchoranalysis.image.bean.channel.ChannelAggregator
ChannelConverter<T> - Class in org.anchoranalysis.image.core.channel.convert: Base class to convert Channels from one type to another specific type.
ChannelConverter(VoxelDataType, VoxelsConverter<T>, VoxelsFactoryTypeBound<T>) - Constructor for class org.anchoranalysis.image.core.channel.convert.ChannelConverter: Creates a new ChannelConverter instance.
ChannelConverterAttached<S,T> - Interface in org.anchoranalysis.image.core.channel.convert.attached: A channel-converter that has been permanently associated with a particular object.
ChannelConverterMulti - Class in org.anchoranalysis.image.core.channel.convert: Converts a channel from one voxel data-type to one of multiple other types.
ChannelConverterMulti() - Constructor for class org.anchoranalysis.image.core.channel.convert.ChannelConverterMulti
ChannelConvertStyle - Class in org.anchoranalysis.plugin.image.task.bean.format.convertstyle: Converts a channel(s) at a particular timepoint into a stack(s).
ChannelConvertStyle() - Constructor for class org.anchoranalysis.plugin.image.task.bean.format.convertstyle.ChannelConvertStyle
ChannelFactory - Class in org.anchoranalysis.image.core.channel.factory: Creates a Channel corresponding to one of several data-types.
ChannelFactoryFloat - Class in org.anchoranalysis.image.core.channel.factory: Creates a Channel with voxel-type FloatVoxelType.
ChannelFactoryFloat() - Constructor for class org.anchoranalysis.image.core.channel.factory.ChannelFactoryFloat: Default constructor.
ChannelFactorySingleType - Class in org.anchoranalysis.image.core.channel.factory: Creates a Channel for a specific data-type.
ChannelFactorySingleType(VoxelDataType, VoxelsFactoryTypeBound<?>) - Constructor for class org.anchoranalysis.image.core.channel.factory.ChannelFactorySingleType
ChannelFactoryUnsignedByte - Class in org.anchoranalysis.image.core.channel.factory: Creates a Channel with voxel-type UnsignedByteVoxelType.
ChannelFactoryUnsignedByte() - Constructor for class org.anchoranalysis.image.core.channel.factory.ChannelFactoryUnsignedByte: Default constructor.
ChannelFactoryUnsignedInt - Class in org.anchoranalysis.image.core.channel.factory: Creates a Channel with voxel-type UnsignedIntVoxelType.
ChannelFactoryUnsignedInt() - Constructor for class org.anchoranalysis.image.core.channel.factory.ChannelFactoryUnsignedInt: Default constructor.
ChannelFactoryUnsignedShort - Class in org.anchoranalysis.image.core.channel.factory: Creates a Channel with voxel-type UnsignedShortVoxelType.
ChannelFactoryUnsignedShort() - Constructor for class org.anchoranalysis.image.core.channel.factory.ChannelFactoryUnsignedShort: Default constructor.
ChannelFixture - Class in org.anchoranalysis.test.image: Creates a Channel to use in tests.
ChannelFixture() - Constructor for class org.anchoranalysis.test.image.ChannelFixture
ChannelFixture(boolean) - Constructor for class org.anchoranalysis.test.image.ChannelFixture: Creates a new ChannelFixture instance.
ChannelFixture.IntensityFunction - Interface in org.anchoranalysis.test.image: Functional interface for creating intensity values for a given location.
ChannelGenerator - Class in org.anchoranalysis.image.io.channel.output: Writes a single channel to a file.
ChannelGenerator() - Constructor for class org.anchoranalysis.image.io.channel.output.ChannelGenerator
ChannelGetter - Interface in org.anchoranalysis.image.io.channel.input: Retrieves a Channel by name from a particular time-point.
ChannelGetterForTimepoint - Class in org.anchoranalysis.plugin.image.task.stack: A wrapper around ChannelGetter that retrieves channels for a specific timepoint.
ChannelGetterForTimepoint(ChannelGetter, int) - Constructor for class org.anchoranalysis.plugin.image.task.stack.ChannelGetterForTimepoint: Creates a new ChannelGetterForTimepoint instance.
ChannelMap - Class in org.anchoranalysis.image.io.channel.input: A mapping of assigned channel-names to particular indices.
ChannelMap() - Constructor for class org.anchoranalysis.image.io.channel.input.ChannelMap
ChannelMapCreator - Class in org.anchoranalysis.image.io.bean.channel: Creates a ChannelMap for a particular OpenedImageFile.
ChannelMapCreator() - Constructor for class org.anchoranalysis.image.io.bean.channel.ChannelMapCreator
ChannelMapper - Class in org.anchoranalysis.image.core.stack: Helps retrieve channel and an associated converter and apply operation on them jointly.
ChannelMapper(IntFunction<Channel>, IntFunction<Optional<ChannelConverterAttached<Channel, UnsignedByteBuffer>>>) - Constructor for class org.anchoranalysis.image.core.stack.ChannelMapper: Creates a new ChannelMapper instance.
channelNames() - Method in class org.anchoranalysis.image.io.channel.map.NamedChannelsConcatenate
channelNames() - Method in interface org.anchoranalysis.image.io.channel.map.NamedChannelsMap: All channel-names.
channelNames() - Method in class org.anchoranalysis.image.io.channel.map.OpenedNamedChannels
channelNames(Logger) - Method in interface org.anchoranalysis.image.io.stack.input.OpenedImageFile: The names of each channel, if they are known.
channelNames(Logger) - Method in class org.anchoranalysis.plugin.io.multifile.OpenedMultiFile
ChannelProvider - Class in org.anchoranalysis.image.bean.provider: Base class for beans that implement Provider to provide a Channel and associated Stack.
ChannelProvider() - Constructor for class org.anchoranalysis.image.bean.provider.ChannelProvider
ChannelProviderBinary - Class in org.anchoranalysis.image.bean.provider: Implementation of ChannelProvider that calls two ChannelProviders that must provide Channels of the same dimensions.
ChannelProviderBinary() - Constructor for class org.anchoranalysis.image.bean.provider.ChannelProviderBinary
ChannelProviderTernary - Class in org.anchoranalysis.image.bean.provider: Implementation of ChannelProvider that calls three ChannelProviders that must provide Channels of the same dimensions.
ChannelProviderTernary() - Constructor for class org.anchoranalysis.image.bean.provider.ChannelProviderTernary
ChannelProviderUnary - Class in org.anchoranalysis.image.bean.provider: Implementation of ChannelProvider that calls a single delegate ChannelProvider.
ChannelProviderUnary() - Constructor for class org.anchoranalysis.image.bean.provider.ChannelProviderUnary
channels() - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitialization: A collection of Channels, indexed by name.
ChannelSource - Class in org.anchoranalysis.plugin.image.task.grouped: Extracts a set of Channels from a NamedStacks, optionally resizing.
ChannelSource(NamedStacks, ConsistentChannelChecker, Optional<SizeXY>, VoxelsResizer) - Constructor for class org.anchoranalysis.plugin.image.task.grouped.ChannelSource: Creates a new ChannelSource instance.
ChannelSpecification - Class in org.anchoranalysis.test.image.stackwriter: Specifies a type and number of channels in a stack.
ChannelSpecification(VoxelDataType, int, boolean) - Constructor for class org.anchoranalysis.test.image.stackwriter.ChannelSpecification: Creates a new ChannelSpecification instance.
channelsPerByteArray(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.Default
channelsPerByteArray(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptions: The number of channels returned with each call to IFormatReader.openBytes(int).
channelsPerByteArray(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptionsDelegate
check(Channel, String, Dimensions) - Static method in class org.anchoranalysis.plugin.image.channel.DimensionsChecker: Checks a channel to make sure it's the same size as an existing channel.
check(Channel, Mask) - Static method in class org.anchoranalysis.plugin.image.channel.DimensionsChecker: Checks if a channel and a mask have the same dimensions.
check(Mask, String, Dimensions) - Static method in class org.anchoranalysis.plugin.image.channel.DimensionsChecker: Checks a mask to make sure it's the same size as an existing channel.
check(T) - Static method in class org.anchoranalysis.test.experiment.BeanTestChecker: Checks if a bean has all necessary items, throwing a run-time exception if it does not.
check(T) - Static method in class org.anchoranalysis.test.image.io.BeanInstanceMapFixture: Checks if a bean has all necessary items, throwing a run-time exception if it does not.
checkAbsolutePath() - Method in class org.anchoranalysis.io.output.path.prefixer.OutputPrefixerSettings: Checks that if a path is defined as the output-directory then it must be absolute.
checkAndInit(T, P, Logger) - Static method in class org.anchoranalysis.test.experiment.BeanTestChecker: Checks if a bean has all necessary items as with BeanTestChecker.check(T) and also initializes the bean.
CheckCacheForSpecificChildren - Class in org.anchoranalysis.feature.session.cache.finder: For particular child-caches, check if a FeatureCalculationInput is available from another LRU-cache and reuse.
CheckCacheForSpecificChildren(Class<?>, CacheTransferSourceCollection) - Constructor for class org.anchoranalysis.feature.session.cache.finder.CheckCacheForSpecificChildren
checkChannelNames(Set<String>, boolean) - Method in class org.anchoranalysis.plugin.image.task.grouped.ConsistentChannelNamesChecker: Checks that the channel-names are consistent.
checkChannelType(Channel) - Method in class org.anchoranalysis.image.bean.nonbean.ConsistentChannelChecker: Checks that a channel has the same type (max value) as the others.
CheckedBiConsumer<S,T,E> - Interface in org.anchoranalysis.core.functional.checked: Like BiConsumer but can also throw a checked exception.
CheckedBiFunction<S,T,V,E> - Interface in org.anchoranalysis.core.functional.checked: Like BiFunction but can also throw a checked exception.
CheckedBooleanSupplier<E> - Interface in org.anchoranalysis.core.functional.checked: Like BooleanSupplier but can also throw an exception.
CheckedConsumer<S,E> - Interface in org.anchoranalysis.core.functional.checked: Consumes a value and throws an exception.
CheckedFunction<S,V,E> - Interface in org.anchoranalysis.core.functional.checked: Like Function but can also thrown an exception.
CheckedFunctionWithInt<S,V,E> - Interface in org.anchoranalysis.core.functional.checked: Like FunctionWithInt but can also throw a checked exception.
CheckedIntConsumer<E> - Interface in org.anchoranalysis.core.functional.checked: Consumes an int and throws an exception.
CheckedIntFunction<T,E> - Interface in org.anchoranalysis.core.functional.checked: Like IntFunction but can also thrown an exception.
CheckedPredicate<T,E> - Interface in org.anchoranalysis.core.functional.checked: Like Predicate but can also throw an exception.
CheckedRunnable<E> - Interface in org.anchoranalysis.core.functional.checked: Like Runnable but can also throw an exception.
CheckedStream - Class in org.anchoranalysis.core.functional: Map operations for streams that can throw checked-exceptions.
CheckedStream.ConvertedToRuntimeException - Exception Class in org.anchoranalysis.core.functional: An exception that wraps another exception, but exposes itself as a RuntimeException.
CheckedSupplier<T,E> - Interface in org.anchoranalysis.core.functional.checked: Like Supplier but can also throw an exception.
CheckedToDoubleBiFunction<T,U,E> - Interface in org.anchoranalysis.core.functional.checked: Like ToDoubleBiFunction but can also thrown an exception.
CheckedToDoubleFunction<T,E> - Interface in org.anchoranalysis.core.functional.checked: Like ToDoubleFunction but can also thrown an exception.
CheckedToIntFunction<S,E> - Interface in org.anchoranalysis.core.functional.checked: Like ToIntFunction but can also thrown an exception.
CheckedUnaryOperator<T,E> - Interface in org.anchoranalysis.core.functional.checked: Like a UnaryOperator but allows an exception to be thrown.
CheckedUnsupportedOperationException - Exception Class in org.anchoranalysis.core.exception: When a particular operation is unsupported in particular circumstances.
CheckedUnsupportedOperationException() - Constructor for exception class org.anchoranalysis.core.exception.CheckedUnsupportedOperationException: Creates with a default message indicating that the operation is unsupported.
CheckedUnsupportedOperationException(String) - Constructor for exception class org.anchoranalysis.core.exception.CheckedUnsupportedOperationException: Creates with a message explaining that the operation is unsupported.
checkExtentMatch(BoundingBox, BoundingBox) - Static method in class org.anchoranalysis.image.voxel.ExtentMatchHelper: Checks that the Extents of two bounding boxes are identical.
checkIdenticalDataType(VoxelDataType) - Method in class org.anchoranalysis.image.voxel.VoxelsUntyped: Do the voxels have a data-type that is equal to match?
CheckIfAllowed - Class in org.anchoranalysis.io.output.writer: Only allows outputs, if the output-name is allowed in the OutputterChecked.
CheckIfAllowed(SingleLevelOutputEnabled, Optional<WriterExecuteBeforeEveryOperation>, Writer) - Constructor for class org.anchoranalysis.io.output.writer.CheckIfAllowed: Creates a new CheckIfAllowed instance.
checkIfConnected() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Determines if an object-mask is connected.
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.bean.AnchorBean: Checks that a bean's properties conform to expectations.
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.bean.permute.property.SequenceInteger
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.image.bean.displayer.IntensityQuantiles
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.image.bean.spatial.arrange.align.Align
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.image.bean.spatial.arrange.fill.Fill
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureEvaluator
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.io.input.bean.path.matcher.MatchRegularExpression
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.io.input.bean.path.NameElementRange
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.io.output.bean.OutputWriteSettings
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromStack
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.slice.ExtractSliceRange
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Erode
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.Sequence
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeChannels
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeColoredObjects
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.FromChannelOrMask
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeature
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureSequenceInteger
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.CombineObjectsForFeatures: Checks if the bean is misconfigured and saves the default instances for later use.
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.Intersection
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.io.bean.file.namer.LastDirectories
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGFeature
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.opencv.bean.stack.OpenCVReader
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.operator.feature.bean.FromDictionary
CheckMisconfigured - Class in org.anchoranalysis.bean.initializable: Routines for checking that particular patterns exist with bean-properties.
CheckParsedFilePathBag - Class in org.anchoranalysis.plugin.io.bean.file.group.check
CheckParsedFilePathBag() - Constructor for class org.anchoranalysis.plugin.io.bean.file.group.check.CheckParsedFilePathBag
checkResultsVector(ResultsVector) - Static method in class org.anchoranalysis.test.feature.ConstantsInListFixture: Checks that a result-vector has the results we expect from the feature-list associated with this fixture.
checkSize(Extent) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters: Throws an exception if an image of size extent cannot be described by these parameters.
checkUnsupported3D(Channel) - Static method in class org.anchoranalysis.image.bean.segment.object.SegmentChannelIntoObjects: Throws an exception if the channel has more than one z-slice, as 3D is unsupported by the implementation.
checkUnsupportedObjectMask(Optional<ObjectMask>) - Static method in class org.anchoranalysis.image.bean.segment.object.SegmentChannelIntoObjects: Throws an exception if object is present, as it is unsupported by the implementation.
checkUnsupportedSeeds(Optional<ObjectCollection>) - Static method in class org.anchoranalysis.image.bean.segment.object.SegmentChannelIntoObjects: Throws an exception if seeds is present, as it is unsupported by the implementation.
ChildCacheFinder - Interface in org.anchoranalysis.feature.session.cache.finder: Strategy to determine which child-cache (among hierarchy) to employ for a particular feature calculation.
childCacheFor(ChildCacheName, Class<? extends FeatureInput>, CacheCreator) - Method in interface org.anchoranalysis.feature.calculate.cache.FeatureCalculationCache: Gets/creates a child-cache for a given name.
childCacheFor(FeatureCalculationCache<?>, CacheCreator, ChildCacheName, V) - Method in class org.anchoranalysis.feature.session.cache.finder.CheckCacheForSpecificChildren
childCacheFor(FeatureCalculationCache<?>, CacheCreator, ChildCacheName, V) - Method in interface org.anchoranalysis.feature.session.cache.finder.ChildCacheFinder: Selects a child-cache given a parent and a child-name.
childCacheFor(FeatureCalculationCache<?>, CacheCreator, ChildCacheName, V) - Method in class org.anchoranalysis.feature.session.cache.finder.DefaultChildCacheFinder
ChildCacheName - Class in org.anchoranalysis.feature.calculate.cache: A unique identifier for a child-cache's name commposed potentially of two elements.
ChildCacheName(Class<?>) - Constructor for class org.anchoranalysis.feature.calculate.cache.ChildCacheName: Uses only the class as an identifier.
ChildCacheName(Class<?>, int) - Constructor for class org.anchoranalysis.feature.calculate.cache.ChildCacheName: Uses only the class combines with an integer part-name.
ChildCacheName(Class<?>, String) - Constructor for class org.anchoranalysis.feature.calculate.cache.ChildCacheName: Uses both the class and a part-name as an identifier.
Circle - Class in org.anchoranalysis.mpp.mark.conic: Represents a 2D circle mark.
Circle() - Constructor for class org.anchoranalysis.mpp.mark.conic.Circle
Circle(Bound) - Constructor for class org.anchoranalysis.mpp.mark.conic.Circle: Creates a circle with a radius within particular bounds.
Circle(Circle) - Constructor for class org.anchoranalysis.mpp.mark.conic.Circle: Copy constructor.
circleAt(Point2d, int) - Static method in class org.anchoranalysis.test.image.object.CircleObjectFixture: Creates a single circular mask at a particular center point and radius.
circleAt(Point2i, double) - Static method in class org.anchoranalysis.test.feature.plugins.objects.CircleObjectFixture: Creates a circular object mask at a specified center point with a given radius.
CircleObjectFixture - Class in org.anchoranalysis.test.feature.plugins.objects: A fixture for creating circular objects and related utilities for testing purposes.
CircleObjectFixture - Class in org.anchoranalysis.test.image.object: Creates object-masks that are circles in different ways
circumference(int) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse: Calculates the circumference of the ellipse for a given region.
clamp(Point3d, Dimensions) - Static method in class org.anchoranalysis.mpp.mark.PointClamper: Clamps a double-precision point to be within the given dimensions.
clamp(Point3i, Dimensions) - Static method in class org.anchoranalysis.mpp.mark.PointClamper: Clamps an integer point to be within the given dimensions.
ClampHistogramMax - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold: Clamps the input-histogram to a certain maximum value, and then delegates the calculate-level.
ClampHistogramMax() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.ClampHistogramMax
clampTo(Extent) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Makes sure an object fits inside an extent, removing any parts which do not.
clampTo(Extent) - Method in class org.anchoranalysis.spatial.box.BoundingBox: Ensures that the box fits inside a Extent by reducing any values to their limits in the respective dimension.
classificationString(boolean) - Static method in class org.anchoranalysis.plugin.image.task.bean.labeller.BinaryOutcomeImageLabeller: Converts a boolean classification result to its string representation.
classInCurrentJar() - Method in class org.anchoranalysis.launcher.config.LauncherConfig: Provides a class which is used to determine the base location for LauncherConfig.pathRelativeProperties().
clean() - Method in class org.anchoranalysis.mpp.feature.mark.EnergyMemoList: Cleans up the energy memo list by setting the list to null.
cleanUp() - Method in interface org.anchoranalysis.mpp.mark.voxelized.VoxelizedMark: Cleans up any resources associated with this voxelized mark.
cleanUp(VoxelPartitionFactory<Histogram>) - Method in class org.anchoranalysis.mpp.index.VoxelPartitionHistogram
cleanUp(VoxelPartitionFactory<T>) - Method in class org.anchoranalysis.mpp.index.IndexByChannel: Cleans up the voxel partitions for all channels using the provided factory.
cleanUp(VoxelPartitionFactory<T>) - Method in class org.anchoranalysis.mpp.index.IndexByRegion: Cleans up the voxel partitions using the provided factory.
cleanUp(VoxelPartitionFactory<T>) - Method in interface org.anchoranalysis.mpp.index.VoxelPartition: Cleans up the voxel partition using the provided factory.
cleanUpRemaining() - Method in class org.anchoranalysis.core.collection.MapCreateCountdown: Applies the clean-up function on any keys remaining in the map.
clear() - Method in class org.anchoranalysis.feature.bean.list.FeatureList: Removes all of the elements from this list.
clear() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer: Clears the buffer ala Buffer.clear().
clipTo(ObjectMask, Extent) - Method in class org.anchoranalysis.image.core.object.scale.AccessObjectMaskSimple
clipTo(T, Extent) - Method in interface org.anchoranalysis.image.core.object.scale.AccessObjectMask: Ensures the element lies within a certain extent.
close() - Method in class org.anchoranalysis.feature.io.csv.FeatureCSVWriter: Closes any open file-handles.
close() - Method in interface org.anchoranalysis.image.io.stack.input.OpenedImageFile: Closes the opened image-file, removing any intermediate data-structures.
close() - Method in class org.anchoranalysis.inference.concurrency.ConcurrentModelPool: Close all models, to indicate they are no longer in use, and to perform tidy-up.
close() - Method in interface org.anchoranalysis.inference.InferenceModel: Indicates that the model will no longer be used, and does appropriate tidying up and freeing of resources.
close() - Method in class org.anchoranalysis.io.generator.tabular.CSVWriter
close() - Method in class org.anchoranalysis.io.input.csv.CSVReader.OpenedCSVFile
close() - Method in class org.anchoranalysis.io.input.csv.ReadByLine: Closes any opened-files
close() - Method in class org.anchoranalysis.plugin.image.task.labeller.SharedStateFilteredImageOutput: Closes the CSV writer.
close() - Method in class org.anchoranalysis.plugin.image.task.stack.SharedStateSelectedSlice: Closes the CSV writer if it exists.
close() - Method in class org.anchoranalysis.plugin.io.multifile.OpenedMultiFile
close() - Method in class org.anchoranalysis.plugin.onnx.model.OnnxModel
close() - Method in class org.anchoranalysis.plugin.opencv.segment.OpenCVModel
close(boolean, boolean) - Method in class org.anchoranalysis.experiment.bean.log.StatefulNullMessageLogger
close(boolean, boolean) - Method in class org.anchoranalysis.experiment.log.ConsoleMessageLogger
close(boolean, boolean) - Method in class org.anchoranalysis.experiment.log.FailureOnlyMessageLogger
close(boolean, boolean) - Method in class org.anchoranalysis.experiment.log.MultipleLoggers
close(boolean, boolean) - Method in interface org.anchoranalysis.experiment.log.StatefulMessageLogger: Stops logging.
close(boolean, boolean) - Method in class org.anchoranalysis.experiment.log.TextFileMessageLogger
close(ErrorReporter) - Method in interface org.anchoranalysis.io.input.InputFromManager: Performs all tidying up, file-closing etc. after we are finished using the InputFromManager
close(ErrorReporter) - Method in class org.anchoranalysis.io.input.InputFromManagerDelegate
close(ErrorReporter) - Method in class org.anchoranalysis.mpp.io.input.MultiInput
close(ErrorReporter) - Method in class org.anchoranalysis.mpp.io.input.StackWithMap: Closes resources and cleans up.
closeAndWriteOutputs(Optional<NamedFeatureStore<FeatureInputResults>>, boolean, Function<InputOutputContext, FeatureCSVWriterFactory>, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.feature.FeatureExporter: Writes all the results that have been collected as a CSV file, and closes open I/O handles and memory structures.
closeAndWriteOutputs(ExportFeaturesStyle) - Method in class org.anchoranalysis.plugin.image.task.segment.SharedStateSegmentInstance: Writes all the results that have been collected as a CSV file, and closes open I/O handles and memory structures.
closeAnyOpenIO() - Method in class org.anchoranalysis.plugin.image.task.feature.FeatureResultsAndThumbnails: Closes any open IO and removes redundant structures stored in memory.
closeLogger() - Method in class org.anchoranalysis.plugin.io.shared.RecordingCounter: Closes the logger.
ClusterByTimestamp - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster: Associates particular timestamp with each file, and clusters.
ClusterByTimestamp() - Constructor for class org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster.ClusterByTimestamp
clusterFor(File) - Method in class org.anchoranalysis.plugin.io.file.copy.ClusterMembership: Finds the corresponding cluster for a particular file.
ClusterIdentifier - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster: Uniquely identifies a cluster.
ClusterIdentifier(String, ZoneOffset) - Constructor for class org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster.ClusterIdentifier: Creates with a constant-name.
ClusterIdentifier(ZoneOffset) - Constructor for class org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster.ClusterIdentifier: Creates with no name.
ClusterMembership - Class in org.anchoranalysis.plugin.io.file.copy: A mapping of files to membership of particular clusters.
ClusterMembership(ClusterIdentifier) - Constructor for class org.anchoranalysis.plugin.io.file.copy.ClusterMembership: Creates a new ClusterMembership instance.
CODE_MINIMA - Static variable in class org.anchoranalysis.plugin.image.segment.watershed.encoding.WatershedEncoding: Code representing a minima voxel.
CODE_PLATEAU - Static variable in class org.anchoranalysis.plugin.image.segment.watershed.encoding.WatershedEncoding: Code representing a plateau voxel.
CODE_TEMPORARY - Static variable in class org.anchoranalysis.plugin.image.segment.watershed.encoding.WatershedEncoding: Code representing a temporary voxel.
CODE_UNVISITED - Static variable in class org.anchoranalysis.plugin.image.segment.watershed.encoding.WatershedEncoding: Code representing an unvisited voxel.
coefficientOfVariation(Histogram) - Static method in class org.anchoranalysis.math.histogram.HistogramStatistics: Calculates the coefficient-of-variation of a distribution of values, represented by their histogram.
CoefficientOfVariation - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic: Calculates the coefficient of variation of all the values in the histogram.
CoefficientOfVariation() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.CoefficientOfVariation
CollapseFileName - Class in org.anchoranalysis.plugin.io.bean.path.derive: Removes the file-name from a path, but keeps the directories and preserves the file-extension.
CollapseFileName() - Constructor for class org.anchoranalysis.plugin.io.bean.path.derive.CollapseFileName
CollectionGenerator<T> - Class in org.anchoranalysis.io.generator.collection: Writes a collection of elements as a subdirectory with each element as a single file in the subdirectory.
CollectionGenerator(Generator<T>, String) - Constructor for class org.anchoranalysis.io.generator.collection.CollectionGenerator: Creates a new CollectionGenerator instance.
collectResult() - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.ProcessChangedPointAbsoluteMasked: Collects the result of the operation after processing neighbor voxels.
collectResult() - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighbor: Collects the result of the operation after processing neighbor pixels.
collectResult() - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsolute: Collects the result of the operation after processing neighbor voxels.
colorAtVoxel(ReadableTuple3i) - Method in class org.anchoranalysis.image.core.stack.RGBStack: Gets the color at a particular voxel.
ColorConverterBase - Class in org.anchoranalysis.plugin.opencv.bean.color: Converts a RGB stack into another color space using OpenCV.
ColorConverterBase() - Constructor for class org.anchoranalysis.plugin.opencv.bean.color.ColorConverterBase
ColoredBase - Class in org.anchoranalysis.plugin.image.bean.stack.provider.color: Base class for providers that draw entities (an outline or filled) on a background.
ColoredBase() - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase
ColoredBaseWithGenerator - Class in org.anchoranalysis.plugin.image.bean.stack.provider.color: Like ColoredBase but uses a generator to determine the colors for the objects.
ColoredBaseWithGenerator() - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBaseWithGenerator
ColoredMarks - Class in org.anchoranalysis.mpp.mark: A collection of marks, each associated with a color.
ColoredMarks - Class in org.anchoranalysis.plugin.mpp.bean.stack.provider: Draws a colored representation (outline or filled) of an MarkCollection on a background
ColoredMarks() - Constructor for class org.anchoranalysis.mpp.mark.ColoredMarks: Creates an empty ColoredMarks instance.
ColoredMarks() - Constructor for class org.anchoranalysis.plugin.mpp.bean.stack.provider.ColoredMarks
ColoredMarks(MarkCollection, ColorIndex, IdentifierGetter) - Constructor for class org.anchoranalysis.mpp.mark.ColoredMarks: Creates a ColoredMarks instance from a MarkCollection and assigns colors based on a ColorIndex.
ColoredMarks(MarkCollection, ColorList) - Constructor for class org.anchoranalysis.mpp.mark.ColoredMarks
ColoredMarks(Mark, RGBColor) - Constructor for class org.anchoranalysis.mpp.mark.ColoredMarks: Creates a ColoredMarks instance with a single mark and color.
ColoredMask - Class in org.anchoranalysis.plugin.image.bean.stack.provider.color: Draws a colored representation (outline or filled) of a ObjectMask on a background
ColoredMask() - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredMask
ColoredObject - Class in org.anchoranalysis.plugin.image.object: An ObjectMask with an associated color.
ColoredObject(ObjectMask, RGBColor) - Constructor for class org.anchoranalysis.plugin.image.object.ColoredObject: Creates a new ColoredObject instance.
ColoredObjectCollection - Class in org.anchoranalysis.plugin.image.object: Associates a ColorList with a ObjectCollection
ColoredObjectCollection() - Constructor for class org.anchoranalysis.plugin.image.object.ColoredObjectCollection: Create with an empty collection.
ColoredObjectCollection(Stream<ColoredObject>) - Constructor for class org.anchoranalysis.plugin.image.object.ColoredObjectCollection: Create from a stream of ColoredObjects.
ColoredObjectCollection(ObjectCollection, ColorList) - Constructor for class org.anchoranalysis.plugin.image.object.ColoredObjectCollection: Create with an existing object and color list.
ColoredObjectCollection(ObjectMask, RGBColor) - Constructor for class org.anchoranalysis.plugin.image.object.ColoredObjectCollection: Create with a single object and color.
ColoredObjects - Class in org.anchoranalysis.plugin.image.bean.stack.provider.color: Draws a colored representation (outline or filled) of an ObjectCollection on a background
ColoredObjects() - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredObjects
coloredObjectsToDraw(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase: Creates colored-objects to be drawn.
coloredObjectsToDraw(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBaseWithGenerator
coloredObjectsToDraw(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredMask
coloredObjectsToDraw(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeColoredObjects
ColoredOverlayCollection - Class in org.anchoranalysis.overlay.collection: Like a OverlayCollection but additionally associates a color with each overlay.
ColoredOverlayCollection() - Constructor for class org.anchoranalysis.overlay.collection.ColoredOverlayCollection: Create an empty collection.
ColoredOverlayCollection(OverlayCollection, ColorList) - Constructor for class org.anchoranalysis.overlay.collection.ColoredOverlayCollection: Creates a new ColoredOverlayCollection instance.
colorFor(ObjectWithProperties, int) - Method in class org.anchoranalysis.overlay.writer.ObjectDrawAttributes: A color for a particular object
colorForEachIndex(int) - Method in class org.anchoranalysis.bean.shared.color.scheme.ColorScheme: Assigns a color to each index value from a list of size numberColors.
ColorIndex - Interface in org.anchoranalysis.core.color: Associates an RGB-color with each index.
ColorIndexModulo - Class in org.anchoranalysis.core.color: Derives a new ColorIndex from an existing ColorIndex applying a modulo operation to each index call.
ColorIndexModulo(ColorIndex) - Constructor for class org.anchoranalysis.core.color.ColorIndexModulo: Creates a new ColorIndexModulo instance.
ColorList - Class in org.anchoranalysis.core.color: A list of colors, each corresponding to a particular index position.
ColorList() - Constructor for class org.anchoranalysis.core.color.ColorList
ColorList(Color...) - Constructor for class org.anchoranalysis.core.color.ColorList: Create for one or more colors of type Color.
ColorList(Stream<RGBColor>) - Constructor for class org.anchoranalysis.core.color.ColorList: Create for one or more colors of type RGBColor.
ColorList(RGBColor...) - Constructor for class org.anchoranalysis.core.color.ColorList: Create for one or more colors of type RGBColor.
ColorProvider - Class in org.anchoranalysis.image.bean.provider: Base class for beans that implement Provider to provide a ColorList.
ColorProvider() - Constructor for class org.anchoranalysis.image.bean.provider.ColorProvider
ColorScheme - Class in org.anchoranalysis.bean.shared.color.scheme: Creates a sequence of related colors.
ColorScheme() - Constructor for class org.anchoranalysis.bean.shared.color.scheme.ColorScheme
ColorSchemeUnary - Class in org.anchoranalysis.bean.shared.color.scheme: Like ColorScheme but employs a unary operator on a call to an existing ColorScheme.
ColorSchemeUnary() - Constructor for class org.anchoranalysis.bean.shared.color.scheme.ColorSchemeUnary
ColorSchemeUnary(ColorScheme) - Constructor for class org.anchoranalysis.bean.shared.color.scheme.ColorSchemeUnary: Creates a new ColorSchemeUnary instance.
colorSpaceCode() - Method in class org.anchoranalysis.plugin.opencv.bean.color.ColorConverterBase: The color space conversion code to use from OpenCV, that defines the color-space to convert to.
colorSpaceCode() - Method in class org.anchoranalysis.plugin.opencv.bean.color.ConvertRGBToHSV
colorSpaceCode() - Method in class org.anchoranalysis.plugin.opencv.bean.color.ConvertRGBToLab
column(int) - Method in class org.anchoranalysis.spatial.orientation.RotationMatrix: Extracts a column from the rotation-matrix as a point.
combine(boolean, boolean) - Method in class org.anchoranalysis.io.output.enabled.multi.MultiLevelAnd
combine(boolean, boolean) - Method in class org.anchoranalysis.io.output.enabled.multi.MultiLevelBinary: Determines whether an output is enabled via a combination of the two MultiLevelOutputEnabled.
combine(boolean, boolean) - Method in class org.anchoranalysis.io.output.enabled.multi.MultiLevelOr
combine(boolean, boolean) - Method in class org.anchoranalysis.io.output.enabled.single.SingleLevelAnd
combine(boolean, boolean) - Method in class org.anchoranalysis.io.output.enabled.single.SingleLevelBinary: Determines whether an output is enabled via a combination of the two MultiLevelOutputEnabled.
combine(boolean, boolean) - Method in class org.anchoranalysis.io.output.enabled.single.SingleLevelOr
combine(List<PermutationAssigner>) - Static method in class org.anchoranalysis.bean.permute.assign.PermutationAssignerFactory: Combines multiple existing assigners into a single PermutationAssigners.
combine(List<RGBStack>, VoxelsResizer, OperationContext) - Method in class org.anchoranalysis.image.bean.spatial.arrange.StackArranger: Creates a new RGBStack of voxel data type unsigned byte that is a combination of other RGBStacks.
combine(List<RGBStack>, VoxelsResizer, ChannelFactorySingleType, OperationContext) - Method in class org.anchoranalysis.image.bean.spatial.arrange.StackArranger: Creates a new RGBStack that is a combination of other RGBStacks.
combine(DualScale, BiFunction<T, U, S>) - Method in class org.anchoranalysis.image.inference.segment.DualScale: Create a derived DualScale by combining the respective elements of this instance with another.
Combine - Class in org.anchoranalysis.plugin.io.bean.file.provider
Combine() - Constructor for class org.anchoranalysis.plugin.io.bean.file.provider.Combine
CombineBase - Class in org.anchoranalysis.plugin.image.bean.mask.provider.combine: Base class for combining two masks.
CombineBase() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.combine.CombineBase
CombineCSV - Class in org.anchoranalysis.plugin.io.bean.task: Combines multiple CSV files into a single CSV file.
CombineCSV() - Constructor for class org.anchoranalysis.plugin.io.bean.task.CombineCSV
combined() - Method in class org.anchoranalysis.core.system.path.PathDifference: The directory-component (if it exists) and filename-component combined.
combined() - Method in class org.anchoranalysis.core.system.path.SplitPath: A path that combines the root together with the remainder.
combineDescription(String, String) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.AddConstantTo
combineDescription(String, String) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.ConstantToThePowerOf
combineDescription(String, String) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.DivideByConstant
combineDescription(String, String) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.MultiplyByConstant
combineDescription(String, String) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.SubtractFrom
combineDescription(String, String) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.ToThePowerOfConstant
combineDescription(String, String) - Method in class org.anchoranalysis.plugin.operator.feature.bean.replace.ReplaceUnusualValue
combineDescription(String, String) - Method in class org.anchoranalysis.plugin.operator.feature.bean.WithValueBase: Combines the descriptions of the constant value and the feature.
combineDescriptionsRecursively(String, String) - Method in exception class org.anchoranalysis.core.exception.combinable.AnchorCombinableException: Traverses through a set of nested-exceptions creating a description for each "combined" exception, and combining them into a single string.
CombinedListGenerator<T> - Class in org.anchoranalysis.io.generator.combined: Several generators combined together with a common element-type.
CombinedListGenerator() - Constructor for class org.anchoranalysis.io.generator.combined.CombinedListGenerator
CombinedListGenerator(Stream<NameValue<Generator<T>>>) - Constructor for class org.anchoranalysis.io.generator.combined.CombinedListGenerator: Create from a stream of named generators.
CombinedListGenerator(NameValue<Generator<T>>) - Constructor for class org.anchoranalysis.io.generator.combined.CombinedListGenerator: Create from a single named generator.
CombinedListGenerator(Generator<T>...) - Constructor for class org.anchoranalysis.io.generator.combined.CombinedListGenerator: Create from multiple named generators.
CombinedName - Class in org.anchoranalysis.feature.io.name: A name which is unique when a primaryName is combined with a secondaryName
CombinedName(String, String) - Constructor for class org.anchoranalysis.feature.io.name.CombinedName: Creates with explicit strings for both parts.
combinedStacks() - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitialization: Exposes several entities that have natural Stack representations as a unified NamedProvider.
CombineObjectsForFeatures<T> - Class in org.anchoranalysis.plugin.image.feature.bean.object.combine: A way to combine (or not combine) objects so that they provide a feature-table.
CombineObjectsForFeatures() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.combine.CombineObjectsForFeatures
CombineObjectsForFeatures(Interpolator) - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.combine.CombineObjectsForFeatures: Create with a specific interpolator.
combineSecond(SingleLevelOutputEnabled, SingleLevelOutputEnabled) - Method in class org.anchoranalysis.io.output.enabled.multi.MultiLevelAnd
combineSecond(SingleLevelOutputEnabled, SingleLevelOutputEnabled) - Method in class org.anchoranalysis.io.output.enabled.multi.MultiLevelBinary: Builds a second-level output by combining enabled1 and enabled2.
combineSecond(SingleLevelOutputEnabled, SingleLevelOutputEnabled) - Method in class org.anchoranalysis.io.output.enabled.multi.MultiLevelOr
combineTypes(VoxelDataType, VoxelDataType) - Static method in class org.anchoranalysis.image.voxel.datatype.CombineTypes: What data-type to use to represent voxels of both type1 and type2?
CombineTypes - Class in org.anchoranalysis.image.voxel.datatype: Calculates which VoxelDataType to use when combining two other voxel-data types, but without losing precision.
combineValueAndFeature(double, double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.AddConstantTo
combineValueAndFeature(double, double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.ConstantToThePowerOf
combineValueAndFeature(double, double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.DivideByConstant
combineValueAndFeature(double, double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.MultiplyByConstant
combineValueAndFeature(double, double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.SubtractFrom
combineValueAndFeature(double, double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.ToThePowerOfConstant
combineValueAndFeature(double, double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.replace.ReplaceUnusualValue
combineValueAndFeature(double, double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.WithValueBase: Combines the constant value with the feature result.
combineWithSuffix(String) - Method in class org.anchoranalysis.core.system.path.FilenameSplitExtension: Inserts a suffix after the base-name, but before the extension, immutably.
CommandLineException - Exception Class in org.anchoranalysis.launcher: An exception thrown at run-time while processing command-line arguments.
CommandLineException(String) - Constructor for exception class org.anchoranalysis.launcher.CommandLineException: Constructs a new CommandLineException with the specified detail message.
CommandLineExtracter - Class in org.anchoranalysis.launcher.options: Adds methods to CommandLine for querying and extracting options, with and without arguments.
CommandLineExtracter(CommandLine) - Constructor for class org.anchoranalysis.launcher.options.CommandLineExtracter: Creates a new CommandLineExtracter instance.
CommandLineOptions - Class in org.anchoranalysis.launcher.options: All command-line options used by the launcher.
common() - Method in class org.anchoranalysis.experiment.io.InitializationContext: Creates a CommonContext a context that contains a subset of this context.
common() - Method in interface org.anchoranalysis.io.output.outputter.InputOutputContext: Creates a CommonContext a context that contains a subset of this context.
CommonContext - Class in org.anchoranalysis.core.log: A logger with additional configuration that are coupled together widely in the code.
CommonContext(Logger, Path) - Constructor for class org.anchoranalysis.core.log.CommonContext: Creates a new CommonContext instance.
CommonPath - Class in org.anchoranalysis.core.system.path: Finds the common root directory of a set of paths.
CommonSize - Class in org.anchoranalysis.plugin.image.task.size: Shared-state that exposes a common-size to all images.
CommonSize(Extent) - Constructor for class org.anchoranalysis.plugin.image.task.size.CommonSize: Creates a new CommonSize instance.
commonType(Stream<VoxelDataType>) - Static method in class org.anchoranalysis.image.voxel.datatype.FindCommonVoxelType: Finds a common type to represent (ideally without loss of precision} of a stream of types.
commonType(VoxelDataType, VoxelDataType) - Static method in class org.anchoranalysis.image.voxel.datatype.FindCommonVoxelType: Finds a common type to represent (ideally without loss of precision} both first and second.
ComparableSource - Class in org.anchoranalysis.annotation.io.bean.comparer: A set of elements, loaded from the file-system, to be compared to another set.
ComparableSource() - Constructor for class org.anchoranalysis.annotation.io.bean.comparer.ComparableSource
Comparator3d<T> - Class in org.anchoranalysis.spatial.point: Imposes an ordering on any sub-type of Tuple3d.
Comparator3d() - Constructor for class org.anchoranalysis.spatial.point.Comparator3d
Comparator3i<T> - Class in org.anchoranalysis.spatial.point: Imposes an ordering on any sub-type of Tuple3i.
Comparator3i() - Constructor for class org.anchoranalysis.spatial.point.Comparator3i
ComparatorOrderByName<V> - Class in org.anchoranalysis.core.identifier.name: Orders two name-values by their name (alphabetic order from standard String.compareTo(String).
ComparatorOrderByName() - Constructor for class org.anchoranalysis.core.identifier.name.ComparatorOrderByName
compare(float, float) - Method in interface org.anchoranalysis.image.voxel.projection.extrema.ComparisonProjection.FloatComparer: Compare a value to an existing value.
compare(int, int) - Method in interface org.anchoranalysis.image.voxel.projection.extrema.ComparisonProjection.IntComparer: Compare a value to an existing value.
compare(long, long) - Method in interface org.anchoranalysis.image.voxel.projection.extrema.ComparisonProjection.LongComparer: Compare a value to an existing value.
compare(NameValue<V>, NameValue<V>) - Method in class org.anchoranalysis.core.identifier.name.ComparatorOrderByName
compare(T, T) - Method in class org.anchoranalysis.spatial.point.Comparator3d
compare(T, T) - Method in class org.anchoranalysis.spatial.point.Comparator3i
CompareAnnotations<T> - Class in org.anchoranalysis.plugin.annotation.bean.comparison: Task to compare a set of annotations to a segmentation or another set of annotations.
CompareAnnotations() - Constructor for class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
compareExplicitDirectoryToTest(Path, String) - Static method in class org.anchoranalysis.test.image.DualComparerFactory: Compares an explicit directory to a directory in Maven's test/resources.
compareTemporaryDirectoryToTest(Path, Optional<String>, String) - Static method in class org.anchoranalysis.test.image.DualComparerFactory: Compares a directory in a temporary-folder to a directory in Maven's test/resources.
compareTo(AssociatedIndex) - Method in class org.anchoranalysis.core.index.Indexable
compareTo(MultiName) - Method in class org.anchoranalysis.feature.io.name.CombinedName
compareTo(MultiName) - Method in class org.anchoranalysis.feature.io.name.SimpleName
compareTo(ExtentToArrange) - Method in class org.anchoranalysis.image.bean.spatial.arrange.fill.ExtentToArrange: Sorts in descending order by extent.
compareTo(ObjectForReduction) - Method in class org.anchoranalysis.image.inference.bean.reduce.ObjectForReduction
compareTo(LabelledWithConfidence<T>) - Method in class org.anchoranalysis.image.inference.segment.LabelledWithConfidence
compareTo(WithConfidence<T>) - Method in class org.anchoranalysis.image.inference.segment.WithConfidence
compareTo(WithPriority<T>) - Method in class org.anchoranalysis.inference.concurrency.WithPriority: Orders so that gpu==true has higher priority in queue to gpu==false.
compareTo(EigenvalueAndVector) - Method in class org.anchoranalysis.math.statistics.moment.EigenvalueAndVector
compareTo(SortedSetChannel) - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetChannel
compareTo(SortedSetSlice) - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetSlice
compareTo(BoundingBox) - Method in class org.anchoranalysis.spatial.box.BoundingBox
compareTo(Extent) - Method in class org.anchoranalysis.spatial.box.Extent
compareTo(ReadableTuple3i) - Method in interface org.anchoranalysis.spatial.point.ReadableTuple3i
compareTwoBinaryFiles(String) - Method in class org.anchoranalysis.test.image.DualComparer: Compare two binary-files.
compareTwoCsvFiles(String, CSVComparer, PrintStream) - Method in class org.anchoranalysis.test.image.DualComparer: Compare two CSV files using a specified comparer.
compareTwoImages(String) - Method in class org.anchoranalysis.test.image.DualComparer: Compare two images that have an identical path, but in two different test loaders.
compareTwoImages(String, String) - Method in class org.anchoranalysis.test.image.io.TestLoaderImage: Compare two images that are located on the file system in the same test-folder
compareTwoImages(String, String, boolean) - Method in class org.anchoranalysis.test.image.DualComparer: Compare two images with different paths, but in two different test loaders.
compareTwoImages(TestLoaderImage, String, TestLoaderImage, String, boolean) - Static method in class org.anchoranalysis.test.image.io.TestLoaderImage: Compare two images that are located on the file system (possibly in different test folders)
compareTwoObjectCollections(String) - Method in class org.anchoranalysis.test.image.DualComparer: Compare two object-mask-collections.
compareTwoObjectCollections(String, String) - Method in class org.anchoranalysis.test.image.io.TestLoaderImage: Compare two obj-mask-collection that are located on the file system in the test-folder
compareTwoSubdirectories(String) - Method in class org.anchoranalysis.test.image.DualComparer: Compare two subdirectories that have an identical path, but in two different test loaders.
compareTwoSubdirectoriesInLoader(TestLoader, String, String) - Static method in class org.anchoranalysis.test.image.DualComparerFactory: Compares two subdirectories within the same TestLoader.
compareTwoSubdirectoriesInLoader(TestLoader, String, TestLoader, String) - Static method in class org.anchoranalysis.test.image.DualComparerFactory: Compares two subdirectories from different TestLoaders.
compareTwoXmlDocuments(String) - Method in class org.anchoranalysis.test.image.DualComparer: Compare two XML documents.
CompareWithRange<T> - Class in org.anchoranalysis.plugin.operator.feature.bean.range: Compares a value with a range, returning specified constants if its inside the range, below it or above it
CompareWithRange() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.range.CompareWithRange
CompareWithRangeFeature<T> - Class in org.anchoranalysis.plugin.operator.feature.bean.range: Like CompareWithRange but uses features to calculate boundary values
CompareWithRangeFeature() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.range.CompareWithRangeFeature
CompareXML - Class in org.anchoranalysis.test: Compares two XML documents to see if they are equal.
comparison() - Method in interface org.anchoranalysis.plugin.annotation.counter.ImageCounterWithStatistics: Creates statistics from counted images and the payload T passed for annotated images.
ComparisonPlan - Class in org.anchoranalysis.test.image.rasterwriter.comparison: A plan on which comparisons to execute for a test.
ComparisonPlan(boolean, Optional<ImageFileFormat>, boolean) - Constructor for class org.anchoranalysis.test.image.rasterwriter.comparison.ComparisonPlan: Creates a plan for particular settings.
ComparisonPlan(boolean, Optional<ImageFileFormat>, boolean, String) - Constructor for class org.anchoranalysis.test.image.rasterwriter.comparison.ComparisonPlan: Creates a plan for particular settings - and which copies any missing images to a particular directory.
ComparisonProjection - Class in org.anchoranalysis.image.voxel.projection.extrema: Base class for different types of projections that compare and replace each voxel.
ComparisonProjection(ComparisonProjection.IntComparer, ComparisonProjection.LongComparer, ComparisonProjection.FloatComparer) - Constructor for class org.anchoranalysis.image.voxel.projection.extrema.ComparisonProjection
ComparisonProjection.FloatComparer - Interface in org.anchoranalysis.image.voxel.projection.extrema: Performs comparison of two values of type long.
ComparisonProjection.IntComparer - Interface in org.anchoranalysis.image.voxel.projection.extrema: Performs comparison for two values of type int.
ComparisonProjection.LongComparer - Interface in org.anchoranalysis.image.voxel.projection.extrema: Performs comparison of two values of type long.
ComparisonSharedState<T> - Class in org.anchoranalysis.plugin.annotation.bean.comparison: Shared state for comparison operations, including grouping and statistics.
ComparisonSharedState(CSVAssignment, int, Function<String, ImageCounterWithStatistics<T>>) - Constructor for class org.anchoranalysis.plugin.annotation.bean.comparison.ComparisonSharedState: Creates a new ComparisonSharedState.
CompatibleWithMark - Interface in org.anchoranalysis.mpp.mark: An interface for objects that can determine compatibility with a Mark.
completeProjection() - Method in interface org.anchoranalysis.image.voxel.buffer.ProjectableBuffer: Performs any final operation before turning the projected buffer.
CompressAnyTIFF - Class in org.anchoranalysis.plugin.io.bean.file.copy.method: Create a voxelwise compressed copy of any TIFF file being copied, and otherwise do a Bytewise copy.
CompressAnyTIFF() - Constructor for class org.anchoranalysis.plugin.io.bean.file.copy.method.CompressAnyTIFF
computeIfAbsent(K) - Method in class org.anchoranalysis.core.collection.MapCreate: Gets an existing element from the map, newly creating and storing the element if it's absent.
computeInitialFeasibleSolution() - Method in class org.anchoranalysis.math.optimization.HungarianAlgorithm: Compute an initial feasible solution by assigning zero labels to the workers and by assigning to each job a label equal to the minimum cost among its incident edges.
Concatenate - Class in org.anchoranalysis.bean.define.adder: Concatenates a list of adders.
Concatenate - Class in org.anchoranalysis.plugin.image.bean.color.provider: Combines one or more ColorProviders into a unitary ColorProvider.
Concatenate - Class in org.anchoranalysis.plugin.image.bean.object.provider: An ObjectCollectionProvider that concatenates multiple ObjectCollections from a list of providers.
Concatenate - Class in org.anchoranalysis.plugin.image.bean.stack.provider: Combines all the channels from one or more sources (stacks, channels etc.)
Concatenate<T> - Class in org.anchoranalysis.plugin.io.bean.input: Concatenates the inputs from multiple InputManagers that all provide the same input-type.
Concatenate() - Constructor for class org.anchoranalysis.bean.define.adder.Concatenate
Concatenate() - Constructor for class org.anchoranalysis.plugin.image.bean.color.provider.Concatenate
Concatenate() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.Concatenate
Concatenate() - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.Concatenate
Concatenate() - Constructor for class org.anchoranalysis.plugin.io.bean.input.Concatenate
ConcurrencyPlan - Class in org.anchoranalysis.inference.concurrency: How many allocated CPUs and CPUs can be used concurrently for inference.
ConcurrentJobMonitor - Class in org.anchoranalysis.experiment.task.processor: Monitors all submitted jobs and their current state of execution.
ConcurrentJobMonitor(long) - Constructor for class org.anchoranalysis.experiment.task.processor.ConcurrentJobMonitor: Creates a new ConcurrentJobMonitor instance.
ConcurrentModel<T> - Class in org.anchoranalysis.inference.concurrency: An instance of model that can be used concurrently for inference.
ConcurrentModel(T, boolean) - Constructor for class org.anchoranalysis.inference.concurrency.ConcurrentModel: Creates a new ConcurrentModel instance.
ConcurrentModelException - Exception Class in org.anchoranalysis.inference.concurrency: This exception indicates that an error occurred when performing inference from a model concurrently.
ConcurrentModelException(Throwable) - Constructor for exception class org.anchoranalysis.inference.concurrency.ConcurrentModelException: Creates with a cause.
ConcurrentModelPool<T> - Class in org.anchoranalysis.inference.concurrency: Keeps concurrent copies of a model to be used by different threads.
ConcurrentModelPool(ConcurrencyPlan, CreateModelForPool<T>, Logger) - Constructor for class org.anchoranalysis.inference.concurrency.ConcurrentModelPool: Creates with a particular plan and function to create models.
ConditionalKernel - Class in org.anchoranalysis.image.voxel.kernel: Executes another BinaryKernel iff a predicate is satisfied for a particular point.
ConditionalKernel(BinaryKernel, Predicate<Point3i>) - Constructor for class org.anchoranalysis.image.voxel.kernel.ConditionalKernel: Creates with a particular delegate BinaryKernel and a predicate that tests each point.
ConfigureBioformatsLogging - Class in org.anchoranalysis.io.bioformats: Singleton class for making sure Bioformats is configured configured.
configurePermuteProperty(PermutePropertySequenceInteger) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteDivideByParam
configurePermuteProperty(PermutePropertySequenceInteger) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureSequenceInteger: Configures the PermutePropertySequenceInteger for this permutation.
configurePermuteProperty(PermutePropertySequenceInteger) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFirstSecondOrder
ConicBase - Class in org.anchoranalysis.mpp.mark.conic: Abstract base class for conic marks (e.g., ellipsoids, spheres).
ConicBase() - Constructor for class org.anchoranalysis.mpp.mark.conic.ConicBase: Default constructor.
ConicBase(MarkWithPosition) - Constructor for class org.anchoranalysis.mpp.mark.conic.ConicBase: Constructor that copies from another MarkWithPosition.
ConicFitterBase - Class in org.anchoranalysis.plugin.points.bean.fitter: Base class for conic fitters, providing common properties and methods.
ConicFitterBase() - Constructor for class org.anchoranalysis.plugin.points.bean.fitter.ConicFitterBase
ConnectedComponentsFromBinarySegmentation - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel: Performs a binary-segmentation of the channel and converts its connected-components into objects
ConnectedComponentsFromBinarySegmentation() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.channel.ConnectedComponentsFromBinarySegmentation
ConnectedComponentsFromMask - Class in org.anchoranalysis.plugin.image.bean.object.provider.connected: Converts a binary-mask into its connected components
ConnectedComponentsFromMask() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.connected.ConnectedComponentsFromMask
ConsistentChannelChecker - Class in org.anchoranalysis.image.bean.nonbean: Checks that all Channels have the same voxel-data-type.
ConsistentChannelChecker() - Constructor for class org.anchoranalysis.image.bean.nonbean.ConsistentChannelChecker
ConsistentChannelNamesChecker - Class in org.anchoranalysis.plugin.image.task.grouped: Checks that each image has an identical set of Channel-names, and RGB-state.
ConsistentChannelNamesChecker() - Constructor for class org.anchoranalysis.plugin.image.task.grouped.ConsistentChannelNamesChecker
ConsoleMessageLogger - Class in org.anchoranalysis.experiment.log: Logs messages to the console, STDOUT.
ConsoleMessageLogger() - Constructor for class org.anchoranalysis.experiment.log.ConsoleMessageLogger
Constant<T> - Class in org.anchoranalysis.feature.bean.operator: A constant value that is entirely invariant to the feature-input.
Constant - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold: A constant value for thresholding.
Constant - Class in org.anchoranalysis.plugin.io.bean.path.derive: Always generates a constant path irrespective of the the input
Constant() - Constructor for class org.anchoranalysis.feature.bean.operator.Constant
Constant() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.Constant
Constant() - Constructor for class org.anchoranalysis.plugin.io.bean.path.derive.Constant
Constant(double) - Constructor for class org.anchoranalysis.feature.bean.operator.Constant: Constructor with a particular value.
Constant(int) - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.Constant
Constant(String) - Constructor for class org.anchoranalysis.plugin.io.bean.path.derive.Constant
Constant(String, double) - Constructor for class org.anchoranalysis.feature.bean.operator.Constant: Constructor with a particular value and a custom-name.
ConstantScaleFactor - Class in org.anchoranalysis.plugin.image.bean.scale: Scale X and Y dimension by a constant floating-point number.
ConstantScaleFactor() - Constructor for class org.anchoranalysis.plugin.image.bean.scale.ConstantScaleFactor
ConstantScaleFactor(double) - Constructor for class org.anchoranalysis.plugin.image.bean.scale.ConstantScaleFactor: Creates a new ConstantScaleFactor instance.
ConstantsInListFixture - Class in org.anchoranalysis.test.feature: A test fixture for creating and validating feature lists with constant values.
ConstantToThePowerOf<T> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic: A feature that raises a constant value to the power of another feature's result.
ConstantToThePowerOf() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.ConstantToThePowerOf
consumeChannelIfSupported(int, BiConsumer<Channel, ChannelConverterAttached<Channel, UnsignedByteBuffer>>, Consumer<Channel>) - Method in class org.anchoranalysis.image.core.stack.ChannelMapper: Like ChannelMapper.mapChannelIfSupported(int, BiFunction, Function) but the mapping has no return-type.
consumeMatchingFiles(List<Path>, Consumer<File>) - Method in class org.anchoranalysis.io.input.path.matcher.DualPathPredicates: Calls a Consumer on any path that matches the predicate file.
containerOptional() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithContainerBase: Retrieves the optional container of objects.
containerRequired() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithContainerBase: Retrieves the required container of objects.
contains() - Method in class org.anchoranalysis.spatial.box.BoundingBox: For evaluating whether this bounding-box contains other points, boxes etc.?
contains(double) - Method in class org.anchoranalysis.mpp.bean.bound.ResolvedBound: Checks if a value is contained within the bound.
contains(double) - Method in class org.anchoranalysis.spatial.rtree.IntervalRTree: Which objects contain a particular point?
contains(int, int, int) - Method in class org.anchoranalysis.spatial.box.Extent: Is a point contained within the extent?
contains(Double) - Method in class org.anchoranalysis.bean.primitive.DoubleList
contains(Double) - Method in class org.anchoranalysis.bean.primitive.DoubleSet
contains(Integer) - Method in class org.anchoranalysis.bean.primitive.IntegerList
contains(Integer) - Method in class org.anchoranalysis.bean.primitive.IntegerSet
contains(Object) - Method in class org.anchoranalysis.mpp.mark.MarkCollection: Checks if the collection contains a specific object.
contains(String) - Method in class org.anchoranalysis.bean.primitive.StringList
contains(String) - Method in class org.anchoranalysis.bean.primitive.StringSet
contains(String) - Method in class org.anchoranalysis.core.collection.StringSetTrie: Does the set contain a particular string?
contains(Feature<FeatureInput>) - Method in class org.anchoranalysis.feature.shared.SharedFeatures: Whether a particular feature is contained in this instance.
contains(ChildCacheName) - Method in class org.anchoranalysis.feature.session.cache.finder.CacheTransferSourceCollection: Whether a particular child-cache exists in the source?
contains(BoundingBox) - Method in class org.anchoranalysis.image.core.dimensions.Dimensions: Is box entirely contained within the extent?
contains(BoundingBox) - Method in class org.anchoranalysis.spatial.box.Extent: Is box entirely contained within the extent?
contains(Point2i) - Method in class org.anchoranalysis.spatial.box.Extent: Is a point of type Point2i contained within the extent in the XY plane?
contains(Point3d) - Method in class org.anchoranalysis.image.core.dimensions.Dimensions: Is a point of type Point3d contained within the extent?
contains(Point3d) - Method in class org.anchoranalysis.spatial.box.Extent: Is a point of type Point3d contained within the extent?
contains(Point3i) - Method in class org.anchoranalysis.image.core.dimensions.Dimensions: Is a point of type ReadableTuple3i contained within the Extent?
contains(Point3i) - Method in class org.anchoranalysis.image.voxel.object.IntersectingObjects: All elements that contain a particular point.
contains(Point3i) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Whether a particular point exists within the object-mask?
contains(ReadableTuple3i) - Method in class org.anchoranalysis.spatial.box.Extent: Is a point of type ReadableTuple3i contained within the extent?
contains(ReadableTuple3i) - Method in class org.anchoranalysis.spatial.rtree.BoundingBoxRTree: Which objects contain a particular point?
contains(T) - Method in interface org.anchoranalysis.bean.primitive.PrimitiveBeanCollection: Whether the collection contains a particular element?
containsChild(ChildCacheName) - Method in class org.anchoranalysis.feature.session.cache.finder.CacheTransferSource: Whether a particular child-cache exists in the source?
containsEdge(V, V) - Method in class org.anchoranalysis.core.graph.GraphWithoutPayload: Does the graph contain a particular edge?
containsEdge(V, V) - Method in class org.anchoranalysis.core.graph.GraphWithPayload: Does the graph contain a particular edge?
containsFamily(Class<?>) - Method in class org.anchoranalysis.bean.BeanInstanceMap: Is a particular family-type contained in the map?
containsKey(String) - Method in class org.anchoranalysis.core.value.Dictionary: Does a parameter exist with a particular key?
containsMark(Mark) - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria: Checks if the collection contains a specific mark.
containsOrEmpty() - Method in class org.anchoranalysis.io.input.bean.DebugModeParameters
containsStream(double) - Method in class org.anchoranalysis.spatial.rtree.IntervalRTree: Like IntervalRTree.contains(double) but returns a Stream instead of a Set.
containsStream(Point) - Method in class org.anchoranalysis.spatial.rtree.RTree: Which objects contain a particular point?
containsStream(ReadableTuple3i) - Method in class org.anchoranalysis.spatial.rtree.BoundingBoxRTree: Like BoundingBoxRTree.contains(org.anchoranalysis.spatial.point.ReadableTuple3i) but returns a Stream instead of a Set.
containsVertex(V) - Method in class org.anchoranalysis.core.graph.GraphWithoutPayload: Does the graph contain a particular vertex?
containsVertex(V) - Method in class org.anchoranalysis.core.graph.GraphWithPayload: Does the graph contain a particular vertex?
containsX(double) - Method in class org.anchoranalysis.spatial.box.Extent: Is a value contained within the extent on the X-axis?
containsX(int) - Method in class org.anchoranalysis.spatial.box.Extent: Is a value contained within the extent on the X-axis?
containsY(double) - Method in class org.anchoranalysis.spatial.box.Extent: Is a value contained within the extent on the Y-axis?
containsY(int) - Method in class org.anchoranalysis.spatial.box.Extent: Is a value contained within the extent on the Y-axis?
containsZ(double) - Method in class org.anchoranalysis.spatial.box.Extent: Is a value contained within the extent on the Z-axis?
containsZ(int) - Method in class org.anchoranalysis.spatial.box.Extent: Is a value contained within the extent on the Z-axis?
Contour - Class in org.anchoranalysis.spatial.point: A path of successively-neighbored points.
Contour() - Constructor for class org.anchoranalysis.spatial.point.Contour
contoursForObject(ObjectMask) - Static method in class org.anchoranalysis.plugin.opencv.CVFindContours: Calculates the extreme outer contours from an ObjectMask as OpenCV defines contours.
ConversionPolicy - Enum Class in org.anchoranalysis.image.core.channel.convert: The different ways of converting the voxel-data-type in a Channel.
convert(int) - Method in class org.anchoranalysis.plugin.io.shared.NumberToStringConverter: Converts number to a string, padding with leading zeros if necessary to ensure the desired width.
convert(ByteBuffer, int, OrientationChange, boolean) - Method in class org.anchoranalysis.io.bioformats.copyconvert.ConvertTo: Converts a slice of single-channel into a newly created buffer of type T T.
convert(ByteBuffer, int, OrientationChange, boolean) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedByte
convert(Set<String>, ChannelGetterForTimepoint, Logger) - Method in class org.anchoranalysis.plugin.image.task.bean.format.convertstyle.ChannelConvertStyle: Converts a particular set of channels.
convert(Set<String>, ChannelGetterForTimepoint, Logger) - Method in class org.anchoranalysis.plugin.image.task.bean.format.convertstyle.ExtractToRGB
convert(Set<String>, ChannelGetterForTimepoint, Logger) - Method in class org.anchoranalysis.plugin.image.task.bean.format.convertstyle.IndependentChannels
convert(Set<String>, ChannelGetterForTimepoint, Logger) - Method in class org.anchoranalysis.plugin.image.task.bean.format.convertstyle.RGBIfNamesMatch
convert(Channel, ConversionPolicy) - Method in class org.anchoranalysis.image.core.channel.convert.attached.channel.QuantileIntensity
convert(Channel, ConversionPolicy) - Method in class org.anchoranalysis.image.core.channel.convert.attached.channel.UpperLowerQuantileIntensity
convert(Channel, ConversionPolicy) - Method in class org.anchoranalysis.image.core.channel.convert.attached.channel.IntensityRange
convert(Channel, ConversionPolicy) - Method in class org.anchoranalysis.image.core.channel.convert.attached.channel.MaxIntensity
convert(Channel, ConversionPolicy) - Method in interface org.anchoranalysis.image.core.channel.convert.attached.ChannelConverterAttached: Converts the voxel-type in a Channel.
convert(Channel, ConversionPolicy) - Method in class org.anchoranalysis.image.core.channel.convert.attached.histogram.MaxIntensityFromHistogram
convert(Channel, ConversionPolicy) - Method in class org.anchoranalysis.image.core.channel.convert.attached.histogram.QuantileIntensityFromHistogram
convert(Channel, ConversionPolicy) - Method in class org.anchoranalysis.image.core.channel.convert.attached.histogram.UpperLowerQuantileIntensityFromHistogram
convert(Channel, ConversionPolicy) - Method in class org.anchoranalysis.image.core.channel.convert.ChannelConverter: Converts channel to have voxels with data-type T.
convert(Channel, VoxelDataType) - Method in class org.anchoranalysis.image.core.channel.convert.ChannelConverterMulti: Converts a Channel's voxels to another type.
convert(DisplayStack, boolean) - Static method in class org.anchoranalysis.image.io.stack.ConvertStackToRGB: Converts all of a DisplayStack to a RGBStack.
convert(Stack, StackDisplayer, boolean) - Static method in class org.anchoranalysis.image.io.stack.ConvertStackToRGB: Converts all of a DisplayStack to a RGBStack.
convert(Stack, ConversionPolicy) - Method in class org.anchoranalysis.image.core.channel.convert.ChannelConverter: Like ChannelConverter.convert(Channel, ConversionPolicy) but converts every channel in a Stack.
convert(VoxelsUntyped, VoxelsFactoryTypeBound<T>) - Method in class org.anchoranalysis.image.voxel.convert.VoxelsConverterMulti: Converts a Voxels to another type.
convert(Mark) - Method in class org.anchoranalysis.mpp.mark.MarkToObjectConverter: Converts a Mark to an equivalent ObjectMask.
Convert<T> - Class in org.anchoranalysis.plugin.image.bean.channel.provider.convert: Converts a channel by applying a converter (no histogram is involved in the conversion).
Convert() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.convert.Convert
convert2iTo3d(List<Point2i>) - Static method in class org.anchoranalysis.spatial.point.PointConverter: Convert a list of Point2i to a list of Point3d.
convert2iTo3f(List<Point2i>) - Static method in class org.anchoranalysis.spatial.point.PointConverter: Convert a list of Point2i to a list of Point3f.
convert3dTo3f(List<Point3d>) - Static method in class org.anchoranalysis.spatial.point.PointConverter: Convert a list of Point3d to a list of Point3f.
convert3fTo3d(List<Point3f>) - Static method in class org.anchoranalysis.spatial.point.PointConverter: Convert a list of Point3f to a list of Point3d.
convert3i(List<Point3d>) - Static method in class org.anchoranalysis.spatial.point.PointConverter: Convert a list of Point3d to a list of Point3i.
convert3i(List<Point3f>, boolean) - Static method in class org.anchoranalysis.spatial.point.PointConverter: Convert a list of Point3f to a list of Point3i, optionally rounding values.
convert3iTo3f(List<Point3i>) - Static method in class org.anchoranalysis.spatial.point.PointConverter: Convert a list of Point3i to a list of Point3f.
ConvertBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider.convert: Base class for channel providers that perform conversions on a single input channel.
ConvertBase() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.convert.ConvertBase
convertBeforeAssign(DisplayStack) - Method in class org.anchoranalysis.image.io.stack.output.generator.DisplayStackGenerator
convertBeforeAssign(Stack) - Method in class org.anchoranalysis.image.io.stack.output.generator.FlattenStackGenerator
convertBeforeAssign(T) - Method in class org.anchoranalysis.image.io.stack.output.generator.RasterGeneratorBridge
convertBeforeAssign(T) - Method in class org.anchoranalysis.image.io.stack.output.generator.RasterGeneratorDelegateToRaster: Converts an element before setting it on the delegate.
convertBeforeTransform(Stack) - Method in class org.anchoranalysis.image.io.stack.output.generator.DisplayStackGenerator
convertBeforeTransform(Stack) - Method in class org.anchoranalysis.image.io.stack.output.generator.FlattenStackGenerator
convertBeforeTransform(Stack) - Method in class org.anchoranalysis.image.io.stack.output.generator.RasterGeneratorBridge
convertBeforeTransform(Stack) - Method in class org.anchoranalysis.image.io.stack.output.generator.RasterGeneratorDelegateToRaster: Converts an element before calling RasterGeneratorDelegateToRaster.transform(T) on the delegate.
ConvertChannelTo<T> - Class in org.anchoranalysis.image.bean.channel: Creates a ChannelConverter for converting a channel to a particular type.
ConvertChannelTo() - Constructor for class org.anchoranalysis.image.bean.channel.ConvertChannelTo
ConvertChannelToWithHistogram<T> - Class in org.anchoranalysis.image.bean.channel: Creates a ChannelConverterAttached<Histogram, T> for converting a channel to a particular type, making use of a Histogram.
ConvertChannelToWithHistogram() - Constructor for class org.anchoranalysis.image.bean.channel.ConvertChannelToWithHistogram
convertCode(int, int, EncodedVoxels, Point3i) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedIntBuffer: Converts the code at the given index to a connected component ID.
convertCropped(DisplayStack, BoundingBox) - Static method in class org.anchoranalysis.image.io.stack.ConvertStackToRGB: Converts a bounding-box region in DisplayStack to a RGBStack.
ConvertedInput - Class in org.anchoranalysis.plugin.mpp.shared: A converted-input, together with any logged messages associated with it.
ConvertedInput(U, StringBuilder) - Constructor for class org.anchoranalysis.plugin.mpp.shared.ConvertedInput: Creates a new ConvertedInput instance.
ConvertedToRuntimeException(Throwable) - Constructor for exception class org.anchoranalysis.core.functional.CheckedStream.ConvertedToRuntimeException: Creates for any exception.
convertFloat(FloatBuffer, FloatBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToFloatNoScaling
convertFloat(FloatBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToUnsignedByteNoScaling
convertFloat(FloatBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToUnsignedByteScaleByMaxValue
convertFloat(FloatBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToUnsignedByteScaleByMinMaxValue
convertFloat(FloatBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToUnsignedByteScaleByType: Converts the current position in a FloatBuffer to the current position in a UnsignedShortBuffer.
convertFloat(FloatBuffer, UnsignedIntBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToUnsignedInt
convertFloat(FloatBuffer, UnsignedShortBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToUnsignedShortNoScaling
convertFloat(FloatBuffer, UnsignedShortBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToUnsignedShortScaleByType: Converts the current position in a FloatBuffer to the current position in a UnsignedShortBuffer.
convertFloat(FloatBuffer, T) - Method in class org.anchoranalysis.image.voxel.convert.VoxelsConverter: Copies a value from the current position in a FloatBuffer to the current position in a buffer of type T.
convertFrom(VoxelsUntyped, VoxelsFactoryTypeBound<T>) - Method in class org.anchoranalysis.image.voxel.convert.VoxelsConverter: Creates a new voxels of type T and copies the voxels from from.
ConvertFromImagePlus - Class in org.anchoranalysis.io.imagej.convert: Converts an ImagePlus into a channel or voxels.
ConvertFromMat - Class in org.anchoranalysis.plugin.opencv.convert: Convert from the OpenCV Mat to a Stack.
ConvertFromPhysicalVolume<T> - Class in org.anchoranalysis.image.feature.bean.physical: Converts a feature from physical volume units to voxel units.
ConvertFromPhysicalVolume() - Constructor for class org.anchoranalysis.image.feature.bean.physical.ConvertFromPhysicalVolume
convertFromUnits(double, String) - Static method in class org.anchoranalysis.image.core.dimensions.SpatialUnits: Converts a value from another unit-type to base units.
convertFromUnits(double, SpatialUnits.UnitSuffix) - Static method in class org.anchoranalysis.image.core.dimensions.SpatialUnits: Converts a value from another unit-type to base units.
ConvertImageFormat - Class in org.anchoranalysis.plugin.image.task.bean.format: Converts each input-image to an output format, optionally changing the bit depth.
ConvertImageFormat() - Constructor for class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat
ConvertNamedChannels<T,S,U> - Class in org.anchoranalysis.plugin.mpp.bean.convert: Converts NamedChannelsInput to a variety of others to match a delegate task.
ConvertNamedChannels() - Constructor for class org.anchoranalysis.plugin.mpp.bean.convert.ConvertNamedChannels
ConvertNamedChannelsInputToStack - Class in org.anchoranalysis.plugin.io.bean.input.stack: An input object that converts NamedChannelsInput to StackSequenceInput.
ConvertNamedChannelsInputToStack(NamedChannelsInput, int, Optional<String>, ExecutionTimeRecorder) - Constructor for class org.anchoranalysis.plugin.io.bean.input.stack.ConvertNamedChannelsInputToStack: Create with an input.
ConvertNamedChannelsInputToStack(NamedChannelsInput, ExecutionTimeRecorder) - Constructor for class org.anchoranalysis.plugin.io.bean.input.stack.ConvertNamedChannelsInputToStack: Create with an input.
ConvertNamedChannelsToStack - Class in org.anchoranalysis.plugin.io.bean.input.stack: Manager that converts (one channel) NamedChannelsInput to StackSequenceInput.
ConvertNamedChannelsToStack() - Constructor for class org.anchoranalysis.plugin.io.bean.input.stack.ConvertNamedChannelsToStack
ConvertRGBToHSV - Class in org.anchoranalysis.plugin.opencv.bean.color: Converts a RGB image to the HSV color space.
ConvertRGBToHSV() - Constructor for class org.anchoranalysis.plugin.opencv.bean.color.ConvertRGBToHSV
ConvertRGBToLab - Class in org.anchoranalysis.plugin.opencv.bean.color: Converts a RGB image to the Lab color space.
ConvertRGBToLab() - Constructor for class org.anchoranalysis.plugin.opencv.bean.color.ConvertRGBToLab
convertSliceOfSingleChannel(ByteBuffer, int, OrientationChange) - Method in class org.anchoranalysis.io.bioformats.copyconvert.ConvertTo: Converts a slice of single-channel into a newly created VoxelBuffer.
ConvertStackToRGB - Class in org.anchoranalysis.image.io.stack: Converts a Stack or DisplayStack to a RGBStack.
ConvertTo<T> - Class in org.anchoranalysis.io.bioformats.copyconvert: Converts a subset of raw voxel bytes in a buffer to a possibly a buffer with different data-type.
ConvertTo(Function<VoxelsUntyped, Voxels<T>>, IntFunction<T>, Function<T, VoxelBuffer<T>>) - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.ConvertTo: Creates a new ConvertTo instance.
convertTo3d(Point2d) - Static method in class org.anchoranalysis.spatial.point.PointConverter: Convert a Point2d to a Point3d using 0 as the value of the Z-axis component.
convertTo3i(Point2i) - Static method in class org.anchoranalysis.spatial.point.PointConverter: Convert a Point2i to a Point3i using 0 as the value of the Z-axis component.
convertTo3i(Point2i, int) - Static method in class org.anchoranalysis.spatial.point.PointConverter: Convert a Point3i to a Point2i using an explicit value for the Z-axis component.
ConvertToFactory - Class in org.anchoranalysis.io.bioformats.copyconvert: Creates a ConvertTo to match the desired voxel-type.
ConvertToImagePlus - Class in org.anchoranalysis.io.imagej.convert: Converts a channel or voxels into a ImagePlus.
ConvertToImageProcessor - Class in org.anchoranalysis.io.imagej.convert: Converts other voxel data-structures (as used by Anchor) to an ImageJ ImageProcessor.
ConvertToImg - Class in org.anchoranalysis.image.voxel.convert.imglib2: Converts the Voxels and VoxelBuffer data-types used in Anchor to the Img used in ImgLib2.
ConvertToMat - Class in org.anchoranalysis.plugin.opencv.convert: Converts common image data-structures used by Anchor to the Mat class used by OpenCV.
ConvertToNativeImg - Class in org.anchoranalysis.image.voxel.convert.imglib2: Converts the Voxels and VoxelBuffer data-types used in Anchor to the NativeImg used in ImgLib2.
convertToObjects(Dimensions) - Method in interface org.anchoranalysis.annotation.mark.AnnotationWithMarks: Creates an object-collection that is a voxelized representation of the marks in the annotation.
convertToOutputType(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientBase: Converts the input channel to the output type specified by GradientBase.outputShort.
convertToPhysical(double, UnitConverter) - Method in class org.anchoranalysis.image.feature.bean.physical.ConvertFromPhysicalVolume: Converts the input value from physical volume units to voxel units.
convertToPhysical(double, UnitConverter) - Method in class org.anchoranalysis.image.feature.bean.physical.ConvertToPhysicalAreaXY: Converts the input value from pixel units to physical area units in an isometric XY plane.
convertToPhysical(double, UnitConverter) - Method in class org.anchoranalysis.image.feature.bean.physical.ConvertToPhysicalDistance: Converts the input value to physical distance along the specified direction.
convertToPhysical(double, UnitConverter) - Method in class org.anchoranalysis.image.feature.bean.physical.ConvertToPhysicalVolume: Converts the input value from voxel units to physical volume units.
convertToPhysical(double, UnitConverter) - Method in class org.anchoranalysis.image.feature.bean.physical.FeatureConvertUnits: Converts the input value to physical units.
ConvertToPhysicalAreaXY<T> - Class in org.anchoranalysis.image.feature.bean.physical: Converts a feature value representing area in pixel units to physical area units in an isometric XY plane.
ConvertToPhysicalAreaXY() - Constructor for class org.anchoranalysis.image.feature.bean.physical.ConvertToPhysicalAreaXY
ConvertToPhysicalDistance<T> - Class in org.anchoranalysis.image.feature.bean.physical: Converts a distance feature to physical units along a specified direction.
ConvertToPhysicalDistance() - Constructor for class org.anchoranalysis.image.feature.bean.physical.ConvertToPhysicalDistance
ConvertToPhysicalDistance(Feature<T>, SpatialUnits.UnitSuffix, DirectionVector) - Constructor for class org.anchoranalysis.image.feature.bean.physical.ConvertToPhysicalDistance: Creates a new instance with specified feature, unit type, and direction vector.
ConvertToPhysicalVolume<T> - Class in org.anchoranalysis.image.feature.bean.physical: Converts a feature value representing volume in voxel units to physical volume units.
ConvertToPhysicalVolume() - Constructor for class org.anchoranalysis.image.feature.bean.physical.ConvertToPhysicalVolume
convertToString(Path) - Static method in class org.anchoranalysis.plugin.io.file.copy.PathOperations: Converts a path to a string, making sure it uses UNIX-style separators.
convertToUnits(double, String) - Static method in class org.anchoranalysis.image.core.dimensions.SpatialUnits: Converts a value in base-units to another unit-type.
convertToUnits(double, SpatialUnits.UnitSuffix) - Static method in class org.anchoranalysis.image.core.dimensions.SpatialUnits: Converts a value in base-units to another unit-type.
ConvertToVoxelBuffer - Class in org.anchoranalysis.io.imagej.convert: Converts a ImageProcessor to a voxel-buffer of particular data-type.
ConvertUnits<T> - Class in org.anchoranalysis.plugin.operator.feature.physical: Converts a feature value from one unit type to another.
ConvertUnits() - Constructor for class org.anchoranalysis.plugin.operator.feature.physical.ConvertUnits
convertUnsignedByte(UnsignedByteBuffer, FloatBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToFloatNoScaling
convertUnsignedByte(UnsignedByteBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToUnsignedByte
convertUnsignedByte(UnsignedByteBuffer, UnsignedIntBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToUnsignedInt
convertUnsignedByte(UnsignedByteBuffer, UnsignedShortBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToUnsignedShortNoScaling
convertUnsignedByte(UnsignedByteBuffer, UnsignedShortBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToUnsignedShortScaleByType
convertUnsignedByte(UnsignedByteBuffer, T) - Method in class org.anchoranalysis.image.voxel.convert.VoxelsConverter: Copies a value from the current position in a UnsignedByteBuffer to the current position in a buffer of type T.
convertUnsignedInt(UnsignedIntBuffer, FloatBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToFloatNoScaling
convertUnsignedInt(UnsignedIntBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToUnsignedByteNoScaling
convertUnsignedInt(UnsignedIntBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToUnsignedByteScaleByMaxValue
convertUnsignedInt(UnsignedIntBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToUnsignedByteScaleByMinMaxValue
convertUnsignedInt(UnsignedIntBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToUnsignedByteScaleByType
convertUnsignedInt(UnsignedIntBuffer, UnsignedIntBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToUnsignedInt
convertUnsignedInt(UnsignedIntBuffer, UnsignedShortBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToUnsignedShortNoScaling
convertUnsignedInt(UnsignedIntBuffer, UnsignedShortBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToUnsignedShortScaleByType
convertUnsignedInt(UnsignedIntBuffer, T) - Method in class org.anchoranalysis.image.voxel.convert.VoxelsConverter: Copies a value from the current position in a UnsignedIntBuffer to the current position in a buffer of type T.
convertUnsignedShort(UnsignedShortBuffer, FloatBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToFloatNoScaling
convertUnsignedShort(UnsignedShortBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToUnsignedByteNoScaling
convertUnsignedShort(UnsignedShortBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToUnsignedByteScaleByMaxValue
convertUnsignedShort(UnsignedShortBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToUnsignedByteScaleByMinMaxValue
convertUnsignedShort(UnsignedShortBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToUnsignedByteScaleByType
convertUnsignedShort(UnsignedShortBuffer, UnsignedIntBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToUnsignedInt
convertUnsignedShort(UnsignedShortBuffer, UnsignedShortBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToUnsignedShortNoScaling
convertUnsignedShort(UnsignedShortBuffer, UnsignedShortBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToUnsignedShortScaleByType
convertUnsignedShort(UnsignedShortBuffer, T) - Method in class org.anchoranalysis.image.voxel.convert.VoxelsConverter: Copies a value from the current position in a UnsignedShortBuffer to the current position in a buffer of type T.
convertValue(short) - Method in class org.anchoranalysis.io.bioformats.copyconvert.toshort.ToUnsignedShort: Converts a value retrieved from the source buffer to the destination form.
convertValue(short) - Method in class org.anchoranalysis.io.bioformats.copyconvert.toshort.UnsignedShortFromSignedShort
convertValue(short) - Method in class org.anchoranalysis.io.bioformats.copyconvert.toshort.UnsignedShortFromUnsignedShort
ConvertWithHistogram<T> - Class in org.anchoranalysis.plugin.image.bean.channel.provider.convert: Converts a channel to a different voxel data-type by applying a converter with an associated histogram.
ConvertWithHistogram() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.convert.ConvertWithHistogram
convexHull2D(List<Point2i>) - Static method in class org.anchoranalysis.plugin.points.convexhull.ConvexHullUtilities: Apply a convex-hull algorithm to filter a set of points using the default minimum number of points.
convexHull2D(List<Point2i>, int) - Static method in class org.anchoranalysis.plugin.points.convexhull.ConvexHullUtilities: Apply a convex-hull algorithm to filter a set of points.
ConvexHull2D - Class in org.anchoranalysis.plugin.points.bean.convexhull: Sets particular voxels to high only if they exist on the convex-hull of the outline of a mask.
ConvexHull2D() - Constructor for class org.anchoranalysis.plugin.points.bean.convexhull.ConvexHull2D
ConvexHull3D - Class in org.anchoranalysis.plugin.points.bean.convexhull: Calculates a 3D convex hull from a binary mask.
ConvexHull3D() - Constructor for class org.anchoranalysis.plugin.points.bean.convexhull.ConvexHull3D
ConvexHullBase - Class in org.anchoranalysis.plugin.points.bean.convexhull: Base class for convex hull implementations.
ConvexHullBase() - Constructor for class org.anchoranalysis.plugin.points.bean.convexhull.ConvexHullBase
ConvexHullUtilities - Class in org.anchoranalysis.plugin.points.convexhull: Utility methods for calculating convex hulls on 2D points.
copyAllChannels(Dimensions, ByteBuffer, DestinationChannelForIndex, int, ImageFileEncoding, OrientationChange) - Method in class org.anchoranalysis.io.bioformats.copyconvert.ConvertTo: Copies the channels in the source buffer into a particular DestinationChannelForIndex.
copyAllFrames(IFormatReader, List<Channel>, ImageFileShape, ConvertTo<?>, ReadOptions, OrientationChange) - Static method in class org.anchoranalysis.io.bioformats.copyconvert.CopyConvert: Copies all frames, channels, z-slices (in a byte-array) into a destination set of Channels converting them if necessary along the way.
copyChangeDictionary(Dictionary) - Method in class org.anchoranalysis.feature.energy.EnergyStack: Makes a copy of the EnergyStack but assigns a new Dictionary.
copyChangeIterationsDilation(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations: Creates a copy of this bean with a new value for iterationsDilation.
copyChangeOrientation(ByteBuffer, boolean, int, FloatBuffer, OrientationChange) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tofloat.FloatFromUnsignedByte
copyChangeOrientation(ByteBuffer, boolean, int, FloatBuffer, OrientationChange) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tofloat.FloatFromUnsignedInt
copyChangeOrientation(ByteBuffer, boolean, int, UnsignedByteBuffer, OrientationChange) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.ToUnsignedByteWithScaling
copyChangeOrientation(ByteBuffer, boolean, int, UnsignedByteBuffer, OrientationChange) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromFloat
copyChangeOrientation(ByteBuffer, boolean, int, UnsignedByteBuffer, OrientationChange) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedByteInterleaving
copyChangeOrientation(ByteBuffer, boolean, int, UnsignedByteBuffer, OrientationChange) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedByteNoInterleaving
copyChangeOrientation(ByteBuffer, boolean, int, UnsignedIntBuffer, OrientationChange) - Method in class org.anchoranalysis.io.bioformats.copyconvert.toint.UnsignedIntFromUnsignedInt
copyChangeOrientation(ByteBuffer, boolean, int, UnsignedShortBuffer, OrientationChange) - Method in class org.anchoranalysis.io.bioformats.copyconvert.toshort.ToUnsignedShort
copyChangeOrientation(ByteBuffer, boolean, int, T, OrientationChange) - Method in class org.anchoranalysis.io.bioformats.copyconvert.ConvertTo: Copy the bytes, changing orientation.
CopyContext<T> - Class in org.anchoranalysis.plugin.io.input.path: Context parameters when copying many files from a source directory to a destination directory.
CopyContext(Path, Path, T) - Constructor for class org.anchoranalysis.plugin.io.input.path.CopyContext: Creates a new CopyContext instance.
CopyConvert - Class in org.anchoranalysis.io.bioformats.copyconvert: Copies the bytes from a IFormatReader to a list of channels, converting if necessary.
CopyFiles<T> - Class in org.anchoranalysis.plugin.io.bean.task: Copy files to the output-directory, possibly changing the name or performing other operations like compression in the process.
CopyFiles() - Constructor for class org.anchoranalysis.plugin.io.bean.task.CopyFiles
CopyFilesMethod - Class in org.anchoranalysis.plugin.io.bean.file.copy.method: A method used for copying files (e.g. bytewise or activating compression etc.).
CopyFilesMethod() - Constructor for class org.anchoranalysis.plugin.io.bean.file.copy.method.CopyFilesMethod
CopyFilesNaming<T> - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming: How an output name (and path) is selected for an input file when copying.
CopyFilesNaming() - Constructor for class org.anchoranalysis.plugin.io.bean.file.copy.naming.CopyFilesNaming
CopyFilesNamingOne - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming
CopyFilesNamingOne() - Constructor for class org.anchoranalysis.plugin.io.bean.file.copy.naming.CopyFilesNamingOne
CopyFilesNamingWithoutSharedState - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming: Base class for implementations of CopyFilesNaming where each file is copied independently of the others.
CopyFilesNamingWithoutSharedState() - Constructor for class org.anchoranalysis.plugin.io.bean.file.copy.naming.CopyFilesNamingWithoutSharedState
copyFrom(int, int, ResultsVector, int) - Method in class org.anchoranalysis.feature.results.ResultsVector: Copies a contiguous subset of results from another vector.
copyFrom(VoxelsUntyped, Voxels<T>) - Method in class org.anchoranalysis.image.voxel.convert.VoxelsConverter: Copies voxels from a source (of any type) to voxels of type T.
copyFromFloat(Voxels<FloatBuffer>, Voxels<T>) - Method in class org.anchoranalysis.image.voxel.convert.VoxelsConverter: Copies voxels from a source of type @{link FloatBuffer} to voxels of type T.
copyFromPath1ToPath2(String) - Method in class org.anchoranalysis.test.image.DualComparer: Copies a file from its path in the first loader, to its path in the second loader.
copyFromUnsignedByte(Voxels<UnsignedByteBuffer>, Voxels<T>) - Method in class org.anchoranalysis.image.voxel.convert.VoxelsConverter: Copies voxels from a source of type @{link UnsignedByteBuffer} to voxels of type T.
copyFromUnsignedInt(Voxels<UnsignedIntBuffer>, Voxels<T>) - Method in class org.anchoranalysis.image.voxel.convert.VoxelsConverter: Copies voxels from a source of type @{link UnsignedIntBuffer} to voxels of type T.
copyFromUnsignedShort(Voxels<UnsignedShortBuffer>, Voxels<T>) - Method in class org.anchoranalysis.image.voxel.convert.VoxelsConverter: Copies voxels from a source of type @{link UnsignedShortBuffer} to voxels of type T.
copyImageInto(Stack, Stack, BoundingBox) - Static method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.StackCopierAtBox: Copies a source stack into a destination stack at a particular BoundingBox.
copyInitialize(Class<?>, NamedProviderStore<S>) - Method in class org.anchoranalysis.image.bean.nonbean.init.PopulateStoreFromDefine: Copies objects of a particular class from the define and initializes.
copyKeepOrientation(ByteBuffer, boolean, int, FloatBuffer) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tofloat.FloatFromUnsignedByte
copyKeepOrientation(ByteBuffer, boolean, int, FloatBuffer) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tofloat.FloatFromUnsignedInt
copyKeepOrientation(ByteBuffer, boolean, int, UnsignedByteBuffer) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.ToUnsignedByteWithScaling
copyKeepOrientation(ByteBuffer, boolean, int, UnsignedByteBuffer) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromFloat
copyKeepOrientation(ByteBuffer, boolean, int, UnsignedByteBuffer) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedByteInterleaving
copyKeepOrientation(ByteBuffer, boolean, int, UnsignedByteBuffer) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedByteNoInterleaving
copyKeepOrientation(ByteBuffer, boolean, int, UnsignedIntBuffer) - Method in class org.anchoranalysis.io.bioformats.copyconvert.toint.UnsignedIntFromUnsignedInt
copyKeepOrientation(ByteBuffer, boolean, int, UnsignedShortBuffer) - Method in class org.anchoranalysis.io.bioformats.copyconvert.toshort.ToUnsignedShort
copyKeepOrientation(ByteBuffer, boolean, int, T) - Method in class org.anchoranalysis.io.bioformats.copyconvert.ConvertTo: Copy the bytes, without changing orientation.
copyPixelsTo(int, BoundingBox, Voxels<UnsignedByteBuffer>, BoundingBox) - Method in class org.anchoranalysis.image.core.stack.DisplayStack: Copies pixels from a particular channel to an output buffer.
copyProviderInitialize(Class<?>, NamedProviderStore<T>) - Method in class org.anchoranalysis.image.bean.nonbean.init.PopulateStoreFromDefine: Copies objects of a particular class (which must be a Provider) from define and initializes each.
copyStackInto(CheckedSupplier<RGBStack, InputReadFailedException>, String, Path, Optional<String>) - Method in class org.anchoranalysis.plugin.image.task.slice.MontageSharedState: Copies a Stack into a BoundingBox in the combined image, resizing if necessary.
copyTo(SharedObjects, Logger) - Method in interface org.anchoranalysis.mpp.io.input.ExportSharedObjects: Adds any exported shared objects to the target container.
copyTo(SharedObjects, Logger) - Method in class org.anchoranalysis.mpp.io.input.MultiInput
copyToDirectory(File) - Method in class org.anchoranalysis.test.TestLoader: Copies all the data in the test-data folder (recursively), preserving file modification times.
copyToDirectory(String[], File) - Method in class org.anchoranalysis.test.TestLoader: Copies specific subdirectories from the test-data folder (recursively), preserving file modification times.
copyVoxelFrom(int, VoxelBuffer<T>, int) - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer: Copies one particular intensity-value from another VoxelBuffer into this buffer.
copyVoxelsTo(ObjectMask, VoxelsUntyped, BoundingBox) - Method in class org.anchoranalysis.image.voxel.VoxelsUntyped: Copies the voxels into a destination, but only those voxels inside an ObjectMask.
copyVoxelsTo(BoundingBox, VoxelsUntyped, BoundingBox) - Method in class org.anchoranalysis.image.voxel.VoxelsUntyped: Copies the voxels into a destination, but only those voxels inside a bounding-box.
copyWithoutInitialize(Class<?>, NamedProviderStore<S>) - Method in class org.anchoranalysis.image.bean.nonbean.init.PopulateStoreFromDefine: Copies objects of a particular class from the define without performing any initialization.
cornerMin() - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: The minimum corner of the bounding box in each dimension.
cornerMin() - Method in class org.anchoranalysis.spatial.box.BoundingBox: The minimum corner of the bounding box in each dimension.
correctedEndIndex(int) - Method in class org.anchoranalysis.core.index.range.IndexRangeNegative: The end-index, maybe corrected so that it is no longer negative.
correctedStartIndex(int) - Method in class org.anchoranalysis.core.index.range.IndexRangeNegative: The start-index, maybe corrected so that it is no longer negative.
CostMatrix<T> - Class in org.anchoranalysis.annotation.io.assignment: Stores costs between all possible pairings between elements from two lists.
CostOverlapWithinMidpointDistance - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap: TODO the center-of-gravity calculation can be turned into a FeatureCalculation which is cacheable
CostOverlapWithinMidpointDistance() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.CostOverlapWithinMidpointDistance
count() - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateAtCorner
count() - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateImplementation
count() - Method in interface org.anchoranalysis.image.voxel.extracter.predicate.VoxelsPredicate: Counts the number of values satisfying the predicate - across all voxels.
count(BoundedVoxels<UnsignedByteBuffer>, BoundedVoxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.mpp.overlap.CountIntersectingVoxels: Counts the number of intersecting voxels between two bounded voxel sets.
Count - Class in org.anchoranalysis.feature.bean.results: The sum of the results from a particular feature.
Count - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic: Counts the number of items in a histogram (posssibly in relation to a threshold: above, below etc.)
Count() - Constructor for class org.anchoranalysis.feature.bean.results.Count
Count() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Count
countByte(BoundedVoxels<UnsignedByteBuffer>, BoundedVoxels<UnsignedByteBuffer>, PredicateTwoBytes) - Static method in class org.anchoranalysis.image.voxel.iterator.intersecting.CountVoxelsIntersectingBounded: Counts all voxels in the intersection of two bounded-voxels of type BoundedVoxels that match a predicate.
countByteMasked(Voxels<UnsignedByteBuffer>, byte, BoundedVoxels<UnsignedByteBuffer>, BoundedVoxels<UnsignedByteBuffer>, PredicateTwoBytes) - Static method in class org.anchoranalysis.image.voxel.iterator.intersecting.CountVoxelsIntersectingBounded: Counts all voxels intersection of two bounded-voxels of type BoundedVoxels but only voxels that lie on an object-mask and match a predicate.
CountedProjectableBuffer<T> - Class in org.anchoranalysis.image.voxel.projection: A projectable buffer that also keeps track of the number of voxels in it.
CountedProjectableBuffer(VoxelsFactoryTypeBound<T>, Extent) - Constructor for class org.anchoranalysis.image.voxel.projection.CountedProjectableBuffer: Creates with minimal parameters, as no preprocessing is necessary.
CountEqual - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.energy: Counts the number of voxels in an object that have a specific intensity value in a channel.
CountEqual() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.CountEqual
Counter - Class in org.anchoranalysis.math.arithmetic: A simple counter that increments.
Counter() - Constructor for class org.anchoranalysis.math.arithmetic.Counter
Counter(int) - Constructor for class org.anchoranalysis.math.arithmetic.Counter: Creates a new Counter instance.
countForObject(ObjectMask) - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateAtCorner
countForObject(ObjectMask) - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateImplementation
countForObject(ObjectMask) - Method in interface org.anchoranalysis.image.voxel.extracter.predicate.VoxelsPredicate: Counts the number of values satisfying the predicate - but restricted to voxels corresponding to on in an object-mask.
countIntersectingVoxels(ObjectMask) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Counts the number of intersecting-voxels between two object-masks.
countIntersectingVoxels(ObjectMask, ObjectMask) - Static method in class org.anchoranalysis.image.voxel.iterator.intersecting.CountVoxelsIntersectingObjects: Counts the number of intersecting-voxels between two object-masks.
CountIntersectingVoxels - Class in org.anchoranalysis.mpp.overlap: Counts the number of intersecting voxels where bytes are encoded as region memberships.
CountIntersectingVoxels(byte) - Constructor for class org.anchoranalysis.mpp.overlap.CountIntersectingVoxels: Creates a new instance with a specific region membership flag.
CountIntersectingVoxels(PredicateRegionMembership) - Constructor for class org.anchoranalysis.mpp.overlap.CountIntersectingVoxels
CountKernel - Class in org.anchoranalysis.image.voxel.kernel.count: Base class for kernels that return a count (positive integer) for every voxel.
CountKernel() - Constructor for class org.anchoranalysis.image.voxel.kernel.count.CountKernel: Creates with a kernel-size of three.
CountKernelNeighborhood - Class in org.anchoranalysis.image.voxel.kernel.count: For every voxel on the outline, count all neighbors that are adjacent.
CountKernelNeighborhood() - Constructor for class org.anchoranalysis.image.voxel.kernel.count.CountKernelNeighborhood
CountKernelNeighborhoodMask - Class in org.anchoranalysis.image.voxel.kernel.count: The number of touching-faces of a voxel with a neighbor, so long as the neighbor is part of an ObjectMask.
CountKernelNeighborhoodMask(ObjectMask) - Constructor for class org.anchoranalysis.image.voxel.kernel.count.CountKernelNeighborhoodMask: Create with object-mask.
countMasked(BoundedVoxels<UnsignedByteBuffer>, BoundedVoxels<UnsignedByteBuffer>, Voxels<UnsignedByteBuffer>, byte) - Method in class org.anchoranalysis.mpp.overlap.CountIntersectingVoxels: Counts the number of intersecting voxels between two bounded voxel sets, considering a global mask.
countMatching(IntPredicate) - Method in class org.anchoranalysis.math.histogram.Histogram: Gets the total count of all values that match a predicate.
countOff() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels: Counts the number of voxels with an off state.
countOn() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels: Counts the number of voxels with an on state.
countThreshold(RelationToThreshold) - Method in interface org.anchoranalysis.image.voxel.statistics.VoxelStatistics: Counts the number of voxels that exist, relative to a threshold.
countThreshold(RelationToThreshold) - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsCombined
countThreshold(RelationToThreshold) - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsFromHistogram
CountVoxelsIntersectingBounded - Class in org.anchoranalysis.image.voxel.iterator.intersecting: Like IterateVoxelsBoundingBox but counts voxels matching a predicate rather than iterating.
CountVoxelsIntersectingObjects - Class in org.anchoranalysis.image.voxel.iterator.intersecting: Like CountVoxelsIntersectingBounded but specifically counts areas of intersection between two ObjectMasks.
countXY() - Method in class org.anchoranalysis.spatial.point.RunningSumPoint: The count for the X or Y dimensions.
countZ() - Method in class org.anchoranalysis.spatial.point.RunningSumPoint: The count for the Z dimension.
create() - Method in class org.anchoranalysis.bean.shared.random.RandomNumberGeneratorBean: Creates the RandomNumberGenerator.
create() - Method in class org.anchoranalysis.bean.shared.relation.EqualToBean
create() - Method in class org.anchoranalysis.bean.shared.relation.GreaterThanBean
create() - Method in class org.anchoranalysis.bean.shared.relation.GreaterThanEqualToBean
create() - Method in class org.anchoranalysis.bean.shared.relation.LessThanBean
create() - Method in class org.anchoranalysis.bean.shared.relation.LessThanEqualToBean
create() - Method in class org.anchoranalysis.bean.shared.relation.RelationBean: Creates a DoubleBiPredicate that implements the relation.
create() - Method in class org.anchoranalysis.bean.shared.StringMap: Derives a Map representation for the mapping.
create() - Static method in class org.anchoranalysis.image.io.object.output.mask.RasterDirectoryObjectsGenerator: Creates the Generator to write each object as a binary Mask in a directory.
create() - Method in class org.anchoranalysis.mpp.bean.mark.factory.MarkEllipseFactory
create() - Method in class org.anchoranalysis.mpp.bean.mark.factory.MarkEllipsoidFactory
create() - Method in class org.anchoranalysis.mpp.bean.mark.factory.MarkFactory: Creates a new Mark object.
create() - Method in class org.anchoranalysis.mpp.bean.mark.factory.MarkPointListFactory
create() - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreator: Creates an EnergyScheme instance.
create() - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement
create() - Method in interface org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFirstSecondOrder.CreateFirstSecondOrder: Creates a new StatisticalBase instance.
create() - Static method in class org.anchoranalysis.test.feature.ConstantsInListFixture: Creates a feature-list associated with the fixture.
create() - Static method in class org.anchoranalysis.test.io.output.OutputterCheckedFixture: Creates with default empty values.
create(boolean) - Static method in class org.anchoranalysis.experiment.time.ExecutionTimeRecorderFactory: Creates either a ExecutionTimeRecorder that records times, or ignores the recording depending on whether any output is enabled that needs the execution-time.
create(boolean) - Method in interface org.anchoranalysis.inference.concurrency.CreateModelForPool: Creates a model.
create(boolean) - Static method in class org.anchoranalysis.test.image.MaskFixture: Creates the Mask with the default corner and no assigned resolution.
create(boolean, boolean) - Static method in class org.anchoranalysis.test.image.EnergyStackFixture: Creates an energy-stack with default settings.
create(boolean, boolean, boolean, boolean) - Static method in class org.anchoranalysis.test.image.EnergyStackFixture: Creates the energy-stack to use.
create(boolean, Supplier<T>) - Static method in class org.anchoranalysis.core.functional.OptionalFactory: Creates only if a boolean flag is true, otherwise returns Optional.empty().
create(boolean, Optional<Resolution>) - Static method in class org.anchoranalysis.test.image.MaskFixture: Creates the Mask with the default corner and a particular resolution.
create(boolean, T) - Static method in class org.anchoranalysis.core.functional.OptionalFactory: Creates only if a boolean flag is true, otherwise returns Optional.empty().
create(int) - Method in class org.anchoranalysis.image.core.object.label.DecodeLabels: Creates a list of elements from voxels that are labelled with unique integers (sequentially increasing).
create(int) - Method in interface org.anchoranalysis.mpp.index.factory.VoxelPartitionFactory: Creates a new VoxelPartition with the specified number of slices.
create(int) - Method in class org.anchoranalysis.mpp.index.factory.VoxelPartitonFactoryHistogram: Creates a new VoxelPartitionHistogram with the specified number of slices.
create(Class<? extends FeatureInput>) - Method in interface org.anchoranalysis.feature.calculate.cache.CacheCreator: Creates a FeatureCalculationCache that accepts a particular input type.
create(Class<? extends FeatureInput>) - Method in class org.anchoranalysis.feature.session.cache.HorizontalCacheCreator
create(String) - Static method in class org.anchoranalysis.core.functional.OptionalFactory: Creates Optional.empty() for an empty string, or otherwise Optional.of().
create(String) - Static method in class org.anchoranalysis.image.core.dimensions.size.suggestion.ImageSizeSuggestionFactory: Creates a suggestion for how to resize an image.
create(String, OutputterChecked, String) - Static method in class org.anchoranalysis.io.generator.text.TextFileOutputter: Creates a TextFileOutput.
create(Path) - Static method in class org.anchoranalysis.io.generator.tabular.CSVWriter: Creates and starts a CSVWriter (it's always allowed, so will never return null)
create(Collection<Point3i>) - Static method in class org.anchoranalysis.image.core.object.ObjectFromPointsFactory: Create an ObjectMask from a collection of points.
create(List<NamedBean<FeatureListProvider<T>>>, LabelHeaders, FeatureOutputNames, Optional<InputGrouper>, FeatureExporterContext) - Static method in class org.anchoranalysis.plugin.image.task.feature.FeatureExporter: Alternative static constructor that creates a shared-state from a list of named FeatureListProviders.
create(List<Point3d>) - Static method in class org.anchoranalysis.mpp.mark.points.PointListFactory: Creates a PointList from a list of Point3d objects.
create(List<Point3d>, int) - Static method in class org.anchoranalysis.mpp.mark.points.PointListFactory: Creates a PointList from a list of Point3d objects with a specified ID.
create(List<T>, List<T>, boolean, CheckedToDoubleBiFunction<T, T, CreateException>) - Static method in class org.anchoranalysis.annotation.io.assignment.CostMatrix: Creates by calculating the cost between elements.
create(List<V>, Function<V, ObjectMask>, Extent, boolean, boolean) - Static method in class org.anchoranalysis.image.voxel.neighborhood.NeighborGraph: Like NeighborGraph.create(ObjectCollection, Extent, boolean, boolean) but extracts objects from a list of elements which form the vertices.
create(Map<Integer, T>, UnaryOperator<T>) - Method in class org.anchoranalysis.image.core.object.label.DecodeLabels: Creates a map of elements to other elements that are labelled with unique integers (sequentially increasing) in voxels.
create(Optional<? extends ExportSharedObjects>, InitializationContext, Optional<Define>) - Static method in class org.anchoranalysis.mpp.io.input.MarksInitializationFactory: Creates a new MarksInitialization instance.
create(Optional<String>, String) - Static method in class org.anchoranalysis.feature.io.name.MultiNameFactory: Creates either a multi-name that is either has a single part or a double part.
create(Optional<SharedObjects>, Optional<EnergyStack>) - Static method in class org.anchoranalysis.image.feature.calculator.InitializationFactory: Creates a FeatureInitialization object from optional SharedObjects and EnergyStack.
create(Optional<MultiLevelOutputEnabled>) - Method in class org.anchoranalysis.io.output.bean.rules.AddToDefaults
create(Optional<MultiLevelOutputEnabled>) - Method in class org.anchoranalysis.io.output.bean.rules.IgnoreUnderscorePrefixUnless
create(Optional<MultiLevelOutputEnabled>) - Method in class org.anchoranalysis.io.output.bean.rules.NoneExcept
create(Optional<MultiLevelOutputEnabled>) - Method in class org.anchoranalysis.io.output.bean.rules.OutputEnabledRules: Creates rules for determining whether an output is enabled or disabled.
create(Optional<MultiLevelOutputEnabled>) - Method in class org.anchoranalysis.io.output.bean.rules.Permissive
create(Optional<MultiLevelOutputEnabled>) - Method in class org.anchoranalysis.io.output.bean.rules.PermissiveExcept
create(IFormatReader, VoxelDataType, int) - Static method in class org.anchoranalysis.io.bioformats.copyconvert.ConvertToFactory: Creates a ConvertTo to match the desired voxel-type.
create(Provider<T>) - Static method in class org.anchoranalysis.bean.OptionalProviderFactory: Creates from a provider if non-null.
create(IntToFloatFunction, Point2i) - Static method in class org.anchoranalysis.mpp.mark.points.RotatableBoundingBoxFactory: Builds a bounding-box from the 5-element floating-point vector returned from the EAST algorithm.
create(SharedObjects) - Static method in class org.anchoranalysis.feature.initialization.FeatureRelatedInitialization: Creates with shared-objects, and otherwise empty initialization.
create(Logger, Path) - Static method in class org.anchoranalysis.feature.initialization.FeatureRelatedInitialization: Creates a log and a model-directory, and otherwise empty initialization.
create(EnergyStackWithoutParameters) - Method in class org.anchoranalysis.mpp.feature.energy.scheme.DictionaryForImageCreator: Creates a dictionary containing calculated image features for a given energy stack.
create(FeatureCSVMetadata) - Method in interface org.anchoranalysis.feature.io.csv.results.FeatureCSVWriterFactory: Maybe creates a FeatureCSVWriter corresponding to particular metadata.
create(FeatureCSVMetadataForOutput, FeatureCSVWriterFactory, Optional<Consumer<LabelledResultsVector>>, boolean) - Static method in class org.anchoranalysis.feature.io.csv.results.LabelledResultsCSVWriterFactory: Creates with appropriate support classes for outputting.
create(FeatureCSVMetadata, Outputter, boolean) - Static method in class org.anchoranalysis.feature.io.csv.FeatureCSVWriter: Maybe creates a FeatureCSVWriter depending if the output is allowed.
create(FeatureOutputNames, FeatureTableCalculator<T>, LabelHeaders, Optional<InputGrouper>, FeatureExporterContext) - Static method in class org.anchoranalysis.plugin.image.task.feature.FeatureExporter: Alternative static constructor that creates a shared-state from a NamedFeatureStore.
create(FeatureNameList, boolean) - Static method in class org.anchoranalysis.feature.io.csv.table.FeatureTableCSVGeneratorFactory: Creates either a FeatureTableCSVGenerator in either horizontal or vertical style.
create(NamedFeatureStore<T>, LabelHeaders, FeatureOutputNames, Optional<InputGrouper>, FeatureExporterContext) - Static method in class org.anchoranalysis.plugin.image.task.feature.FeatureExporter: Alternative static constructor that creates a shared-state from a NamedFeatureStore.
create(ImageInitialization, SharedObjects) - Static method in class org.anchoranalysis.mpp.init.PointsInitialization: Creates a new PointsInitialization instance.
create(Dimensions, VoxelDataType) - Method in class org.anchoranalysis.image.core.channel.factory.ChannelFactory: Creates an empty initialized channel for a particular data-type.
create(Stack) - Static method in class org.anchoranalysis.image.core.bufferedimage.BufferedImageFromStack: Creates a BufferedImage from a Stack.
create(OpenedImageFile, Logger) - Method in class org.anchoranalysis.image.io.bean.channel.ChannelMapCreator: Creates the ChannelMap.
create(OpenedImageFile, Logger) - Method in class org.anchoranalysis.plugin.io.bean.channel.map.Autoname
create(OpenedImageFile, Logger) - Method in class org.anchoranalysis.plugin.io.bean.channel.map.FromEntries
create(OpenedImageFile, Logger) - Method in class org.anchoranalysis.plugin.io.bean.channel.map.FromMetadata
create(OpenedImageFile, Logger) - Method in class org.anchoranalysis.plugin.io.bean.channel.map.SingleChannel
create(SliceBufferIndex<T>) - Method in interface org.anchoranalysis.image.voxel.factory.VoxelsFactoryTypeBound: Create a new Voxels that has been initialized with buffers from SliceBufferIndex.
create(VoxelDataType, Extent) - Method in class org.anchoranalysis.image.voxel.projection.Projection: Creates a buffer for the projection for a particular voxel-type and size (extent).
create(VoxelDataType, Extent) - Method in class org.anchoranalysis.plugin.image.bean.channel.aggregator.MaxProjection
create(VoxelDataType, Extent) - Method in class org.anchoranalysis.plugin.image.bean.channel.aggregator.MeanProjection
create(VoxelDataType, Extent) - Method in class org.anchoranalysis.plugin.image.bean.channel.aggregator.MinProjection
create(VoxelDataType, Extent) - Method in class org.anchoranalysis.plugin.image.bean.channel.aggregator.ProjectableBufferAggregator: Creates the ProjectableBuffer used for aggregation.
create(VoxelDataType, Extent) - Method in class org.anchoranalysis.plugin.image.bean.channel.aggregator.StandardDeviationProjection
create(ObjectCollection) - Static method in class org.anchoranalysis.image.voxel.object.IntersectingObjects: Creates from an ObjectCollection.
create(ObjectCollection, Extent, boolean, boolean) - Static method in class org.anchoranalysis.image.voxel.neighborhood.NeighborGraph: Create the graph with object-masks as vertices, where edges represent the number of neighboring voxels between objects.
create(Voxels<?>) - Method in class org.anchoranalysis.image.core.channel.factory.ChannelFactory: Create a Channel from particular voxels.
create(Voxels<?>, Optional<Resolution>) - Method in class org.anchoranalysis.image.core.channel.factory.ChannelFactory: Create a Channel from particular voxels.
create(Voxels<?>, Optional<Resolution>) - Method in class org.anchoranalysis.image.core.channel.factory.ChannelFactorySingleType: Create a Channel from voxels and a resolution.
create(InputManagerParameters) - Method in class org.anchoranalysis.io.input.bean.files.FilesProvider: Creates or provides a list of files.
create(InputManagerParameters) - Method in class org.anchoranalysis.io.input.bean.files.FilesProviderUnary
create(InputManagerParameters) - Method in class org.anchoranalysis.io.input.bean.files.FilesProviderWithDirectory
create(InputManagerParameters) - Method in class org.anchoranalysis.io.input.bean.files.SpecificPathList
create(InputManagerParameters) - Method in class org.anchoranalysis.plugin.annotation.bean.file.FromAnnotations
create(InputManagerParameters) - Method in class org.anchoranalysis.plugin.io.bean.file.provider.Combine
create(InputManagerParameters) - Method in class org.anchoranalysis.plugin.io.bean.file.provider.Rooted
create(InputOutputContext) - Static method in class org.anchoranalysis.image.io.ImageInitializationFactory: Create from an InputOutputContext - without any suggested size.
create(InputOutputContext, Optional<ImageSizeSuggestion>) - Static method in class org.anchoranalysis.image.io.ImageInitializationFactory: Create from an InputOutputContext - with a suggested size.
create(OutputterChecked, ErrorReporter, ExecutionArguments, boolean) - Method in class org.anchoranalysis.experiment.bean.log.LoggingDestination: Creates a logger for this destination
create(OutputterChecked, ErrorReporter, ExecutionArguments, boolean) - Method in class org.anchoranalysis.experiment.bean.log.OnlyIf
create(OutputterChecked, ErrorReporter, ExecutionArguments, boolean) - Method in class org.anchoranalysis.experiment.bean.log.SwitchDetailedLogging
create(OutputterChecked, ErrorReporter, ExecutionArguments, boolean) - Method in class org.anchoranalysis.experiment.bean.log.ToConsole
create(OutputterChecked, ErrorReporter, ExecutionArguments, boolean) - Method in class org.anchoranalysis.experiment.bean.log.ToMultiple
create(OutputterChecked, ErrorReporter, ExecutionArguments, boolean) - Method in class org.anchoranalysis.experiment.bean.log.ToTextFile
create(OutputterChecked, ErrorReporter, ExecutionArguments, boolean) - Method in class org.anchoranalysis.experiment.bean.log.ToTextFileOnlyIfFailure
create(Mark) - Method in class org.anchoranalysis.mpp.proposer.ProposerContext: Creates a VoxelizedMarkMemo for the given mark.
create(Mark, EnergyStackWithoutParameters, RegionMap) - Static method in class org.anchoranalysis.mpp.mark.voxelized.memo.VoxelizedMarkMemoFactory: Creates a new VoxelizedMarkMemo instance.
create(Mark, EnergyStackWithoutParameters, RegionMap) - Static method in class org.anchoranalysis.mpp.mark.voxelized.VoxelizedMarkFactory: Creates a new VoxelizedMarkHistogram instance.
create(Point3i, boolean) - Static method in class org.anchoranalysis.test.image.MaskFixture: Creates the Mask with a particular corner and no assigned resolution.
create(Point3i, boolean, Optional<Resolution>) - Static method in class org.anchoranalysis.test.image.MaskFixture: Creates the Mask with a particular corner and a particular resolution.
create(ChannelSpecification, Extent) - Method in class org.anchoranalysis.test.image.StackFixture: Creates a stack with a particular number of the channels of particular size.
create(CommandLine, Path, Path) - Static method in class org.anchoranalysis.launcher.executor.ExperimentExecutorFactory: Creates an experiment-executor from a command line that EITHER: uses a default-experiment OR accepts a path passed as the first command-line argument.
create1() - Method in class org.anchoranalysis.test.image.object.CutOffCornersObjectFixture: Create the first object.
create2() - Method in class org.anchoranalysis.test.image.object.CutOffCornersObjectFixture: Create the second object.
create3() - Method in class org.anchoranalysis.test.image.object.CutOffCornersObjectFixture: Create the third object.
createAddCriteria() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergySchemeWithSharedFeatures: Creates an AddCriteriaEnergyPair based on the energy scheme.
createAggregateFeature(Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.FeatureListProviderAggregatePair: Creates an aggregate feature from individual features for first, second, and merged objects.
createAggregateFeature(Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.ReduceFirstAndSecond
createAggregateFeature(Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.ReduceRatioFirstAndSecond
createAggregateFeature(Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.SubtractReducedFromMerged
createAll() - Method in class org.anchoranalysis.test.image.object.CutOffCornersObjectFixture: Creates all three objects.
createAndConsumeListBeans(String, HierarchicalConfiguration, Object, Collection<T>) - Static method in class org.anchoranalysis.bean.xml.creator.BeanListCreator: Extracts a list of instantiated bean objects from an XML configuration, and adds them to addTo.
createArguments(CommandLine) - Method in class org.anchoranalysis.launcher.config.LauncherConfig: Creates execution arguments from the command line.
createAscending() - Static method in class org.anchoranalysis.test.feature.plugins.HistogramFixture: Creates an ascending histogram from 0 to 255 (inclusive).
createAssignment(ObjectCollection, ObjectCollection, double, Dimensions) - Method in class org.anchoranalysis.annotation.io.assignment.AssignOverlappingObjects: Creates an assignment from the objects in left to those in right.
createAssignment(ObjectsToCompare, Dimensions, boolean, InputOutputContext) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.AnnotationComparisonAssigner: Creates an assignment based on the objects to compare.
createAssignment(ObjectsToCompare, Dimensions, boolean, InputOutputContext) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner
createAssignment(ObjectsToCompare, Dimensions, boolean, InputOutputContext) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.MaskIntersectionAssigner
createAxisArray() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientBaseAddSum: Creates an array of booleans indicating which axes to calculate the gradient for.
createAxisArray() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientForAxis
createAxisArray() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientXY
createBackground(NamedProviderStore<Stack>, String, StackDisplayer) - Static method in class org.anchoranalysis.mpp.io.output.BackgroundCreator: Creates a background DisplayStack from a named stack in a collection.
createBean(Class<?>, BeanDeclaration, Object) - Method in class org.anchoranalysis.bean.xml.factory.AnchorDefaultBeanFactory
createBean(Class, BeanDeclaration, Object) - Method in class org.anchoranalysis.bean.define.DefineFactory
createBean(Class, BeanDeclaration, Object) - Method in class org.anchoranalysis.bean.xml.factory.IncludeBeanFactory
createBean(Class, BeanDeclaration, Object) - Method in class org.anchoranalysis.bean.xml.factory.IncludeListBeanFactory
createBean(Class, BeanDeclaration, Object) - Method in class org.anchoranalysis.bean.xml.factory.ListBeanFactory
createBean(Class, BeanDeclaration, Object) - Method in class org.anchoranalysis.bean.xml.factory.primitive.DoubleListFactory
createBean(Class, BeanDeclaration, Object) - Method in class org.anchoranalysis.bean.xml.factory.primitive.DoubleSetFactory
createBean(Class, BeanDeclaration, Object) - Method in class org.anchoranalysis.bean.xml.factory.primitive.IntegerListFactory
createBean(Class, BeanDeclaration, Object) - Method in class org.anchoranalysis.bean.xml.factory.primitive.IntegerSetFactory
createBean(Class, BeanDeclaration, Object) - Method in class org.anchoranalysis.bean.xml.factory.primitive.StringListFactory
createBean(Class, BeanDeclaration, Object) - Method in class org.anchoranalysis.bean.xml.factory.primitive.StringSetFactory
createBean(Class, BeanDeclaration, Object) - Method in class org.anchoranalysis.bean.xml.factory.ReplacePropertyBeanFactory
createBeanFromConfig(HierarchicalConfiguration, Object) - Static method in class org.anchoranalysis.bean.xml.creator.BeanCreator: Creates a bean from a HierarchicalConfiguration.
createBeanFromXML(XMLBeanDeclaration, String, Object) - Static method in class org.anchoranalysis.bean.xml.creator.BeanCreator: Creates a bean from XML.
createBetweenTwoPoints(Point3d, Point3d) - Static method in class org.anchoranalysis.spatial.orientation.DirectionVector: Creates a DirectionVector representing the direction between two points of type Point3d.
createBetweenTwoPoints(Point3i, Point3i) - Static method in class org.anchoranalysis.spatial.orientation.DirectionVector: Creates a DirectionVector representing the direction between two points of type Point3i.
createBounded(BoundingBox) - Method in interface org.anchoranalysis.image.voxel.factory.VoxelsFactoryTypeBound: Creates and initializes voxels that correspond to a particular bounding-box region.
createBuilderWithDefaultErrorHandler() - Static method in class org.anchoranalysis.core.serialize.XMLParser: Creates a document-builder with default error-handling.
createCachedCalculationForDerived(CalculationPartResolver<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.DerivedObject: Creates a CalculationPart for deriving the object mask.
createCachedCalculationForDerived(CalculationPartResolver<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.Erode: Creates a CalculationPart for eroding the object mask.
createCachedCalculationForDerived(CalculationPartResolver<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.Shell
createCalculationContext(Optional<String>, ExecutionTimeRecorder, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.feature.FeatureExporter: Creates a FeatureCalculationContext for calculating features to later use this exporter.
createCalculationContext(ExecutionTimeRecorder, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.segment.SharedStateSegmentInstance: Creates a FeatureCalculationContext for calculating features to later use this exporter.
createCalculator(CreateCalculatorHelper, ImageInitialization, BoundReplaceStrategy<FeatureInputStack, ? extends ReplaceStrategy<FeatureInputStack>>) - Method in class org.anchoranalysis.image.feature.calculator.merged.MergedPairsFeatures: Creates a feature calculator for stack features.
createChannel(int, boolean) - Method in class org.anchoranalysis.image.core.stack.DisplayStack: Create Channel for a particular index after applying conversion.
createChannel(Extent, ChannelFixture.IntensityFunction, VoxelDataType) - Method in class org.anchoranalysis.test.image.ChannelFixture: Creates a channel with specified extent, intensity function, and voxel data type.
createChannelDeriver(ChannelSource) - Method in class org.anchoranalysis.plugin.image.task.bean.combine.AggregateChannelTask
createChannelDeriver(ChannelSource) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase: A function to derive the individual type used for aggregation from a Channel.
createChannelDeriver(ChannelSource) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.histogram.ExportImageHistograms
createChannelsForSeries(int, Logger) - Method in class org.anchoranalysis.image.io.channel.input.NamedChannelsInput: Creates a NamedChannelsMap representing the channels for a particular series in this input.
createChecked(boolean, CheckedSupplier<T, E>) - Static method in class org.anchoranalysis.core.functional.OptionalFactory: Like OptionalFactory.create(boolean, T) but accepts a supplier that throws a checked/exception.
createCollection(Channel, ObjectCollection, CalculateLevel, int, MessageLogger) - Static method in class org.anchoranalysis.plugin.image.intensity.level.LevelResultCollectionFactory: Creates a LevelResultCollection from a channel and object collection.
createColor(ColoredMarks, RegionMembershipWithFlags) - Static method in class org.anchoranalysis.mpp.overlay.OverlayCollectionMarkFactory: Creates a ColoredOverlayCollection from ColoredMarks.
createColors(int) - Method in class org.anchoranalysis.annotation.io.assignment.generator.AssignmentColorPool: Creates a list of colors to describe the assignment.
createComparer(Path, String) - Method in class org.anchoranalysis.test.image.rasterwriter.comparison.ComparisonPlan: Creates the ImageComparer to use to compare between images loaded in a temporary-directory and saved-images.
createComparer(Path, String) - Static method in class org.anchoranalysis.test.image.stackwriter.SavedFiles: Creates a comparer between a directory and saved-files in a directory in the resources.
createComparisonStacks(AnnotationWithMarks, DisplayStack, Path, ColorScheme, Path, OperationContext, boolean) - Method in class org.anchoranalysis.annotation.io.bean.comparer.MultipleComparer: Creates a Stack illustrating the comparison between annotation and each source in sources.
createContextForWriting(Optional<ImageFileFormat>, ExecutionTimeRecorder) - Method in class org.anchoranalysis.io.output.bean.OutputManager: Creates the OutputWriteContext needed for writing files.
createConverter() - Method in class org.anchoranalysis.image.bean.channel.ConvertChannelTo: Creates the converter.
createConverter() - Method in class org.anchoranalysis.image.bean.channel.ConvertChannelToWithHistogram: Creates the converter.
createConverter() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByDictionary
createConverter() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByMinMaxValue
createConverter() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByTypeToByte
createConverter() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ToByte
createConverter() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ToByteUpperLowerQuantileIntensity
createConverterFor(VoxelDataType) - Method in class org.anchoranalysis.image.bean.displayer.IntensityQuantiles
createConverterFor(VoxelDataType) - Method in class org.anchoranalysis.image.bean.displayer.StackDisplayer: Determines what kind of converter to use for a particular channel, to map it to an unsigned 8-bit channel.
createCountKernelMask(ObjectMask) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.TouchingVoxels: Creates a CountKernel for the given object mask.
createDelegate(Feature<T>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteDivideByParam
createDelegate(Feature<T>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureSequenceInteger: Creates a delegate PermuteFeature for the given feature.
createDelegate(Feature<T>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFirstSecondOrder
createDescending() - Static method in class org.anchoranalysis.test.feature.plugins.HistogramFixture: Creates a descending histogram from 0 to 255 (inclusive).
createDescriptor(Extent) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters: Creates an empty HOGDescriptor to describe an image of a particular size.
createDesignMatrix(List<Point3f>) - Method in class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresViaNormalEquationBase: Creates the design matrix from the input points.
createDictionary() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergyScheme: Creates and returns the associated Dictionary or an empty dictionary if none is associated.
createDim() - Method in class org.anchoranalysis.plugin.points.bean.fitter.PointsFitterToMark: Creates and returns the Dimensions using the specified provider.
createDimensions() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithDimensionsBase: Creates the dimensions using the specified DimensionsProvider.
createDims() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithOptionalDimensionsBase: Creates the dimensions if a DimensionsProvider is specified.
createDistanceMapForVoxels(BinaryVoxels<UnsignedByteBuffer>, Optional<Resolution>, float) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D: Creates a distance map for binary voxels.
createDuplicate(ReadableTuple3i, Extent) - Static method in class org.anchoranalysis.spatial.box.BoundingBox: Creates a bounding-box from a corner and an extent - duplicating cornerMin.
createDuplicate(ReadableTuple3i, ReadableTuple3i) - Static method in class org.anchoranalysis.spatial.box.BoundingBox: Creates from two int points (a minimum corner and a maximum corner) - reusing cornerMinInclusive internally.
createEmpty(Extent, VoxelDataType) - Method in class org.anchoranalysis.image.voxel.factory.VoxelsFactory: Creates empty voxels to match a particular size.
createEmptyInitialised(Dimensions) - Method in class org.anchoranalysis.image.core.channel.factory.ChannelFactorySingleType: Create a Channel initialized with zero-valued voxel-buffers.
createEmptyInitialisedToSupportMaxValue(Dimensions, long) - Method in class org.anchoranalysis.image.core.channel.factory.ChannelFactory: Creates an empty initialized channel with discrete type with as minimal as needed data-type to support a maximum value.
createEmptyMat(Extent, int) - Static method in class org.anchoranalysis.plugin.opencv.convert.ConvertToMat: Creates a Mat which contains only zero-values.
createEmptyOff(Extent) - Static method in class org.anchoranalysis.image.voxel.binary.BinaryVoxelsFactory: Creates binary-voxels using unsigned 8-bit byte type and with all voxels set to off (0).
createEmptyOff(Extent, VoxelDataType) - Static method in class org.anchoranalysis.image.voxel.binary.BinaryVoxelsFactory: Creates an empty binary-voxels of a particular data-type with all voxels initialized to off. (0).
createEmptyOn(Extent) - Static method in class org.anchoranalysis.image.voxel.binary.BinaryVoxelsFactory: Creates binary-voxels using unsigned 8-bit byte type and with all voxels set to on (255).
createEmptyStackFor(Dimensions) - Static method in class org.anchoranalysis.image.io.object.output.rgb.ObjectsAsRGBGenerator: Creates an empty RGBStack.
createEmptyUninitialised(Dimensions) - Method in class org.anchoranalysis.image.core.channel.factory.ChannelFactorySingleType: Create a Channel without initialization with voxel-buffers.
CreateException - Exception Class in org.anchoranalysis.core.exception: A generic exception that be thrown when the creation of a new object fails.
CreateException(String) - Constructor for exception class org.anchoranalysis.core.exception.CreateException: Creates with a message, but without a cause.
CreateException(String, AnchorCombinableException) - Constructor for exception class org.anchoranalysis.core.exception.CreateException: Creates with a message, and a combinable-exception as a cause.
CreateException(String, HasFriendlyErrorMessage) - Constructor for exception class org.anchoranalysis.core.exception.CreateException: Creates with a message, and a cause with a user-friendly error message.
CreateException(Throwable) - Constructor for exception class org.anchoranalysis.core.exception.CreateException: Creates with a cause, but without a message.
createExperimentExecutor(CommandLine) - Method in class org.anchoranalysis.launcher.config.LauncherConfig: Creates an experiment executor from the command line.
createExperimentOutputter(Optional<String>, MultiLevelOutputEnabled, Optional<MultiLevelRecordedOutputs>, OutputWriteContext, PathPrefixerContext, Optional<Consumer<Path>>, Optional<Logger>) - Method in class org.anchoranalysis.io.output.bean.OutputManager: Creates an outputter for the experiment in general.
createExporter(LabelHeaders, List<NamedBean<FeatureListProvider<S>>>, FeatureOutputNames, Optional<InputGrouper>, FeatureExporterContext) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.SingleRowPerInput
createExporter(LabelHeaders, List<NamedBean<FeatureListProvider>>, FeatureOutputNames, Optional<InputGrouper>, FeatureExporterContext) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FeatureSource: Creates the FeatureExporter to be used for calculating and exporting feature-results.
createFeatureList(String, TestLoader) - Static method in class org.anchoranalysis.test.feature.plugins.FeaturesFromXMLFixture: Creates a feature list from an XML file.
createFeatureNames() - Method in interface org.anchoranalysis.image.feature.calculator.FeatureTableCalculator: Creates a list of names for each feature (columns of the table).
createFeatureNames() - Method in class org.anchoranalysis.image.feature.calculator.merged.PairsTableCalculator
createFeatureNames() - Method in class org.anchoranalysis.image.feature.calculator.SingleTableCalculator
createFeatures(List<NamedBean<FeatureListProvider<FeatureInputSingleObject>>>, NamedFeatureStoreFactory, boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.CombineObjectsForFeatures: Creates features that will be applied on the objects.
createFeatures(List<NamedBean<FeatureListProvider<FeatureInputSingleObject>>>, NamedFeatureStoreFactory, boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.EachObjectIndependently
createFeatures(List<NamedBean<FeatureListProvider<FeatureInputSingleObject>>>, NamedFeatureStoreFactory, boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
createFeatures(NamedFeatureStore<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.EachObjectIndependently: Creates a FeatureTableCalculator from a NamedFeatureStore.
createFeatureSession() - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureEvaluator: Creates session for evaluating feature optionally adding an energy-stack.
createFeatureSession(UnaryOperator<FeatureList<T>>, SharedObjects) - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureListEvaluator: Creates session for evaluating features.
createFilenameForWriting(String, String) - Method in class org.anchoranalysis.io.output.writer.AlwaysAllowed
createFilenameForWriting(String, String) - Method in class org.anchoranalysis.io.output.writer.CheckIfAllowed
createFilenameForWriting(String, String) - Method in interface org.anchoranalysis.io.output.writer.Writer: The path to write a particular output to.
createFilenameForWriting(String, String) - Method in class org.anchoranalysis.io.output.writer.WriterRouterErrors: The path to write a particular output to.
createFitResultFromMatrixAandCenter(DoubleMatrix2D, DoubleMatrix2D, boolean) - Static method in class org.anchoranalysis.plugin.points.bean.fitter.EllipsoidFitHelper: Creates a FitResult from the matrix A and center matrix.
createFlat(boolean, Supplier<Optional<T>>) - Static method in class org.anchoranalysis.core.functional.OptionalFactory: Creates an Optional from a boolean flag and a supplier that returns an Optional.
createFloat(Voxels<FloatBuffer>) - Static method in class org.anchoranalysis.image.voxel.extracter.VoxelsExtracterFactory: Create voxels-extracter for FloatBuffer.
createFloat(Voxels<FloatBuffer>, int) - Static method in class org.anchoranalysis.image.voxel.assigner.VoxelsAssignerFactory: Create a VoxelsAssigner for a FloatBuffer.
createFloat(Extent) - Method in class org.anchoranalysis.image.voxel.projection.extrema.ComparisonProjection
createFloat(Extent) - Method in class org.anchoranalysis.image.voxel.projection.MeanIntensityProjection
createFloat(Extent) - Method in class org.anchoranalysis.image.voxel.projection.Projection: Creates a buffer for a maximum-intensity projection for float voxels.
createFloat(Extent) - Method in class org.anchoranalysis.image.voxel.projection.StandardDeviationIntensityProjection
createFloat(Extent, IntFunction<FloatBuffer>) - Static method in class org.anchoranalysis.image.voxel.arithmetic.VoxelsArithmeticFactory: Create a VoxelsArithmetic for FloatBuffer.
createForDirectoryPermissive(Path, DirectoryCreationParameters, Optional<Logger>) - Static method in class org.anchoranalysis.io.output.outputter.OutputterChecked: Creates, defaulting to a permissive output-manager in a particular directory.
createForSingle(AnchorBean<?>, String) - Static method in class org.anchoranalysis.bean.permute.assign.PermutationAssignerFactory: Creates an assigner for one or more properties, as identified by propertyPath.
createForSubdirectory(String) - Method in class org.anchoranalysis.test.TestLoader: Creates a new test-loader for a subdirectory of the current test.
createForVoxelBuffer(VoxelBuffer<T>, Extent) - Method in interface org.anchoranalysis.image.voxel.factory.VoxelsFactoryTypeBound: Create a new Voxels that has been initialized with a single-slice's memory buffers.
createFrom(int, ObjectMask) - Method in interface org.anchoranalysis.image.core.object.label.DecodeLabels.CreateElementFromScaledObject: Create from an index and it's scaled-object.
createFrom(int, ObjectMask) - Method in interface org.anchoranalysis.image.core.object.scale.AccessObjectMask: Creates an element of type T from an object-representation and index.
createFrom(int, ObjectMask) - Method in class org.anchoranalysis.image.core.object.scale.AccessObjectMaskSimple
createFrom(BufferedImage) - Static method in class org.anchoranalysis.image.core.bufferedimage.CreateStackFromBufferedImage: Create a Stack by converting a BufferedImage.
createFrom(Channel, Optional<Mask>) - Static method in class org.anchoranalysis.image.core.object.HistogramFromObjectsFactory: Creates a Histogram of all voxel intensity values in channel, or only those in mask if it is dfined.
createFrom(Channel, Mask) - Static method in class org.anchoranalysis.image.core.object.HistogramFromObjectsFactory: Creates a Histogram of all voxel intensity values in channel corresponding to Mask.
createFrom(Channel, ObjectCollection) - Static method in class org.anchoranalysis.image.core.object.HistogramFromObjectsFactory: Creates a Histogram of voxel intensity values in channel corresponding to objects.
createFrom(Channel, ObjectMask) - Static method in class org.anchoranalysis.image.core.object.HistogramFromObjectsFactory: Creates a Histogram of voxel intensity values in channel corresponding to object.
createFrom(Mask, int, boolean, boolean) - Static method in class org.anchoranalysis.image.core.contour.FindContour: Creates an contour from a Mask at the boundary of depth 1 pixel.
createFrom(SliceBufferIndex<T>, VoxelDataType) - Method in class org.anchoranalysis.image.voxel.factory.VoxelsFactory: Creates voxels from a particular SliceBufferIndex with specified type.
createFrom(VoxelBuffer<?>) - Static method in class org.anchoranalysis.image.voxel.statistics.HistogramFactory: Creates a Histogram of the aggregated voxel intensities in a VoxelBuffer.
createFrom(ObjectMask, int, boolean, boolean) - Static method in class org.anchoranalysis.image.core.contour.FindContour: Creates an contour from a ObjectMask.
createFrom(VoxelsUntyped) - Static method in class org.anchoranalysis.image.voxel.statistics.HistogramFactory: Creates a Histogram of the aggregated voxel intensities in a VoxelsUntyped.
createFrom(VoxelsUntyped, Optional<ObjectMask>) - Static method in class org.anchoranalysis.image.core.object.HistogramFromObjectsFactory: Creates a Histogram of voxel intensity values in voxels, all or only those in object.
createFrom(OutputManager) - Static method in class org.anchoranalysis.test.io.output.OutputterCheckedFixture: Creates a OutputterChecked from an OutputManager - that permits all outputs.
createFrom(OutputManager, OutputEnabledRules) - Static method in class org.anchoranalysis.test.io.output.OutputterCheckedFixture: Creates a OutputterChecked from an OutputManager - that outputs in accordance to the rules in outputsEnabled.
createFromChannel(Channel) - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderUnary: Creates a Channel given the entity provided by the delegate.
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.AnisotropicDiffusion
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.MinimumFilter
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.Invert
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromDictionary
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromIntersectingObjects
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.convert.Convert
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.convert.ConvertWithHistogram
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.Duplicate
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientBaseAddSum
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.Sobel
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.IfParamEquals
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.Blur
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.IfVoxelZero
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.Median
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.QuantileStretch
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.ScaleXY
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.mask.UnaryWithMaskBase
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectBase
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.slice.ExtractCenterSlice
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.slice.ExtractSliceRange
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.slice.MaximumIntensityProjection
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.slice.MeanIntensityProjection
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.UnaryWithObjectsBase
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.UnaryWithValueBase
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentChannel
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentWithSeeds
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithChannelBase: Creates an ObjectCollection from a source Channel.
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.EdgeFilterIJ
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.GaussianBlur2D
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank.MedianFilter3D
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.WithRadiusBase
createFromChannel(Channel, int) - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.BackgroundSubtractor
createFromChannel(Channel, int) - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.WithFilterBase
createFromChannel(Channel, int) - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.WithRadiusBase: Creates a new channel from an existing channel and a radius.
createFromChannel(Channel, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.NormalizeDifferenceToMedian
createFromChannel(Channel, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.NormalizeObjectIntensity
createFromChannel(Channel, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.IdentifyObjects
createFromChannel(Channel, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreObjects
createFromChannel(Channel, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.UnaryWithObjectsBase: Creates a new channel from an existing channel and a collection of objects.
createFromChannelWithConstant(Channel, double) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.ArithmeticWithConstantBase
createFromChannelWithConstant(Channel, double) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.ArithmeticWithConstantConditionallyWriteBase
createFromChannelWithConstant(Channel, double) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.UnaryWithValueBase: Creates a new channel from an existing channel and a scalar value.
createFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransformForEachObject3D
createFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.CreateNew
createFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromDimensionsBase: Creates a channel from the given dimensions.
createFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.slice.RepeatSlice
createFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.AllValuesOff
createFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.AllValuesOn
createFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromObjects
createFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.FromDimensionsBase: Creates a Mask from the given Dimensions.
createFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Box
createFromExisting(InitializationContext, Optional<Define>, Optional<SharedObjects>, Optional<Dictionary>) - Static method in class org.anchoranalysis.mpp.io.input.MarksInitializationFactory: Creates a new MarksInitialization instance from existing shared objects and dictionary.
createFromExplicitDirectory(String) - Static method in class org.anchoranalysis.test.TestLoader: Creates a new test-data loader using an explicit file path as root.
createFromExplicitDirectory(Path) - Static method in class org.anchoranalysis.test.TestLoader: Creates a new test-data loader using an explicit file path as root.
createFromGenerator(TransformingGenerator<BoundingBox, Stack>, int, ColorIndex) - Static method in class org.anchoranalysis.image.io.stack.output.box.DrawObjectOnStackGenerator: Creates an extracted-object generator that draws an outline - with default color green and flattened in Z.
createFromGuess3D(Mask, int, boolean, boolean) - Static method in class org.anchoranalysis.image.core.contour.FindContour: Like FindContour.createFrom(Mask, int, boolean, boolean), but guesses whether to do this in 2D or 3D.
createFromHistogram(Histogram) - Method in class org.anchoranalysis.image.bean.provider.HistogramProviderUnary: Creates a Histogram given the entity provided by the delegate.
createFromHistogram(Histogram) - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.CutBelowThreshold
createFromHistogram(Histogram) - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.GreaterThanThreshold
createFromList(List<T>, Function<T, BoundingBox>) - Static method in class org.anchoranalysis.spatial.box.BoundedList: Creates for a list, minimally fitting a bounding-box around all elements
createFromMask(Mask) - Method in class org.anchoranalysis.image.bean.provider.MaskProviderUnary: Creates a Mask given the entity provided by the delegate.
createFromMask(Mask) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D
createFromMask(Mask) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.mask.FromMask
createFromMask(Mask) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.mask.FromMaskBase: Creates a Channel from the provided Mask.
createFromMask(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.combine.CombineBase
createFromMask(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.Duplicate
createFromMask(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.Invert
createFromMask(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.ExteriorContour
createFromMask(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.FitBoxToOnVoxels
createFromMask(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.MorphologicalOperatorBase
createFromMask(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfPredicateBase
createFromMask(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.ScaleXY
createFromMask(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.slice.FlattenZ
createFromMask(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.slice.RepeatSlice
createFromMask(Mask) - Method in class org.anchoranalysis.plugin.imagej.bean.mask.provider.FillHoles
createFromMask(Mask) - Method in class org.anchoranalysis.plugin.imagej.bean.mask.provider.MorphologicalOperation
createFromMask(Mask) - Method in class org.anchoranalysis.plugin.points.bean.convexhull.ConvexHullBase
createFromMask(Mask, Mask) - Method in class org.anchoranalysis.plugin.points.bean.convexhull.ConvexHull2D
createFromMask(Mask, Mask) - Method in class org.anchoranalysis.plugin.points.bean.convexhull.ConvexHull3D
createFromMask(Mask, Mask) - Method in class org.anchoranalysis.plugin.points.bean.convexhull.ConvexHullBase: Creates a convex hull from a mask and its outline.
createFromMaskedChannel(Channel, Mask) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.SubtractMean
createFromMaskedChannel(Channel, Mask) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromChannel
createFromMaskedChannel(Channel, Mask) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignValue
createFromMaskedChannel(Channel, Mask) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.mask.UnaryWithMaskBase: Creates a new Channel from the input channel and mask.
createFromMaskedChannel(Channel, Mask) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.mask.ZeroOutsideMask
createFromMavenWorkingDirectory() - Static method in class org.anchoranalysis.test.TestLoader: Creates a new test-data loader finding PATH_RESOURCES using the Maven working directory.
createFromMavenWorkingDirectory(String) - Static method in class org.anchoranalysis.test.TestLoader: Creates a new test-data loader finding PATH_RESOURCES/PLUS_SOMETHING using the Maven working directory.
createFromNotObjects(ObjectCollection, Dimensions, BinaryValuesInt) - Static method in class org.anchoranalysis.image.core.mask.MaskFromObjects: Create a Mask corresponding to all off voxels in an ObjectCollection.
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.image.bean.provider.ObjectCollectionProviderUnary: Creates a ObjectCollection given the entity provided by the delegate.
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.AtIndex
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.DecomposeIntoConnectedComponents
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.RejectIfNotConnected
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Duplicate
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.feature.ObjectWithMaximumFeature
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.feature.ObjectWithMaximumFeatureFromEachMatchedCollection
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.feature.SortByFeature
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.IntersectsWithContainer
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.Match
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.NotInContainer
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.ObjectCollectionProviderFilterBase
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.RemoveTouchingBorder
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.mask.AndObjectsWithMasks
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeGreedyToIncreaseObjectFeature
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithFeature
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.ObjectCollectionProviderMorphological
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Scale
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.slice.ExtendInZ
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.slice.ExtendInZWithinContainer
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.slice.FlattenZ
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.slice.SliceAt
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.split.RemoveIntersectingVoxels
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.split.SplitByObjects
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.split.SplitIntoSquares
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.UnaryWithChannelBase
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.imagej.bean.object.provider.DrawLineAlongConvexHull
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.imagej.bean.object.provider.FillHoles
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.points.bean.SplitContourAtSaddlePoints
createFromObjects(ObjectCollection, Optional<List<ObjectMask>>, Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.Filter
createFromObjects(ObjectCollection, Optional<List<ObjectMask>>, Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.FilterByGroup
createFromObjects(ObjectCollection, Optional<List<ObjectMask>>, Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.ObjectCollectionProviderFilterBase: Creates an ObjectCollection from the given objects, potentially applying a filter and considering dimensions.
createFromObjects(ObjectCollection, Channel) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.BinarySegmentByObject
createFromObjects(ObjectCollection, Channel) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentChannelByObject
createFromObjects(ObjectCollection, Channel) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.UnaryWithChannelBase: Creates objects from a source collection and a channel.
createFromObjects(ObjectCollection, Dimensions, BinaryValuesInt) - Static method in class org.anchoranalysis.image.core.mask.MaskFromObjects: Create a Mask corresponding to all on voxels in an ObjectCollection.
createFromOutputter(String, OutputterChecked) - Static method in class org.anchoranalysis.io.generator.tabular.CSVWriter: Creates and starts a CSVWriter if it's allowed, otherwise returns Optional.empty().
createFromOutputterWithHeaders(String, OutputterChecked, Supplier<List<String>>, ErrorReporter) - Static method in class org.anchoranalysis.io.generator.tabular.CSVWriter: Like CSVWriter.createFromOutputter(String, OutputterChecked) but suppresses any exceptions into an error log - and writes headers.
createFromPath(Path, OperationContext) - Static method in class org.anchoranalysis.image.io.object.input.ObjectCollectionReader: Reads an object-collection from a path (or path prefix) trying different methods to read the objects.
createFromSource(Channel) - Method in class org.anchoranalysis.plugin.fiji.bean.mask.provider.AutoLocalThreshold
createFromSource(Channel) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromChannel
createFromSource(Channel) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.FromChannelBase: Creates a Mask from the source Channel.
createFromSource(Channel) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.segment.SegmentChannel
createFromSource(Channel) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.segment.Threshold
createFromStack(Optional<ScaleableBackground>, int, ColorIndex) - Static method in class org.anchoranalysis.image.io.stack.output.box.DrawObjectOnStackGenerator: Creates the generator with maybe a stack as the background, or else an empty background - and with default color green and flattened in Z.
createFromStack(Stack) - Method in class org.anchoranalysis.image.bean.provider.stack.StackProviderUnary: Creates a Stack given the entity provided by the delegate.
createFromStack(Stack) - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices
createFromStack(Stack) - Method in class org.anchoranalysis.plugin.opencv.bean.color.ColorConverterBase
createFromStack(ScaleableBackground, int, ColorIndex) - Static method in class org.anchoranalysis.image.io.stack.output.box.DrawObjectOnStackGenerator: Creates the generator with a stack as the background - and with default color green and flattened across the Z-dimension.
createFromString(String) - Static method in class org.anchoranalysis.spatial.axis.AxisConverter: Maps a string of x, y, z (case ignored) to a corresponding axis type.
createFromTupleDuplicate(ReadableTuple3i) - Static method in class org.anchoranalysis.spatial.box.Extent: Creates from a ReadableTuple3i representing the sizes in each dimension, where the tuple is not used internally.
createFromTupleReuse(ReadableTuple3i) - Static method in class org.anchoranalysis.spatial.box.Extent: Creates from a ReadableTuple3i representing the sizes in each dimension, where the tuple is used internally.
createFromTwoMasks(Mask, Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.combine.And
createFromTwoMasks(Mask, Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.combine.CombineBase: Creates a mask from some combination of two masks.
createFromTwoMasks(Mask, Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.combine.IfHighLow
createFromTwoMasks(Mask, Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.combine.Or
createFromTwoMasks(Mask, Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.combine.Xor
createGrayscaleByte(Voxels<UnsignedByteBuffer>) - Static method in class org.anchoranalysis.image.voxel.convert.bufferedimage.BufferedImageFromVoxels: Creates a BufferedImage from a Voxels<UnsignedByteBuffer>.
createGrayscaleShort(Voxels<UnsignedShortBuffer>) - Static method in class org.anchoranalysis.image.voxel.convert.bufferedimage.BufferedImageFromVoxels: Creates a BufferedImage from a Voxels<UnsignedShortBuffer>.
createGroupMap(ConsistentChannelChecker, Optional<Stream<String>>, Optional<InputOutputContext>, OperationContext) - Method in class org.anchoranalysis.plugin.image.task.bean.combine.AggregateChannelTask
createGroupMap(ConsistentChannelChecker, Optional<Stream<String>>, Optional<InputOutputContext>, OperationContext) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase: Creates a map for the storing an aggregate-data-object for each group.
createGroupMap(ConsistentChannelChecker, Optional<Stream<String>>, Optional<InputOutputContext>, OperationContext) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.histogram.ExportImageHistograms
createHashMapToId() - Method in class org.anchoranalysis.mpp.mark.MarkCollection: Creates a map of marks to their indices in the collection.
createHeaders(String[], Optional<String>, boolean) - Static method in class org.anchoranalysis.plugin.image.task.feature.LabelHeadersForCSV: Creates the label-headers (the headers for columns not associated with features).
createIdArr() - Method in class org.anchoranalysis.mpp.mark.MarkCollection: Creates an array of mark IDs.
createIdHashMap() - Method in class org.anchoranalysis.mpp.mark.MarkCollection: Creates a map of marks indexed by their IDs.
createImageFormat(String) - Static method in class org.anchoranalysis.core.format.FileFormatFactory: Creates a ImageFileFormat from an identifier string if its equal to any extension associated with the image file formats in ImageFileFormat.
createInitialization(InitializationContext, Optional<SharedObjects>, Optional<Dictionary>) - Method in class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputter: Creates an ImageInitialization from the given context, shared objects, and dictionary.
createInitialization(InitializationContext, ExportSharedObjects) - Method in class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputter: Creates an ImageInitialization from the given context and input.
createInitializationContext() - Method in class org.anchoranalysis.experiment.task.InputBound: Creates an InitializationContext from the current instance.
createInitialized(Extent) - Static method in class org.anchoranalysis.image.voxel.buffer.slice.FromByte: Create a buffer of a particular size, that has been initialized.
createInitialized(Extent) - Static method in class org.anchoranalysis.image.voxel.buffer.slice.FromFloat: Create a buffer of a particular size, that has been initialized.
createInitialized(Extent) - Static method in class org.anchoranalysis.image.voxel.buffer.slice.FromInt: Create a buffer of a particular size, that has been initialized.
createInitialized(Extent) - Static method in class org.anchoranalysis.image.voxel.buffer.slice.FromShort: Create a buffer of a particular size, that has been initialized.
createInitialized(Extent) - Method in interface org.anchoranalysis.image.voxel.factory.VoxelsFactoryTypeBound: Create a new Voxels that has been initialized with memory buffers.
createInputGrouper(Optional<IndexRangeNegative>) - Method in class org.anchoranalysis.io.input.bean.grouper.FromDerivePath: Creates an InputGrouper that can be used to derive a group-key from a particular input.
createInputGrouper(Optional<IndexRangeNegative>) - Method in class org.anchoranalysis.io.input.bean.grouper.Grouper: Creates an InputGrouper that can be used to derive a group-key from a particular input.
createInputGrouper(Optional<IndexRangeNegative>) - Method in class org.anchoranalysis.io.input.bean.grouper.WithoutGrouping
createInputGrouper(Optional<IndexRangeNegative>) - Method in class org.anchoranalysis.plugin.io.bean.grouper.IfGroupIndexRange
createInputsFromFiles(FilesProvider, InputManagerParameters, Function<NamedFile, T>) - Method in class org.anchoranalysis.plugin.io.bean.input.files.NamedFilesBase: Creates a list of inputs from a FilesProvider which together with the namer can create the inputs.
createInverted() - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValuesInt: Inverts the values so off becomes on, and vice-versa.
createKernel() - Method in class org.anchoranalysis.image.voxel.kernel.morphological.DilationContext: Creates a kernel for performing the dilation.
createLabelledChannel(BoundedList<T>, Optional<Map<Integer, T>>) - Method in class org.anchoranalysis.image.core.object.label.LabelObjects: Creates a channel that contains a unique integer (label) for each element's object-representation.
createList(int) - Method in class org.anchoranalysis.bean.shared.color.scheme.ColorScheme: Creates a sequence of related colors.
createList(int) - Method in class org.anchoranalysis.bean.shared.color.scheme.ColorSchemeUnary
createList(int) - Method in class org.anchoranalysis.bean.shared.color.scheme.FromList
createList(int) - Method in class org.anchoranalysis.bean.shared.color.scheme.FromSingle
createList(int) - Method in class org.anchoranalysis.bean.shared.color.scheme.HSB
createList(int) - Method in class org.anchoranalysis.bean.shared.color.scheme.VeryBright
createListBeans(String, HierarchicalConfiguration, Object) - Static method in class org.anchoranalysis.bean.xml.creator.BeanListCreator: A list of instantiated bean objects from an XML configuration.
createListChildFeatures() - Method in class org.anchoranalysis.feature.bean.Feature: Returns a list of Features that exist as bean-properties of this feature, either directly or in lists.
createListMembershipWithFlags() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMap: Creates a list of all region memberships with their corresponding flags.
createLoader(String) - Static method in class org.anchoranalysis.test.image.stackwriter.SavedFiles: Creates a loader for reading from a particular set of saved-files in a directory in the resources.
createMapToIndex() - Method in class org.anchoranalysis.feature.name.FeatureNameList: Creates a map from the feature-names to their indices in the list.
createMarkEllipsoidLeastSquares(CheckedSupplier<List<Point3i>, CreateException>, Dimensions, boolean, double) - Static method in class org.anchoranalysis.plugin.points.calculate.ellipsoid.EllipsoidFactory: Creates a Ellipsoid using least-squares fitting to a supplied list of points.
createMarkEllipsoidLeastSquares(ObjectMask, Dimensions, boolean, double) - Static method in class org.anchoranalysis.plugin.points.calculate.ellipsoid.EllipsoidFactory: Creates a Ellipsoid using least-squares fitting to the points on the outline of an ObjectMask.
createMarkFromPoint(Point3d, int, boolean) - Static method in class org.anchoranalysis.mpp.mark.conic.MarkConicFactory: Creates a mark from a double-precision 3D point.
createMarkFromPoint(Point3i, int, boolean) - Static method in class org.anchoranalysis.mpp.mark.conic.MarkConicFactory: Creates a mark from an integer 3D point.
CreateMarkFromPoints - Class in org.anchoranalysis.mpp.bean.points: Creates a mark by fitting it to a set of points extracted from other marks.
CreateMarkFromPoints() - Constructor for class org.anchoranalysis.mpp.bean.points.CreateMarkFromPoints
createMarkFromPoints3f(List<Point3f>) - Static method in class org.anchoranalysis.mpp.mark.points.PointListFactory: Creates a PointList from a list of Point3f objects.
createMarkFromPoints3i(List<Point3i>) - Static method in class org.anchoranalysis.mpp.mark.points.PointListFactory: Creates a PointList from a list of Point3i objects.
createMaskOff(Dimensions) - Static method in class org.anchoranalysis.image.core.mask.MaskFactory: Creates a binary-mask for specific dimensions with all voxels set to off.
createMaskOff(Dimensions, BinaryValuesInt) - Static method in class org.anchoranalysis.image.core.mask.MaskFactory: Creates a binary-mask for specific dimensions with all voxels set to off.
createMaskOn(Dimensions) - Static method in class org.anchoranalysis.image.core.mask.MaskFactory: Creates a binary-mask for specific dimensions with all voxels set to on.
createMaskOn(Dimensions, BinaryValuesInt) - Static method in class org.anchoranalysis.image.core.mask.MaskFactory: Creates a binary-mask for specific dimensions with all voxels set to on.
createMatcherFile(Path, Optional<InputContextParameters>) - Method in class org.anchoranalysis.io.input.bean.path.matcher.FilePathMatcher: Create a predicate to be used for matching against path.
createMatcherFile(Path, Optional<InputContextParameters>) - Method in class org.anchoranalysis.io.input.bean.path.matcher.MatchExtensions
createMatcherFile(Path, Optional<InputContextParameters>) - Method in class org.anchoranalysis.io.input.bean.path.matcher.MatchGlob
createMatcherFile(Path, Optional<InputContextParameters>) - Method in class org.anchoranalysis.io.input.bean.path.matcher.MatchRegularExpression
createMerged(ColoredMarks) - Method in class org.anchoranalysis.mpp.mark.ColoredMarks: Merges this ColoredMarks with another, avoiding duplicates.
createMerged(MarkCollection) - Method in class org.anchoranalysis.mpp.mark.MarkCollection: Creates a new collection by merging this collection with another.
createMessageForDescription(String) - Method in exception class org.anchoranalysis.bean.xml.exception.BeanMisconfiguredXMLException
createMessageForDescription(String) - Method in exception class org.anchoranalysis.bean.xml.exception.LocalisedBeanException
createMessageForDescription(String) - Method in exception class org.anchoranalysis.core.exception.combinable.AnchorCombinableException: Creates a message for the exception from the description.
createMessageForDescription(String) - Method in exception class org.anchoranalysis.core.identifier.provider.NamedProviderGetException
createMinusOne() - Method in class org.anchoranalysis.spatial.box.Extent: Creates a new Extent with each dimension decreased by one.
createMockFeatureWithCalculation() - Static method in class org.anchoranalysis.test.feature.plugins.mockfeature.MockFeatureWithCalculationFixture: Creates a mock feature that counts the number of pixels in an object.
createMockFeatureWithCalculation(ToDoubleFunction<T>) - Static method in class org.anchoranalysis.test.feature.plugins.mockfeature.MockFeatureWithCalculationFixture: Creates a mock feature with a custom calculation function.
CreateModelFailedException - Exception Class in org.anchoranalysis.inference.concurrency: When creating a model to be used for inference fails.
CreateModelFailedException(Throwable) - Constructor for exception class org.anchoranalysis.inference.concurrency.CreateModelFailedException: Creates with a cause only.
CreateModelForPool<T> - Interface in org.anchoranalysis.inference.concurrency: Creates a model to use in the pool.
createModelPool(ConcurrencyPlan, Logger) - Method in class org.anchoranalysis.image.inference.bean.segment.instance.SegmentStackIntoObjectsPooled: Creates the model pool (to be used by multiple threads).
createModelPool(ConcurrencyPlan, Logger) - Method in class org.anchoranalysis.image.inference.bean.segment.instance.SuppressNonMaximum
createModelPool(ConcurrencyPlan, Logger) - Method in class org.anchoranalysis.plugin.onnx.bean.object.segment.stack.SegmentObjectsFromONNXModel
createModelPool(ConcurrencyPlan, Logger) - Method in class org.anchoranalysis.plugin.opencv.bean.object.segment.stack.SegmentObjectsFromTensorFlowModel
createNamedFeatureList(List<NamedBean<FeatureListProvider<T>>>) - Method in class org.anchoranalysis.feature.store.NamedFeatureStoreFactory: Create a NamedFeatureStore from a list of beans.
createNamedFeatureProviders(String, TestLoader) - Static method in class org.anchoranalysis.test.feature.plugins.FeaturesFromXMLFixture: Creates a list of named feature list providers from an XML file.
createNecessaryDirectories(Path) - Static method in class org.anchoranalysis.core.system.path.DirectoryCreator: Creates necessary directories to make a path to a file valid.
CreateNew - Class in org.anchoranalysis.plugin.image.bean.channel.provider: Creates a new channel with all values initialized to a constant (by default zero)
CreateNew - Class in org.anchoranalysis.plugin.mpp.bean.provider.collection: Creates a new empty collection of marks
CreateNew() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.CreateNew
CreateNew() - Constructor for class org.anchoranalysis.plugin.mpp.bean.provider.collection.CreateNew
createNewDocument() - Static method in class org.anchoranalysis.core.serialize.XMLParser: Creates a new XML document.
createObject(Dimensions, BinaryValuesByte) - Method in class org.anchoranalysis.mpp.overlay.OverlayMark
createObject(Dimensions, BinaryValuesByte) - Method in class org.anchoranalysis.overlay.object.OverlayObjectMask
createObject(Dimensions, BinaryValuesByte) - Method in class org.anchoranalysis.overlay.Overlay: Derives an object-mask representation of the overlay to be drawn with overlayWriter.
createObjects() - Method in class org.anchoranalysis.plugin.points.bean.fitter.PointsFitterToMark: Creates and returns the ObjectCollection using the specified provider.
createObjectsImage(Assignment<ObjectMask>, boolean, AssignmentColorPool) - Method in class org.anchoranalysis.annotation.io.assignment.generator.DrawColoredObjects: Creates an image with the objects colored, as indicated in the class description.
createOneToMany(Generator<T>, CheckedFunction<S, Stream<T>, ?>) - Static method in class org.anchoranalysis.io.generator.GeneratorBridge: Creates a bridge that maps ONE-TO-MANY from source to destination (i.e. one or more calls to the generator for each source item)
createOneToOne(Generator<T>, CheckedFunction<S, T, ?>) - Static method in class org.anchoranalysis.io.generator.GeneratorBridge: Creates a bridge that maps ONE-TO-ONE from source to destination (i.e. one call to the generator for each source item)
createOrReuse(Throwable) - Static method in exception class org.anchoranalysis.core.exception.InitializeException: Wraps exception in a InitializeException, unless it already its cause is a InitializeException.
createOrReuse(FeatureList<T>, FeatureInitialization, SharedFeatures, Logger) - Method in class org.anchoranalysis.feature.session.replace.BoundReplaceStrategy: Creates a ReplaceStrategy for a particular CacheCreator, or reuses any previously-created ReplaceStrategy if it exists.
createOrReuse(T) - Method in class org.anchoranalysis.feature.session.replace.AlwaysNew
createOrReuse(T) - Method in class org.anchoranalysis.feature.session.replace.CacheAndReuseStrategy
createOrReuse(T) - Method in interface org.anchoranalysis.feature.session.replace.ReplaceStrategy: Find or create a FeatureCalculationInput to associate with input.
createOrReuse(T) - Method in class org.anchoranalysis.feature.session.replace.ReuseSingletonStrategy
createOutputManager(Optional<Path>, Optional<OutputEnabledRules>) - Static method in class org.anchoranalysis.test.io.output.OutputManagerFixture: Creates the OutputManager fixture.
createPair(CreateCalculatorHelper, ImageInitialization, CacheTransferSourceCollection) - Method in class org.anchoranalysis.image.feature.calculator.merged.MergedPairsFeatures: Creates a feature calculator for pair object features.
createPairsUnique() - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria: Creates a set of unique pairs from the graph.
createPairsUnique() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedPairs: Creates a set of unique energy pairs.
createParam(String, boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureSequenceInteger: Creates a parameter feature for the permutation.
createParameters() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.TouchingVoxels: Creates KernelApplicationParameters based on the current configuration.
createParameters(boolean, boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.surface.SurfaceNumberVoxelFaces
createParameters(boolean, boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.surface.SurfaceNumberVoxels
createParameters(boolean, boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.surface.SurfaceNumberVoxelsBase: Creates the calculation parameters for the surface voxel count.
createPayloadCalculator() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergePairs
createPayloadCalculator() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeToIncreaseObjectFeature
createPayloadCalculator() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithFeature: Determines the payload for any given or potential vertex.
createPermutedCopies(List<T>, PermuteProperty<S>, PermutationAssigner) - Method in class org.anchoranalysis.bean.permute.PermutedCopyCreator: Applies a permutation to a copy of each element in a list of beans, updating the custom name of each bean to reflect the permutation.
createPermutedFeaturesFor(Feature<T>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeature
createPermutedFeaturesFor(Feature<T>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureBase: Creates permuted features for the given feature.
createPermutedFeaturesFor(Feature<T>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureSequenceInteger
createPolicy() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.convert.ConvertBase: Creates a ConversionPolicy based on the changeExisting property.
createPrioritizer() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergePairs
createPrioritizer() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeToIncreaseObjectFeature
createPrioritizer() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithFeature: Determines the priority (and selection criteria) used to allow merges between neighbors.
createPriority(ObjectVertex, ObjectVertex, Logger) - Method in interface org.anchoranalysis.plugin.image.object.merge.priority.Prioritizer: Creates a prioritized vertex based on the source and destination vertices.
createRadiiArray() - Method in class org.anchoranalysis.mpp.mark.conic.ConicBase: Creates an array of radii in their original units.
createRadiiArray() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
createRadiiArray() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
createRadiiArrayResolved(Optional<Resolution>) - Method in class org.anchoranalysis.mpp.mark.conic.ConicBase: Creates an array of radii resolved to the given resolution.
createRadiiArrayResolved(Optional<Resolution>) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
createRadiiArrayResolved(Optional<Resolution>) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
createReducedFeature(Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.FeatureListProviderAggregatePair: Creates a reduced feature from features for the first and second objects.
createReuse(Point3d, Point3d) - Static method in class org.anchoranalysis.spatial.box.BoundingBox: Creates from two double points (a minimum corner and a maximum corner).
createReuse(ReadableTuple3i, Extent) - Static method in class org.anchoranalysis.spatial.box.BoundingBox: Creates a bounding-box from a corner and an extent - reusing cornerMin internally.
createReuse(ReadableTuple3i, ReadableTuple3i) - Static method in class org.anchoranalysis.spatial.box.BoundingBox: Creates from two int points (a minimum corner and a maximum corner) - reusing cornerMinInclusive internally.
createRGB(Voxels<UnsignedByteBuffer>, Voxels<UnsignedByteBuffer>, Voxels<UnsignedByteBuffer>, Extent) - Static method in class org.anchoranalysis.image.core.bufferedimage.BufferedImageFromStack: Creates a BufferedImage from three Voxels<UnsignedByteBuffer> representing respectively, red, green, blue color components.
createRGBStack(Channel, Channel, Channel, VoxelDataType) - Static method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeChannels: Creates an RGB stack from up to three channels.
createSameSize(ChannelProvider, String, Channel) - Static method in class org.anchoranalysis.plugin.image.channel.DimensionsChecker: Creates a new channel from a provider, making sure it's the same size as an existing channel.
createSameSize(MaskProvider, String, Channel) - Static method in class org.anchoranalysis.plugin.image.channel.DimensionsChecker: Creates a new mask from a provider, making sure it's the same size as an existing channel.
createSecondLevelFromSet(StringSet) - Method in class org.anchoranalysis.io.output.bean.rules.AddToDefaults
createSecondLevelFromSet(StringSet) - Method in class org.anchoranalysis.io.output.bean.rules.IgnoreUnderscorePrefixUnless
createSecondLevelFromSet(StringSet) - Method in class org.anchoranalysis.io.output.bean.rules.NoneExcept
createSecondLevelFromSet(StringSet) - Method in class org.anchoranalysis.io.output.bean.rules.OutputEnableRulesSpecify: Creates a new second-level SingleLevelOutputEnabled from the relevant set of strings.
createSecondLevelFromSet(StringSet) - Method in class org.anchoranalysis.io.output.bean.rules.PermissiveExcept
createSegmenter() - Method in class org.anchoranalysis.test.image.segment.InstanceSegmentationTestBase: Creates the segmentation implementation to be tested.
createSequence(VoxelDataType) - Method in class org.anchoranalysis.plugin.io.multifile.buffer.MultiBufferSized
createSession() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.feature.ObjectCollectionProviderWithFeature: Creates a feature calculation session for single objects.
createSet() - Method in class org.anchoranalysis.mpp.mark.MarkCollection: Creates a set of all marks in the collection.
createSetter(AnchorBean<?>) - Method in class org.anchoranalysis.bean.permute.property.PermuteProperty: Creates a PermutationAssigner which allows the particular property to be changed.
createSharedStateJob(InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat: Sets a new output-sequence for the series.
createSharedStateJob(InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.RasterTask: Creates a shared-state for the duration of a particular input-job.
createSingle(CreateCalculatorHelper, ImageInitialization, BoundReplaceStrategy<FeatureInputSingleObject, CacheAndReuseStrategy<FeatureInputSingleObject>>) - Method in class org.anchoranalysis.image.feature.calculator.merged.MergedPairsFeatures: Creates a feature calculator for single object features.
createSingle(T, Function<T, BoundingBox>) - Static method in class org.anchoranalysis.spatial.box.BoundedList: Creates for a single element using its current bounding-box.
CreateStackFromBufferedImage - Class in org.anchoranalysis.image.core.bufferedimage: Converts a BufferedImage from the AWT library to a Stack.
createStackSequenceForSeries(int, Logger) - Method in interface org.anchoranalysis.image.io.stack.input.StackSequenceInput: Creates a supplier of a TimeSeries of stacks for a particular series number.
createStackSequenceForSeries(int, Logger) - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertNamedChannelsInputToStack
createStatisticsFor(VoxelizedMarkMemo, Dimensions) - Method in class org.anchoranalysis.mpp.bean.mark.MarkRegion: Creates voxel statistics for the mark region based on the given memo and dimensions.
createSubdirectory(String, boolean) - Method in class org.anchoranalysis.io.output.writer.AlwaysAllowed
createSubdirectory(String, boolean) - Method in class org.anchoranalysis.io.output.writer.CheckIfAllowed
createSubdirectory(String, boolean) - Method in interface org.anchoranalysis.io.output.writer.Writer: Maybe creates a subdirectory for writing to.
createSubdirectory(String, boolean) - Method in class org.anchoranalysis.io.output.writer.WriterRouterErrors: Maybe creates a subdirectory for writing to.
createSubset(Collection<Integer>) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection: A subset of the collection identified by particular indices.
createToColorUnselectedObjects(Interpolator) - Static method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize: Alternative constructor that switches on the coloring of unselected objects by default.
createTransformerFactory() - Static method in class org.anchoranalysis.core.serialize.XMLParser: Creates a TransformerFactory that ignores any DTDs in the document and disables external entities (to prevent XXE attacks).
createUninitialised(Dimensions, VoxelDataType) - Method in class org.anchoranalysis.image.core.channel.factory.ChannelFactory: Create a Channel without initialization with voxel-buffers.
createUninitialized(Extent) - Static method in class org.anchoranalysis.image.voxel.buffer.slice.FromByte: Create a buffer of a particular size, that has not been initialized.
createUninitialized(Extent) - Static method in class org.anchoranalysis.image.voxel.buffer.slice.FromFloat: Create a buffer of a particular size, that has not been initialized.
createUninitialized(Extent) - Static method in class org.anchoranalysis.image.voxel.buffer.slice.FromInt: Create a buffer of a particular size, that has not been initialized.
createUninitialized(Extent) - Static method in class org.anchoranalysis.image.voxel.buffer.slice.FromShort: Create a buffer of a particular size, that has not been initialized.
createUninitialized(Extent) - Method in interface org.anchoranalysis.image.voxel.factory.VoxelsFactoryTypeBound: Create a new Voxels that has not yet been initialized with memory buffers.
createUnsignedByte(BinaryVoxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.image.voxel.binary.connected.ObjectsFromConnectedComponentsFactory: Finds the connected-components in unsigned byte voxels.
createUnsignedByte(Voxels<UnsignedByteBuffer>) - Static method in class org.anchoranalysis.image.voxel.extracter.VoxelsExtracterFactory: Create voxels-extracter for UnsignedByteBuffer.
createUnsignedByte(Voxels<UnsignedByteBuffer>, int) - Static method in class org.anchoranalysis.image.voxel.assigner.VoxelsAssignerFactory: Create a VoxelsAssigner for a UnsignedByteBuffer.
createUnsignedByte(Extent) - Method in class org.anchoranalysis.image.voxel.projection.extrema.ComparisonProjection
createUnsignedByte(Extent) - Method in class org.anchoranalysis.image.voxel.projection.MeanIntensityProjection
createUnsignedByte(Extent) - Method in class org.anchoranalysis.image.voxel.projection.Projection: Creates a buffer for a maximum-intensity projection for unsigned byte voxels.
createUnsignedByte(Extent) - Method in class org.anchoranalysis.image.voxel.projection.StandardDeviationIntensityProjection
createUnsignedByte(Extent, IntFunction<UnsignedByteBuffer>) - Static method in class org.anchoranalysis.image.voxel.arithmetic.VoxelsArithmeticFactory: Create a VoxelsArithmetic for UnsignedByteBuffer.
createUnsignedInt(BinaryVoxels<UnsignedIntBuffer>) - Method in class org.anchoranalysis.image.voxel.binary.connected.ObjectsFromConnectedComponentsFactory: Finds the connected-components in unsigned int voxels.
createUnsignedInt(Voxels<UnsignedIntBuffer>) - Static method in class org.anchoranalysis.image.voxel.extracter.VoxelsExtracterFactory: Create voxels-extracter for UnsignedIntBuffer.
createUnsignedInt(Voxels<UnsignedIntBuffer>, int) - Static method in class org.anchoranalysis.image.voxel.assigner.VoxelsAssignerFactory: Create a a VoxelsAssigner for a UnsignedIntBuffer.
createUnsignedInt(Extent) - Method in class org.anchoranalysis.image.voxel.projection.extrema.ComparisonProjection
createUnsignedInt(Extent) - Method in class org.anchoranalysis.image.voxel.projection.MeanIntensityProjection
createUnsignedInt(Extent) - Method in class org.anchoranalysis.image.voxel.projection.Projection: Creates a buffer for a maximum-intensity projection for unsigned int voxels.
createUnsignedInt(Extent) - Method in class org.anchoranalysis.image.voxel.projection.StandardDeviationIntensityProjection
createUnsignedInt(Extent, IntFunction<UnsignedIntBuffer>) - Static method in class org.anchoranalysis.image.voxel.arithmetic.VoxelsArithmeticFactory: Create a VoxelsArithmetic for UnsignedIntBuffer.
createUnsignedShort(Voxels<UnsignedShortBuffer>) - Static method in class org.anchoranalysis.image.voxel.extracter.VoxelsExtracterFactory: Create voxels-extracter for UnsignedShortBuffer.
createUnsignedShort(Voxels<UnsignedShortBuffer>, int) - Static method in class org.anchoranalysis.image.voxel.assigner.VoxelsAssignerFactory: Create a VoxelsAssigner for a UnsignedShortBuffer.
createUnsignedShort(Extent) - Method in class org.anchoranalysis.image.voxel.projection.extrema.ComparisonProjection
createUnsignedShort(Extent) - Method in class org.anchoranalysis.image.voxel.projection.MeanIntensityProjection
createUnsignedShort(Extent) - Method in class org.anchoranalysis.image.voxel.projection.Projection: Creates a buffer for a maximum-intensity projection for unsigned short voxels.
createUnsignedShort(Extent) - Method in class org.anchoranalysis.image.voxel.projection.StandardDeviationIntensityProjection
createUnsignedShort(Extent, IntFunction<UnsignedShortBuffer>) - Static method in class org.anchoranalysis.image.voxel.arithmetic.VoxelsArithmeticFactory: Create a VoxelsArithmetic for UnsignedShortBuffer.
createVector() - Method in class org.anchoranalysis.image.bean.spatial.direction.AxisAlignedUnitVector
createVector() - Method in class org.anchoranalysis.image.bean.spatial.direction.DirectionVectorBean: Creates a vector in a particular direction.
createVector() - Method in class org.anchoranalysis.image.bean.spatial.direction.SpecifyVector
createVoxelsResizer() - Method in class org.anchoranalysis.image.bean.interpolator.ImgLib2Lanczos
createVoxelsResizer() - Method in class org.anchoranalysis.image.bean.interpolator.ImgLib2Linear
createVoxelsResizer() - Method in class org.anchoranalysis.image.bean.interpolator.Interpolator: Create a VoxelsResizer that can be used for resizing voxel-buffers.
createVoxelsResizer() - Method in class org.anchoranalysis.image.bean.interpolator.None
createVoxelsResizer() - Method in class org.anchoranalysis.io.imagej.bean.interpolator.ImageJ
createVoxelsResizer() - Method in class org.anchoranalysis.plugin.opencv.bean.interpolate.OpenCV
createWithConsoleFallback(OutputterChecked, ExecutionArguments, boolean) - Method in class org.anchoranalysis.experiment.bean.log.LoggingDestination: Creates a logger for this destination - and if anything goes wrong reporting fallback into the console.
createWithEmptyBackground(int, ColorIndex) - Static method in class org.anchoranalysis.image.io.stack.output.box.DrawObjectOnStackGenerator: Creates the generator with an empty background - and with default color green and flattened in Z-dimension.
createWithEmptyList() - Static method in class org.anchoranalysis.io.input.bean.files.SpecificPathList: Factory method for creating the class with an empty list of paths.
createWithLeftUnassigned(ObjectCollection) - Static method in class org.anchoranalysis.annotation.io.assignment.OverlappingObjects: Creates with only left unassigned objects.
createWithLogFallback(OutputterChecked, MessageLogger, ExecutionArguments, boolean) - Method in class org.anchoranalysis.experiment.bean.log.LoggingDestination: Creates a logger for this destination - and if anything goes wrong reporting fallback into a log.
createWithoutColor(MarkCollection, RegionMembershipWithFlags) - Static method in class org.anchoranalysis.mpp.overlay.OverlayCollectionMarkFactory: Creates an OverlayCollection from a MarkCollection without color information.
createWithoutStacks(InitializationContext) - Static method in class org.anchoranalysis.plugin.image.task.stack.InitializationFactory: Creates an ImageInitialization without adding any stacks.
createWithPrefix(DirectoryWithPrefix, MultiLevelOutputEnabled, OutputWriteContext, Optional<MultiLevelRecordedOutputs>, DirectoryCreationParameters, Optional<Logger>) - Static method in class org.anchoranalysis.io.output.outputter.OutputterChecked: Creates a bound output-manager from an existing OutputManager with a prefix.
createWithRight(ObjectCollection) - Static method in class org.anchoranalysis.annotation.io.assignment.OverlappingObjects: Creates with only right unassigned objects.
createWithStacks(ProvidesStackInput, InitializationContext) - Static method in class org.anchoranalysis.plugin.image.task.stack.InitializationFactory: Creates an ImageInitialization with stacks added from the input.
createWithXY(double) - Static method in class org.anchoranalysis.image.core.dimensions.Resolution: Creates with only XY resolution, identical in both dimensions.
createWithXYAndZ(double, double) - Static method in class org.anchoranalysis.image.core.dimensions.Resolution: Creates with XY resolution and Z resolution.
createWriter() - Method in class org.anchoranalysis.io.bioformats.bean.writer.BioformatsWriter: Creates or gets an instance of IFormatWriter which dictates the file format to use for writing.
createWriter() - Method in class org.anchoranalysis.io.bioformats.bean.writer.OMETiff
createWriter() - Method in class org.anchoranalysis.io.bioformats.bean.writer.OMEXML
createWriter() - Method in class org.anchoranalysis.io.bioformats.bean.writer.Tiff
createWriter() - Method in class org.anchoranalysis.test.image.stackwriter.StackWriterTestBase: Creates the StackWriter to be tested.
createWriter(FeatureCSVMetadata) - Method in class org.anchoranalysis.feature.io.csv.results.LabelledResultsCSVWriter: Creates a CSVWriter.
cropRemoveLargerValues(long) - Method in class org.anchoranalysis.math.histogram.Histogram: Like Histogram.cropRemoveSmallerValues(long) but larger values are removed rather than smaller values if the total count is too high.
cropRemoveSmallerValues(long) - Method in class org.anchoranalysis.math.histogram.Histogram: Creates a Histogram reusing the bins in the current histogram, but with an upper limit on the total count.
crossProduct(Vector3d) - Method in class org.anchoranalysis.spatial.point.Vector3d: Computes the cross-product of the tuple with another.
CSV - Enum constant in enum class org.anchoranalysis.core.format.NonImageFileFormat: CSV (Comma Separated Value) files.
csvAggregated(FeatureNameList) - Method in class org.anchoranalysis.feature.io.results.FeatureOutputMetadata: Specific metadata for writing an aggregated CSV file.
CSVComparer - Class in org.anchoranalysis.test.image.csv: Compares two CSV files to determine if they are identical or not.
CSVComparer(String, boolean, int, boolean, boolean) - Constructor for class org.anchoranalysis.test.image.csv.CSVComparer: Creates a new CSVComparer instance.
CSVGenerator<T> - Class in org.anchoranalysis.io.generator.tabular: A generator that writes the contents of a CSV file to the file-system.
CSVGenerator() - Constructor for class org.anchoranalysis.io.generator.tabular.CSVGenerator
csvNonAggregated() - Method in class org.anchoranalysis.feature.io.results.FeatureOutputMetadata: Specific metadata for writing a non-aggregated CSV file.
CSVReader - Class in org.anchoranalysis.io.input.csv: Reads a CSV File from the file-system.
CSVReader(String, boolean) - Constructor for class org.anchoranalysis.io.input.csv.CSVReader: Create, expecting unquoted strings.
CSVReader(String, boolean, boolean) - Constructor for class org.anchoranalysis.io.input.csv.CSVReader: Creates a new CSVReader instance.
CSVReader.OpenedCSVFile - Class in org.anchoranalysis.io.input.csv: A CSV file that has been opened for reading from the file-system.
CSVReaderByLine - Class in org.anchoranalysis.io.input.csv: Reads a CSV file line-by-line.
CSVReaderException - Exception Class in org.anchoranalysis.io.input.csv: When an error occurs reading a CSV file.
CSVReaderException(String) - Constructor for exception class org.anchoranalysis.io.input.csv.CSVReaderException: Create with a message only.
CSVReaderException(Throwable) - Constructor for exception class org.anchoranalysis.io.input.csv.CSVReaderException: Create with a cause only.
csvWriter(FeatureCSVMetadata) - Method in class org.anchoranalysis.plugin.image.task.feature.FeatureExporterContext: Creates a FeatureCSVWriter for the non-aggregated results.
CSVWriter - Class in org.anchoranalysis.io.generator.tabular: Writes a CSV file to the file-system.
CUBIC_MICRO - Enum constant in enum class org.anchoranalysis.image.core.dimensions.SpatialUnits.UnitSuffix: 1e-6 cubed.
CUBIC_MILLI - Enum constant in enum class org.anchoranalysis.image.core.dimensions.SpatialUnits.UnitSuffix: 1e-3 cubed.
CUBIC_NANO - Enum constant in enum class org.anchoranalysis.image.core.dimensions.SpatialUnits.UnitSuffix: 1e-9 cubed.
currentStateDescription() - Method in class org.anchoranalysis.experiment.task.processor.ConcurrentJobMonitor: A human-understandable string describing the aggregate state.
customizeExperimentExecutor(ExperimentExecutor, CommandLine) - Method in class org.anchoranalysis.launcher.config.LauncherConfig: Customizes the experiment executor with additional configuration.
CutBelowThreshold - Class in org.anchoranalysis.plugin.image.bean.histogram.provider: This cuts a Histogram below a threshold BUT TRANSFERS ALL THE COUNT greater than equal to the threshold into the bin just below the threshold value
CutBelowThreshold() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.provider.CutBelowThreshold
CutOffCorners - Class in org.anchoranalysis.test.image.object: The bounding box is filled apart from cuboids cut out of the corners
CutOffCorners(int, int, Extent) - Constructor for class org.anchoranalysis.test.image.object.CutOffCorners: Constructs a CutOffCorners pattern.
CutOffCornersObjectFixture - Class in org.anchoranalysis.test.image.object: Creates one or more objects that are otherwise rectangles with on values, but with corner voxels as off.
CutOffCornersObjectFixture() - Constructor for class org.anchoranalysis.test.image.object.CutOffCornersObjectFixture: Create without any check on dimensions.
CutOffCornersObjectFixture(Dimensions) - Constructor for class org.anchoranalysis.test.image.object.CutOffCornersObjectFixture: Create with any check on dimensions.
CVFindContours - Class in org.anchoranalysis.plugin.opencv: Wrapper around OpenCV's findContours function.
CVInit - Class in org.anchoranalysis.plugin.opencv: Provides for initialization of the JavaCPP bridge to OpenCV.

D

dataType() - Method in class org.anchoranalysis.image.core.channel.factory.ChannelFactorySingleType
dataType() - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer: Data-type of each voxel in the buffer.
dataType() - Method in interface org.anchoranalysis.image.voxel.factory.VoxelsFactoryTypeBound: The data-type of the voxels, as created by this factory.
dataType() - Method in class org.anchoranalysis.image.voxel.Voxels: The underlying data-type of the voxels, represented by a VoxelDataType instance.
DataTypeMaxIntensity<T> - Class in org.anchoranalysis.plugin.image.feature.bean.stack.intensity: The maximum-intensity allowed by the data-type of the stack.
DataTypeMaxIntensity() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.stack.intensity.DataTypeMaxIntensity
DateStyle - Enum Class in org.anchoranalysis.plugin.io.naming.interval: How to style a date in a file-name.
DebugDependentProcessor<T,S> - Class in org.anchoranalysis.experiment.bean.processor: Executes different processors depending on whether we are in debug mode or not.
DebugDependentProcessor() - Constructor for class org.anchoranalysis.experiment.bean.processor.DebugDependentProcessor
DebugModeParameters - Class in org.anchoranalysis.io.input.bean: An alternative mode of option where behaviours change.
DebugModeParameters(Optional<String>) - Constructor for class org.anchoranalysis.io.input.bean.DebugModeParameters: Creates a new DebugModeParameters instance.
decode(int) - Static method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.ChainCodesDirection: Decodes a chain-code into a point.
decode(List<OnnxTensor>, ImageInferenceContext) - Method in class org.anchoranalysis.plugin.onnx.bean.object.segment.decode.instance.maskrcnn.DecodeMaskRCNN
decode(List<OnnxTensor>, ImageInferenceContext) - Method in class org.anchoranalysis.plugin.onnx.bean.object.segment.decode.instance.text.DecodeEAST
decode(List<T>, ImageInferenceContext) - Method in class org.anchoranalysis.image.inference.bean.segment.instance.DecodeInstanceSegmentation: Decodes the output tensors from inference into ObjectMasks with confidence and labels.
decodeConnectedComponentID(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.WatershedEncoding: Decodes a connected component ID from its encoded form.
DecodeEAST - Class in org.anchoranalysis.plugin.onnx.bean.object.segment.decode.instance.text: Extracts text from a RGB image by using the EAST deep neural network model and the ONNX Runtime.
DecodeEAST() - Constructor for class org.anchoranalysis.plugin.onnx.bean.object.segment.decode.instance.text.DecodeEAST
DecodeInstanceSegmentation<T> - Class in org.anchoranalysis.image.inference.bean.segment.instance: Decodes inference output into segmented-objects.
DecodeInstanceSegmentation() - Constructor for class org.anchoranalysis.image.inference.bean.segment.instance.DecodeInstanceSegmentation
DecodeLabels<T> - Class in org.anchoranalysis.image.core.object.label: Decodes a labelled raster into derived objects or object-like elements.
DecodeLabels(Voxels<?>, int, int, DecodeLabels.CreateElementFromScaledObject<T>) - Constructor for class org.anchoranalysis.image.core.object.label.DecodeLabels: Creates a new DecodeLabels instance.
DecodeLabels.CreateElementFromScaledObject<T> - Interface in org.anchoranalysis.image.core.object.label: Creates an element from the scaled-object and its index.
DecodeMaskRCNN - Class in org.anchoranalysis.plugin.onnx.bean.object.segment.decode.instance.maskrcnn: Decodes the inference output from a Mask-RCNN implementation.
DecodeMaskRCNN() - Constructor for class org.anchoranalysis.plugin.onnx.bean.object.segment.decode.instance.maskrcnn.DecodeMaskRCNN
DecomposeIntoConnectedComponents - Class in org.anchoranalysis.plugin.image.bean.object.provider.connected: Ensures each object in a collection is a connected-component, decomposing it if necessary into multiple objects.
DecomposeIntoConnectedComponents() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.connected.DecomposeIntoConnectedComponents
decrement() - Method in class org.anchoranalysis.math.arithmetic.Counter: Decreases the counter by one.
decrementX() - Method in class org.anchoranalysis.image.voxel.kernel.KernelPointCursor: Decrements the point and associated index by one in the X dimension.
decrementX() - Method in class org.anchoranalysis.spatial.point.Tuple3i: Decrements the X component's value by one.
decrementX(int) - Method in class org.anchoranalysis.spatial.point.Tuple3i: Decrements the X component's value by a shift.
decrementY() - Method in class org.anchoranalysis.image.voxel.kernel.KernelPointCursor: Decrements the point and associated index by one in the Y dimension.
decrementY() - Method in class org.anchoranalysis.spatial.point.Tuple3i: Decrements the Y component's value by one.
decrementY(int) - Method in class org.anchoranalysis.spatial.point.Tuple3i: Decrements the Y component's value by a shift.
decrementYTwice() - Method in class org.anchoranalysis.image.voxel.kernel.KernelPointCursor: Decrements the point and associated index by two in the Y dimension.
decrementZ() - Method in class org.anchoranalysis.image.voxel.kernel.KernelPointCursor: Decrements the point by one in the Z dimension.
decrementZ() - Method in class org.anchoranalysis.spatial.point.Tuple3i: Decrements the Z component's value by one.
decrementZ(int) - Method in class org.anchoranalysis.spatial.point.Tuple3i: Decrements the Z component's value by a shift.
deepCopy() - Method in class org.anchoranalysis.core.color.ColorList: Creates a new list, containing the duplicates of same elements as the current list.
deepCopy() - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria: Creates a deep copy of this RandomCollectionWithAddCriteria.
deepCopy() - Method in class org.anchoranalysis.mpp.feature.energy.EnergyTotal: Creates a deep copy of this EnergyTotal instance.
deepCopy() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown: Creates a deep copy of this instance.
deepCopy() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy: Makes a deep copy of this instance (except the energyScheme which is reused).
deepCopy() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedAll: Creates a deep copy of this instance.
deepCopy() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedIndividual: Creates a deep copy of this instance.
deepCopy() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedPairs: Creates a deep copy of this instance.
deepCopy() - Method in class org.anchoranalysis.mpp.mark.ColoredMarks: Creates a deep copy of this ColoredMarks instance.
deepCopy() - Method in class org.anchoranalysis.mpp.mark.MarkCollection: Creates a deep copy of the collection.
Default - Class in org.anchoranalysis.io.bioformats.bean.options: A default set of ReadOptions without special behavior.
Default() - Constructor for class org.anchoranalysis.io.bioformats.bean.options.Default
DEFAULT_CHARACTER - Static variable in class org.anchoranalysis.core.log.Divider: The default character used in the divider, if not otherwise specified in the constructor.
DEFAULT_COLOR_SET_GENERATOR - Static variable in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase: The default ColorScheme used for generating colors.
DEFAULT_FUNC_NUM_PIXELS - Static variable in class org.anchoranalysis.test.feature.plugins.mockfeature.MockFeatureWithCalculationFixture: A default function for counting the number of pixels (voxels) in a single object.
DEFAULT_IMAGE_INPUT_NAME - Static variable in class org.anchoranalysis.mpp.io.input.MultiInput: The default name for the input image stack.
DEFAULT_NUMBER_CHARACTERS_IN_BANNER - Static variable in class org.anchoranalysis.core.log.Divider: The default total nubmer of characters to use in the divier, if not otherwise specified in the constructor.
DEFAULT_NUMBER_GPUS - Static variable in class org.anchoranalysis.inference.concurrency.ConcurrencyPlan: The default number of GPUs used for numberGPUs in certain constructors.
DefaultChildCacheFinder - Class in org.anchoranalysis.feature.session.cache.finder: The default strategy for finding children by always directly taking (or creating a child-cache) as necessary.
defaultExperimentOrCustom(CommandLine, Path) - Static method in class org.anchoranalysis.launcher.executor.selectparam.experiment.ExperimentFactory: Chooses either a path to the default-experiment or a path to a custom experiment.
DefaultInstance - Annotation Interface in org.anchoranalysis.bean.annotation: Indicates a default bean-instance is available.
defaultOutputs() - Method in class org.anchoranalysis.experiment.bean.io.InputOutputExperiment
defaultOutputs() - Method in class org.anchoranalysis.experiment.bean.io.OutputExperiment: If specified, default rules for determine which outputs are enabled or not.
defaultOutputs() - Method in class org.anchoranalysis.experiment.bean.task.Task: If specified, default rules for determine which outputs are enabled or not.
defaultOutputs() - Method in class org.anchoranalysis.plugin.annotation.bean.aggregate.AggregateAnnotations
defaultOutputs() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
defaultOutputs() - Method in class org.anchoranalysis.plugin.image.task.bean.combine.AggregateChannelTask
defaultOutputs() - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage
defaultOutputs() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures
defaultOutputs() - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat
defaultOutputs() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.histogram.ExportImageHistograms
defaultOutputs() - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageAssignLabel
defaultOutputs() - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage
defaultOutputs() - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel
defaultOutputs() - Method in class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice
defaultOutputs() - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
defaultOutputs() - Method in class org.anchoranalysis.plugin.io.bean.task.CopyFiles
defaultOutputs() - Method in class org.anchoranalysis.plugin.mpp.bean.convert.ConvertNamedChannels
defaultOutputs() - Method in class org.anchoranalysis.plugin.mpp.bean.define.Develop
Define - Class in org.anchoranalysis.bean.define: A bean where the definitions of many different NamedBeans can be specified.
Define<T> - Class in org.anchoranalysis.feature.bean.list: Specifies a list of features directly without assigning any custom-naming.
Define() - Constructor for class org.anchoranalysis.bean.define.Define
Define() - Constructor for class org.anchoranalysis.feature.bean.list.Define
Define(List<Feature<T>>) - Constructor for class org.anchoranalysis.feature.bean.list.Define: Creates a new Define instance.
Define(Feature<T>) - Constructor for class org.anchoranalysis.feature.bean.list.Define: Create from a single Feature.
DefineAdder - Interface in org.anchoranalysis.bean.define.adder: Indicates that an object can add one or more items to a Define.
DefineAdderBean - Class in org.anchoranalysis.bean.define.adder: Base class for AnchorBeans that can add items to a Define.
DefineAdderBean() - Constructor for class org.anchoranalysis.bean.define.adder.DefineAdderBean
DefineAdderWithPrefixBean - Class in org.anchoranalysis.bean.define.adder: Like DefineAdderBean but adds a prefix to the name of beans when adding.
DefineAdderWithPrefixBean() - Constructor for class org.anchoranalysis.bean.define.adder.DefineAdderWithPrefixBean
DefineAddException - Exception Class in org.anchoranalysis.bean.define: Called when a bean fails to be added to a Define.
DefineAddException(String) - Constructor for exception class org.anchoranalysis.bean.define.DefineAddException: Creates with a message only.
DefineAddException(String, Throwable) - Constructor for exception class org.anchoranalysis.bean.define.DefineAddException: Creates with a message and cause.
DefineAddException(Throwable) - Constructor for exception class org.anchoranalysis.bean.define.DefineAddException: Creates with a cause only.
DefinedNamed<T> - Class in org.anchoranalysis.feature.bean.list: Specifies features via a list of names and associated with features.
DefinedNamed() - Constructor for class org.anchoranalysis.feature.bean.list.DefinedNamed
DefineFactory - Class in org.anchoranalysis.bean.define: Creates a new Define.
DefineFactory() - Constructor for class org.anchoranalysis.bean.define.DefineFactory
DefineOutputter - Class in org.anchoranalysis.plugin.mpp.bean.define: Applies a Define on inputs and outputs produced entities (images, histograms, objects etc.).
DefineOutputter() - Constructor for class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputter
DefineOutputter.Processor<T> - Interface in org.anchoranalysis.plugin.mpp.bean.define: Functional interface for processing an ImageInitialization.
DefineOutputterWithEnergy - Class in org.anchoranalysis.plugin.mpp.bean.define: Like a Define but outputs also an energy-stack.
DefineOutputterWithEnergy() - Constructor for class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputterWithEnergy
DefineOutputterWithEnergy.ProcessWithEnergyStack<T,S> - Interface in org.anchoranalysis.plugin.mpp.bean.define: Functional interface for processing with an energy stack.
DefineSingle<T> - Class in org.anchoranalysis.feature.bean.list: Specifies a single feature directly without assigning any custom-naming.
DefineSingle() - Constructor for class org.anchoranalysis.feature.bean.list.DefineSingle
DefineSingle(Feature<T>) - Constructor for class org.anchoranalysis.feature.bean.list.DefineSingle: Creates a new DefineSingle instance.
delegate() - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptionsDelegate: The ReadOptions that is used as a delegate by sub-classes.
delete(Path) - Method in interface org.anchoranalysis.annotation.io.AnnotationDeleter: Deletes all files at this path (or any other paths derived from this one.
delete(Path) - Method in class org.anchoranalysis.annotation.io.mark.DualMarksAnnotationDeleter
delete(Path) - Method in class org.anchoranalysis.annotation.io.SimpleAnnotationDeleter
depth(boolean) - Static method in class org.anchoranalysis.test.image.MaskFixture: The **depth** of the mask that will be created.
deriveColorList() - Method in class org.anchoranalysis.plugin.image.object.ColoredObjectCollection: Derives a ColorList from the collection.
deriveContext(InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeaturesStyle: Derives a FeatureExporterContext from the current style and given context.
DerivedObject - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.morphological: A base class for features that operate on a derived object mask and calculate a feature on it.
DerivedObject() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.DerivedObject
deriveExtent() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.ObjectCollectionProviderMorphological: Derives the extent from the dimensions, if available.
deriveFrom(Path, boolean) - Method in class org.anchoranalysis.io.input.bean.path.DerivePath: Derives a new path from an existing path.
deriveFrom(Path, boolean) - Method in class org.anchoranalysis.io.input.bean.path.Identity
deriveFrom(Path, boolean) - Method in class org.anchoranalysis.io.input.bean.path.NameElementRange
deriveFrom(Path, boolean) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.CollapseFileName
deriveFrom(Path, boolean) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Constant
deriveFrom(Path, boolean) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.InsertRegExGroups
deriveFrom(Path, boolean) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.JoinRegExGroups
deriveFrom(Path, boolean) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.RemoveTrailingDirectory
deriveFrom(Path, boolean) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Replace
deriveFrom(Path, boolean) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Rooted
deriveFrom(Supplier<Optional<Path>>, boolean) - Method in class org.anchoranalysis.io.input.bean.path.DerivePath: Derives a new path from an existing path.
deriveFrom(Channel) - Method in class org.anchoranalysis.image.bean.displayer.StackDisplayer: Creates from a Channel.
deriveFrom(RGBStack) - Method in class org.anchoranalysis.image.bean.displayer.StackDisplayer: Derives a DisplayStack from a RGBStack.
deriveFrom(Stack) - Method in class org.anchoranalysis.image.bean.displayer.StackDisplayer: Derives a DisplayStack from a RGBStack.
deriveFromDelegate(FeatureInputSingleObject, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.CalculateIntersecting
deriveFromDelegate(T, U) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegate: Derives the result from the delegate calculation.
DeriveFromPair - Class in org.anchoranalysis.plugin.image.feature.bean.list.pair: Embeds each feature in a FeatureDeriveFromPair feature (first, second or merge) and prepends with a string.
DeriveFromPair() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.pair.DeriveFromPair
deriveGroupKeyOptional(Path) - Method in interface org.anchoranalysis.io.input.grouper.InputGrouper: Derives a key for the group from identifier.
deriveIndex(String) - Static method in class org.anchoranalysis.image.core.stack.RGBChannelNames: Derives the index of a channel for a channel name.
deriveInitializationContext() - Method in class org.anchoranalysis.experiment.task.ParametersExperiment: Derives an InitializationContext from the parameters.
deriveInput(Stack, Optional<double[]>) - Method in class org.anchoranalysis.image.inference.bean.segment.instance.SegmentStackIntoObjectsScaleDecode: Derives the input tensor from an image.
deriveInput(Stack, Optional<double[]>) - Method in class org.anchoranalysis.plugin.onnx.bean.object.segment.stack.SegmentObjectsFromONNXModel
deriveInput(Stack, Optional<double[]>) - Method in class org.anchoranalysis.plugin.opencv.bean.object.segment.stack.SegmentObjectsFromTensorFlowModel
deriveInputsStartBatch(ObjectCollection, EnergyStack, boolean, OperationContext) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.CombineObjectsForFeatures: Derives a list of inputs (i.e. rows in a feature table) and starts a batch of related thumbnail generation.
deriveLabels(String, Optional<String>, int) - Method in interface org.anchoranalysis.plugin.image.task.feature.calculator.LabelsForInput: Calculates labels for a given input (and index).
deriveName(File, Optional<Path>, int) - Method in class org.anchoranalysis.io.input.bean.namer.FileNamerIndependent: Derives a unique name for this file.
deriveName(File, Optional<Path>, int) - Method in class org.anchoranalysis.plugin.io.bean.file.namer.FromOutputName
deriveName(File, Optional<Path>, int) - Method in class org.anchoranalysis.plugin.io.bean.file.namer.LastDirectories
deriveName(File, Optional<Path>, int) - Method in class org.anchoranalysis.plugin.io.bean.file.namer.NormalizedPath
deriveName(File, Optional<Path>, int) - Method in class org.anchoranalysis.plugin.io.bean.file.namer.RegExMatcher
deriveName(File, Optional<Path>, int) - Method in class org.anchoranalysis.plugin.io.bean.file.namer.RelativeToDirectory
deriveName(File, FileNamerContext) - Method in class org.anchoranalysis.io.input.bean.namer.FileNamer: A name for a file.
deriveName(List<File>, FileNamerContext) - Method in class org.anchoranalysis.io.input.bean.namer.FileNamer: Derives a list of names (associated with each file) for some files.
deriveName(List<File>, FileNamerContext) - Method in class org.anchoranalysis.io.input.bean.namer.FileNamerIndependent
deriveName(List<File>, FileNamerContext) - Method in class org.anchoranalysis.plugin.io.bean.file.namer.IfRelativeToDirectory
deriveName(List<File>, FileNamerContext) - Method in class org.anchoranalysis.plugin.io.bean.file.namer.patternspan.PatternSpan
deriveName(List<File>, FileNamerContext) - Method in class org.anchoranalysis.plugin.io.bean.file.namer.RemoveExtension
deriveName(List<File>, FileNamerContext) - Method in class org.anchoranalysis.plugin.io.bean.file.namer.SubsetRangeIfRequested
deriveNames() - Method in class org.anchoranalysis.feature.bean.list.FeatureList: Derives the names of the features.
deriveNameUnique(List<File>, FileNamerContext) - Method in class org.anchoranalysis.io.input.bean.namer.FileNamer: Like FileNamer.deriveName(List, FileNamerContext) but checks that the final list of named-files all have unique names.
deriveObject() - Method in class org.anchoranalysis.image.voxel.object.DeriveObjectFromPoints: Derives an ObjectMask that includes all points that were previously added.
deriveObject(Dimensions, RegionMembershipWithFlags, BinaryValuesByte) - Method in class org.anchoranalysis.mpp.mark.Mark: Creates an ObjectMask representation of the mark.
deriveObject(BoundingBox) - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateAtCorner
deriveObject(BoundingBox) - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateImplementation
deriveObject(BoundingBox) - Method in interface org.anchoranalysis.image.voxel.extracter.predicate.VoxelsPredicate: Creates an ObjectMask for all the voxels inside the bounding-box satisfying the predicate.
DeriveObjectFromPoints - Class in org.anchoranalysis.image.voxel.object: Derive an ObjectMask by incrementally adding points.
DeriveObjectFromPoints() - Constructor for class org.anchoranalysis.image.voxel.object.DeriveObjectFromPoints
deriveObjects(Dimensions, RegionMembershipWithFlags) - Method in class org.anchoranalysis.mpp.mark.MarkCollection: Derives objects from the marks in the collection.
deriveObjectTight() - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateAtCorner
deriveObjectTight() - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateImplementation
deriveObjectTight() - Method in interface org.anchoranalysis.image.voxel.extracter.predicate.VoxelsPredicate: Creates an ObjectMask for all the voxels satisfying the predicate, minimally fitting the bounding-box to the on voxels only.
derivePath(DerivePath, Path) - Static method in class org.anchoranalysis.plugin.annotation.bean.strategy.PathFromGenerator: Derives a path using a DerivePath generator and a binding path.
DerivePath - Class in org.anchoranalysis.io.input.bean.path: Derives a path from an existing path.
DerivePath() - Constructor for class org.anchoranalysis.io.input.bean.path.DerivePath
DerivePathException - Exception Class in org.anchoranalysis.io.input.path: When an error occurs deriving a path from another path.
DerivePathException(String) - Constructor for exception class org.anchoranalysis.io.input.path.DerivePathException: Create with a message only.
DerivePathException(String, Throwable) - Constructor for exception class org.anchoranalysis.io.input.path.DerivePathException: Create with a message and cause.
DerivePathException(Throwable) - Constructor for exception class org.anchoranalysis.io.input.path.DerivePathException: Create with a cause only.
derivePathPrefixerContext() - Method in class org.anchoranalysis.experiment.arguments.ExecutionArguments: Derive a PathPrefixerContext from the arguments in this class.
derivePointsLocal() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Creates a list of all on voxels as points, using local coordinates i.e.
deriveRootedPath(Path, String, boolean, boolean) - Static method in class org.anchoranalysis.plugin.io.input.path.RootedFilePathUtilities
deriveRotationMatrix() - Method in class org.anchoranalysis.spatial.orientation.Orientation: Derives a RotationMatrix that can be applied to rotate an entity anti-clockwise to the current orientation.
deriveRotationMatrix() - Method in class org.anchoranalysis.spatial.orientation.Orientation2D
deriveRotationMatrix() - Method in class org.anchoranalysis.spatial.orientation.Orientation3DEulerAngles
deriveRotationMatrix() - Method in class org.anchoranalysis.spatial.orientation.OrientationAxisAngle
deriveRotationMatrix() - Method in class org.anchoranalysis.spatial.orientation.OrientationRotationMatrix
deriveScalingFactor(int, int) - Static method in class org.anchoranalysis.spatial.scale.Scaler: Calculates a scaling-factor (for one dimension) by doing a floating point division of two integers.
deriveScore(double, double, FeatureResultSupplier) - Method in class org.anchoranalysis.plugin.operator.feature.bean.statistics.GaussianCumulative
deriveScore(double, double, FeatureResultSupplier) - Method in class org.anchoranalysis.plugin.operator.feature.bean.statistics.StatisticalBase: Derive scores given the value, mean and standard deviation.
deriveScore(double, double, FeatureResultSupplier) - Method in class org.anchoranalysis.plugin.operator.feature.bean.statistics.ZScore
deriveScoreFromVoxel(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevelBase
deriveScoreFromVoxel(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.NormalizeByConstant
deriveScoreFromVoxel(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.NormalizeByMax
deriveScoreFromVoxel(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.SingleChannel: Derives a score from a single voxel intensity.
deriveStack(boolean) - Method in class org.anchoranalysis.image.core.stack.DisplayStack: Derives a Stack from the display-stack that will be converted to 8-bit if necessary.
deriveStatistic(DoubleArrayList) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.MeanAcrossObjects
deriveStatistic(DoubleArrayList) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.ObjectAggregationBase: Derives a statistic from the calculated feature values for all objects.
deriveStatistic(DoubleArrayList) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.QuantileAcrossObjects
deriveStatistics() - Method in class org.anchoranalysis.experiment.task.processor.ConcurrentJobMonitor: Derive statistics on the aggregate state of jobs.
deriveSubdirectory(String, boolean) - Method in class org.anchoranalysis.io.output.outputter.Outputter: Creates a new Outputter by appending a relative folder-path to the current Outputter
deriveSubdirectory(String, boolean) - Method in class org.anchoranalysis.io.output.outputter.OutputterChecked: Derives a bound-output-manager for a (possibly newly created) subdirectory of the existing manager
deriveSubdirectory(String, boolean) - Method in class org.anchoranalysis.io.output.writer.ElementOutputter: Derives a bound-output-manager for a (possibly newly created) subdirectory of the existing manager.
deriveUnsignedBytePredicate() - Method in interface org.anchoranalysis.image.voxel.iterator.predicate.PredicateTwoBytes: Derives a predicate with a different interface for operating on UnsignedByteBuffer.
deriveUnsignedByteProcessor() - Method in interface org.anchoranalysis.image.voxel.iterator.predicate.PredicateTwoBytes: Derives a processor with a different interface for operating on UnsignedByteBuffer.
describe() - Method in class org.anchoranalysis.core.graph.GraphWithoutPayload: Describes the graph in a multi-line string.
describe() - Method in interface org.anchoranalysis.launcher.executor.selectparam.SelectParam: Provides a string that can be displayed to the user to describe this particular SelectParam.
describe() - Method in class org.anchoranalysis.launcher.executor.selectparam.UseDefaultManager
describe() - Method in class org.anchoranalysis.plugin.image.object.merge.DescribeGraph: Generates a string describing the entire graph (vertices and edges).
describe() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.image.SummarizerImageMetadata
describe() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.input.SummarizerInputFromManager
describe() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.path.ExtensionCount
describe() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.path.FilePathPattern
describe() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.path.FileSizeStatistics
describe() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.Summarizer: A string summarizing this item.
describe() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerAggregate
describe() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerCount
describe() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerListMultiline
describe() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerSplitMoreThan
describe(boolean) - Method in class org.anchoranalysis.core.graph.GraphWithPayload: Describes the graph in a multi-line string.
describe(String) - Method in class org.anchoranalysis.plugin.io.shared.FrequencyMap: Describes the frequency map contents in human-readable language.
describeAcceptedClasses() - Method in class org.anchoranalysis.bean.initializable.property.AssignerMatchClass
describeAcceptedClasses() - Method in interface org.anchoranalysis.bean.initializable.property.InitializationParameterAssigner: A string describing which classes of initialization-parameters are accepted or not.
describeBean() - Method in class org.anchoranalysis.bean.AnchorBean: A (maybe longer) description identifying the bean and perhaps its key parameters.
describeBean() - Method in class org.anchoranalysis.feature.bean.Feature
describeBean() - Method in class org.anchoranalysis.feature.bean.list.FeatureList
describeBean() - Method in class org.anchoranalysis.image.bean.spatial.arrange.overlay.Overlay
describeBean() - Method in class org.anchoranalysis.mpp.bean.bound.BoundMinMax
describeBean() - Method in class org.anchoranalysis.mpp.bean.bound.BoundUnitless
describeBean() - Method in class org.anchoranalysis.mpp.bean.bound.rotation.BoundRotation2D
describeBean() - Method in class org.anchoranalysis.mpp.bean.bound.rotation.BoundRotation3D
describeBean() - Method in class org.anchoranalysis.mpp.bean.mark.factory.MarkWithIdentifierFactory
describeBean() - Method in class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaPair
describeBean() - Method in class org.anchoranalysis.mpp.feature.mark.MarkPairCollection
describeChildren() - Method in class org.anchoranalysis.bean.AnchorBean: Generates a string describing the children of the current bean.
describeEdge(ObjectVertex, ObjectVertex, ObjectVertex, double, boolean) - Method in class org.anchoranalysis.plugin.image.object.merge.DescribeGraph: Generates a string to describe a potential merge.
describeEdge(ObjectVertex, ObjectVertex, ObjectVertex, double, boolean) - Method in class org.anchoranalysis.plugin.image.object.merge.GraphLogger: Logs a description of a potential edge merge.
describeExecutionTimes(RunningSum, RecordedExecutionTimes, long) - Static method in class org.anchoranalysis.experiment.time.DescribeExecutionTimeStatistics: Describes how long operations took to complete en aggregate with related-statistics.
DescribeExecutionTimeStatistics - Class in org.anchoranalysis.experiment.time: Generates report of the execution-times of different operations.
DescribeGraph - Class in org.anchoranalysis.plugin.image.object.merge: Builds string-descriptions of a NeighborGraph.
DescribeGraph(NeighborGraph, boolean) - Constructor for class org.anchoranalysis.plugin.image.object.merge.DescribeGraph: Creates a new DescribeGraph instance.
describeMarks(MarkCollection) - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedIndividual: Generates a string description of the marks and their associated energies.
describeMerge(ObjectVertex, TypedEdge<ObjectVertex, PrioritisedVertex>) - Method in class org.anchoranalysis.plugin.image.object.merge.DescribeGraph: Describes a merge operation that has been decided upon.
describeMerge(ObjectVertex, TypedEdge<ObjectVertex, PrioritisedVertex>) - Method in class org.anchoranalysis.plugin.image.object.merge.GraphLogger: Logs a description of a merge operation that has been decided upon.
describeNoun() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.image.BitDepth
describeNoun() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.image.ImageSize
describeNoun() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.image.NumberChannels
describeNoun() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.image.SummarizerImageMetadata
describeParameters() - Method in class org.anchoranalysis.feature.bean.Feature: A human-readable description of the parameterization of the bean.
describeParameters() - Method in class org.anchoranalysis.feature.bean.operator.Constant
describeParameters() - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.AsSingle
describeParameters() - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.ForSpecificAxis
describeParameters() - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Count
describeParameters() - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.RatioThreshold
describeParameters() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxAlongAxisBase
describeParameters() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase
describeParameters() - Method in class org.anchoranalysis.plugin.image.feature.bean.physical.UnitsWithinRange
describeParameters() - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGFeature
describeParameters() - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.InvertedMax
describeParameters() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.CompareWithRange
describeParameters() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.CompareWithRangeFeature
describeParameters() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareBase
describeParameters() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareFromScalars
describeParameters() - Method in class org.anchoranalysis.plugin.operator.feature.bean.statistics.StatisticalBase
describePropertiesFriendly() - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations: Creates a string that uniquely identifies all properties in the bean, in a human-friendly format.
describePropertyValue(Double) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyDoubleSet
describePropertyValue(Double) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequenceDouble
describePropertyValue(Integer) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequenceInteger
describePropertyValue(String) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyStringSet
describePropertyValue(T) - Method in class org.anchoranalysis.bean.permute.property.PermuteProperty: Describes a particular property-value in a unique but human-readable way.
describeTo(boolean) - Method in class org.anchoranalysis.core.graph.TypedEdge: Describes the edge by showing the to vertex, and optionally the payload.
describeUncompletedJobs(int) - Method in class org.anchoranalysis.experiment.task.processor.ConcurrentJobMonitor: A string that describes all jobs that are not tey completed, but only if there are fewer than a certain number.
descriptionForList(String) - Method in class org.anchoranalysis.feature.bean.operator.FeatureFromList: Derive a string description of all the items of the list concatenated together.
descriptionLong() - Method in class org.anchoranalysis.feature.bean.Feature: A long human-readable description of the feature and some or all of its parameterization.
descriptionLong() - Method in class org.anchoranalysis.feature.bean.operator.Constant
descriptionLong() - Method in class org.anchoranalysis.feature.bean.operator.Reference
descriptionLong() - Method in class org.anchoranalysis.feature.bean.operator.Sum
descriptionLong() - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.intensity.Intensity
descriptionLong() - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.AbsoluteValue
descriptionLong() - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.Divide
descriptionLong() - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.InvertedMax
descriptionLong() - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.Multiply
descriptionLong() - Method in class org.anchoranalysis.plugin.operator.feature.bean.list.MeanGeometric
descriptionLong() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.NormalizedRange
descriptionLong() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.Range
descriptionLong() - Method in class org.anchoranalysis.plugin.operator.feature.bean.WithValueBase
descriptiveIdentifier() - Method in interface org.anchoranalysis.core.format.FileFormat: An identifier that describes the format, that is meaningful to the end-user.
descriptiveIdentifier() - Method in enum class org.anchoranalysis.core.format.ImageFileFormat
descriptiveIdentifier() - Method in enum class org.anchoranalysis.core.format.NonImageFileFormat
DescriptiveNameContainsImageLabeller - Class in org.anchoranalysis.plugin.image.task.bean.labeller: Labels images based on whether their descriptive name contains a specific string.
DescriptiveNameContainsImageLabeller() - Constructor for class org.anchoranalysis.plugin.image.task.bean.labeller.DescriptiveNameContainsImageLabeller
DeserializationFailedException - Exception Class in org.anchoranalysis.core.serialize: When a deserialization operation fails.
DeserializationFailedException(Exception) - Constructor for exception class org.anchoranalysis.core.serialize.DeserializationFailedException: Creates with a cause, but without a message.
DeserializationFailedException(String) - Constructor for exception class org.anchoranalysis.core.serialize.DeserializationFailedException: Creates with a message, but without a cause.
DeserializationFailedException(String, Throwable) - Constructor for exception class org.anchoranalysis.core.serialize.DeserializationFailedException: Creates with message and cause.
deserialize(Path, OperationContext) - Method in interface org.anchoranalysis.core.serialize.Deserializer: Deserializes a representation of an object stored on the filesystem.
deserialize(Path, OperationContext) - Method in class org.anchoranalysis.core.serialize.DictionaryDeserializer
deserialize(Path, OperationContext) - Method in class org.anchoranalysis.core.serialize.ObjectInputStreamDeserializer
deserialize(Path, OperationContext) - Method in class org.anchoranalysis.core.serialize.XStreamDeserializer
Deserializer<T> - Interface in org.anchoranalysis.core.serialize: Creates an object from a serialized representation on the file-system.
DestinationChannelForIndex - Interface in org.anchoranalysis.io.bioformats: Selects a destination-channel for the byte-copier, given an index
destinationPath(File, DirectoryWithPrefix, int, CopyContext<T>) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.CopyFilesNaming: Returns the output path (destination to to be copied to) for a given single file.
destinationPathRelative(File, DirectoryWithPrefix, int, CopyContext<NoSharedState>) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.CopyFilesNamingOne
destinationPathRelative(File, DirectoryWithPrefix, int, CopyContext<NoSharedState>) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.OutputPrefixWithExtension
destinationPathRelative(File, DirectoryWithPrefix, int, CopyContext<NoSharedState>) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.PreserveName
destinationPathRelative(File, DirectoryWithPrefix, int, CopyContext<ClusterMembership>) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster.ClusterByTimestamp
destinationPathRelative(File, DirectoryWithPrefix, int, CopyContext<AnonymizeSharedState>) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.Anonymize
destinationPathRelative(File, DirectoryWithPrefix, int, CopyContext<T>) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.CopyFilesNaming: Calculates the relative-output path (to be appended to destDir)
destinationPathRelative(Path) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.CopyFilesNamingOne
destinationPathRelative(Path) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.RegularExpressionBase
destinationPathRelative(Path) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.RemoveWhitespace
destinationPathRelative(Path, String) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.FilterWithRegularExpression
destinationPathRelative(Path, String) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.RegularExpressionBase
destinationPathRelative(Path, String) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.SubstituteRegularExpression
destinationSize - Variable in class org.anchoranalysis.io.bioformats.copyconvert.ConvertTo: The total number of elements (whatever the destination type is) in the destination buffer.
determineChannelNames(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.Default
determineChannelNames(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptions: A list of channel-names, if available.
determineChannelNames(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptionsDelegate
determineChannelNames(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.SwitchChannelTime
determineEnabledOutputs(RecordedOutputsWithRules) - Method in class org.anchoranalysis.io.output.bean.OutputManager: Determines which outputs are enabled or not.
determineInputType(Class<? extends FeatureInput>, Class<? extends FeatureInput>) - Static method in class org.anchoranalysis.feature.input.FeatureInputType: Finds a common input-type for two classes, throwing an exception if the two types aren't compatible.
determineInputType(List<Feature<T>>) - Static method in class org.anchoranalysis.feature.input.FeatureInputType: Finds a common input-type for classes in the list, throwing an exception if any two types aren't compatible.
determineOrientationCorrection(Metadata) - Static method in class org.anchoranalysis.io.bioformats.metadata.OrientationReader: Determines the needed correction to orientation for the voxels if an EXIF orientation tag is present.
determineOrientationCorrection(Path) - Static method in class org.anchoranalysis.io.bioformats.metadata.OrientationReader: Determines the needed correction to orientation for the voxels if an EXIF orientation tag is present.
Develop - Class in org.anchoranalysis.plugin.mpp.bean.define: Derives various types of outputs (images, histograms etc.) from MultiInputs.
Develop() - Constructor for class org.anchoranalysis.plugin.mpp.bean.define.Develop
dictionaries() - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitialization: Named-store of Dictionarys.
dictionary() - Method in class org.anchoranalysis.mpp.init.MarksInitialization: Gets the DictionaryInitialization associated with this MarksInitialization.
dictionary() - Method in class org.anchoranalysis.mpp.io.input.MultiInput: Gets the map of Dictionarys.
Dictionary - Class in org.anchoranalysis.core.value: Collection of parameters represented by key-value pairs.
Dictionary() - Constructor for class org.anchoranalysis.core.value.Dictionary: Creates empty, with no parameters.
DICTIONARY_IDENTIFIER - Static variable in class org.anchoranalysis.image.bean.nonbean.init.ImageInitialization: The name of the dictionary added by ImageInitialization.addSharedObjectsDictionary(java.util.Optional<org.anchoranalysis.core.identifier.provider.store.SharedObjects>, java.util.Optional<org.anchoranalysis.core.value.Dictionary>).
DictionaryBean<T> - Class in org.anchoranalysis.bean.shared.dictionary: Base class for beans that require initialization with DictionaryInitialization.
DictionaryBean() - Constructor for class org.anchoranalysis.bean.shared.dictionary.DictionaryBean
DictionaryCondition - Class in org.anchoranalysis.plugin.image.bean.dictionary: Checks if a value in a Dictionary is equal to an expected value.
DictionaryCondition() - Constructor for class org.anchoranalysis.plugin.image.bean.dictionary.DictionaryCondition
dictionaryDeriver() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy: Gets the dictionary deriver path if set.
DictionaryDeserializer<T> - Class in org.anchoranalysis.core.serialize: Deserializes a Dictionary from a file-system representation as a Java properties file.
DictionaryDeserializer() - Constructor for class org.anchoranalysis.core.serialize.DictionaryDeserializer
DictionaryForImageCreator - Class in org.anchoranalysis.mpp.feature.energy.scheme: Creates a Dictionary for a particular EnergyStack that is associated with an EnergyScheme.
DictionaryForImageCreator(EnergyScheme, SharedFeatures, Logger) - Constructor for class org.anchoranalysis.mpp.feature.energy.scheme.DictionaryForImageCreator: Creates a new DictionaryForImageCreator instance.
DictionaryGenerator - Class in org.anchoranalysis.io.generator.serialized: A generator that writes the contents of a Dictionary to the file-system as XML.
DictionaryGenerator() - Constructor for class org.anchoranalysis.io.generator.serialized.DictionaryGenerator
dictionaryInitialization() - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitialization: The associated initialization for a DictionaryBean.
DictionaryInitialization - Class in org.anchoranalysis.bean.shared.dictionary: Initialization parameters that provide a named-mapping to Dictionarys.
DictionaryInitialization(SharedObjects) - Constructor for class org.anchoranalysis.bean.shared.dictionary.DictionaryInitialization: Creates using a SharedObjects to create a NamedProviderStore for the dictionaries.
DictionaryProvider - Class in org.anchoranalysis.bean.shared.dictionary: Base class for beans that implement Provider to provide a Dictionary.
DictionaryProvider() - Constructor for class org.anchoranalysis.bean.shared.dictionary.DictionaryProvider
DictionaryProviderReference - Class in org.anchoranalysis.bean.shared.dictionary: References a particular Dictionary in shared-object-space.
DictionaryProviderReference() - Constructor for class org.anchoranalysis.bean.shared.dictionary.DictionaryProviderReference
Difference - Class in org.anchoranalysis.plugin.image.feature.bean.score
Difference() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.Difference
DifferenceCalculateLevelStandardDeviation - Class in org.anchoranalysis.plugin.image.feature.bean.score: Similar to Difference but calculates the width as the standard-deviation of the histogram
DifferenceCalculateLevelStandardDeviation() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.DifferenceCalculateLevelStandardDeviation
differenceFrom(Path, Path) - Static method in class org.anchoranalysis.core.system.path.PathDifference: Finds the difference between a path and a base.
diffModulo(int, int, int) - Static method in class org.anchoranalysis.test.image.ChannelFixture: Calculates intensity as the difference of coordinates modulo 256.
dilate(boolean, Optional<Extent>) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: Grow bounding-box by 1 pixel in all directions.
dilate(BinaryVoxels<UnsignedByteBuffer>, int, DilationContext) - Static method in class org.anchoranalysis.image.voxel.object.morphological.MorphologicalDilation: Performs a morphological dilation operation.
dilate(ObjectMask, Optional<Extent>, boolean, int, boolean) - Static method in class org.anchoranalysis.image.voxel.object.morphological.MorphologicalDilation: Dilates an ObjectMask, growing the bounding-box as necessary.
Dilate - Class in org.anchoranalysis.plugin.image.bean.mask.provider.morphological: Performs a dilation morphological operation on BinaryVoxels.
Dilate - Class in org.anchoranalysis.plugin.image.bean.object.provider.morphological: Dilates each object in the collection, growing bounding-boxes as necessary in relevant dimensions.
Dilate() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Dilate
Dilate() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Dilate
DilationContext - Class in org.anchoranalysis.image.voxel.kernel.morphological: Additional parameters for influencing a morphologicla dilation opperation.
DilationContext(OutsideKernelPolicy, boolean, boolean, Optional<Predicate<Point3i>>) - Constructor for class org.anchoranalysis.image.voxel.kernel.morphological.DilationContext: Create without a post-condition.
DilationContext(OutsideKernelPolicy, boolean, boolean, Optional<Predicate<Point3i>>, Optional<AcceptIterationPredicate>) - Constructor for class org.anchoranalysis.image.voxel.kernel.morphological.DilationContext: Create with a post-condition.
DilationKernel - Class in org.anchoranalysis.image.voxel.kernel.morphological: Morphological dilation with a 3x3 or 3x3x3 kernel size.
DilationKernel(boolean) - Constructor for class org.anchoranalysis.image.voxel.kernel.morphological.DilationKernel: Creates with a type of neighborhood.
dimensionIndexFor(Axis) - Static method in class org.anchoranalysis.spatial.axis.AxisConverter: A corresponding index representing for the dimension an Axis represents.
dimensions() - Method in class org.anchoranalysis.feature.energy.EnergyStack: The image-dimensions associated with the energy-stack.
dimensions() - Method in class org.anchoranalysis.feature.energy.EnergyStackWithoutParameters: The dimensions of all channels in the stack.
dimensions() - Method in class org.anchoranalysis.feature.input.FeatureInputDimensions: The dimensions of the associated image.
dimensions() - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy
dimensions() - Method in class org.anchoranalysis.image.core.channel.Channel: The size and voxel-resolution of the channel.
dimensions() - Method in class org.anchoranalysis.image.core.mask.Mask: The size and voxel-resolution of the channel.
dimensions() - Method in class org.anchoranalysis.image.core.stack.DisplayStack: The dimensions of all channels in the stack.
dimensions() - Method in class org.anchoranalysis.image.core.stack.RGBStack: The dimensions of all channels in the stack.
dimensions() - Method in class org.anchoranalysis.image.core.stack.Stack: The dimensions of all channels in the stack.
dimensions() - Method in class org.anchoranalysis.image.feature.input.FeatureInputImageMetadata
dimensions() - Method in class org.anchoranalysis.image.io.object.output.grayscale.ObjectsAsGrayscaleGenerator: The dimensions associated with the objects (assumed to be constant across any change in element).
dimensions() - Method in class org.anchoranalysis.mpp.feature.bean.mark.collection.FeatureInputMarkCollection: Gets the optional dimensions associated with the mark collection.
dimensions() - Method in class org.anchoranalysis.mpp.proposer.ProposerContext: Gets the dimensions of the energy stack.
dimensions(int, Logger) - Method in class org.anchoranalysis.image.io.channel.input.NamedChannelsInput: Dimensions of a particular series.
dimensions(Logger) - Method in class org.anchoranalysis.image.io.channel.map.NamedChannelsConcatenate
dimensions(Logger) - Method in interface org.anchoranalysis.image.io.channel.map.NamedChannelsMap: The dimensions of each Channel.
dimensions(Logger) - Method in class org.anchoranalysis.image.io.channel.map.OpenedNamedChannels
dimensions(Dimensions) - Method in enum class org.anchoranalysis.image.core.dimensions.OrientationChange: A Dimensions that describes {code dimensions} after the orientation change.
Dimensions - Class in org.anchoranalysis.image.core.dimensions: The size of an image (in voxels), together with the image resolution.
Dimensions(int, int, int) - Constructor for class org.anchoranalysis.image.core.dimensions.Dimensions: Construct with an explicit extent and no resolution.
Dimensions(Extent) - Constructor for class org.anchoranalysis.image.core.dimensions.Dimensions: Construct with an explicit extent and no resolution.
Dimensions(Extent, Optional<Resolution>) - Constructor for class org.anchoranalysis.image.core.dimensions.Dimensions: Creates a new Dimensions instance.
Dimensions(ReadableTuple3i) - Constructor for class org.anchoranalysis.image.core.dimensions.Dimensions: Construct with an explicit extent and no resolution.
DimensionsChecker - Class in org.anchoranalysis.plugin.image.channel: Utility class for checking and ensuring consistency of dimensions across channels and masks.
DimensionsCreator - Class in org.anchoranalysis.io.bioformats: Infers Dimensions for a particular image-file.
DimensionsCreator(IMetadata) - Constructor for class org.anchoranalysis.io.bioformats.DimensionsCreator
dimensionsForSeries(int, Logger) - Method in interface org.anchoranalysis.image.io.stack.input.OpenedImageFile: The Dimensions associated with a particular series.
dimensionsForSeries(int, Logger) - Method in class org.anchoranalysis.plugin.io.multifile.OpenedMultiFile
dimensionsOptional() - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy: The image-dimensions associated with the energy-stack, if it exists.
DimensionsProvider - Class in org.anchoranalysis.image.bean.provider: Base class for beans that implement Provider to provide Dimensions.
DimensionsProvider() - Constructor for class org.anchoranalysis.image.bean.provider.DimensionsProvider
dimensionsRequired() - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy: The image-dimensions associated with the energy-stack, or an exception if no energy-stack exists.
DirectionVector - Class in org.anchoranalysis.spatial.orientation: A vector indicating a direction in space.
DirectionVector() - Constructor for class org.anchoranalysis.spatial.orientation.DirectionVector: Creates with each dimension's value set to 0.
DirectionVector(double, double, double) - Constructor for class org.anchoranalysis.spatial.orientation.DirectionVector: Creates for a particular value in each dimension.
DirectionVector(Axis) - Constructor for class org.anchoranalysis.spatial.orientation.DirectionVector: Creates a direction aligned to a particular axis.
DirectionVector(Tuple3d) - Constructor for class org.anchoranalysis.spatial.orientation.DirectionVector: Creates reusing Tuple3d internally for the dimension's values.
DirectionVectorBean - Class in org.anchoranalysis.image.bean.spatial.direction: A bean that creates a DirectionVector.
DirectionVectorBean() - Constructor for class org.anchoranalysis.image.bean.spatial.direction.DirectionVectorBean
directory - Variable in class org.anchoranalysis.test.image.stackwriter.StackWriterTestBase: A temporary directory created for each test method.
directory() - Method in class org.anchoranalysis.io.input.InputsWithDirectory: The directory associated with the inputs.
DirectoryCreationParameters - Class in org.anchoranalysis.io.output.outputter: Options that influence how an output directory is created.
DirectoryCreationParameters() - Constructor for class org.anchoranalysis.io.output.outputter.DirectoryCreationParameters: Creates to not delete directories, and with no consumer called upon directory creation.
DirectoryCreationParameters(boolean, Optional<Consumer<Path>>) - Constructor for class org.anchoranalysis.io.output.outputter.DirectoryCreationParameters: Creates a new DirectoryCreationParameters instance.
DirectoryCreator - Class in org.anchoranalysis.core.system.path: Creates necessary directories on a file-system to make a path valid.
DirectoryDepth - Class in org.anchoranalysis.plugin.io.bean.input.files.provider: Lists all directories to a certain depth
DirectoryDepth() - Constructor for class org.anchoranalysis.plugin.io.bean.input.files.provider.DirectoryDepth
DirectoryStructure - Class in org.anchoranalysis.plugin.io.bean.file.path.prefixer: Reuses the directories between a path and its root to form the output - and also the filename.
DirectoryStructure() - Constructor for class org.anchoranalysis.plugin.io.bean.file.path.prefixer.DirectoryStructure
DirectoryWithPrefix - Class in org.anchoranalysis.io.output.path.prefixer: A directory into which files can be written, and a prefix for the name of each written file.
DirectoryWithPrefix(Path) - Constructor for class org.anchoranalysis.io.output.path.prefixer.DirectoryWithPrefix: Creates for a directory, with no prefix.
DirectoryWithPrefix(Path, String, String) - Constructor for class org.anchoranalysis.io.output.path.prefixer.DirectoryWithPrefix: Creates a new DirectoryWithPrefix instance.
disableAdditionalOutputs(MultiLevelOutputEnabled) - Method in class org.anchoranalysis.io.output.recorded.OutputEnabledDelta: Assigns additional outputs to disable.
disableGPUs() - Method in class org.anchoranalysis.inference.concurrency.ConcurrencyPlan: Derive a ConcurrencyPlan that preserves the number of CPUs but disables all GPUs.
DiscardOutliers - Class in org.anchoranalysis.plugin.image.bean.object.filter.collective: Calculates features values for all objects, and discards any object less than quantile - (minRatio * stdDev)
DiscardOutliers() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.collective.DiscardOutliers
DisplayStack - Class in org.anchoranalysis.image.core.stack: Stack that contains 1 or 3 channels so that we and display it as either grayscale or as an RGB unsigned 8-bit image, respectively.
DisplayStack(Stack) - Constructor for class org.anchoranalysis.image.core.stack.DisplayStack: Create for a particular Stack where all channels are already guaranteed to be unsigned-bit.
DisplayStack(Stack, boolean, Function<VoxelDataType, ChannelConverterAttached<Channel, UnsignedByteBuffer>>) - Constructor for class org.anchoranalysis.image.core.stack.DisplayStack: Create for a particular Stack that may needed to be converted.
DisplayStackGenerator - Class in org.anchoranalysis.image.io.stack.output.generator: Writes a display-stack to the filesystem.
DisplayStackGenerator(boolean) - Constructor for class org.anchoranalysis.image.io.stack.output.generator.DisplayStackGenerator: Creates the generator.
distance(BoundingBox, BoundingBox, boolean) - Static method in class org.anchoranalysis.spatial.box.BoundingBoxDistance: Calculates the distance between two BoundingBoxes.
distance(Point2d) - Method in class org.anchoranalysis.spatial.point.Point2d: The square of the Euclidean distance between this point and another Point2d.
distance(Point3d) - Method in class org.anchoranalysis.spatial.point.Point3d: The Euclidean distance between this point and another Point3d.
distance(Point3f) - Method in class org.anchoranalysis.spatial.point.Point3f: The Euclidean distance between this point and another.
distance(Point3i) - Method in class org.anchoranalysis.spatial.point.Point3i: The Euclidean distance between this point and another.
DistanceCondition - Class in org.anchoranalysis.plugin.image.object.merge.condition: A BeforeCondition that checks if two ObjectMasks are within a specified maximum distance.
DistanceCondition(Optional<UnitValueDistance>, boolean, MessageLogger) - Constructor for class org.anchoranalysis.plugin.image.object.merge.condition.DistanceCondition: Creates a new DistanceCondition instance.
distanceMax(Point3i) - Method in class org.anchoranalysis.spatial.point.Point3i: The maximum distance across any individual axis to another point.
DistancePhysical - Class in org.anchoranalysis.image.bean.unitvalue.distance: Implementation of UnitValueDistance that specifies a value in physical units, as described by particular recognized strings.
DistancePhysical() - Constructor for class org.anchoranalysis.image.bean.unitvalue.distance.DistancePhysical
distanceSquared(Point2d) - Method in class org.anchoranalysis.spatial.point.Point2d: The square of the Euclidean distance between this point and another Point2d.
distanceSquared(Point3d) - Method in class org.anchoranalysis.spatial.point.Point3d: The square of the Euclidean distance between this point and another Point3d.
distanceSquared(Point3d) - Method in class org.anchoranalysis.spatial.point.Point3i: The square of the Euclidean distance between this point and another Point3d.
distanceSquared(Point3f) - Method in class org.anchoranalysis.spatial.point.Point3f: The square of the Euclidean distance between this point and another.
distanceSquared(Point3i) - Method in class org.anchoranalysis.spatial.point.Point3d: The square of the Euclidean distance between this point and another Point3i.
distanceSquared(Point3i) - Method in class org.anchoranalysis.spatial.point.Point3i: The square of the Euclidean distance between this point and another Point3i.
distanceSquaredTo(Point3i) - Method in class org.anchoranalysis.plugin.image.intensity.level.LevelResult: Calculates the squared distance from the midpoint of this level's object to a given point.
DistanceTransform3D - Class in org.anchoranalysis.plugin.fiji.bean.channel.provider.distance: Euclidian Distance Transform from ImageJ that works on 2D as well as 3D z-stacks.
DistanceTransform3D() - Constructor for class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D
DistanceTransformForEachObject3D - Class in org.anchoranalysis.plugin.fiji.bean.channel.provider.distance: Like DistanceTransform3D but applies the distance transform separately for each object in a collection.
DistanceTransformForEachObject3D() - Constructor for class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransformForEachObject3D
DistanceVoxels - Class in org.anchoranalysis.image.bean.unitvalue.distance: Implementation of UnitValueDistance that specifies a value in voxels, ignoring any physical image resolution.
DistanceVoxels() - Constructor for class org.anchoranalysis.image.bean.unitvalue.distance.DistanceVoxels
DistanceVoxels(double) - Constructor for class org.anchoranalysis.image.bean.unitvalue.distance.DistanceVoxels: Create with a particular value.
Divide<T> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic: A feature that divides the results of multiple features sequentially.
Divide() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.Divide
divideBy(double) - Method in class org.anchoranalysis.spatial.point.Tuple3d: Arithmetically divide values across each dimension.
divideBy(int) - Method in interface org.anchoranalysis.image.voxel.arithmetic.VoxelsArithmetic: Divides the value of all voxels by a scalar constant.
divideBy(int) - Method in class org.anchoranalysis.spatial.point.Tuple3d: Arithmetically divide values across each dimension.
divideBy(int) - Method in class org.anchoranalysis.spatial.point.Tuple3i: Arithmetically divide by a value across each dimension.
DivideByConstant<T> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic: A feature that divides the result of another feature by a constant value.
DivideByConstant() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.DivideByConstant
divideByZeroReplace(double, double, double) - Static method in class org.anchoranalysis.math.arithmetic.DoubleUtilities: Replaces a value with a constant if the denominator is 0.
Divider - Class in org.anchoranalysis.core.log: Creates a line of text that span a certain width with a repeated character, optionally containing a label.
Divider() - Constructor for class org.anchoranalysis.core.log.Divider: A banner using dashes.
Divider(char) - Constructor for class org.anchoranalysis.core.log.Divider: A banner using a particular repeated character.
Divider(char, int) - Constructor for class org.anchoranalysis.core.log.Divider: A banner using a particular repeated character.
Divider(int) - Constructor for class org.anchoranalysis.core.log.Divider: A banner using dashes, with a particular number of characters.
divideVoxelsByCount(Voxels<FloatBuffer>) - Method in class org.anchoranalysis.image.voxel.projection.CountedProjectableBuffer: Divides all voxel values by the count of added voxels.
DO_NOT_CHANGE_EXISTING - Enum constant in enum class org.anchoranalysis.image.core.channel.convert.ConversionPolicy: Do not change the existing channel, rather make a new channel.
doDuplicate(PointListBase) - Method in class org.anchoranalysis.mpp.mark.points.PointListBase: Duplicates this PointListBase into a new instance.
doesClassInheritFromAny(Class<? extends InputFromManager>) - Method in class org.anchoranalysis.experiment.task.InputTypesExpected: Does the child-class inherit from any one of expected input-types?
doesNeighborQualify(boolean, KernelPointCursor, Supplier<UnsignedByteBuffer>, int) - Method in class org.anchoranalysis.image.voxel.kernel.morphological.BinaryKernelMorphological: Does a particular neighboring-point satisfy the conditions.
doesNeighborQualify(boolean, KernelPointCursor, Supplier<UnsignedByteBuffer>, int) - Method in class org.anchoranalysis.image.voxel.kernel.morphological.DilationKernel
doesNeighborQualify(boolean, KernelPointCursor, Supplier<UnsignedByteBuffer>, int) - Method in class org.anchoranalysis.image.voxel.kernel.morphological.ErosionKernel: Checks whether a particular neighbor voxel qualifies to make the current voxel an outline voxel.
doesNeighborQualify(boolean, KernelPointCursor, Supplier<UnsignedByteBuffer>, int) - Method in class org.anchoranalysis.image.voxel.kernel.outline.OutlineKernel: Checks whether a particular neighbor voxel qualifies to make the current voxel an outline voxel.
doesNeighborQualify(boolean, KernelPointCursor, Supplier<UnsignedByteBuffer>, int) - Method in class org.anchoranalysis.image.voxel.kernel.outline.OutlineKernelNeighborMatchValue: Checks whether a particular neighbor voxel qualifies to make the current voxel an outline voxel.
doesNeighborVoxelQualify(Point3i) - Method in class org.anchoranalysis.image.voxel.kernel.count.CountKernel: Whether a particular neighboring voxel is accepted or not.
doesNeighborVoxelQualify(Point3i) - Method in class org.anchoranalysis.image.voxel.kernel.count.CountKernelNeighborhood
doesNeighborVoxelQualify(Point3i) - Method in class org.anchoranalysis.image.voxel.kernel.count.CountKernelNeighborhoodMask
doesPathExist(String) - Method in class org.anchoranalysis.test.image.io.TestLoaderImage: Checks if a test path exists.
doesPathExist(String) - Method in class org.anchoranalysis.test.TestLoader: Does a resource exist with a particular folderPath + fileName.
doesPathExist(String, String) - Method in class org.anchoranalysis.test.TestLoader: Does a resource exist with a particular folderPath + fileName.
doJobOnInput(InputBound<AnnotationWithStrategy<S>, AggregateSharedState>) - Method in class org.anchoranalysis.plugin.annotation.bean.aggregate.AggregateAnnotations
doJobOnInput(InputBound<NamedChannelsInput, SharedStateSelectedSlice>) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice
doJobOnInput(InputBound<NamedChannelsInput, S>) - Method in class org.anchoranalysis.plugin.image.task.bean.RasterTask
doJobOnInput(InputBound<ProvidesStackInput, GroupedSharedState<S, T>>) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase
doJobOnInput(InputBound<ProvidesStackInput, SharedStateFilteredImageOutput<T>>) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageAssignLabel
doJobOnInput(InputBound<StackSequenceInput, SharedStateSegmentInstance<T>>) - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel
doJobOnInput(InputBound<StackSequenceInput, MontageSharedState>) - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage
doJobOnInput(InputBound<StackSequenceInput, S>) - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage
doJobOnInput(InputBound<FileInput, CSVWriter>) - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
doJobOnInput(InputBound<FileWithDirectoryInput, RecordingCounter<T>>) - Method in class org.anchoranalysis.plugin.io.bean.task.CopyFiles
doJobOnInput(InputBound<MultiInput, NoSharedState>) - Method in class org.anchoranalysis.plugin.mpp.bean.define.Develop
doJobOnInput(InputBound<AnnotationComparisonInput<ProvidesStackInput>, ComparisonSharedState<T>>) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
doJobOnInput(InputBound<S, NoSharedState>) - Method in class org.anchoranalysis.launcher.run.tasks.HelloWorld
doJobOnInput(InputBound<T, FeatureExporter<S>>) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures
doJobOnInput(InputBound<T, Summarizer<S>>) - Method in class org.anchoranalysis.plugin.io.bean.task.SummarizeBase
doJobOnInput(InputBound<T, SharedStateRememberConverted<U, S>>) - Method in class org.anchoranalysis.plugin.mpp.bean.convert.ConvertNamedChannels
doJobOnInput(InputBound<T, S>) - Method in class org.anchoranalysis.experiment.bean.task.Task: Performs the task on a particular input.
doStack(InputBound<NamedChannelsInput, NoSharedState>, OutputSequenceIndexed<Stack, String>, int, int, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat
doStack(InputBound<NamedChannelsInput, S>, U, int, int, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.RasterTask: Processes one stack from a series.
dotProduct(Tuple3d) - Method in class org.anchoranalysis.spatial.point.Tuple3d: Computes the dot-product of the tuple with another.
double3DFromFloat(Point2f) - Static method in class org.anchoranalysis.spatial.point.PointConverter: Convert a Point2f to a Point3d.
DoubleBiPredicate - Interface in org.anchoranalysis.math.relation: Like BiPredicate but operates on doubles.
doubleFromFloat(Point2f) - Static method in class org.anchoranalysis.spatial.point.PointConverter: Convert a Point2f to a Point2d.
doubleFromFloat(Point3f) - Static method in class org.anchoranalysis.spatial.point.PointConverter: Convert a Point3f to a Point3d.
doubleFromInt(Point2i) - Static method in class org.anchoranalysis.spatial.point.PointConverter: Convert a Point2i to a Point3d using 0 as the value of the Z-axis component.
doubleFromInt(ReadableTuple3i) - Static method in class org.anchoranalysis.spatial.point.PointConverter: Convert a ReadableTuple3i to a Point3d.
DoubleList - Class in org.anchoranalysis.bean.primitive: A bean defining a list of Doubles.
DoubleList(Double...) - Constructor for class org.anchoranalysis.bean.primitive.DoubleList: Constructs with one or more values added to the list.
DoubleListFactory - Class in org.anchoranalysis.bean.xml.factory.primitive: Creates a DoubleList from a XML element.
DoubleListFactory() - Constructor for class org.anchoranalysis.bean.xml.factory.primitive.DoubleListFactory
DoubleSet - Class in org.anchoranalysis.bean.primitive: A bean defining a set of Doubles.
DoubleSet() - Constructor for class org.anchoranalysis.bean.primitive.DoubleSet
DoubleSet(Double...) - Constructor for class org.anchoranalysis.bean.primitive.DoubleSet: Constructs with one or more values added to the set.
DoubleSetFactory - Class in org.anchoranalysis.bean.xml.factory.primitive: Creates a DoubleSet from a XML element.
DoubleSetFactory() - Constructor for class org.anchoranalysis.bean.xml.factory.primitive.DoubleSetFactory
DoubleUtilities - Class in org.anchoranalysis.math.arithmetic: Utilities for arithmetic operations involving type double.
drawAllLabels(double, BoxAligner) - Method in class org.anchoranalysis.plugin.image.task.slice.MontageSharedState: Draw all labels that have been queued during calls to MontageSharedState.copyStackInto(org.anchoranalysis.core.functional.checked.CheckedSupplier<org.anchoranalysis.image.core.stack.RGBStack, org.anchoranalysis.io.input.InputReadFailedException>, java.lang.String, java.nio.file.Path, java.util.Optional<java.lang.String>).
drawCollection(ObjectCollectionWithProperties, RGBStack, ObjectDrawAttributes) - Method in class org.anchoranalysis.overlay.bean.DrawObject: Writes object-masks onto of a RGBStack - across all of the stack.
drawCollection(ObjectCollectionWithProperties, RGBStack, ObjectDrawAttributes, BoundingBox) - Method in class org.anchoranalysis.overlay.bean.DrawObject: Writes object-masks onto of a RGBStack - within a bounding box only.
DrawColoredObjects - Class in org.anchoranalysis.annotation.io.assignment.generator: Outlines or completely fills in each ObjectMask with a color.
DrawColoredObjects(DisplayStack, boolean, int) - Constructor for class org.anchoranalysis.annotation.io.assignment.generator.DrawColoredObjects: Creates a new DrawColoredObjects instance.
DrawCroppedObjectsGenerator - Class in org.anchoranalysis.image.io.object.output.rgb: Similar to DrawObjectsGenerator, but with the background stack cropped to focus only on the region containing objects.
DrawCroppedObjectsGenerator(DrawObject, DisplayStack, Padding, ColorIndex) - Constructor for class org.anchoranalysis.image.io.object.output.rgb.DrawCroppedObjectsGenerator: Create with a particular background and method for drawing-objects.
DrawLineAlongConvexHull - Class in org.anchoranalysis.plugin.imagej.bean.object.provider: Draws a lines between successive points on the convex-hull of an object.
DrawLineAlongConvexHull() - Constructor for class org.anchoranalysis.plugin.imagej.bean.object.provider.DrawLineAlongConvexHull
DrawObject - Class in org.anchoranalysis.overlay.bean: Draws a representation of an ObjectMask on a RGBStack.
DrawObject() - Constructor for class org.anchoranalysis.overlay.bean.DrawObject
DrawObjectOnStackGenerator - Class in org.anchoranalysis.image.io.stack.output.box: Creates images of object(s) drawn on a background only in a local region around their bounding box.
DrawObjectsGenerator - Class in org.anchoranalysis.image.io.object.output.rgb: Generates stacks of RGB images using a DrawObject to draw objects on a background.
DrawOverlay - Class in org.anchoranalysis.overlay.writer: Draws an ovleray onto a RGBStack
DrawOverlay(DrawObject) - Constructor for class org.anchoranalysis.overlay.writer.DrawOverlay: Creates a new DrawOverlay instance.
drawOverlays(ColoredOverlayCollection, RGBStack, IdentifierGetter<Overlay>) - Method in class org.anchoranalysis.overlay.writer.DrawOverlay: Draw a collection of colored-overlays on top of a RGBStack.
drawSingle(ObjectWithProperties, RGBStack, ObjectDrawAttributes, int, BoundingBox) - Method in class org.anchoranalysis.image.io.bean.object.draw.Filled
drawSingle(ObjectWithProperties, RGBStack, ObjectDrawAttributes, int, BoundingBox) - Method in class org.anchoranalysis.image.io.bean.object.draw.Flatten
drawSingle(ObjectWithProperties, RGBStack, ObjectDrawAttributes, int, BoundingBox) - Method in class org.anchoranalysis.image.io.bean.object.draw.IfElse
drawSingle(ObjectWithProperties, RGBStack, ObjectDrawAttributes, int, BoundingBox) - Method in class org.anchoranalysis.image.io.bean.object.draw.Outline
drawSingle(ObjectWithProperties, RGBStack, ObjectDrawAttributes, int, BoundingBox) - Method in class org.anchoranalysis.overlay.bean.DrawObject: Draws a single-object on top of a RGB-stack.
drawText(String, BufferedImage, Extent) - Method in class org.anchoranalysis.image.io.bean.stack.combine.TextStyle: Draws text on a BufferedImage.
dropKey() - Method in exception class org.anchoranalysis.feature.calculate.NamedFeatureCalculateException: Removes any feature-name from the exception.
dropZ() - Method in class org.anchoranalysis.spatial.point.Point3d: Creates a new point with identical x and y values, but with z set to 0.
DualComparer - Class in org.anchoranalysis.test.image: Allows for comparison of objects that exist on different test loaders
DualComparer(TestLoader, TestLoader) - Constructor for class org.anchoranalysis.test.image.DualComparer: Creates a new DualComparer instance.
DualComparerFactory - Class in org.anchoranalysis.test.image: Factory for creating DualComparer instances to compare directories.
DualMarks - Interface in org.anchoranalysis.annotation.mark: Two mark-collections, one considered accepted and the other rejected.
DualMarksAnnotation<T> - Class in org.anchoranalysis.annotation.mark: An annotation that consists of two sets of marks, accepted and rejected.
DualMarksAnnotation() - Constructor for class org.anchoranalysis.annotation.mark.DualMarksAnnotation
DualMarksAnnotationDeleter - Class in org.anchoranalysis.annotation.io.mark: Deletes DualMarksAnnotations from the file-system.
DualMarksAnnotationDeleter() - Constructor for class org.anchoranalysis.annotation.io.mark.DualMarksAnnotationDeleter
DualMarksAnnotationWriter<T> - Class in org.anchoranalysis.annotation.io.mark: Writes DualMarksAnnotations to the file-system.
DualMarksAnnotationWriter() - Constructor for class org.anchoranalysis.annotation.io.mark.DualMarksAnnotationWriter
DualMarksAnnotationWriter(boolean) - Constructor for class org.anchoranalysis.annotation.io.mark.DualMarksAnnotationWriter: Creates a new DualMarksAnnotationWriter instance.
DualPathPredicates - Class in org.anchoranalysis.io.input.path.matcher: A Predicate<Path for both a file and a directory.
DualPathPredicates(CheckedPredicate<Path, IOException>, CheckedPredicate<Path, IOException>) - Constructor for class org.anchoranalysis.io.input.path.matcher.DualPathPredicates: Creates a new DualPathPredicates instance.
DualScale<T> - Class in org.anchoranalysis.image.inference.segment: Stores two versions of the same object, representing two different scales.
DualScale(T, T) - Constructor for class org.anchoranalysis.image.inference.segment.DualScale: Creates a new DualScale instance.
duplicate() - Method in class org.anchoranalysis.core.color.RGBColor: Creates a deep-copy of the current object.
duplicate() - Method in class org.anchoranalysis.core.value.Dictionary: Deep-copy of existing dictionary.
duplicate() - Method in class org.anchoranalysis.feature.shared.SharedFeatures: A deep copy of the current instance.
duplicate() - Method in class org.anchoranalysis.feature.store.NamedFeatureStore: Deep-copies the store, including duplicating each feature.
duplicate() - Method in class org.anchoranalysis.image.core.channel.Channel: A deep-copy.
duplicate() - Method in class org.anchoranalysis.image.core.mask.Mask: Deep-copies the object.
duplicate() - Method in class org.anchoranalysis.image.core.object.properties.ObjectWithProperties: Deep copies the current instance.
duplicate() - Method in class org.anchoranalysis.image.core.stack.RGBStack: A deep copy.
duplicate() - Method in class org.anchoranalysis.image.core.stack.StackNotUniformSized: A deep-copy.
duplicate() - Method in class org.anchoranalysis.image.feature.calculator.merged.MergedPairsFeatures: Creates a duplicate of this MergedPairsFeatures instance.
duplicate() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels: Deep-copy of the object, including duplicating voxel buffers in memory.
duplicate() - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: A deep-copy of the current structure.
duplicate() - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer: Creates a deep copy of the current object, including deep-copying the associated buffer.
duplicate() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection: Deep copy, including duplicating ObjectMasks.
duplicate() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Creates a deep-copy of the current object-mask.
duplicate() - Method in class org.anchoranalysis.image.voxel.Voxels: A deep-copy.
duplicate() - Method in class org.anchoranalysis.io.output.namestyle.IndexableOutputNameStyle
duplicate() - Method in class org.anchoranalysis.io.output.namestyle.IntegerSuffixOutputNameStyle
duplicate() - Method in class org.anchoranalysis.io.output.namestyle.OutputNameStyle: Deep copy the current object.
duplicate() - Method in class org.anchoranalysis.io.output.namestyle.SimpleOutputNameStyle
duplicate() - Method in class org.anchoranalysis.io.output.namestyle.StringSuffixOutputNameStyle
duplicate() - Method in class org.anchoranalysis.io.output.namestyle.WithoutOutputNameStyle
duplicate() - Method in class org.anchoranalysis.math.arithmetic.RunningSum: Deep-copy.
duplicate() - Method in class org.anchoranalysis.math.histogram.Histogram: Creates a deep-copy of the current object.
duplicate() - Method in class org.anchoranalysis.math.statistics.moment.EigenvalueAndVector: Creates a deep-copy of the current object.
duplicate() - Method in class org.anchoranalysis.math.statistics.moment.ImageMoments: Creates a deep-copy of the current object.
duplicate() - Method in class org.anchoranalysis.mpp.bean.bound.Bound: Creates a duplicate of this bound.
duplicate() - Method in class org.anchoranalysis.mpp.bean.bound.BoundDegrees
duplicate() - Method in class org.anchoranalysis.mpp.bean.bound.BoundPhysicalExtent
duplicate() - Method in class org.anchoranalysis.mpp.bean.bound.BoundUnitless
duplicate() - Method in class org.anchoranalysis.mpp.mark.conic.Circle
duplicate() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
duplicate() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
duplicate() - Method in class org.anchoranalysis.mpp.mark.conic.Sphere
duplicate() - Method in class org.anchoranalysis.mpp.mark.Mark: Creates a duplicate of this mark.
duplicate() - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
duplicate() - Method in class org.anchoranalysis.mpp.mark.points.PointList
duplicate() - Method in class org.anchoranalysis.mpp.mark.points.Polygon
duplicate() - Method in class org.anchoranalysis.mpp.mark.points.PolygonCurve
duplicate() - Method in class org.anchoranalysis.mpp.mark.points.RotatableBoundingBox
duplicate() - Method in interface org.anchoranalysis.mpp.mark.voxelized.VoxelizedMark: Creates a duplicate of this voxelized mark.
duplicate() - Method in class org.anchoranalysis.spatial.orientation.RotationMatrix: Deep-copy of the current rotation-matrix.
Duplicate - Class in org.anchoranalysis.plugin.image.bean.channel.provider: Creates a duplicate of the input channel.
Duplicate - Class in org.anchoranalysis.plugin.image.bean.mask.provider: A provider that creates a duplicate of a given Mask.
Duplicate - Class in org.anchoranalysis.plugin.image.bean.object.provider: Duplicates (deep copy) an object-collection.
Duplicate() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.Duplicate
Duplicate() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.Duplicate
Duplicate() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.Duplicate
duplicateBean() - Method in class org.anchoranalysis.bean.AnchorBean: Creates a new bean that deep-copies every property value.
duplicateBean() - Method in class org.anchoranalysis.bean.define.Define
duplicateBean() - Method in class org.anchoranalysis.bean.primitive.DoubleList: Duplicate the bean.
duplicateBean() - Method in class org.anchoranalysis.bean.primitive.DoubleSet: Duplicate the bean.
duplicateBean() - Method in class org.anchoranalysis.bean.primitive.IntegerList: Duplicate the bean.
duplicateBean() - Method in class org.anchoranalysis.bean.primitive.IntegerSet: Duplicate the bean.
duplicateBean() - Method in class org.anchoranalysis.bean.primitive.StringList: Duplicate the bean.
duplicateBean() - Method in class org.anchoranalysis.bean.primitive.StringSet: Duplicate the bean.
duplicateBean() - Method in class org.anchoranalysis.bean.shared.color.RGBColorBean
duplicateBean() - Method in class org.anchoranalysis.image.bean.spatial.arrange.align.Align
duplicateChangeExtent(Extent) - Method in class org.anchoranalysis.image.core.dimensions.Dimensions: Deep-copies the current object, but assigns a different Extent.
duplicateChangeName(String) - Method in class org.anchoranalysis.feature.bean.Feature: Duplicates the feature as per AnchorBean.duplicateBean() but sets a particular custom-name.
duplicateChangeResolution(Optional<Resolution>) - Method in class org.anchoranalysis.image.core.dimensions.Dimensions: Deep-copies the current object, but assigns a different Resolution.
duplicateChangeX(int) - Method in class org.anchoranalysis.spatial.box.Extent: Creates a copy of the current Extent with the value for the X-dimension changed.
duplicateChangeY(int) - Method in class org.anchoranalysis.spatial.box.Extent: Creates a copy of the current Extent with the value for the Y-dimension changed.
duplicateChangeZ(int) - Method in class org.anchoranalysis.image.core.dimensions.Dimensions: Deep-copies the current object, but assigns a different size for the Z-dimension.
duplicateChangeZ(int) - Method in class org.anchoranalysis.spatial.box.Extent: Creates a copy of the current Extent with the value for the Z-dimension changed.
duplicateChangeZ(int) - Method in class org.anchoranalysis.spatial.point.Point3i
duplicateChangeZ(int) - Method in interface org.anchoranalysis.spatial.point.ReadableTuple3i: Creates a copy of the current tuple, but with a different Z-component value.
duplicateDeep() - Method in class org.anchoranalysis.image.core.stack.Stack: Performs a deep copy of the stack, so that all channels are duplicated.
duplicateForNewThread() - Method in interface org.anchoranalysis.image.feature.calculator.FeatureTableCalculator: Makes a copy of the feature-store for a new thread.
duplicateForNewThread() - Method in class org.anchoranalysis.image.feature.calculator.merged.PairsTableCalculator
duplicateForNewThread() - Method in class org.anchoranalysis.image.feature.calculator.SingleTableCalculator
duplicateFresh() - Method in class org.anchoranalysis.mpp.mark.voxelized.memo.VoxelizedMarkMemo: Duplicates the current mark memo, resetting the calculation state.
duplicateShallow() - Method in class org.anchoranalysis.feature.initialization.FeatureInitialization: A shallow-copy of the current initialization.
duplicateShallow() - Method in class org.anchoranalysis.feature.name.FeatureNameList: Shallow copy of the current instance.
duplicateShallow() - Method in class org.anchoranalysis.image.core.stack.Stack: Performs a shallow copy of the stack, so that all channels are reused.
duplicateShallow() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection: Shallow copy of objects.

E

EachObjectIndependently - Class in org.anchoranalysis.plugin.image.feature.bean.object.combine: Selects features and objects directly from the input list, treating each object independently.
EachObjectIndependently() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.combine.EachObjectIndependently
EachObjectIndependently(Interpolator) - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.combine.EachObjectIndependently: Create with a specific interpolator.
EagerEvaluationStore<T> - Class in org.anchoranalysis.core.identifier.provider.store: Evaluates items immediately via the StoreSupplier as soon as they are added.
EagerEvaluationStore() - Constructor for class org.anchoranalysis.core.identifier.provider.store.EagerEvaluationStore
EdgeFilterIJ - Class in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter: Applies an edge detection filter to each slice of a Channel independently using ImageJ's FIND_EDGES filter.
EdgeFilterIJ() - Constructor for class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.EdgeFilterIJ
edgesMaybeDuplicates() - Method in class org.anchoranalysis.core.graph.GraphWithPayload: The edges in the graph, all of them, but with some edges possibly duplicated.
edgesUnique() - Method in class org.anchoranalysis.core.graph.GraphWithPayload: The edges in the graph, all of them, without any duplicates.
effectiveBitsPerPixel(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.Default
effectiveBitsPerPixel(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptions: The number of bits used per pixel.
effectiveBitsPerPixel(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptionsDelegate
EigenvalueAndVector - Class in org.anchoranalysis.math.statistics.moment: An eigenvalue and its corresponding eigenvector.
EigenvalueAndVector(double, DoubleMatrix1D) - Constructor for class org.anchoranalysis.math.statistics.moment.EigenvalueAndVector: Creates a new EigenvalueAndVector instance.
ElementOutputter - Class in org.anchoranalysis.io.output.writer: Outputs an element to the file-system.
ElementOutputter(OutputterChecked, ExecutionTimeRecorder, Supplier<Optional<Logger>>) - Constructor for class org.anchoranalysis.io.output.writer.ElementOutputter: Creates a new ElementOutputter instance.
ElementSupplier<T> - Interface in org.anchoranalysis.io.output.writer: Creates or gets a element to output files together with a ElementWriter.
elementwiseOperation(ReadableTuple3i, ReadableTuple3i, IntBinaryOperator) - Static method in class org.anchoranalysis.spatial.point.Point3i: Creates a new point by applying a pairwise operation to each dimension's values for two tuples.
ElementWriter<T> - Interface in org.anchoranalysis.io.output.writer: Writes an element (with or without an index) to the file system.
ElementWriterSupplier<T> - Interface in org.anchoranalysis.io.output.writer: Creates or gets a element-writer to output files.
Ellipse - Class in org.anchoranalysis.mpp.mark.conic: Represents a 2D ellipse mark.
Ellipse() - Constructor for class org.anchoranalysis.mpp.mark.conic.Ellipse: Creates a new Ellipse with default values.
Ellipse(Ellipse) - Constructor for class org.anchoranalysis.mpp.mark.conic.Ellipse: Creates a new Ellipse by copying an existing one.
EllipseStandardFormConverter - Class in org.anchoranalysis.plugin.points.bean.fitter: Extracts forms for 'standard form' representation of an ellipse from the coefficients for a 2nd order polynomial describing the ellipse.
EllipseStandardFormConverter(DoubleMatrix1D) - Constructor for class org.anchoranalysis.plugin.points.bean.fitter.EllipseStandardFormConverter: Creates a new EllipseStandardFormConverter and performs the conversion.
Ellipsoid - Class in org.anchoranalysis.mpp.mark.conic: Represents a 3D ellipsoid mark with multiple sub-regions.
Ellipsoid() - Constructor for class org.anchoranalysis.mpp.mark.conic.Ellipsoid: Creates a new Ellipsoid with default values.
Ellipsoid(Ellipsoid) - Constructor for class org.anchoranalysis.mpp.mark.conic.Ellipsoid: Creates a new Ellipsoid by copying an existing one.
EllipsoidBase - Class in org.anchoranalysis.plugin.points.bean.feature: Base class for features that calculate properties of an Ellipsoid fitted to an object.
EllipsoidBase() - Constructor for class org.anchoranalysis.plugin.points.bean.feature.EllipsoidBase
EllipsoidFactory - Class in org.anchoranalysis.plugin.points.calculate.ellipsoid: Factory for creating Ellipsoid objects using least-squares fitting.
EllipsoidFitHelper - Class in org.anchoranalysis.plugin.points.bean.fitter: Helper class for fitting ellipsoids to point data.
Ellipsoidicity - Class in org.anchoranalysis.plugin.points.bean.feature: Calculates the ellipsoidicity of an object by fitting an Ellipsoid to it.
Ellipsoidicity() - Constructor for class org.anchoranalysis.plugin.points.bean.feature.Ellipsoidicity
EllipsoidUtilities - Class in org.anchoranalysis.mpp.mark.conic: Utility class for operations related to Ellipsoid marks.
Ellipticity - Class in org.anchoranalysis.plugin.points.bean.feature: Calculates the ellipticity of an ObjectMask (on the center of gravity slice if it's a z-stack).
Ellipticity() - Constructor for class org.anchoranalysis.plugin.points.bean.feature.Ellipticity
empty() - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory: Creates an empty list of features
empty() - Static method in class org.anchoranalysis.image.voxel.object.ObjectCollectionFactory: Creates a newly created object-collection that is empty.
Empty - Class in org.anchoranalysis.plugin.image.bean.object.provider: Creates an empty object-collection.
Empty() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.Empty
emptyFirstComparator() - Static method in class org.anchoranalysis.core.functional.OptionalComparator: Creates a Comparator for elements of type T where empty-values are first.
EmptyHistogramConstant - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold: Specifies a constant if a histogram is empty, otherwise delegates to another {#link org.anchoranalysis.image.bean.threshold.CalculateLevel}
EmptyHistogramConstant() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.EmptyHistogramConstant
emptyLastComparator() - Static method in class org.anchoranalysis.core.functional.OptionalComparator: Creates a Comparator for elements of type T where empty-values are last.
enableAdditionalOutputs(MultiLevelOutputEnabled) - Method in class org.anchoranalysis.io.output.recorded.OutputEnabledDelta: Assigns additional outputs to enable.
encodeConnectedComponentID(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.WatershedEncoding: Encodes a connected component ID.
EncodedIntBuffer - Class in org.anchoranalysis.plugin.image.segment.watershed.encoding: A wrapper around UnsignedIntBuffer that provides methods for encoding and decoding watershed-related information.
EncodedIntBuffer(UnsignedIntBuffer, WatershedEncoding) - Constructor for class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedIntBuffer
encodeDirection(int, int, int) - Method in interface org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodeDirection: Encodes a 3D direction into an integer representation.
encodeDirection(int, int, int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.WatershedEncoding: Encodes a 3D direction into an integer representation.
EncodeDirection - Interface in org.anchoranalysis.plugin.image.segment.watershed.encoding: An interface for encoding a 3D direction into an integer representation.
EncodedVoxels - Class in org.anchoranalysis.plugin.image.segment.watershed.encoding: Represents voxels encoded with watershed-related information.
EncodedVoxels(Voxels<UnsignedIntBuffer>) - Constructor for class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels: Creates a new EncodedVoxels instance.
ENCODING - Static variable in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels: The encoding used for the direction-vectors.
end() - Method in class org.anchoranalysis.feature.io.csv.results.LabelledResultsCSVWriter: Stops writing the CSV file.
end() - Method in class org.anchoranalysis.io.generator.text.TextFileOutput: This should be called once after writing all content with TextFileOutput.getWriter()
end() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.collective.DiscardOutliers
end() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.collective.RelationWithMatches
end() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.GreaterIntersectionWith
end() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntensityGreaterEqualThan
end() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntersectsWith
end() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.NotTouchingSceneBorder
end() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedFeature
end() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterPredicate: Performs any necessary cleanup after filtering is complete.
end() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterRelation
endSeries(NoSharedState, OutputSequenceIndexed<Stack, String>, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat
endSeries(S, U, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.RasterTask: Ends processing of a series.
ENERGY_STACK - Static variable in class org.anchoranalysis.image.io.stack.StackIdentifiers: The channels selected as inputs to an optimization routine or for feature calculation.
EnergyMemoList - Class in org.anchoranalysis.mpp.feature.mark: A collection of memoized marks on which energies can be derived.
EnergyMemoList() - Constructor for class org.anchoranalysis.mpp.feature.mark.EnergyMemoList: Creates an empty energy memo list.
EnergyMemoList(EnergySavedIndividual, EnergyStackWithoutParameters, MarkCollection, EnergySchemeWithSharedFeatures) - Constructor for class org.anchoranalysis.mpp.feature.mark.EnergyMemoList: Creates an energy memo list with the given parameters.
EnergyMemoList(EnergyMemoList) - Constructor for class org.anchoranalysis.mpp.feature.mark.EnergyMemoList: Creates a copy of an existing energy memo list.
EnergyPair - Class in org.anchoranalysis.mpp.feature.energy: Represents a pair of Marks with their associated total energy.
EnergyPair(MarkPair, EnergyTotal) - Constructor for class org.anchoranalysis.mpp.feature.energy.EnergyPair: Creates a new EnergyPair instance.
EnergySavedAll - Class in org.anchoranalysis.mpp.feature.energy.saved: Saves and manages the total energy for all items in a collection.
EnergySavedAll() - Constructor for class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedAll
EnergySavedIndividual - Class in org.anchoranalysis.mpp.feature.energy.saved: Stores and manages individual energy values for a collection of marks.
EnergySavedIndividual() - Constructor for class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedIndividual
EnergySavedPairs - Class in org.anchoranalysis.mpp.feature.energy.saved: Stores and manages pairwise energy interactions between marks.
EnergySavedPairs(AddCriteria<EnergyPair>) - Constructor for class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedPairs: Creates a new instance with the specified add criteria for energy pairs.
EnergyScheme - Class in org.anchoranalysis.mpp.feature.energy.scheme: The energy for a feature-list as factorized into different cliques.
EnergyScheme(FeatureList<FeatureInputSingleMemo>, FeatureList<FeatureInputPairMemo>, FeatureList<FeatureInputAllMemo>, RegionMap, AddCriteriaPair) - Constructor for class org.anchoranalysis.mpp.feature.energy.scheme.EnergyScheme: Creates an energy scheme with the specified features and region map.
EnergyScheme(FeatureList<FeatureInputSingleMemo>, FeatureList<FeatureInputPairMemo>, FeatureList<FeatureInputAllMemo>, RegionMap, AddCriteriaPair, Optional<DictionaryProvider>, List<NamedBean<Feature<FeatureInputStack>>>) - Constructor for class org.anchoranalysis.mpp.feature.energy.scheme.EnergyScheme: Creates an energy scheme with the specified features, region map, and additional options.
EnergySchemeCreator - Class in org.anchoranalysis.mpp.feature.bean.energy.scheme: An abstract class for creating EnergyScheme instances.
EnergySchemeCreator() - Constructor for class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreator
EnergySchemeCreatorByElement - Class in org.anchoranalysis.mpp.feature.bean.energy.scheme: Creates an EnergyScheme by combining individual elements and their interactions.
EnergySchemeCreatorByElement() - Constructor for class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement
EnergySchemeSet - Class in org.anchoranalysis.mpp.feature.energy.scheme: A set of EnergySchemes, each associated with a unique name.
EnergySchemeSet(SharedFeatures) - Constructor for class org.anchoranalysis.mpp.feature.energy.scheme.EnergySchemeSet: Creates a new EnergySchemeSet instance.
EnergySchemeWithSharedFeatures - Class in org.anchoranalysis.mpp.feature.energy.scheme: Combines an EnergyScheme with SharedFeatures for energy calculations.
EnergySchemeWithSharedFeatures(EnergyScheme, SharedFeatures, Logger) - Constructor for class org.anchoranalysis.mpp.feature.energy.scheme.EnergySchemeWithSharedFeatures: Creates a new EnergySchemeWithSharedFeatures.
energyStack() - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureEvaluator: The specified energy stack.
energyStack() - Static method in class org.anchoranalysis.test.feature.plugins.objects.CircleObjectFixture: Creates an EnergyStack with the fixture's dimensions.
EnergyStack - Class in org.anchoranalysis.feature.energy: A EnergyStackWithoutParameters with associated parameters in a Dictionary.
EnergyStack(EnergyStackWithoutParameters) - Constructor for class org.anchoranalysis.feature.energy.EnergyStack: Create from a EnergyStackWithoutParameters without any additional parameters.
EnergyStack(EnergyStackWithoutParameters, Dictionary) - Constructor for class org.anchoranalysis.feature.energy.EnergyStack: Creates a new EnergyStack instance.
EnergyStack(Channel) - Constructor for class org.anchoranalysis.feature.energy.EnergyStack: Create from a single Channel.
EnergyStack(Dimensions) - Constructor for class org.anchoranalysis.feature.energy.EnergyStack: Create a new stack of Dimensions with zero-voxel values, without any additional parameters.
EnergyStack(Stack) - Constructor for class org.anchoranalysis.feature.energy.EnergyStack: Create from a EnergyStack without any additional parameters.
EnergyStack(Stack, Dictionary) - Constructor for class org.anchoranalysis.feature.energy.EnergyStack: Create from a Stack with associated parameters in a Dictionary.
EnergyStackFixture - Class in org.anchoranalysis.test.image: A fixture for creating EnergyStack objects for testing purposes.
EnergyStackWithoutParameters - Class in org.anchoranalysis.feature.energy: A stack of channels used as context to calculate features (or calculating energy more broadly).
EnergyStackWithoutParameters(Channel) - Constructor for class org.anchoranalysis.feature.energy.EnergyStackWithoutParameters: Create a energy-stack comprised of a single channel
EnergyStackWithoutParameters(Dimensions) - Constructor for class org.anchoranalysis.feature.energy.EnergyStackWithoutParameters: Create a energy-stack with no channels - but with associated dimensions.
EnergyStackWithoutParameters(Stack) - Constructor for class org.anchoranalysis.feature.energy.EnergyStackWithoutParameters: Create a energy-stack comprised of all channels from a stack
EnergyStackWriter - Class in org.anchoranalysis.mpp.io.output: Writes an energy-stack to the file-system.
EnergyStackWriter(EnergyStack, Outputter) - Constructor for class org.anchoranalysis.mpp.io.output.EnergyStackWriter: Creates a new EnergyStackWriter instance.
EnergyTotal - Class in org.anchoranalysis.mpp.feature.energy: Represents the total energy of a system, which can be modified and queried.
EnergyTotal() - Constructor for class org.anchoranalysis.mpp.feature.energy.EnergyTotal
EnergyTotal(double) - Constructor for class org.anchoranalysis.mpp.feature.energy.EnergyTotal: Creates a new EnergyTotal instance.
ensureImageMetadataReader() - Static method in class org.anchoranalysis.test.image.io.BeanInstanceMapFixture: Ensure a ImageMetadataReader instance exists in the underlying BeanInstanceMap.
ensureInterpolator() - Static method in class org.anchoranalysis.test.image.io.BeanInstanceMapFixture: Ensure a default Interpolator instance exists in the underlying BeanInstanceMap.
ensureInterpolator(Interpolator) - Static method in class org.anchoranalysis.test.image.io.BeanInstanceMapFixture: Ensure a specific Interpolator instance exists in the underlying BeanInstanceMap.
ensureStackDisplayer() - Static method in class org.anchoranalysis.test.image.io.BeanInstanceMapFixture: Ensure a StackDisplayer instance exists in the underlying BeanInstanceMap.
ensureStackReader() - Static method in class org.anchoranalysis.test.image.io.BeanInstanceMapFixture: Ensure a StackReader instance exists in the underlying BeanInstanceMap.
ensureStackWriter(boolean) - Static method in class org.anchoranalysis.test.image.io.BeanInstanceMapFixture: Ensure a StackWriter instance exists in the underlying BeanInstanceMap.
entrySet() - Method in class org.anchoranalysis.core.collection.MapCreate: The entries in the map.
entrySet() - Method in class org.anchoranalysis.plugin.image.task.labeller.FileLabelMap: Gets the entry set of the internal map.
equalMask(BoundingBox, int) - Method in class org.anchoranalysis.image.core.channel.Channel: Creates a ObjectMask representing all the voxels in box equal to equalValue.
equals(Object) - Method in class org.anchoranalysis.annotation.image.ImageLabelAnnotation
equals(Object) - Method in class org.anchoranalysis.annotation.io.assignment.CostMatrix
equals(Object) - Method in class org.anchoranalysis.annotation.io.image.findable.Found
equals(Object) - Method in class org.anchoranalysis.annotation.io.image.findable.NotFound
equals(Object) - Method in interface org.anchoranalysis.bean.GenerateUniqueParameterization
equals(Object) - Method in class org.anchoranalysis.bean.primitive.DoubleList
equals(Object) - Method in class org.anchoranalysis.bean.primitive.DoubleSet
equals(Object) - Method in class org.anchoranalysis.bean.primitive.IntegerList
equals(Object) - Method in class org.anchoranalysis.bean.primitive.IntegerSet
equals(Object) - Method in class org.anchoranalysis.bean.primitive.StringList
equals(Object) - Method in class org.anchoranalysis.bean.primitive.StringSet
equals(Object) - Method in class org.anchoranalysis.bean.shared.path.RootPath
equals(Object) - Method in class org.anchoranalysis.bean.shared.relation.EqualToBean
equals(Object) - Method in class org.anchoranalysis.bean.shared.relation.GreaterThanBean
equals(Object) - Method in class org.anchoranalysis.bean.shared.relation.GreaterThanEqualToBean
equals(Object) - Method in class org.anchoranalysis.bean.shared.relation.LessThanBean
equals(Object) - Method in class org.anchoranalysis.bean.shared.relation.LessThanEqualToBean
equals(Object) - Method in class org.anchoranalysis.bean.shared.relation.RelationBean
equals(Object) - Method in class org.anchoranalysis.bean.shared.relation.threshold.RelationToConstant
equals(Object) - Method in class org.anchoranalysis.core.color.RGBColor
equals(Object) - Method in class org.anchoranalysis.core.graph.TypedEdge
equals(Object) - Method in class org.anchoranalysis.core.index.Indexable
equals(Object) - Method in class org.anchoranalysis.core.index.range.IndexRangeNegative
equals(Object) - Method in class org.anchoranalysis.core.log.CommonContext
equals(Object) - Method in class org.anchoranalysis.core.system.path.FilenameSplitExtension
equals(Object) - Method in class org.anchoranalysis.core.system.path.SplitPath
equals(Object) - Method in class org.anchoranalysis.core.time.OperationContext
equals(Object) - Method in class org.anchoranalysis.core.value.TypedValue
equals(Object) - Method in class org.anchoranalysis.experiment.task.ParametersUnbound
equals(Object) - Method in class org.anchoranalysis.experiment.task.processor.JobDescription
equals(Object) - Method in class org.anchoranalysis.experiment.task.processor.SubmittedJob
equals(Object) - Method in class org.anchoranalysis.experiment.time.RunningSumParented
equals(Object) - Method in class org.anchoranalysis.feature.calculate.cache.ChildCacheName
equals(Object) - Method in class org.anchoranalysis.feature.calculate.cache.part.ResolvedPart
equals(Object) - Method in class org.anchoranalysis.feature.calculate.cache.part.ResolvedPartMap
equals(Object) - Method in class org.anchoranalysis.feature.calculate.part.CalculationPart
equals(Object) - Method in class org.anchoranalysis.feature.calculate.part.CalculationPartMap
equals(Object) - Method in class org.anchoranalysis.feature.initialization.FeatureInitialization
equals(Object) - Method in class org.anchoranalysis.feature.input.FeatureInputDimensions
equals(Object) - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy
equals(Object) - Method in class org.anchoranalysis.feature.input.FeatureInputNull
equals(Object) - Method in class org.anchoranalysis.feature.input.FeatureInputResults
equals(Object) - Method in class org.anchoranalysis.feature.io.csv.metadata.FeatureCSVMetadata
equals(Object) - Method in class org.anchoranalysis.feature.io.name.CombinedName
equals(Object) - Method in interface org.anchoranalysis.feature.io.name.MultiName: If another name is equal to the current name.
equals(Object) - Method in class org.anchoranalysis.feature.io.name.SimpleName
equals(Object) - Method in class org.anchoranalysis.feature.io.results.LabelledResultsVector
equals(Object) - Method in class org.anchoranalysis.feature.results.ResultsVector
equals(Object) - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.StackArrangement
equals(Object) - Method in class org.anchoranalysis.image.bean.spatial.arrange.fill.ExtentToArrange: To correspond to ExtentToArrange.compareTo(ExtentToArrange).
equals(Object) - Method in class org.anchoranalysis.image.bean.spatial.SizeXY
equals(Object) - Method in class org.anchoranalysis.image.bean.threshold.CalculateLevel
equals(Object) - Method in class org.anchoranalysis.image.bean.threshold.CalculateLevelUnary
equals(Object) - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryNotOffVoxels
equals(Object) - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryNotOnVoxels
equals(Object) - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryOffVoxels
equals(Object) - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryOnVoxels
equals(Object) - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryVoxelsBase
equals(Object) - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
equals(Object) - Method in class org.anchoranalysis.image.core.dimensions.Resolution
equals(Object) - Method in class org.anchoranalysis.image.core.mask.Mask
equals(Object) - Method in class org.anchoranalysis.image.core.object.label.OverlappingObject
equals(Object) - Method in class org.anchoranalysis.image.core.object.MatchedObject
equals(Object) - Method in class org.anchoranalysis.image.core.object.properties.ObjectWithProperties
equals(Object) - Method in class org.anchoranalysis.image.core.stack.ImagePyramidMetadata
equals(Object) - Method in class org.anchoranalysis.image.core.stack.Stack
equals(Object) - Method in class org.anchoranalysis.image.feature.calculation.CalculateInputFromPair
equals(Object) - Method in class org.anchoranalysis.image.feature.calculation.CalculateNumberVoxels
equals(Object) - Method in class org.anchoranalysis.image.feature.calculator.NamedFeatureCalculatorMulti
equals(Object) - Method in class org.anchoranalysis.image.feature.input.FeatureInputImageMetadata
equals(Object) - Method in class org.anchoranalysis.image.feature.input.FeatureInputObjectCollection
equals(Object) - Method in class org.anchoranalysis.image.feature.input.FeatureInputPairObjects
equals(Object) - Method in class org.anchoranalysis.image.feature.input.FeatureInputSingleObject
equals(Object) - Method in class org.anchoranalysis.image.feature.input.FeatureInputStack
equals(Object) - Method in class org.anchoranalysis.image.inference.bean.reduce.ObjectForReduction
equals(Object) - Method in class org.anchoranalysis.image.inference.ImageInferenceContext
equals(Object) - Method in class org.anchoranalysis.image.inference.segment.LabelledWithConfidence
equals(Object) - Method in class org.anchoranalysis.image.inference.segment.WithConfidence
equals(Object) - Method in class org.anchoranalysis.image.io.stack.input.ImageTimestampsAttributes
equals(Object) - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte
equals(Object) - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValuesInt
equals(Object) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer
equals(Object) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBufferAsInt
equals(Object) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
equals(Object) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer
equals(Object) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
equals(Object) - Method in class org.anchoranalysis.image.voxel.datatype.VoxelDataType
equals(Object) - Method in class org.anchoranalysis.image.voxel.iterator.MinMaxRange
equals(Object) - Method in class org.anchoranalysis.image.voxel.kernel.KernelApplicationParameters
equals(Object) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection: Checks if two collections are equal in a shallow way.
equals(Object) - Method in class org.anchoranalysis.inference.concurrency.ConcurrentModel
equals(Object) - Method in class org.anchoranalysis.inference.concurrency.WithPriority
equals(Object) - Method in class org.anchoranalysis.io.bioformats.copyconvert.ImageFileEncoding
equals(Object) - Method in class org.anchoranalysis.io.bioformats.copyconvert.ImageFileShape
equals(Object) - Method in class org.anchoranalysis.io.generator.combined.OptionalNameValue
equals(Object) - Method in class org.anchoranalysis.io.generator.sequence.BoundOutputter
equals(Object) - Method in class org.anchoranalysis.io.input.file.FileNamerContext
equals(Object) - Method in class org.anchoranalysis.io.input.file.NamedFile
equals(Object) - Method in class org.anchoranalysis.io.input.InputsWithDirectory
equals(Object) - Method in class org.anchoranalysis.io.input.path.GlobExtractor.GlobWithDirectory
equals(Object) - Method in class org.anchoranalysis.io.output.outputter.directory.OutputterTarget
equals(Object) - Method in class org.anchoranalysis.io.output.outputter.DirectoryCreationParameters
equals(Object) - Method in class org.anchoranalysis.io.output.outputter.Outputter
equals(Object) - Method in class org.anchoranalysis.io.output.path.prefixer.NamedPath
equals(Object) - Method in class org.anchoranalysis.launcher.config.HelpConfig
equals(Object) - Method in class org.anchoranalysis.math.equation.QuadraticEquationSolver.QuadraticRoots
equals(Object) - Method in class org.anchoranalysis.math.statistics.MeanScale
equals(Object) - Method in class org.anchoranalysis.math.statistics.moment.EigenvalueAndVector
equals(Object) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMap
equals(Object) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
equals(Object) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipWithFlags
equals(Object) - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.CalculateDeriveSingleMemoFromPair
equals(Object) - Method in class org.anchoranalysis.mpp.feature.bean.mark.FeatureInputMark
equals(Object) - Method in class org.anchoranalysis.mpp.feature.energy.EnergyPair
equals(Object) - Method in class org.anchoranalysis.mpp.feature.energy.IndexableMarksWithEnergy
equals(Object) - Method in class org.anchoranalysis.mpp.feature.input.FeatureInputAllMemo
equals(Object) - Method in class org.anchoranalysis.mpp.feature.input.FeatureInputPairMemo
equals(Object) - Method in class org.anchoranalysis.mpp.feature.input.FeatureInputSingleMemo
equals(Object) - Method in class org.anchoranalysis.mpp.feature.mark.MemoList
equals(Object) - Method in class org.anchoranalysis.mpp.overlay.OverlayMark
equals(Object) - Method in class org.anchoranalysis.mpp.pair.MarkPair
equals(Object) - Method in class org.anchoranalysis.mpp.pair.PairVoxelizedMarkMemo
equals(Object) - Method in class org.anchoranalysis.mpp.proposer.ProposerContext
equals(Object) - Method in class org.anchoranalysis.overlay.object.OverlayObjectMask
equals(Object) - Method in class org.anchoranalysis.overlay.Overlay
equals(Object) - Method in class org.anchoranalysis.overlay.writer.ObjectDrawAttributes
equals(Object) - Method in class org.anchoranalysis.plugin.annotation.comparison.ObjectsToCompare
equals(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelListBase
equals(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelRelativeToThreshold
equals(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.ClampHistogramMax
equals(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Constant
equals(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.EmptyHistogramConstant
equals(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.IfGreaterThan
equals(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.IfLessThan
equals(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Maximum
equals(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Minimum
equals(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Otsu
equals(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.OtsuWeighted
equals(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Quantile
equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations
equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.CalculateIntersecting
equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.CalculateDeriveObjectInput
equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegate
equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegateOption
equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateIncrementalOperationMap
equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateObjectMask
equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateShellObjectMask
equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateDilation
equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateDilationMap
equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateErosion
equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateErosionMap
equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.stack.calculation.CalculateHistogram
equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.stack.calculation.CalculateHistogramMasked
equals(Object) - Method in class org.anchoranalysis.plugin.image.object.ColoredObject
equals(Object) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ChangeableOutputSequence
equals(Object) - Method in class org.anchoranalysis.plugin.image.task.feature.FeatureExporterContext
equals(Object) - Method in class org.anchoranalysis.plugin.image.task.feature.InitializationWithEnergyStack
equals(Object) - Method in class org.anchoranalysis.plugin.image.task.feature.LabelledResultsVectorWithThumbnail
equals(Object) - Method in class org.anchoranalysis.plugin.image.task.feature.ResultsVectorWithThumbnail
equals(Object) - Method in class org.anchoranalysis.plugin.image.task.grouped.NamedChannel
equals(Object) - Method in class org.anchoranalysis.plugin.image.task.labeller.ImageCSVLabellerInitialization
equals(Object) - Method in class org.anchoranalysis.plugin.image.task.labeller.ImageLabellerStringMapInitialization
equals(Object) - Method in class org.anchoranalysis.plugin.io.input.path.CopyContext
equals(Object) - Method in class org.anchoranalysis.plugin.io.multifile.FileDetails
equals(Object) - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetChannel
equals(Object) - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetSlice
equals(Object) - Method in class org.anchoranalysis.plugin.io.shared.AnonymizeSharedState
equals(Object) - Method in class org.anchoranalysis.plugin.mpp.shared.ConvertedInput
equals(Object) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters
equals(Object) - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult
equals(Object) - Method in class org.anchoranalysis.plugin.points.calculate.ellipse.CalculateEllipseLeastSquares
equals(Object) - Method in class org.anchoranalysis.plugin.points.calculate.ellipse.ObjectWithEllipse
equals(Object) - Method in class org.anchoranalysis.plugin.points.calculate.ellipsoid.CalculateEllipsoidLeastSquares
equals(Object) - Method in class org.anchoranalysis.spatial.box.BoundingBox
equals(Object) - Method in class org.anchoranalysis.spatial.box.Extent
equals(Object) - Method in class org.anchoranalysis.spatial.orientation.Orientation
equals(Object) - Method in class org.anchoranalysis.spatial.orientation.Orientation2D
equals(Object) - Method in class org.anchoranalysis.spatial.orientation.Orientation3DEulerAngles
equals(Object) - Method in class org.anchoranalysis.spatial.orientation.OrientationAxisAngle
equals(Object) - Method in class org.anchoranalysis.spatial.orientation.OrientationRotationMatrix
equals(Object) - Method in class org.anchoranalysis.spatial.point.Point2d
equals(Object) - Method in class org.anchoranalysis.spatial.point.Point2f
equals(Object) - Method in class org.anchoranalysis.spatial.point.Point2i
equals(Object) - Method in class org.anchoranalysis.spatial.point.Point3d
equals(Object) - Method in class org.anchoranalysis.spatial.point.Point3f
equals(Object) - Method in class org.anchoranalysis.spatial.point.Point3i
equals(Object) - Method in class org.anchoranalysis.spatial.point.Tuple3d
equals(Object) - Method in class org.anchoranalysis.spatial.point.Tuple3f
equals(Object) - Method in class org.anchoranalysis.spatial.point.Tuple3i
equals(Object) - Method in class org.anchoranalysis.spatial.point.Vector3d
equals(Object) - Method in class org.anchoranalysis.spatial.scale.ScaleFactor
equals(Object) - Method in class org.anchoranalysis.test.image.rasterwriter.comparison.ComparisonPlan
equals(Object) - Method in class org.anchoranalysis.test.image.stackwriter.ChannelSpecification
equals(Object...) - Method in class org.anchoranalysis.feature.results.ResultsVector: Does the instance have exactly these values?
equals(Dimensions, boolean) - Method in class org.anchoranalysis.image.core.dimensions.Dimensions: Checks equality between this object and another Dimensions, but possibly skipping a comparison of image-resolution in the check.
equalsDeep(Channel, boolean) - Method in class org.anchoranalysis.image.core.channel.Channel: Are the two channels equal using a deep voxel by voxel comparison?
equalsDeep(Stack, boolean) - Method in class org.anchoranalysis.image.core.stack.Stack: Are the two stack equal using a deep voxel by voxel comparison of each channel?
equalsDeep(BoundedVoxels<?>) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: Performs a deep equality check, that includes checking that each voxel has an identical value.
equalsDeep(ObjectCollection) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection: Checks if two collections are equal in a deeper way.
equalsDeep(ObjectMask) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: A deep equality check with another ObjectMask.
equalsDeep(Voxels<?>) - Method in class org.anchoranalysis.image.voxel.Voxels: Are the voxels identical to another voxels (deep equals)?
equalsDeep(Mark) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
equalsDeep(Mark) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
equalsDeep(Mark) - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
equalsDeep(Mark) - Method in class org.anchoranalysis.mpp.mark.Mark: Checks if this mark is deeply equal to another mark.
equalsDeep(Mark) - Method in class org.anchoranalysis.mpp.mark.MarkWithPosition: Checks if this mark is equal to another mark by comparing all attributes.
equalsDeep(Mark) - Method in class org.anchoranalysis.mpp.mark.points.PointListBase
equalsDeep(MarkCollection) - Method in class org.anchoranalysis.mpp.mark.MarkCollection: Checks if this collection is deeply equal to another.
equalsID(Object) - Method in class org.anchoranalysis.mpp.mark.Mark: Checks if this mark has the same ID as another object.
equalsIgnoreZ(Extent) - Method in class org.anchoranalysis.spatial.box.Extent: Checks for equality with another extent ignoring any differences in the Z dimension.
equalsPrecision(double, Object...) - Method in class org.anchoranalysis.feature.results.ResultsVector: Like ResultsVector.equals(Object) but includes a tolerance for checking equality of the doubles.
equalsTolerance(Point3d, double) - Method in class org.anchoranalysis.spatial.point.Point3d: Checks if this point is equal to another Point3d accepting a tolerance between double values.
EqualTo - Class in org.anchoranalysis.math.relation: Returns true if two values are equal, and false otherwise.
EqualTo() - Constructor for class org.anchoranalysis.math.relation.EqualTo
EqualToBean - Class in org.anchoranalysis.bean.shared.relation: A relation double1 == double2.
EqualToBean() - Constructor for class org.anchoranalysis.bean.shared.relation.EqualToBean
equalToPrimitive(Voxels<UnsignedByteBuffer>, byte, ScalarThreeDimensionalConsumer) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsEqualTo: Iterates through all points with a specific voxel intensity-value, passing coordinates as primitive types.
equalToPrimitiveSlice(Voxels<UnsignedByteBuffer>, int, byte, ScalarThreeDimensionalConsumer) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsEqualTo: Like IterateVoxelsEqualTo.equalToPrimitive(org.anchoranalysis.image.voxel.Voxels<org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer>, byte, org.anchoranalysis.spatial.point.consumer.ScalarThreeDimensionalConsumer) but only iterates over one specific z-slice.
equalToReusePoint(Voxels<UnsignedByteBuffer>, byte, Consumer<Point3i>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsEqualTo: Iterates all points with a specific voxel intensity-value, reusing the Point3i in each iteration.
erode(BinaryVoxels<UnsignedByteBuffer>, int, boolean, Optional<Predicate<Point3i>>) - Static method in class org.anchoranalysis.image.voxel.object.morphological.MorphologicalErosion: Performs a morphological erosion on a BinaryVoxels<UnsignedByteBuffer> voxels.
erode(ObjectMask, int, boolean) - Static method in class org.anchoranalysis.image.voxel.object.morphological.MorphologicalErosion: Performs a morphological erosion on an ObjectMask.
erode(ObjectMask, int, boolean, Optional<AcceptIterationPredicate>) - Static method in class org.anchoranalysis.image.voxel.object.morphological.MorphologicalErosion: Performs a morphological erosion on an ObjectMask - with a postcondition.
Erode - Class in org.anchoranalysis.plugin.image.bean.mask.provider.morphological: Performs an erosion morphological operation on BinaryVoxels.
Erode - Class in org.anchoranalysis.plugin.image.bean.object.provider.morphological: Erodes each object in the collection, growing bounding-boxes as necessary in relevant dimensions.
Erode - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.morphological: A feature that erodes an object mask and then calculates another feature on the eroded object.
Erode() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Erode
Erode() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Erode
Erode() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.Erode
ErosionKernel - Class in org.anchoranalysis.image.voxel.kernel.morphological: Erosion with a 3x3 or 3x3x3 kernel size.
ErosionKernel() - Constructor for class org.anchoranalysis.image.voxel.kernel.morphological.ErosionKernel: Default constructor.
errorMessageIfTooFewPixels() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.ImageMomentsBase: Generates an error message when there are too few pixels to calculate moments.
errorMessageIfTooFewPixels() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.PrincipalAxisEccentricity
errorMessageIfTooFewPixels() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.PrincipalAxisLength
errorMessageIfTooFewPixels() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.PrincipalAxisOrientation
errorMessageIfTooFewPixels() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.RatioPrincipalAxisLength
ErrorNode - Class in org.anchoranalysis.mpp.proposer.error: An abstract class representing a node in an error tree structure.
ErrorNode() - Constructor for class org.anchoranalysis.mpp.proposer.error.ErrorNode
ErrorNodeException - Exception Class in org.anchoranalysis.mpp.proposer.error: An exception that adds a string to the current error node.
ErrorNodeException(Exception) - Constructor for exception class org.anchoranalysis.mpp.proposer.error.ErrorNodeException: Constructs a new ErrorNodeException from another exception.
ErrorNodeException(String) - Constructor for exception class org.anchoranalysis.mpp.proposer.error.ErrorNodeException: Constructs a new ErrorNodeException with the specified error message.
ErrorNodeNull - Class in org.anchoranalysis.mpp.proposer.error: A singleton implementation of ErrorNode that does nothing with errors.
errorReporter() - Method in class org.anchoranalysis.core.log.Logger: Where errors are reported to.
ErrorReporter - Interface in org.anchoranalysis.core.log.error: Reports errors as they occur.
ErrorReporterBase - Class in org.anchoranalysis.core.log.error: Utility base class for common error-reporting formatting.
ErrorReporterBase(Consumer<String>) - Constructor for class org.anchoranalysis.core.log.error.ErrorReporterBase: Creates a new ErrorReporterBase instance.
ErrorReporterForTask - Class in org.anchoranalysis.experiment.task: An error-reporter that replaces particular errors/exceptions with user-friendly messages.
ErrorReporterForTask(MessageLogger) - Constructor for class org.anchoranalysis.experiment.task.ErrorReporterForTask: Create to use a particular logger to report errors.
ErrorReporterIntoLog - Class in org.anchoranalysis.core.log.error: Records errors, by writing them into a logger.
ErrorReporterIntoLog(MessageLogger) - Constructor for class org.anchoranalysis.core.log.error.ErrorReporterIntoLog: Create for a message-logger.
ErrorReporterIntoString - Class in org.anchoranalysis.core.log.error: Logs error messages into a String via StringBuilder.
ErrorReporterIntoString(StringBuilder) - Constructor for class org.anchoranalysis.core.log.error.ErrorReporterIntoString: Creates for a particular StringBuilder.
EXCEPTED_DOUBLE_EXTENSIONS - Static variable in class org.anchoranalysis.core.system.path.ExtensionUtilities: Particular extensions with a double period, that are exceptionally checked for, and treated as a single extension.
exchange(int, EnergyTotal) - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedIndividual: Exchanges an energy total at a specific index with a new one and updates the total energy.
exchange(int, Mark) - Method in class org.anchoranalysis.mpp.mark.MarkCollection: Replaces the mark at a specific index.
exchange(int, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown: Exchanges a mark at a specific index with a new mark.
exchange(int, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy: Exchanges a mark at a particular index with a new mark.
exchange(EnergySavedIndividual, int, VoxelizedMarkMemo, EnergyStackWithoutParameters, EnergySchemeWithSharedFeatures) - Method in class org.anchoranalysis.mpp.feature.mark.EnergyMemoList: Exchanges a mark at a specific index with a new mark and recalculates energies.
exchange(EnergyMemoList, int, VoxelizedMarkMemo, EnergyStack) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown: Exchanges a mark at a specific index with a new mark and updates energies.
exchange(MemoForIndex, VoxelizedMarkMemo, int, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
exchange(MemoForIndex, VoxelizedMarkMemo, int, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedPairs
exchange(MemoForIndex, VoxelizedMarkMemo, int, VoxelizedMarkMemo) - Method in interface org.anchoranalysis.mpp.mark.UpdatableMarks: Exchanges an existing mark with a new one.
Exclude<T> - Class in org.anchoranalysis.plugin.io.bean.input: Excludes all inputs whose identifiers match a regular expression.
Exclude() - Constructor for class org.anchoranalysis.plugin.io.bean.input.Exclude
execute() - Method in interface org.anchoranalysis.io.output.writer.WriterExecuteBeforeEveryOperation: To be called before every operation.
execute() - Method in class org.anchoranalysis.math.optimization.HungarianAlgorithm: Execute the algorithm.
execute(FeatureInputPairObjects) - Method in class org.anchoranalysis.image.feature.calculation.CalculateInputFromPair: Executes the calculation to extract a single object from the pair.
execute(FeatureInputSingleObject) - Method in class org.anchoranalysis.image.feature.calculation.CalculateNumberVoxels: Executes the calculation to count the number of voxels in the object.
execute(FeatureInputSingleObject) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateObjectMask
execute(FeatureInputSingleObject) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateShellObjectMask
execute(FeatureInputSingleObject) - Method in class org.anchoranalysis.plugin.points.calculate.ellipse.CalculateEllipseLeastSquares
execute(FeatureInputSingleObject) - Method in class org.anchoranalysis.plugin.points.calculate.ellipsoid.CalculateEllipsoidLeastSquares
execute(FeatureInputSingleObject, Integer) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateIncrementalOperationMap
execute(FeatureInputStack) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.CalculateDeriveObjectInput
execute(FeatureInputStack) - Method in class org.anchoranalysis.plugin.image.feature.stack.calculation.CalculateHistogram
execute(FeatureInputStack) - Method in class org.anchoranalysis.plugin.image.feature.stack.calculation.CalculateHistogramMasked
execute(Outputter, List<T>, ParametersExperiment) - Method in class org.anchoranalysis.experiment.bean.processor.DebugDependentProcessor
execute(Outputter, List<T>, ParametersExperiment) - Method in class org.anchoranalysis.experiment.bean.processor.JobProcessor: Executes the task on all inputs.
execute(Outputter, List<T>, ParametersExperiment) - Method in class org.anchoranalysis.experiment.bean.processor.ParallelProcessor
execute(Outputter, List<T>, ParametersExperiment) - Method in class org.anchoranalysis.experiment.bean.processor.SequentialProcessor
execute(FeatureInputPairMemo) - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.CalculateDeriveSingleMemoFromPair
execute(T) - Method in class org.anchoranalysis.feature.calculate.part.CalculationPart: This performs the actual calculation when needed.
execute(T) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegate
execute(T, U) - Method in class org.anchoranalysis.feature.calculate.part.CalculationPartMap: Calculates a result for a particular input and key.
executeAndAssertCount(int, int, CheckedRunnable<OperationFailedException>) - Static method in class org.anchoranalysis.test.feature.plugins.mockfeature.MockFeatureWithCalculationFixture: Executes an operation and asserts the expected number of calls to internal methods.
executeEachWithMonitor(String, List<T>) - Method in class org.anchoranalysis.experiment.task.processor.MonitoredSequentialExecutor: Executes code for each element of inputs in serial, providing log-reports as to how many are finished, remain etc.
executeExperiment(ExecutionArguments) - Method in class org.anchoranalysis.experiment.bean.Experiment: Executes the experiment.
executeExperiment(ExecutionArguments) - Method in class org.anchoranalysis.experiment.bean.io.OutputExperiment: Executes the experiment for given arguments.
executeExperiment(ExecutionArguments, boolean, Logger) - Method in class org.anchoranalysis.launcher.executor.ExperimentExecutor: Executes an experiment after finding a single experiment XML file, and reading the experiment from this file.
executeExperimentWithParameters(ParametersExperiment) - Method in class org.anchoranalysis.experiment.bean.io.InputOutputExperiment
executeExperimentWithParameters(ParametersExperiment) - Method in class org.anchoranalysis.experiment.bean.io.OutputExperiment: Executes the experiment for parameters.
executeJob(ParametersUnbound<T, S>) - Method in class org.anchoranalysis.experiment.bean.task.Task: Runs the task on one particular input (a job).
executeLogStatistics(Outputter, List<T>, ParametersExperiment) - Method in class org.anchoranalysis.experiment.bean.processor.JobProcessor: Executes the task on all inputs and logs statistics about this to the file-systen.
executeOrWait(CheckedFunction<ConcurrentModel<T>, S, ConcurrentModelException>) - Method in class org.anchoranalysis.inference.concurrency.ConcurrentModelPool: Execute on the next available model (or wait until one becomes available).
executePhase() - Method in class org.anchoranalysis.math.optimization.HungarianAlgorithm: Execute a single phase of the algorithm.
ExecuteTaskHelper - Class in org.anchoranalysis.test.experiment.task: Executes a task on a single-input outputting into a specific directory.
ExecuteTaskHelper() - Constructor for class org.anchoranalysis.test.experiment.task.ExecuteTaskHelper: Create so that all outputs occur, and with default TaskArguments.
ExecuteTaskHelper(boolean) - Constructor for class org.anchoranalysis.test.experiment.task.ExecuteTaskHelper: Create so that all outputs occur, and with default TaskArguments.
ExecuteTaskHelper(Optional<String>, TaskArguments, boolean) - Constructor for class org.anchoranalysis.test.experiment.task.ExecuteTaskHelper: Create with specific arguments, not necessarily the defaults.
ExecutionArguments - Class in org.anchoranalysis.experiment.arguments: Arguments that can further specify an experiment's execution (in its entirety) in addition to its bean specification.
ExecutionArguments() - Constructor for class org.anchoranalysis.experiment.arguments.ExecutionArguments: Creates with neither a model-directory nor initial task-arguments.
ExecutionArguments(Path, TaskArguments) - Constructor for class org.anchoranalysis.experiment.arguments.ExecutionArguments: Creates with a model-directory and an image-size suggestion.
ExecutionTimeRecorder - Class in org.anchoranalysis.core.time: Records the execution-time of particular operations.
ExecutionTimeRecorder() - Constructor for class org.anchoranalysis.core.time.ExecutionTimeRecorder
ExecutionTimeRecorderFactory - Class in org.anchoranalysis.experiment.time: Creates an instance of ExecutionTimeRecorder depending in what outputs are enabled.
ExecutionTimeRecorderIgnore - Class in org.anchoranalysis.core.time: An implementation of ExecutionTimeRecorder that is a simple placeholder that does nothing.
ExecutionTimeRecorderIgnore() - Constructor for class org.anchoranalysis.core.time.ExecutionTimeRecorderIgnore
executionTimeStatistics() - Method in class org.anchoranalysis.experiment.task.ParametersExperiment: The execution-times that have been recorded.
executionTimeTotal() - Method in class org.anchoranalysis.experiment.task.TaskStatistics: Execution-time of all jobs in milliseconds, ignoring any parallelism.
existingDimensions() - Method in class org.anchoranalysis.image.bean.channel.ChannelAggregator: The Dimensions to use for the aggregation.
existingDimensions() - Method in class org.anchoranalysis.plugin.image.bean.channel.aggregator.ProjectableBufferAggregator
existsWith(BoundingBox) - Method in class org.anchoranalysis.spatial.box.BoundingBoxIntersection: Does intersection exist with another bounding-box?
existsWithAny(List<BoundingBox>) - Method in class org.anchoranalysis.spatial.box.BoundingBoxIntersection: Does intersection exist with with any of the others in the list?
expectedOutputs() - Method in class org.anchoranalysis.image.inference.bean.segment.instance.DecodeInstanceSegmentation: Ordered names of the tensors we are interested in processing, as outputted from inference.
expectedOutputs() - Method in class org.anchoranalysis.plugin.onnx.bean.object.segment.decode.instance.maskrcnn.DecodeMaskRCNN
expectedOutputs() - Method in class org.anchoranalysis.plugin.onnx.bean.object.segment.decode.instance.text.DecodeEAST
Experiment - Class in org.anchoranalysis.experiment.bean: A base class for a type of task that produces some kind of result of interest.
Experiment() - Constructor for class org.anchoranalysis.experiment.bean.Experiment
ExperimentExecutionException - Exception Class in org.anchoranalysis.experiment: An exception that occurs when an experiment is executed.
ExperimentExecutionException(String) - Constructor for exception class org.anchoranalysis.experiment.ExperimentExecutionException: Creates with a message only.
ExperimentExecutionException(String, Throwable) - Constructor for exception class org.anchoranalysis.experiment.ExperimentExecutionException: A string message displayed to the user as well as a stack-trace of the cause.
ExperimentExecutionException(Throwable) - Constructor for exception class org.anchoranalysis.experiment.ExperimentExecutionException: Creates with a cause only.
ExperimentExecutor - Class in org.anchoranalysis.launcher.executor: Runs a particular experiment after identifying necessary paths and input files.
ExperimentExecutorFactory - Class in org.anchoranalysis.launcher.executor: Creates an ExperimentExecutor.
ExperimentFactory - Class in org.anchoranalysis.launcher.executor.selectparam.experiment: SelectParam<Path> factory for experiments.
ExperimentFeedbackContext - Class in org.anchoranalysis.experiment.task: Objects to give the user feedback about different aspects of the experiment.
ExperimentFeedbackContext(StatefulMessageLogger, boolean, ExecutionTimeRecorder) - Constructor for class org.anchoranalysis.experiment.task.ExperimentFeedbackContext: Creates a new ExperimentFeedbackContext instance.
ExperimentIdentifier - Class in org.anchoranalysis.experiment.bean.identifier: A method to produce an identifier for an experiment.
ExperimentIdentifier() - Constructor for class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifier
ExperimentIdentifierAuto - Class in org.anchoranalysis.experiment.bean.identifier: Automatically populates a experiment-name and version number
ExperimentIdentifierAuto() - Constructor for class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierAuto
ExperimentIdentifierConstant - Class in org.anchoranalysis.experiment.bean.identifier: Defines constants for name and version of an experiment
ExperimentIdentifierConstant() - Constructor for class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierConstant
ExperimentIdentifierConstant(String, String) - Constructor for class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierConstant
experimentIdentifierForOutputPath() - Method in class org.anchoranalysis.experiment.task.ParametersExperiment: The experiment-identifier to use in the output-path, if one should be used.
ExperimentLauncherFromShell - Class in org.anchoranalysis.test.experiment.launcher: Launches an experiment by calling the application 'anchor' via the shell.
ExperimentLauncherFromShell(TestLoader) - Constructor for class org.anchoranalysis.test.experiment.launcher.ExperimentLauncherFromShell: Create with a specific loader.
experimentSelectParam(CommandLine, Path) - Static method in class org.anchoranalysis.launcher.executor.selectparam.SelectParamFactory: Creates a SelectParam for experiment selection.
ExportFeatures<T,S,U> - Class in org.anchoranalysis.plugin.image.task.bean.feature: Calculates features and exports them as a CSV file.
ExportFeatures() - Constructor for class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures
ExportFeaturesStyle - Class in org.anchoranalysis.plugin.image.task.bean.feature: Visual style for how features are exported.
ExportFeaturesStyle() - Constructor for class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeaturesStyle
ExportFeaturesStyle(boolean, boolean, boolean) - Constructor for class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeaturesStyle: Creates a new ExportFeaturesStyle instance.
ExportImageHistograms - Class in org.anchoranalysis.plugin.image.task.bean.grouped.histogram: Exports a histogram of voxel intensities as a CSV file for each channel of an image.
ExportImageHistograms() - Constructor for class org.anchoranalysis.plugin.image.task.bean.grouped.histogram.ExportImageHistograms
ExportSharedObjects - Interface in org.anchoranalysis.mpp.io.input: An interface for exporting shared objects to a target container.
ExtendInZ - Class in org.anchoranalysis.plugin.image.bean.object.provider.slice: Creates a 3D version of an object by replicating each input-object across the z-dimension to meet (3D) dimensions.
ExtendInZ() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.slice.ExtendInZ
ExtendInZWithinContainer - Class in org.anchoranalysis.plugin.image.bean.object.provider.slice: Extends an object (2D/3D) as much as it can within the z-slices of a containing object
ExtendInZWithinContainer() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.slice.ExtendInZWithinContainer
extendWith(int) - Method in class org.anchoranalysis.image.voxel.resizer.VoxelsResizerImgLib2: Switches to extend constant-value out-of-bounds strategy
extension() - Method in class org.anchoranalysis.image.core.stack.ImageFileAttributes: The file extension of the file-path.
ExtensionAdder - Class in org.anchoranalysis.test.image.stackwriter: Utility class for adding file extensions to filenames.
extensionAsArray() - Method in enum class org.anchoranalysis.core.format.NonImageFileFormat: The extension (without a period) as an array.
ExtensionCount - Class in org.anchoranalysis.plugin.io.bean.summarizer.path: Remembers each unique extension, and associated count
ExtensionCount() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.path.ExtensionCount
extensionSuffix(OutputWriteSettings) - Method in class org.anchoranalysis.io.generator.serialized.ObjectOutputStreamGenerator
extensionSuffix(OutputWriteSettings) - Method in class org.anchoranalysis.io.generator.serialized.SerializedGenerator: Appended to the standard "serialized" extension, to form the complete extension.
extensionSuffix(OutputWriteSettings) - Method in class org.anchoranalysis.io.generator.serialized.XStreamGenerator
ExtensionUtilities - Class in org.anchoranalysis.core.system.path: Extracting a file-extension from a path according to rules.
extensionWithoutPeriod() - Method in enum class org.anchoranalysis.core.format.NonImageFileFormat: The extension without any leading period.
extensionWithPeriod() - Method in enum class org.anchoranalysis.core.format.NonImageFileFormat: The extension with a leading period.
extent - Variable in class org.anchoranalysis.io.bioformats.copyconvert.ConvertTo: The size of the source and destination buffers.
extent() - Method in class org.anchoranalysis.feature.energy.EnergyStack: The width and height and depth of all Channels in the stack.
extent() - Method in class org.anchoranalysis.feature.energy.EnergyStackWithoutParameters: The width and height and depth of all Channels in the stack.
extent() - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.StackArrangement: The size of the larger image in which all the BoundingBoxes in list must fully reside.
extent() - Method in class org.anchoranalysis.image.core.channel.Channel: The size of the voxels across three dimensions.
extent() - Method in class org.anchoranalysis.image.core.dimensions.Dimensions: The width and height and depth of the image.
extent() - Method in class org.anchoranalysis.image.core.mask.Mask: The size of the voxels across three dimensions.
extent() - Method in class org.anchoranalysis.image.core.stack.DisplayStack: The width and height and depth of all channels in the Stack.
extent() - Method in class org.anchoranalysis.image.core.stack.RGBStack: The width and height and depth of the image.
extent() - Method in class org.anchoranalysis.image.core.stack.Stack: The width and height and depth of the image.
extent() - Method in class org.anchoranalysis.image.inference.segment.SegmentedObjectsAtScale: The width and height and depth of the background image, associated with the objects.
extent() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels: The size of the voxels across three dimensions.
extent() - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: The size of the voxels across three dimensions, and also the size of the associated bounding-box.
extent() - Method in class org.anchoranalysis.image.voxel.buffer.slice.FromByte
extent() - Method in class org.anchoranalysis.image.voxel.buffer.slice.FromFloat
extent() - Method in class org.anchoranalysis.image.voxel.buffer.slice.FromInt
extent() - Method in class org.anchoranalysis.image.voxel.buffer.slice.FromShort
extent() - Method in interface org.anchoranalysis.image.voxel.buffer.slice.SliceBufferIndex: The size of each buffer.
extent() - Method in class org.anchoranalysis.image.voxel.buffer.SlidingBuffer: The size of the voxels across three dimensions.
extent() - Method in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsoluteWithSlidingBuffer: The size of the associated SlidingBuffer.
extent() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: The size of the object-mask's bounding-box across three dimensions.
extent() - Method in class org.anchoranalysis.image.voxel.Voxels: The size of the voxels across three dimensions.
extent() - Method in class org.anchoranalysis.image.voxel.VoxelsUntyped: The size of the voxels across three dimensions.
extent() - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels: Gets the extent of the voxels.
extent() - Method in class org.anchoranalysis.plugin.image.task.size.CommonSize: The common-size of all images.
extent() - Method in class org.anchoranalysis.spatial.box.BoundingBox: Dimensions in pixels needed to represent the bounding box.
extent(Extent) - Method in enum class org.anchoranalysis.image.core.dimensions.OrientationChange: A Extent that describes extent after the orientation change.
Extent<T> - Class in org.anchoranalysis.plugin.image.feature.bean.dimensions: Width/height/depth of energy-stack in pixels depending on axis.
Extent - Class in org.anchoranalysis.spatial.box: The sizes: width, height, depth etc. of an entity in 2 or 3 dimensions.
Extent() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.dimensions.Extent
Extent(int, int) - Constructor for class org.anchoranalysis.spatial.box.Extent: Creates with with only X and Y dimensions.
Extent(int, int, int) - Constructor for class org.anchoranalysis.spatial.box.Extent: Creates with X and Y and Z dimensions.
EXTENT_IDENTIFIER - Static variable in class org.anchoranalysis.test.image.stackwriter.StackTester: A constant identifier used to represent a small extent in file names.
EXTENT_X - Static variable in class org.anchoranalysis.image.io.object.HDF5PathHelper: Attribute for x dimension of the extent.
EXTENT_Y - Static variable in class org.anchoranalysis.image.io.object.HDF5PathHelper: Attribute for y dimension of the extent.
EXTENT_Z - Static variable in class org.anchoranalysis.image.io.object.HDF5PathHelper: Attribute for z dimension of the extent.
ExtentMatchHelper - Class in org.anchoranalysis.image.voxel: Checks if the Extents of two BoundingBoxes are identical.
ExtentToArrange - Class in org.anchoranalysis.image.bean.spatial.arrange.fill: A particular Extent to be arranged, with calculated aspect-ratio, and its unique index position.
ExtentToArrange(int, Extent) - Constructor for class org.anchoranalysis.image.bean.spatial.arrange.fill.ExtentToArrange: Create with a particular index and size.
ExteriorContour - Class in org.anchoranalysis.plugin.image.bean.mask.provider.morphological: Finds the exterior outer contour for a Mask that forms its outline.
ExteriorContour() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.ExteriorContour
extract() - Method in class org.anchoranalysis.image.core.channel.Channel: Interface that allows read/copy/duplication operations to be performed regarding the voxels intensities.
extract() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels: Interface that allows read/copy/duplication operations to be performed regarding the voxels intensities.
extract() - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: Extracts value from voxels using global coordinates (relative to the image as a whole).
extract() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Provides methods to read/copy/duplicate regions of voxels.
extract() - Method in class org.anchoranalysis.image.voxel.Voxels: Interface that allows read/copy/duplication operations to be performed regarding the voxels intensities.
extract() - Method in class org.anchoranalysis.image.voxel.VoxelsFloat
extract() - Method in class org.anchoranalysis.image.voxel.VoxelsUnsignedByte
extract() - Method in class org.anchoranalysis.image.voxel.VoxelsUnsignedInt
extract() - Method in class org.anchoranalysis.image.voxel.VoxelsUnsignedShort
extract() - Method in class org.anchoranalysis.image.voxel.VoxelsUntyped: Interface that allows read/copy/duplication operations to be performed regarding the voxels intensities.
extract(int, IntFunction<T>) - Method in class org.anchoranalysis.core.index.range.IndexRangeNegative: Extracts a subset of elements from a collection according to the specified index/range.
extract(String) - Static method in class org.anchoranalysis.io.input.path.GlobExtractor: Extracts a glob, and a directory portion if it exists from a string with a wildcard.
extract(Path, IndexRangeNegative) - Static method in class org.anchoranalysis.io.input.path.ExtractPathElementRange: Extracts a sub-path from a Path by only retaining a range of elements.
extract(List<T>) - Method in class org.anchoranalysis.core.index.range.IndexRangeNegative: Extracts a subset of elements from a list according to the specified index/range.
extractAsDouble(Dictionary, String) - Static method in class org.anchoranalysis.plugin.image.feature.bean.score.FromDictionaryBase: Extracts a double value from the dictionary for a given key.
ExtractBoundingBoxAreaFromStackGenerator - Class in org.anchoranalysis.image.io.stack.output.box: An iterable-generator that outputs the portion of a stack corresponding to a bounding-box
ExtractBoundingBoxAreaFromStackGenerator(ScaleableBackground) - Constructor for class org.anchoranalysis.image.io.stack.output.box.ExtractBoundingBoxAreaFromStackGenerator
ExtractCenterSlice - Class in org.anchoranalysis.plugin.image.bean.channel.provider.slice: Extracts the slice at the center (rounding down) of the range of z-stacks.
ExtractCenterSlice() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.slice.ExtractCenterSlice
extractChannel(String, boolean) - Method in class org.anchoranalysis.plugin.image.task.grouped.ChannelSource: Extracts a Channel from a particular Stack in stackStore.
extractChannel(String, boolean, int) - Method in class org.anchoranalysis.plugin.image.task.grouped.ChannelSource: Extracts a Channel from a particular Stack in stackStore.
extractChannel(Stack, boolean, int) - Method in class org.anchoranalysis.plugin.image.task.grouped.ChannelSource: Extracts a Channel from a given Stack.
extractChannelForBoundingBox(int, BoundingBox) - Method in class org.anchoranalysis.image.core.stack.DisplayStack: Creates a new Channel that refers to only a BoundingBox portion of the DisplayStack.
ExtractDerivedParameter<S,T> - Class in org.anchoranalysis.bean.initializable.property: Extracts one type of parameter from another, if possible.
ExtractDerivedParameter(Class<?>, Function<S, T>) - Constructor for class org.anchoranalysis.bean.initializable.property.ExtractDerivedParameter: Creates with only a targetClass.
ExtractDerivedParameter(Class<?>, Function<S, T>, Class<?>) - Constructor for class org.anchoranalysis.bean.initializable.property.ExtractDerivedParameter: Creates with a classOfTarget and a baseClassOfSource.
extractExtension(String) - Static method in class org.anchoranalysis.core.system.path.ExtensionUtilities: Extracts the extension from a filename.
extractExtension(Path) - Static method in class org.anchoranalysis.core.system.path.ExtensionUtilities: Like ExtensionUtilities.extractExtension(String) but accepts a Path instead of a String.
ExtractFrameStore - Class in org.anchoranalysis.image.io.stack.time: Exposes a NamedProviderStore<TimeSeries> as a NamedProviderStore<Stack> by extracting a frame from each series.
ExtractFrameStore(NamedProviderStore<Stack>) - Constructor for class org.anchoranalysis.image.io.stack.time.ExtractFrameStore: Creates to extract at time-index 0.
ExtractFrameStore(NamedProviderStore<Stack>, int) - Constructor for class org.anchoranalysis.image.io.stack.time.ExtractFrameStore: Creates to extract at time-index timeIndex.
extractFrom(DualScale<T>, Function<T, ObjectMask>) - Static method in class org.anchoranalysis.image.inference.segment.MultiScaleObject: Creates a new MultiScaleObject by extracting a ObjectMask from a DualScale.
extractFrom(DualScale<T>, DualScale<S>, BiFunction<T, S, ObjectMask>) - Static method in class org.anchoranalysis.image.inference.segment.MultiScaleObject: Creates a new MultiScaleObject by extracting a ObjectMask from two DualScales.
extractFrom(T) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.input.ExtractIdentifier
extractFrom(T) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.input.ExtractIdentifierAndPath
extractFrom(T) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.input.ExtractPath
extractFrom(T) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.input.SummarizerInputFromManager
ExtractIdentifier<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer.input: Extracts the identifier from an InputFromManager to summarize further.
ExtractIdentifier() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.input.ExtractIdentifier
ExtractIdentifierAndPath<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer.input: Extracts the identifier and path from an InputFromManager to summarize further.
ExtractIdentifierAndPath() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.input.ExtractIdentifierAndPath
extractIfPossible(S) - Method in class org.anchoranalysis.bean.initializable.property.ExtractDerivedParameter: Extracts a derived parameter if possible from parameter.
extractKey(ImageMetadataInput) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.image.BitDepth
extractKey(ImageMetadataInput) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.image.NumberChannels
extractKey(ImageMetadataInput) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.image.SummarizerImageMetadataSimple
ExtractMidpoint - Class in org.anchoranalysis.image.io.object: Extracts a Point3i representing the mid-point of an ObjectWithProperties.
extractObjectForSummary(T) - Method in class org.anchoranalysis.plugin.io.bean.task.SummarizeBase: Extract object for summary.
extractObjectForSummary(T) - Method in class org.anchoranalysis.plugin.io.bean.task.SummarizeInputs
ExtractPath<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer.input: Extracts a Path from an input to summarize further.
ExtractPath() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.input.ExtractPath
ExtractPathElementRange - Class in org.anchoranalysis.io.input.path: Extracts a range of elements from a Path.
extractRegionFromStack(BoundingBox) - Method in class org.anchoranalysis.image.io.stack.output.box.ScaleableBackground: Extracts a portion of a stack (flattened and maybe scaled) corresponding to a bounding-box
extractScaledValue(byte[], int, boolean) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.ToUnsignedByteWithScaling: Extracts a value from the source-array, and apply any scaling and clamping.
extractScaledValue(byte[], int, boolean) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedByteNoInterleavingScale
extractScaledValue(byte[], int, boolean) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedInt
extractScaledValue(byte[], int, boolean) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedShort
extractSlice(int) - Method in class org.anchoranalysis.feature.energy.EnergyStack: Extract a particular z-slice from the EnergyStack as a new stack.
extractSlice(int) - Method in class org.anchoranalysis.feature.energy.EnergyStackWithoutParameters: Extract a particular z-slice from the EnergyStackWithoutParameters as a new stack.
extractSlice(int) - Method in class org.anchoranalysis.image.core.channel.Channel: Creates a new Channel containing only one particular slice.
extractSlice(int) - Method in class org.anchoranalysis.image.core.mask.Mask: Creates a new Mask containing only one particular slice.
extractSlice(int) - Method in class org.anchoranalysis.image.core.stack.DisplayStack: Extract a particular z-slice from the DisplayStack as a new stack, applying any applicable conversion.
extractSlice(int) - Method in class org.anchoranalysis.image.core.stack.RGBStack: Extract a particular z-slice from the Stack as a new stack.
extractSlice(int) - Method in class org.anchoranalysis.image.core.stack.Stack: Extract a particular z-slice from the Stack as a new stack.
extractSlice(int) - Method in class org.anchoranalysis.image.core.stack.StackNotUniformSized: Creates a new StackNotUniformSized containing only one particular slice for each respective channel.
extractSlice(int) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: Extracts a particular slice.
extractSlice(int, boolean) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Extracts one particular slice as an object-mask
ExtractSlice - Class in org.anchoranalysis.plugin.image.task.bean.slice: Reduces a z-stack to a single-slice by taking the optima of a feature calculated for each slice.
ExtractSlice() - Constructor for class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice
ExtractSliceRange - Class in org.anchoranalysis.plugin.image.bean.channel.provider.slice: Extracts slices from sliceStart (inclusive) to sliceEnd (inclusive).
ExtractSliceRange() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.slice.ExtractSliceRange
extractStack(ProvidesStackInput, StackProvider, InputOutputContext) - Static method in class org.anchoranalysis.plugin.image.task.feature.calculator.FeatureCalculatorRepeated: Extracts an EnergyStack from the given input and stack provider.
ExtractToRGB - Class in org.anchoranalysis.plugin.image.task.bean.format.convertstyle: Extracts three channels to make an RGB image.
ExtractToRGB() - Constructor for class org.anchoranalysis.plugin.image.task.bean.format.convertstyle.ExtractToRGB
extractTupleForBoundingBox(BoundingBox) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxAlongAxisBase: Extracts a ReadableTuple3i from the given BoundingBox.
extractTupleForBoundingBox(BoundingBox) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxExtentAlongAxis
extractTupleForBoundingBox(BoundingBox) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxMaximumAlongAxis
extractTupleForBoundingBox(BoundingBox) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxMinimumAlongAxis
extractUpToThreeChannels() - Method in class org.anchoranalysis.image.core.stack.Stack: Extracts the first three Channels as a new Stack.

F

factory() - Method in class org.anchoranalysis.image.voxel.Voxels: A factory for creating voxels with a particular buffer-type.
FailureOnlyMessageLogger - Class in org.anchoranalysis.experiment.log: Writes text to a file, but only if FailureOnlyMessageLogger.close(boolean, boolean) is called with successful==true.
FailureOnlyMessageLogger(String, OutputterChecked, ErrorReporter, boolean) - Constructor for class org.anchoranalysis.experiment.log.FailureOnlyMessageLogger: Creates a new FailureOnlyMessageLogger instance.
feature() - Method in class org.anchoranalysis.mpp.init.MarksInitialization: Gets the FeatureRelatedInitialization associated with this MarksInitialization.
Feature<T> - Class in org.anchoranalysis.feature.bean: Base class for a measurement that calculates a result (double) given input parameters.
Feature() - Constructor for class org.anchoranalysis.feature.bean.Feature: Creates with the default initializer.
Feature(BeanInitializer<FeatureInitialization>) - Constructor for class org.anchoranalysis.feature.bean.Feature: Creates with a custom initializer.
FeatureAllMemo - Class in org.anchoranalysis.mpp.feature.bean.energy.element: An abstract base class for features that operate on FeatureInputAllMemo.
FeatureAllMemo() - Constructor for class org.anchoranalysis.mpp.feature.bean.energy.element.FeatureAllMemo
FeatureBinary<T> - Class in org.anchoranalysis.feature.bean.operator: A base class for a Feature that is a binary-function of the results from two other features.
FeatureBinary() - Constructor for class org.anchoranalysis.feature.bean.operator.FeatureBinary
FeatureCalculationCache<T> - Interface in org.anchoranalysis.feature.calculate.cache: A context in which to calculate features while caching certain duplicated internal calculations among the features.
FeatureCalculationContext<S> - Class in org.anchoranalysis.plugin.image.task.feature: The context in which features are calculated, so as to be later exported as a CSV.
FeatureCalculationContext(FeatureResultsAndThumbnails, S, FeatureNameList, Optional<String>, ExecutionTimeRecorder, boolean, InputOutputContext) - Constructor for class org.anchoranalysis.plugin.image.task.feature.FeatureCalculationContext: Creates a new FeatureCalculationContext.
FeatureCalculationException - Exception Class in org.anchoranalysis.feature.calculate: When the calculation of a feature cannot complete successfully.
FeatureCalculationException(String) - Constructor for exception class org.anchoranalysis.feature.calculate.FeatureCalculationException: Creates with a message only.
FeatureCalculationException(String, Throwable) - Constructor for exception class org.anchoranalysis.feature.calculate.FeatureCalculationException: Creates with both a message and a cause.
FeatureCalculationException(Throwable) - Constructor for exception class org.anchoranalysis.feature.calculate.FeatureCalculationException: Creates with a cause only.
FeatureCalculationInput<T> - Interface in org.anchoranalysis.feature.calculate: Gives a FeatureInput the necessary context for feature-calculation, including associating it with a cache.
FeatureCalculator<T> - Interface in org.anchoranalysis.feature.calculate: Calculates FeatureCalculationInput when passed a particular Feature and corresponding FeatureCalculationInput.
FeatureCalculatorCache - Class in org.anchoranalysis.feature.session.calculator: Adds a cache to a FeatureCalculatorSingle or FeatureCalculatorMulti.
FeatureCalculatorFromProvider<T> - Class in org.anchoranalysis.plugin.image.task.feature.calculator: Calculates feature or feature values.
FeatureCalculatorFromProvider(ProvidesStackInput, Optional<StackProvider>, InputOutputContext) - Constructor for class org.anchoranalysis.plugin.image.task.feature.calculator.FeatureCalculatorFromProvider: Creates a new FeatureCalculatorFromProvider.
FeatureCalculatorMulti<T> - Interface in org.anchoranalysis.feature.calculate.bound: Like a FeatureCalculator but is permanently associated with one or more Features.
FeatureCalculatorMultiChangeInput<T> - Class in org.anchoranalysis.feature.calculate.bound: A FeatureCalculatorMulti but changes the input before calculation.
FeatureCalculatorMultiChangeInput(FeatureCalculatorMulti<T>, Consumer<T>) - Constructor for class org.anchoranalysis.feature.calculate.bound.FeatureCalculatorMultiChangeInput: Creates a new FeatureCalculatorMultiChangeInput instance.
FeatureCalculatorRepeated - Class in org.anchoranalysis.plugin.image.task.feature.calculator: Utility class for extracting an EnergyStack from a StackProvider.
FeatureCalculatorSingle<T> - Interface in org.anchoranalysis.feature.calculate.bound: Like a FeatureCalculator but is permanently associated with a single Feature.
FeatureCalculatorSingleChangeInput<T> - Class in org.anchoranalysis.feature.calculate.bound: A FeatureCalculatorSingle but changes the input before calculation.
FeatureCalculatorSingleChangeInput(FeatureCalculatorSingle<T>, Consumer<T>) - Constructor for class org.anchoranalysis.feature.calculate.bound.FeatureCalculatorSingleChangeInput: Creates a new FeatureCalculatorSingleChangeInput instance.
FeatureCalculatorSingleFromMulti<T> - Class in org.anchoranalysis.feature.calculate.bound: Exposes a FeatureCalculatorMulti as a FeatureCalculatorSingle.
FeatureCalculatorSingleFromMulti(FeatureCalculatorMulti<T>) - Constructor for class org.anchoranalysis.feature.calculate.bound.FeatureCalculatorSingleFromMulti: Creates from a FeatureCalculatorMulti.
FeatureConvertUnits<T> - Class in org.anchoranalysis.image.feature.bean.physical: An abstract base class for features that convert units between physical and voxel space.
FeatureConvertUnits() - Constructor for class org.anchoranalysis.image.feature.bean.physical.FeatureConvertUnits
FeatureConvertUnits(Feature<T>, SpatialUnits.UnitSuffix) - Constructor for class org.anchoranalysis.image.feature.bean.physical.FeatureConvertUnits: Constructs a FeatureConvertUnits with a specified feature and unit type.
FeatureCostAssigner - Class in org.anchoranalysis.plugin.annotation.bean.comparison.assigner: Assigns an objects from one set of objects to another based upon a cost (degree of overlap).
FeatureCostAssigner() - Constructor for class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner
FeatureCSVMetadata - Class in org.anchoranalysis.feature.io.csv.metadata: Needed non-result information to output a feature-values CSV file.
FeatureCSVMetadata(String, String[], FeatureNameList) - Constructor for class org.anchoranalysis.feature.io.csv.metadata.FeatureCSVMetadata: Create for a particular output-name.
FeatureCSVMetadata(String, List<String>) - Constructor for class org.anchoranalysis.feature.io.csv.metadata.FeatureCSVMetadata: Creates a new FeatureCSVMetadata instance.
FeatureCSVMetadataForOutput - Class in org.anchoranalysis.feature.io.csv.metadata: Like a FeatureCSVMetadata but additionally associates an output-name.
FeatureCSVMetadataForOutput(String[], FeatureNameList, String) - Constructor for class org.anchoranalysis.feature.io.csv.metadata.FeatureCSVMetadataForOutput: Creates a new FeatureCSVMetadataForOutput instance.
FeatureCSVWriter - Class in org.anchoranalysis.feature.io.csv: Writes the results of feature-calculations as a CSV file.
FeatureCSVWriter(CSVWriter, boolean) - Constructor for class org.anchoranalysis.feature.io.csv.FeatureCSVWriter: Creates for a CSVWriter.
FeatureCSVWriterFactory - Interface in org.anchoranalysis.feature.io.csv.results: To facilitate creation of a FeatureCSVWriter from corresponding FeatureCSVMetadata.
FeatureDeriveFromPair - Class in org.anchoranalysis.image.feature.bean.object.pair: Base class for evaluating FeaturePairObjects in terms of another feature that operates on elements (first, second, merged etc.).
FeatureDeriveFromPair() - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.FeatureDeriveFromPair
FeatureDeriveFromPair(Feature<FeatureInputSingleObject>) - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.FeatureDeriveFromPair: Creates a new FeatureDeriveFromPair instance.
FeatureEnergy<T> - Class in org.anchoranalysis.image.feature.bean: A base class for features that only require an input that extends from FeatureInputEnergy
FeatureEnergy() - Constructor for class org.anchoranalysis.image.feature.bean.FeatureEnergy
FeatureEnergyChannel - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity: A feature that uses a channel from the energy-stack as identified by an index.
FeatureEnergyChannel() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.FeatureEnergyChannel
FeatureEvaluator<T> - Class in org.anchoranalysis.image.feature.bean.evaluator: Defines a feature and provides a means to calculate inputs for it, a session.
FeatureEvaluator() - Constructor for class org.anchoranalysis.image.feature.bean.evaluator.FeatureEvaluator
FeatureExporter<S> - Class in org.anchoranalysis.plugin.image.task.feature: Shared-state for an ExportFeatures task.
FeatureExporter(FeatureOutputMetadata, Supplier<S>, Optional<InputGrouper>, FeatureExporterContext) - Constructor for class org.anchoranalysis.plugin.image.task.feature.FeatureExporter: Creates the shared state.
FeatureExporterContext - Class in org.anchoranalysis.plugin.image.task.feature: Context for exporting features, containing configuration and output settings.
FeatureExporterContext(InputOutputContext, boolean, boolean, boolean) - Constructor for class org.anchoranalysis.plugin.image.task.feature.FeatureExporterContext: Creates a new FeatureExporterContext instance.
FeatureFromList<T> - Class in org.anchoranalysis.feature.bean.operator: A base class for a Feature that is a function of the results from a list of other features.
FeatureFromList() - Constructor for class org.anchoranalysis.feature.bean.operator.FeatureFromList
FeatureFromList(FeatureList<T>) - Constructor for class org.anchoranalysis.feature.bean.operator.FeatureFromList: Create from a list of features.
FeatureGeneric<T> - Class in org.anchoranalysis.feature.bean.operator: Base class for features that broadly accept any type of feature-input.
FeatureGeneric() - Constructor for class org.anchoranalysis.feature.bean.operator.FeatureGeneric
FeatureHistogram - Class in org.anchoranalysis.image.feature.bean: A base class for features that accept a histogram as input.
FeatureHistogram() - Constructor for class org.anchoranalysis.image.feature.bean.FeatureHistogram
FeatureHistogramStatistic - Class in org.anchoranalysis.image.feature.bean.histogram: Base class for FeatureHistogram implementations that calculate a statistic from the Histogram.
FeatureHistogramStatistic() - Constructor for class org.anchoranalysis.image.feature.bean.histogram.FeatureHistogramStatistic
FeatureImageMetadata - Class in org.anchoranalysis.image.feature.bean: A base class for a feature that accepts a FeatureInputImageMetadata as input.
FeatureImageMetadata() - Constructor for class org.anchoranalysis.image.feature.bean.FeatureImageMetadata
FeatureInitialization - Class in org.anchoranalysis.feature.initialization: Parameters used to initialize a Feature before any calculation occurs.
FeatureInitialization() - Constructor for class org.anchoranalysis.feature.initialization.FeatureInitialization: Create without any dictionary, energy-stack or shared-objects.
FeatureInitialization(Optional<Dictionary>, Optional<EnergyStackWithoutParameters>, Optional<SharedObjects>) - Constructor for class org.anchoranalysis.feature.initialization.FeatureInitialization: Creates a new FeatureInitialization instance.
FeatureInitialization(SharedObjects) - Constructor for class org.anchoranalysis.feature.initialization.FeatureInitialization: Create only with shared-objects.
FeatureInitialization(Dictionary) - Constructor for class org.anchoranalysis.feature.initialization.FeatureInitialization: Create only with a dictionary.
FeatureInitialization(EnergyStack) - Constructor for class org.anchoranalysis.feature.initialization.FeatureInitialization: Create only with an energy-stack.
FeatureInput - Interface in org.anchoranalysis.feature.input: A single input used for feature-calculation to produce a result.
FeatureInputAllMemo - Class in org.anchoranalysis.mpp.feature.input: Feature input that contains a list of memoized energy calculations for all marks.
FeatureInputAllMemo(EnergyMemoList, EnergyStack) - Constructor for class org.anchoranalysis.mpp.feature.input.FeatureInputAllMemo: Creates a new instance with a list of memoized energy calculations and an energy stack.
FeatureInputDictionary - Interface in org.anchoranalysis.feature.input: A FeatureInputWithResolution that has an optional associated Dictionary.
FeatureInputDimensions - Class in org.anchoranalysis.feature.input: A FeatureInput that exposes the Dimensions of an image or scene.
FeatureInputDimensions() - Constructor for class org.anchoranalysis.feature.input.FeatureInputDimensions
FeatureInputEnergy - Class in org.anchoranalysis.feature.input: A FeatureInputDimensions that has an optional EnergyStack associated with it.
FeatureInputEnergy() - Constructor for class org.anchoranalysis.feature.input.FeatureInputEnergy: Creates without an associated energy-stack.
FeatureInputEnergy(Optional<EnergyStack>) - Constructor for class org.anchoranalysis.feature.input.FeatureInputEnergy
FeatureInputHistogram - Class in org.anchoranalysis.image.feature.input: A feature input that contains a histogram and optional resolution information.
FeatureInputHistogram(Histogram, Optional<Resolution>) - Constructor for class org.anchoranalysis.image.feature.input.FeatureInputHistogram: Creates a new FeatureInputHistogram instance.
FeatureInputImageMetadata - Class in org.anchoranalysis.image.feature.input: A FeatureInput that provides ImageMetadata.
FeatureInputImageMetadata(ImageMetadata) - Constructor for class org.anchoranalysis.image.feature.input.FeatureInputImageMetadata: Creates a new FeatureInputImageMetadata instance.
FeatureInputMark - Class in org.anchoranalysis.mpp.feature.bean.mark: A feature input that wraps a Mark along with optional dimensions and dictionary.
FeatureInputMark(Mark, Optional<Dimensions>) - Constructor for class org.anchoranalysis.mpp.feature.bean.mark.FeatureInputMark: Constructs a new instance with a mark and optional dimensions.
FeatureInputMark(Mark, Optional<Dimensions>, Optional<Dictionary>) - Constructor for class org.anchoranalysis.mpp.feature.bean.mark.FeatureInputMark: Creates a new FeatureInputMark instance.
FeatureInputMark(Mark, Dimensions, Dictionary) - Constructor for class org.anchoranalysis.mpp.feature.bean.mark.FeatureInputMark: Constructs a new instance with a mark, dimensions, and dictionary.
FeatureInputMarkCollection - Class in org.anchoranalysis.mpp.feature.bean.mark.collection: Feature input that contains a collection of marks and optional dimensions.
FeatureInputMarkCollection(MarkCollection, Optional<Dimensions>) - Constructor for class org.anchoranalysis.mpp.feature.bean.mark.collection.FeatureInputMarkCollection: Creates a new FeatureInputMarkCollection instance.
FeatureInputNull - Class in org.anchoranalysis.feature.input: A FeatureInput with no associated parameterization.
FeatureInputObjectCollection - Class in org.anchoranalysis.image.feature.input: A feature input representing a collection of objects, optionally associated with an energy stack.
FeatureInputObjectCollection(ObjectCollection) - Constructor for class org.anchoranalysis.image.feature.input.FeatureInputObjectCollection: Constructs a FeatureInputObjectCollection with a collection of objects.
FeatureInputObjectCollection(ObjectCollection, Optional<EnergyStack>) - Constructor for class org.anchoranalysis.image.feature.input.FeatureInputObjectCollection: Constructs a FeatureInputObjectCollection with a collection of objects and an optional energy stack.
FeatureInputOverlappingCircleFixture - Class in org.anchoranalysis.test.feature.plugins.objects: A fixture for creating FeatureInputPairObjects with circular object masks.
FeatureInputPairMemo - Class in org.anchoranalysis.mpp.feature.input: Feature input that contains a pair of memoized voxelized marks and an energy stack.
FeatureInputPairMemo(VoxelizedMarkMemo, VoxelizedMarkMemo, EnergyStack) - Constructor for class org.anchoranalysis.mpp.feature.input.FeatureInputPairMemo: Creates a new instance with two memoized voxelized marks and an energy stack.
FeatureInputPairObjects - Class in org.anchoranalysis.image.feature.input: A pair of objects (first and second) and optionally a merged version of both.
FeatureInputPairObjects(FeatureInputPairObjects) - Constructor for class org.anchoranalysis.image.feature.input.FeatureInputPairObjects: Copy constructor for FeatureInputPairObjects.
FeatureInputPairObjects(ObjectMask, ObjectMask) - Constructor for class org.anchoranalysis.image.feature.input.FeatureInputPairObjects: Constructs a FeatureInputPairObjects with two ObjectMasks.
FeatureInputPairObjects(ObjectMask, ObjectMask, Optional<EnergyStack>) - Constructor for class org.anchoranalysis.image.feature.input.FeatureInputPairObjects: Constructs a FeatureInputPairObjects with two ObjectMasks and an optional EnergyStack.
FeatureInputPairObjects(ObjectMask, ObjectMask, Optional<EnergyStack>, Optional<ObjectMask>) - Constructor for class org.anchoranalysis.image.feature.input.FeatureInputPairObjects: Constructs a FeatureInputPairObjects with two ObjectMasks, an optional EnergyStack, and an optional merged ObjectMask.
FeatureInputPairObjects(ObjectMask, ObjectMask, EnergyStack) - Constructor for class org.anchoranalysis.image.feature.input.FeatureInputPairObjects: Constructs a FeatureInputPairObjects with two ObjectMasks and an EnergyStack.
FeatureInputResults - Class in org.anchoranalysis.feature.input: A FeatureInput with the stored results from a prior feature-calculation.
FeatureInputResults(ResultsVectorList, FeatureNameMapToIndex) - Constructor for class org.anchoranalysis.feature.input.FeatureInputResults: Creates a new FeatureInputResults instance.
FeatureInputSingleMemo - Class in org.anchoranalysis.mpp.feature.input: Feature input that contains a single memoized voxelized mark and an optional energy stack.
FeatureInputSingleMemo(VoxelizedMarkMemo, Optional<EnergyStack>) - Constructor for class org.anchoranalysis.mpp.feature.input.FeatureInputSingleMemo: Creates a new instance with a memoized voxelized mark and an optional energy stack.
FeatureInputSingleMemo(VoxelizedMarkMemo, EnergyStack) - Constructor for class org.anchoranalysis.mpp.feature.input.FeatureInputSingleMemo: Creates a new instance with a memoized voxelized mark and a non-optional energy stack.
FeatureInputSingleObject - Class in org.anchoranalysis.image.feature.input: An input representing a single object-mask (with maybe an energy-stack associated).
FeatureInputSingleObject(ObjectMask) - Constructor for class org.anchoranalysis.image.feature.input.FeatureInputSingleObject: Constructs a FeatureInputSingleObject with an ObjectMask.
FeatureInputSingleObject(ObjectMask, Optional<EnergyStack>) - Constructor for class org.anchoranalysis.image.feature.input.FeatureInputSingleObject: Constructs a FeatureInputSingleObject with an ObjectMask and an optional EnergyStack.
FeatureInputSingleObject(ObjectMask, EnergyStack) - Constructor for class org.anchoranalysis.image.feature.input.FeatureInputSingleObject: Constructs a FeatureInputSingleObject with an ObjectMask and an EnergyStack.
FeatureInputStack - Class in org.anchoranalysis.image.feature.input: A feature input that represents an energy stack.
FeatureInputStack() - Constructor for class org.anchoranalysis.image.feature.input.FeatureInputStack: Constructs a FeatureInputStack with an empty energy stack.
FeatureInputStack(Optional<EnergyStackWithoutParameters>) - Constructor for class org.anchoranalysis.image.feature.input.FeatureInputStack: Constructs a FeatureInputStack with an optional energy stack.
FeatureInputStack(EnergyStackWithoutParameters) - Constructor for class org.anchoranalysis.image.feature.input.FeatureInputStack: Constructs a FeatureInputStack with the given energy stack.
FeatureInputType - Class in org.anchoranalysis.feature.input: Performs checks and aggregations on feature-input types are compatible with others
FeatureInputWithResolution - Interface in org.anchoranalysis.feature.input: A FeatureInput that exposes the Resolution of an image or scene.
FeatureIntersectingObjects - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting: An abstract base class for features that calculate values based on intersecting objects.
FeatureIntersectingObjects() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjects
FeatureIntersectingObjectsSingleElement - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting: A feature that calculates a value based on intersecting objects, considering each intersecting object individually.
FeatureIntersectingObjectsSingleElement() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjectsSingleElement
FeatureIntersectingObjectsThreshold - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting: An abstract feature that calculates a value based on intersecting objects, considering each intersecting object individually and applying a threshold.
FeatureIntersectingObjectsThreshold() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjectsThreshold
FeatureList<T> - Class in org.anchoranalysis.feature.bean.list: A list of features with the same input-type.
FeatureList() - Constructor for class org.anchoranalysis.feature.bean.list.FeatureList: Creates with an empty list.
FeatureList(int) - Constructor for class org.anchoranalysis.feature.bean.list.FeatureList: Creates with an empty list of particular capacity.
FeatureList(List<Feature<T>>) - Constructor for class org.anchoranalysis.feature.bean.list.FeatureList: Wraps an existing list.
FeatureList(Stream<Feature<T>>) - Constructor for class org.anchoranalysis.feature.bean.list.FeatureList: Creates from a stream of Features.
FeatureList(Feature<T>) - Constructor for class org.anchoranalysis.feature.bean.list.FeatureList: Creates with a single Feature.
FeatureListEvaluator<T> - Class in org.anchoranalysis.image.feature.bean.evaluator: Defines a list of features and provides a means to calculate inputs for it, a session.
FeatureListEvaluator() - Constructor for class org.anchoranalysis.image.feature.bean.evaluator.FeatureListEvaluator
FeatureListFactory - Class in org.anchoranalysis.feature.bean.list: Factory for creating FeatureList in different ways.
FeatureListProvider<T> - Class in org.anchoranalysis.feature.bean.list: Provides a list of Features with identical input-type.
FeatureListProvider() - Constructor for class org.anchoranalysis.feature.bean.list.FeatureListProvider
FeatureListProviderAggregatePair - Class in org.anchoranalysis.plugin.image.feature.bean.list.pair: Calculates features on each part of a pair (first, second, merged etc.) and then reduces the calculation to a single number.
FeatureListProviderAggregatePair() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.pair.FeatureListProviderAggregatePair
FeatureNameList - Class in org.anchoranalysis.feature.name: A list of Strings representing feature names.
FeatureNameList() - Constructor for class org.anchoranalysis.feature.name.FeatureNameList: Create with no names (an empty list).
FeatureNameList(List<String>) - Constructor for class org.anchoranalysis.feature.name.FeatureNameList
FeatureNameList(Stream<String>) - Constructor for class org.anchoranalysis.feature.name.FeatureNameList: Create from a stream of names.
FeatureNameMapToIndex - Class in org.anchoranalysis.feature.name: A map of feature-names (strings) to indexes (int).
FeatureNameMapToIndex() - Constructor for class org.anchoranalysis.feature.name.FeatureNameMapToIndex
featureNames() - Method in class org.anchoranalysis.feature.io.csv.metadata.FeatureCSVMetadataForOutput: Names of each feature in the feature columns.
featureNames() - Method in class org.anchoranalysis.feature.store.NamedFeatureStore: The names of all Features in the store, in identical order to the store.
featureNamesNonAggregated() - Method in class org.anchoranalysis.feature.io.results.FeatureOutputMetadata: Names of each feature in the feature columns, for non-aggregated features.
FeatureObjectCollection - Class in org.anchoranalysis.image.feature.bean.object.collection: A base class for a feature that accepts a ObjectCollection as input.
FeatureObjectCollection() - Constructor for class org.anchoranalysis.image.feature.bean.object.collection.FeatureObjectCollection
FeatureOutputMetadata - Class in org.anchoranalysis.feature.io.results: Information needed for the outputting differnt types of feature-table CSV files.
FeatureOutputMetadata(LabelHeaders, FeatureNameList, FeatureOutputNames) - Constructor for class org.anchoranalysis.feature.io.results.FeatureOutputMetadata: Creates a new FeatureOutputMetadata instance.
FeatureOutputNames - Class in org.anchoranalysis.feature.io.results: The customizable output names used by LabelledResultsCollector, which all follow a pattern based on a prefix.
FeatureOutputNames() - Constructor for class org.anchoranalysis.feature.io.results.FeatureOutputNames: Creates using default names, equivalent to a prefix of features.
FeatureOutputNames(String, boolean, boolean) - Constructor for class org.anchoranalysis.feature.io.results.FeatureOutputNames: Creates output-names based upon a prefix.
FeaturePairMemo - Class in org.anchoranalysis.mpp.feature.bean.energy.element: An abstract base class for features that operate on pairs of memoized objects.
FeaturePairMemo() - Constructor for class org.anchoranalysis.mpp.feature.bean.energy.element.FeaturePairMemo
FeaturePairObjects - Class in org.anchoranalysis.image.feature.bean.object.pair: An abstract base class for features that operate on pairs of objects.
FeaturePairObjects() - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.FeaturePairObjects
FeatureProvider<T> - Class in org.anchoranalysis.feature.bean.provider: Provides a single Feature.
FeatureProvider() - Constructor for class org.anchoranalysis.feature.bean.provider.FeatureProvider
FeatureProviderBean<B,P> - Class in org.anchoranalysis.feature.bean.provider: Base class for FeatureRelatedBeans that implement Provider to provide an object of type S.
FeatureProviderBean() - Constructor for class org.anchoranalysis.feature.bean.provider.FeatureProviderBean
FeatureProviderDefine<T> - Class in org.anchoranalysis.feature.bean.provider: Defines a single Feature to provide via a bean property.
FeatureProviderDefine() - Constructor for class org.anchoranalysis.feature.bean.provider.FeatureProviderDefine
FeatureProviderDefine(Feature<T>) - Constructor for class org.anchoranalysis.feature.bean.provider.FeatureProviderDefine: Creates a new FeatureProviderDefine instance.
FeatureProviderReference - Class in org.anchoranalysis.feature.bean.provider: Provides an existing Feature identified by its name and optionally a feature-list in which is resides.
FeatureProviderReference() - Constructor for class org.anchoranalysis.feature.bean.provider.FeatureProviderReference
FeatureRelatedBean<T> - Class in org.anchoranalysis.feature.bean: Beans-related to Features, and which require initialization with FeatureRelatedInitialization.
FeatureRelatedBean() - Constructor for class org.anchoranalysis.feature.bean.FeatureRelatedBean: Create with default initializers.
FeatureRelatedInitialization - Class in org.anchoranalysis.feature.initialization: Parameters for initializing a FeatureRelatedBean.
FeatureResults - Class in org.anchoranalysis.feature.bean.results: Features that process ResultsVectorList.
FeatureResults() - Constructor for class org.anchoranalysis.feature.bean.results.FeatureResults
FeatureResultsAndThumbnails - Class in org.anchoranalysis.plugin.image.task.feature: A collection of results from feature calculation, and associated thumbnails.
FeatureResultsAndThumbnails(FeatureOutputMetadata, FeatureExporterContext) - Constructor for class org.anchoranalysis.plugin.image.task.feature.FeatureResultsAndThumbnails: Creates a new FeatureResultsAndThumbnails.
FeatureResultsStatistic - Class in org.anchoranalysis.feature.bean.results: Base class for an instance of FeatureResults that calculating a statistic across all results in the ResultsVectorList for a particular feature-value.
FeatureResultsStatistic() - Constructor for class org.anchoranalysis.feature.bean.results.FeatureResultsStatistic
FeatureResultSupplier - Interface in org.anchoranalysis.plugin.operator.feature.statistics: Supplies the result of a feature calculation.
features() - Method in class org.anchoranalysis.feature.store.NamedFeatureStore: All Features in the store, in identical order.
FeatureSession - Class in org.anchoranalysis.feature.session: A single-point in the code for creating feature-sessions (a factory).
FeaturesFromXMLFixture - Class in org.anchoranalysis.test.feature.plugins: A fixture for creating feature lists and feature list providers from XML files.
FeatureSingleMemo - Class in org.anchoranalysis.mpp.feature.bean.energy.element: An abstract base class for features that operate on a single memoized object.
FeatureSingleMemo() - Constructor for class org.anchoranalysis.mpp.feature.bean.energy.element.FeatureSingleMemo
FeatureSingleObject - Class in org.anchoranalysis.image.feature.bean.object.single: An abstract base class for features that operate on a single object.
FeatureSingleObject() - Constructor for class org.anchoranalysis.image.feature.bean.object.single.FeatureSingleObject
FeatureSingleObjectFromShared<T> - Class in org.anchoranalysis.plugin.image.feature.bean.shared.object: Calculates object-masks from entities in shared, using the feature-input only for an energy-stack.
FeatureSingleObjectFromShared() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.shared.object.FeatureSingleObjectFromShared
featuresInitialization() - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitialization: The associated initialization for a FeatureRelatedBean.
FeatureSource<T,S,U> - Class in org.anchoranalysis.plugin.image.task.bean.feature.source: Extracts features from some kind of inputs to produce one or more rows in a feature-table.
FeatureSource() - Constructor for class org.anchoranalysis.plugin.image.task.bean.feature.source.FeatureSource
FeatureStack - Class in org.anchoranalysis.image.feature.bean: An abstract base class for features that operate on image stacks.
FeatureStack() - Constructor for class org.anchoranalysis.image.feature.bean.FeatureStack
FeatureSymbolCalculator<T> - Interface in org.anchoranalysis.feature.calculate.cache: Resolves and calculates a feature by a symbol.
FeatureTableCalculator<T> - Interface in org.anchoranalysis.image.feature.calculator: A feature-calculator with additional functions for encoding the output in a tabular format with column names.
FeatureTableCSVGenerator<T> - Class in org.anchoranalysis.feature.io.csv.table: Base class for a Generator that outputs a feature-table in CSV format.
FeatureTableCSVGenerator(List<String>) - Constructor for class org.anchoranalysis.feature.io.csv.table.FeatureTableCSVGenerator: Creates a new FeatureTableCSVGenerator instance.
FeatureTableCSVGeneratorFactory - Class in org.anchoranalysis.feature.io.csv.table: Creates a FeatureTableCSVGenerator.
FeatureTestCalculator - Class in org.anchoranalysis.test.feature.plugins: Utility class for testing feature calculations in a controlled environment.
FeatureTestCalculatorDuo - Class in org.anchoranalysis.test.feature.plugins: Utility class for testing features with both positive and negative cases.
featureToCalcInputValue() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.CompareWithRange
featureToCalcInputValue() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.CompareWithRangeFeature
featureToCalcInputValue() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.IfConditionWithinRange
featureToCalcInputValue() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.IfOutsideRange
featureToCalcInputValue() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareBase: Specifies which feature to calculate the input value.
FeatureUnary<T,S> - Class in org.anchoranalysis.feature.bean.operator: A feature that contains another feature as a bean-parameter.
FeatureUnary() - Constructor for class org.anchoranalysis.feature.bean.operator.FeatureUnary
FeatureUnary(Feature<S>) - Constructor for class org.anchoranalysis.feature.bean.operator.FeatureUnary
FeatureUnaryGeneric<T> - Class in org.anchoranalysis.feature.bean.operator: A FeatureUnary that accepts any FeatureInput irrespective of type.
FeatureUnaryGeneric() - Constructor for class org.anchoranalysis.feature.bean.operator.FeatureUnaryGeneric
FeatureUnaryGeneric(Feature<T>) - Constructor for class org.anchoranalysis.feature.bean.operator.FeatureUnaryGeneric: Create with a specific feature, that provides the input to the unary function.
fetchUnmatchedWorker() - Method in class org.anchoranalysis.math.optimization.HungarianAlgorithm
FieldAccessor - Class in org.anchoranalysis.bean: Utilities to access a Field of an AnchorBean.
fieldFromBean(AnchorBean<?>, Field) - Static method in class org.anchoranalysis.bean.FieldAccessor: Retrieves the value of a Field from a AnchorBean.
fields() - Method in class org.anchoranalysis.bean.AnchorBean: A list of all bean-fields that are associated with this bean directly (fields of children are not checked).
FileDetails - Class in org.anchoranalysis.plugin.io.multifile
FileDetails(Path, Optional<Integer>, Optional<Integer>, Optional<Integer>) - Constructor for class org.anchoranalysis.plugin.io.multifile.FileDetails
fileExtensionWriter(OutputWriteSettings, StackWriteOptions, Optional<Logger>) - Static method in class org.anchoranalysis.image.io.stack.output.generator.GeneratorOutputter: The file extension to use for the default StackWriter, as returned by GeneratorOutputter.writer(OutputWriteSettings).
fileFormat(StackWriteOptions) - Method in class org.anchoranalysis.image.io.bean.stack.writer.OneOrThreeChannelsWriter
fileFormat(StackWriteOptions) - Method in class org.anchoranalysis.image.io.bean.stack.writer.StackWriter: The file format that will be written by the generator.
fileFormat(StackWriteOptions) - Method in class org.anchoranalysis.io.bioformats.bean.writer.OMETiff
fileFormat(StackWriteOptions) - Method in class org.anchoranalysis.io.bioformats.bean.writer.OMEXML
fileFormat(StackWriteOptions) - Method in class org.anchoranalysis.io.bioformats.bean.writer.Tiff
fileFormat(StackWriteOptions) - Method in class org.anchoranalysis.io.imagej.bean.stack.writer.PNG
fileFormat(StackWriteOptions) - Method in class org.anchoranalysis.io.imagej.bean.stack.writer.Tiff
fileFormat(StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.StackWriterDelegateBase
fileFormat(StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.WriteResolutionXml
FileFormat - Interface in org.anchoranalysis.core.format: A file-format that is read or written to the filesystem.
FileFormatFactory - Class in org.anchoranalysis.core.format: Creates a FileFormat from a string.
fileFormatWarnUnexpected(StackWriteOptions, Optional<Logger>) - Method in class org.anchoranalysis.image.io.bean.stack.writer.StackWriter: The file format that will be written by the generator, warning with a log message if different to suggestion.
FileInput - Class in org.anchoranalysis.io.input.file: An input pertaining to a single file on the file-system.
FileInput(NamedFile) - Constructor for class org.anchoranalysis.io.input.file.FileInput: Creates for a single file.
FileLabelMap<T> - Class in org.anchoranalysis.plugin.image.task.labeller: A map that associates file identifiers with labels, typically loaded from a CSV file.
filenameFromOutputFormatString(String, String) - Method in class org.anchoranalysis.io.output.namestyle.IndexableOutputNameStyle: Constructs a file name from the output format string and an index.
filenameFromOutputFormatString(String, String) - Method in class org.anchoranalysis.io.output.namestyle.IntegerSuffixOutputNameStyle
filenameFromOutputFormatString(String, String) - Method in class org.anchoranalysis.io.output.namestyle.StringSuffixOutputNameStyle
FileNamer - Class in org.anchoranalysis.io.input.bean.namer: Associates a name (a compact unique identifier) with a file.
FileNamer() - Constructor for class org.anchoranalysis.io.input.bean.namer.FileNamer
FileNamerContext - Class in org.anchoranalysis.io.input.file: Provides useful additional objects when assigning a name to a file.
FileNamerContext(String, Logger) - Constructor for class org.anchoranalysis.io.input.file.FileNamerContext: Creates with a fallback-name and a logger, but otherwise using sensible defaults.
FileNamerContext(Optional<Path>, boolean, String, Optional<IndexRangeNegative>, Logger) - Constructor for class org.anchoranalysis.io.input.file.FileNamerContext: Creates a new FileNamerContext instance.
FileNamerContext(Optional<Path>, boolean, Optional<IndexRangeNegative>, Logger) - Constructor for class org.anchoranalysis.io.input.file.FileNamerContext: Creates with specific parameters.
FileNamerContext(Logger) - Constructor for class org.anchoranalysis.io.input.file.FileNamerContext: Creates with a logger, and otherwise uses sensible defaults.
FileNamerIndependent - Class in org.anchoranalysis.io.input.bean.namer: Base class for methods that derive the name independently for each file.
FileNamerIndependent() - Constructor for class org.anchoranalysis.io.input.bean.namer.FileNamerIndependent
FilenameSplitExtension - Class in org.anchoranalysis.core.system.path: A file-name with the base (without extension) split from the extension.
FilenameSplitExtension(String, Optional<String>) - Constructor for class org.anchoranalysis.core.system.path.FilenameSplitExtension: Creates from a path without an extension.
filenameWithoutExtension() - Method in class org.anchoranalysis.io.output.namestyle.IndexableOutputNameStyle
filenameWithoutExtension() - Method in class org.anchoranalysis.io.output.namestyle.OutputNameStyle: The filename to be written, including prefix, suffix, etc. but excluding extension (and any period before the extension).
filenameWithoutExtension() - Method in class org.anchoranalysis.io.output.namestyle.SimpleOutputNameStyle
filenameWithoutExtension() - Method in class org.anchoranalysis.io.output.namestyle.WithoutOutputNameStyle
filenameWithoutExtension(int) - Method in class org.anchoranalysis.io.output.namestyle.IndexableOutputNameStyle: Like IndexableOutputNameStyle.filenameWithoutExtension() but incorporates an integer index.
filenameWithoutExtension(File) - Static method in class org.anchoranalysis.core.system.path.ExtensionUtilities: Retrieves filename from a File but without any extension.
filenameWithoutExtension(String) - Method in class org.anchoranalysis.io.output.namestyle.IndexableOutputNameStyle: Like IndexableOutputNameStyle.filenameWithoutExtension() but incorporates an string index.
filePath() - Method in class org.anchoranalysis.mpp.io.input.MultiInput: Gets the map of Paths.
FilePath - Class in org.anchoranalysis.plugin.io.bean.file.path
FilePath() - Constructor for class org.anchoranalysis.plugin.io.bean.file.path.FilePath
FilePathBean<T> - Class in org.anchoranalysis.bean.shared.path: Base class for beans that require initialization with FilePathInitialization.
FilePathBean() - Constructor for class org.anchoranalysis.bean.shared.path.FilePathBean
filePathDifference(Path, Path) - Static method in class org.anchoranalysis.plugin.io.file.copy.PathOperations: Finds the difference between a path and a base.
FilePathInitialization - Class in org.anchoranalysis.bean.shared.path: Initialization parameters for a named-set of file-paths.
FilePathInitialization(SharedObjects) - Constructor for class org.anchoranalysis.bean.shared.path.FilePathInitialization: Creates using a SharedObjects to create a NamedProviderStore for the file-paths.
FilePathMatcher - Class in org.anchoranalysis.io.input.bean.path.matcher: Matches file-paths against some kind of pattern.
FilePathMatcher() - Constructor for class org.anchoranalysis.io.input.bean.path.matcher.FilePathMatcher
FilePathParser - Class in org.anchoranalysis.plugin.io.bean.file.group.parser
FilePathParser() - Constructor for class org.anchoranalysis.plugin.io.bean.file.group.parser.FilePathParser
FilePathPattern - Class in org.anchoranalysis.plugin.io.bean.summarizer.path: Converts a list of file-paths into a form that tries to find a pattern in the naming style using the path-pattern-finder library.
FilePathPattern() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.path.FilePathPattern
FilePathPattern(String...) - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.path.FilePathPattern: Create with one or more paths.
FilePathProvider - Class in org.anchoranalysis.io.input.bean.path.provider: Base class for beans that implement Provider to provide a Path.
FilePathProvider() - Constructor for class org.anchoranalysis.io.input.bean.path.provider.FilePathProvider
FilePathProviderReference - Class in org.anchoranalysis.io.input.bean.path.provider: Calls an existing FilePathProvider indirectly to provide an identical result.
FilePathProviderReference() - Constructor for class org.anchoranalysis.io.input.bean.path.provider.FilePathProviderReference
filePaths() - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitialization: Named-store of file-paths.
FilePathToUnixStyleConverter - Class in org.anchoranalysis.core.system.path: Conversion to Unix-style separators.
FileSetFromStringSet - Class in org.anchoranalysis.plugin.io.bean.file.provider
FileSetFromStringSet() - Constructor for class org.anchoranalysis.plugin.io.bean.file.provider.FileSetFromStringSet
FileSizeStatistics - Class in org.anchoranalysis.plugin.io.bean.summarizer.path: Tracks the range of file-size.
FileSizeStatistics() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.path.FileSizeStatistics
FilesProvider - Class in org.anchoranalysis.io.input.bean.files: Base class for providing a list of Files.
FilesProvider() - Constructor for class org.anchoranalysis.io.input.bean.files.FilesProvider
FilesProviderException - Exception Class in org.anchoranalysis.io.input.file: When an error occurs providing a set of files.
FilesProviderException(String) - Constructor for exception class org.anchoranalysis.io.input.file.FilesProviderException: Create with a message only.
FilesProviderException(Throwable) - Constructor for exception class org.anchoranalysis.io.input.file.FilesProviderException: Create with a cause only.
FilesProviderUnary - Class in org.anchoranalysis.io.input.bean.files: Like FilesProvider but employs a unary operator on a call to an existing FilesProvider.
FilesProviderUnary() - Constructor for class org.anchoranalysis.io.input.bean.files.FilesProviderUnary
FilesProviderWithDirectory - Class in org.anchoranalysis.io.input.bean.files: Base class for implementations of FilesProvider which do have an associated directory.
FilesProviderWithDirectory() - Constructor for class org.anchoranalysis.io.input.bean.files.FilesProviderWithDirectory
FilesProviderWithDirectoryString - Class in org.anchoranalysis.io.input.bean.files: A FilesProviderWithDirectory where the directory is optionally specified as a string constant
FilesProviderWithDirectoryString() - Constructor for class org.anchoranalysis.io.input.bean.files.FilesProviderWithDirectoryString
FilesProviderWithDirectoryUnary - Class in org.anchoranalysis.io.input.bean.files: Like FilesProviderWithDirectory but employs a unary operator on a call to an existing FilesProviderWithDirectory.
FilesProviderWithDirectoryUnary() - Constructor for class org.anchoranalysis.io.input.bean.files.FilesProviderWithDirectoryUnary
FilesProviderWithoutDirectory - Class in org.anchoranalysis.io.input.bean.files: Base class for implementations of FilesProvider which do not have an associated directory.
FilesProviderWithoutDirectory() - Constructor for class org.anchoranalysis.io.input.bean.files.FilesProviderWithoutDirectory
FileWithDirectoryInput - Class in org.anchoranalysis.io.input.file: An input pertaining to a single file on the file-system - and a directory in which it resides.
FileWithDirectoryInput(NamedFile, Path) - Constructor for class org.anchoranalysis.io.input.file.FileWithDirectoryInput: Create for a particular file and directory.
fill(BinaryVoxels<UnsignedByteBuffer>) - Static method in class org.anchoranalysis.plugin.imagej.mask.ApplyImageJMorphologicalOperation: Applies the fill operation to the given binary voxels.
Fill - Class in org.anchoranalysis.image.bean.spatial.arrange.fill: Montages Extents together to completely fill the available space, while preserving aspect ratio.
Fill() - Constructor for class org.anchoranalysis.image.bean.spatial.arrange.fill.Fill
Fill(int) - Constructor for class org.anchoranalysis.image.bean.spatial.arrange.fill.Fill: Create with a particular number of rows.
Fill(int, boolean, int, double) - Constructor for class org.anchoranalysis.image.bean.spatial.arrange.fill.Fill: Creates a new Fill instance.
Filled - Class in org.anchoranalysis.image.io.bean.object.draw: Draws a filled-in shape for each object.
Filled() - Constructor for class org.anchoranalysis.image.io.bean.object.draw.Filled
FillHoles - Class in org.anchoranalysis.plugin.imagej.bean.mask.provider: Fills holes in a mask, with options to skip holes touching the border or exceeding a maximum volume.
FillHoles - Class in org.anchoranalysis.plugin.imagej.bean.object.provider: Fills holes in an object.
FillHoles() - Constructor for class org.anchoranalysis.plugin.imagej.bean.mask.provider.FillHoles
FillHoles() - Constructor for class org.anchoranalysis.plugin.imagej.bean.object.provider.FillHoles
filter(Predicate<ObjectMask>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream: Filters a ObjectCollection to include certain items based on a predicate
filter(Stream<T>, Class<? extends Exception>, CheckedPredicate<T, E>) - Static method in class org.anchoranalysis.core.functional.CheckedStream: Performs a Stream.filter(java.util.function.Predicate<? super T>) but accepts a predicate that can throw a checked-exception.
filter(CheckedPredicate<ObjectMask, E>, Class<? extends Exception>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream: Filters a ObjectCollection to include certain items based on a predicate
filter(ObjectCollection, Optional<Dimensions>) - Method in class org.anchoranalysis.image.bean.object.ObjectFilter: Filters an ObjectCollection to remove objects.
filter(ObjectCollection, Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.combine.And
filter(ObjectCollection, Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.combine.Or
filter(ObjectCollection, Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterPredicate
filter(ObjectCollection, Optional<Dimensions>, Optional<List<ObjectMask>>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.ObjectCollectionProviderFilterBase: Filters the given object collection using the specified filter.
Filter - Class in org.anchoranalysis.plugin.image.bean.object.provider.filter: Filters an ObjectCollection using the specified ObjectFilter.
Filter - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel: Applies an object-filter to the results of an upstream segmentation.
Filter() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.filter.Filter
Filter() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.channel.Filter
filterAndMap(Predicate<Feature<T>>, CheckedFunction<Feature<T>, Feature<S>, E>) - Method in class org.anchoranalysis.feature.bean.list.FeatureList: Filters inputs and then performs a FeatureList.map(org.anchoranalysis.core.functional.checked.CheckedFunction<org.anchoranalysis.feature.bean.Feature<T>, org.anchoranalysis.feature.bean.Feature<S>, E>).
filterAndMap(Predicate<ObjectMask>, UnaryOperator<ObjectMask>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream: Performs a ObjectMaskStream.filter(java.util.function.Predicate<org.anchoranalysis.image.voxel.object.ObjectMask>) and then a ObjectMaskStream.map(org.anchoranalysis.core.functional.checked.CheckedFunction<org.anchoranalysis.image.voxel.object.ObjectMask, org.anchoranalysis.image.voxel.object.ObjectMask, E>).
filterAndMapFrom(Collection<T>, Predicate<T>, Class<? extends E>, CheckedFunction<T, ObjectMask, E>) - Static method in class org.anchoranalysis.image.voxel.object.ObjectCollectionFactory: Creates a new collection by filtering an iterable and then mapping it to ObjectMask.
filterAndMapFrom(Collection<T>, Predicate<T>, Function<T, ObjectMask>) - Static method in class org.anchoranalysis.image.voxel.object.ObjectCollectionFactory: Creates a new collection by filtering an iterable and then mapping it to ObjectMask.
filterAndMapToList(List<S>, CheckedPredicate<S, E>, CheckedFunction<S, T, E>) - Static method in class org.anchoranalysis.core.functional.FunctionalList: Creates a new collection by filtering a list and then mapping to a list of another type.
filterAndMapWithIndexFrom(List<T>, Predicate<T>, Class<? extends E>, CheckedBiFunction<T, Integer, ObjectMask, E>) - Static method in class org.anchoranalysis.image.voxel.object.ObjectCollectionFactory: Creates a new collection by filtering a list and then mapping from it to ObjectMask.
filterAndMapWithIndexToList(List<S>, Predicate<S>, CheckedFunctionWithInt<S, T, E>) - Static method in class org.anchoranalysis.core.functional.FunctionalList: Creates a new collection by filtering a list and then mapping (with an index) to a list of another type.
FilterByGroup - Class in org.anchoranalysis.plugin.image.bean.object.provider.filter: Filters an ObjectCollection by grouping objects and then applying a filter to each group.
FilterByGroup() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.filter.FilterByGroup
FilterCSVColumn<T> - Class in org.anchoranalysis.plugin.io.bean.input.filter: Finds a CSV file with the names of an input as the first-column.
FilterCSVColumn() - Constructor for class org.anchoranalysis.plugin.io.bean.input.filter.FilterCSVColumn
FilterDescriptiveName<T> - Class in org.anchoranalysis.plugin.io.bean.input.filter: Filters all the input objects for only those with certain types of descriptive-names.
FilterDescriptiveName() - Constructor for class org.anchoranalysis.plugin.io.bean.input.filter.FilterDescriptiveName
FilterDescriptiveNameEqualsContains - Class in org.anchoranalysis.plugin.io.input.filter: Filters a list of input-objects by the descriptive name.
FilterDescriptiveNameEqualsContains(String, String) - Constructor for class org.anchoranalysis.plugin.io.input.filter.FilterDescriptiveNameEqualsContains: Creates a new FilterDescriptiveNameEqualsContains instance.
filterExclude(Predicate<ObjectMask>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream: Filters a ObjectCollection to exclude certain items based on a predicate
FilterForExistingFiles - Class in org.anchoranalysis.plugin.io.bean.input.files.provider
FilterForExistingFiles() - Constructor for class org.anchoranalysis.plugin.io.bean.input.files.provider.FilterForExistingFiles
FilterHelper - Class in org.anchoranalysis.plugin.imagej.channel.provider: Helper class for applying filters to Channels and BinaryVoxels using ImageJ operations.
FilterIfDebug<T> - Class in org.anchoranalysis.plugin.io.bean.input.filter: Filters a list of inputs when in debug-mode
FilterIfDebug() - Constructor for class org.anchoranalysis.plugin.io.bean.input.filter.FilterIfDebug
filterSubset(Predicate<ObjectMask>, Collection<Integer>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream: Like ObjectMaskStream.filter(java.util.function.Predicate<org.anchoranalysis.image.voxel.object.ObjectMask>) but only operates on certain indices of the collection.
filterSubsetStream(Predicate<ObjectMask>, Collection<Integer>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream: Like ObjectMaskStream.filterSubset(java.util.function.Predicate<org.anchoranalysis.image.voxel.object.ObjectMask>, java.util.Collection<java.lang.Integer>) but returns a stream rather than a ObjectCollection.
filterToList(Collection<T>, Class<? extends Exception>, CheckedPredicate<T, E>) - Static method in class org.anchoranalysis.core.functional.FunctionalList: Filters a collection and maps the result to a list.
filterToList(Collection<T>, Predicate<T>) - Static method in class org.anchoranalysis.core.functional.FunctionalList: Filters a collection and maps the result to a list.
FilterWithRegularExpression - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming: Rejects files that fail to match a particular regular-expression
FilterWithRegularExpression() - Constructor for class org.anchoranalysis.plugin.io.bean.file.copy.naming.FilterWithRegularExpression
Findable<T> - Interface in org.anchoranalysis.annotation.io.image.findable: Parent class for an element that exists in one of two-states, either Found or NotFound.
findAllNonInputFiles() - Method in class org.anchoranalysis.io.input.InputsWithDirectory: Find all files in the input directory are not used as inputs.
findArbitraryOnVoxel() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Finds any arbitrary on voxel on the object.
findClosestResult(Point3i) - Method in class org.anchoranalysis.plugin.image.intensity.level.LevelResultCollection: Finds the LevelResult closest to a given point.
FindCommonVoxelType - Class in org.anchoranalysis.image.voxel.datatype: Finds a common voxel-data type to represent two types.
FindContour - Class in org.anchoranalysis.image.core.contour: Finds contour voxels, the pixels forming a continuous path along the boundary of the object or mask.
findConvertedInputFor(NamedChannelsInput, MessageLogger) - Method in class org.anchoranalysis.plugin.mpp.shared.SharedStateRememberConverted: Finds a converted-input that has been remembered.
findDirectoryWithName(Metadata, Class<T>, String) - Static method in class org.anchoranalysis.io.bioformats.metadata.ReadMetadataUtilities: Finds the first Directory in the metadata with type directoryType and whose name is equal to directoryName.
finderForGrandchild() - Method in class org.anchoranalysis.feature.session.cache.finder.CheckCacheForSpecificChildren
finderForGrandchild() - Method in interface org.anchoranalysis.feature.session.cache.finder.ChildCacheFinder: What finder to use for children-of-children?
finderForGrandchild() - Method in class org.anchoranalysis.feature.session.cache.finder.DefaultChildCacheFinder
findFieldsOfClass(Class<?>) - Method in class org.anchoranalysis.bean.AnchorBean: Finds all bean-fields that are instances of a certain class.
FindFilesException - Exception Class in org.anchoranalysis.io.input.path.matcher: When an error occurs finding files.
FindFilesException(String) - Constructor for exception class org.anchoranalysis.io.input.path.matcher.FindFilesException: Create with a message only.
FindFilesException(String, Throwable) - Constructor for exception class org.anchoranalysis.io.input.path.matcher.FindFilesException: Create with a message and cause.
findMatch(ObjectCollection) - Method in class org.anchoranalysis.image.bean.object.ObjectMatcher: Finds matches for objects.
findMatch(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.match.Always
findMatch(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.match.Bridge
findMatch(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.match.Intersection
findMaxPriority() - Method in class org.anchoranalysis.plugin.image.object.merge.MergeGraph: Finds the edge with the maximum priority for merging.
findMostDeepCombinableException() - Method in exception class org.anchoranalysis.core.exception.combinable.AnchorCombinableException: Traverses through the nested-exceptions and finds the most deep exception that is combinable.
findOptimalInput(int) - Method in class org.anchoranalysis.math.optimization.SearchClosestValueMonoticallyIncreasing: Finds the input value that produces a calculated-value that is closest to target.
findRoot(String, boolean) - Method in class org.anchoranalysis.plugin.io.input.path.RootPathMap: Finds a root to match a name and debug/status
first() - Method in class org.anchoranalysis.io.output.recorded.MultiLevelRecordedOutputs: For recording first-level outputs.
First - Class in org.anchoranalysis.image.feature.bean.object.pair: Evaluates a feature on the first object in a pair of objects.
First() - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.First
First(Feature<FeatureInputSingleObject>) - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.First: Creates a new instance that will evaluate the given feature on the first object of a pair.
FIRST - Enum constant in enum class org.anchoranalysis.image.feature.calculation.CalculateInputFromPair.Extract: Extract the first object from the pair.
firstCheck(KernelPointCursor, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.kernel.morphological.BinaryKernelMorphological: The first check done on the kernel center-point, before checking any neighbors.
firstCheck(KernelPointCursor, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.kernel.morphological.DilationKernel
firstCheck(KernelPointCursor, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.kernel.morphological.ErosionKernel
firstCheck(KernelPointCursor, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.kernel.outline.OutlineKernelBase
firstLevelContains(String) - Method in class org.anchoranalysis.io.output.bean.rules.OutputEnableRulesSpecify: Whether the first-level names contain a particular output (if defined)?
firstPart() - Method in class org.anchoranalysis.feature.io.name.CombinedName
firstPart() - Method in interface org.anchoranalysis.feature.io.name.MultiName: The first part, and grouping key.
firstPart() - Method in class org.anchoranalysis.feature.io.name.SimpleName
fit(List<Point3f>, Mark, Dimensions) - Method in class org.anchoranalysis.mpp.bean.points.fitter.PointsFitter: Fits a mark to a set of points within given dimensions.
fit(List<Point3f>, Mark, Dimensions) - Method in class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresEllipseFitter
fit(List<Point3f>, Mark, Dimensions) - Method in class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresEllipsoidFitter
fit(List<Point3f>, Mark, Dimensions) - Method in class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresViaNormalEquationBase
fit(List<Point3f>, Mark, Dimensions) - Method in class org.anchoranalysis.plugin.points.bean.fitter.Reference
fit(List<Point3f>, Mark, Dimensions) - Method in class org.anchoranalysis.plugin.points.bean.fitter.ReflectInAxesWithinDistance
FitBoxToOnVoxels - Class in org.anchoranalysis.plugin.image.bean.mask.provider.morphological: Fits a box around the on voxels.
FitBoxToOnVoxels() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.FitBoxToOnVoxels
FitCombinedScaler - Class in org.anchoranalysis.image.bean.spatial.arrange.fill: Scales the size of images to match the target image, preserving aspect-ratio.
fitMarkToPointsFromMarks(MarkCollection, Dimensions) - Method in class org.anchoranalysis.mpp.bean.points.CreateMarkFromPoints: Extracts points from marks, creates a new mark, and fits this mark to the extracted points.
FitPoints - Class in org.anchoranalysis.plugin.points.bean: A MarkProposer that fits points to a mark using a PointsProposer and a PointsFitter.
FitPoints() - Constructor for class org.anchoranalysis.plugin.points.bean.FitPoints
FitPointsFromObjects - Class in org.anchoranalysis.plugin.points.bean: A MarkCollectionProvider that fits points from objects to create marks.
FitPointsFromObjects() - Constructor for class org.anchoranalysis.plugin.points.bean.FitPointsFromObjects
fitPointsToMark(List<Point3f>, Mark, Dimensions) - Method in class org.anchoranalysis.plugin.points.bean.fitter.PointsFitterToMark: Fits a list of points to a mark using the specified points fitter.
FitResult - Class in org.anchoranalysis.plugin.points.bean.fitter: Represents the result of fitting an ellipsoid to a set of points.
FitResult() - Constructor for class org.anchoranalysis.plugin.points.bean.fitter.FitResult
FitTo - Class in org.anchoranalysis.plugin.image.bean.scale: Scales an image to approximately similar in size to a SizeXY.
FitTo() - Constructor for class org.anchoranalysis.plugin.image.bean.scale.FitTo
flagForNoRegion() - Static method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipUtilities: Gets the flag representing no region membership.
flagForRegion(int) - Static method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipUtilities: Gets the flag for a specific region index.
flagForRegion(int, int) - Static method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipUtilities: Combines flags for two regions.
flagForRegion(int, int, int) - Static method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipUtilities: Combines flags for three regions.
flags() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership: Calculates the flags as a byte based on the current region memberships.
flatMap(Class<? extends Exception>, CheckedFunction<ObjectMask, ObjectCollection, E>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream: Like a typical flatMap() operation but accepts a mapping function that throws a checked exception.
flatMap(Function<ObjectMask, ObjectCollection>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream: Creates a new ObjectCollection after mapping each item to several others.
flatMap(Optional<S>, CheckedFunction<S, Optional<T>, E>) - Static method in class org.anchoranalysis.core.functional.OptionalUtilities: Like Optional.flatMap(java.util.function.Function<? super T, ? extends java.util.Optional<? extends U>>) but tolerates an exception in the mapping function, which is immediately thrown.
flatMap(Stream<S>, Class<? extends Exception>, CheckedFunction<S, Stream<? extends T>, E>) - Static method in class org.anchoranalysis.core.functional.CheckedStream: Performs a Stream.flatMap(java.util.function.Function<? super T, ? extends java.util.stream.Stream<? extends R>>) but accepts a function that can throw a checked-exception
flatMapFrom(Collection<T>, Function<T, ObjectCollection>) - Static method in class org.anchoranalysis.image.voxel.object.ObjectCollectionFactory: Creates a new collection by flat-mapping an incoming stream to ObjectCollection.
flatMapFrom(Stream<T>, Class<? extends Exception>, CheckedFunction<T, ObjectCollection, E>) - Static method in class org.anchoranalysis.image.voxel.object.ObjectCollectionFactory: Creates a new collection by flat-mapping an incoming stream to ObjectCollection and rethrowing any exception during mapping.
flatMapFromCollection(Stream<T>, Class<? extends Exception>, CheckedFunction<T, Stream<? extends ObjectMask>, E>) - Static method in class org.anchoranalysis.image.voxel.object.ObjectCollectionFactory: Creates a new ObjectCollection by flatMapping an incoming stream to Collection<ObjectMask> and rethrowing any exception during mapping.
flatMapFromOptional(Iterable<S>, CheckedFunction<S, Optional<FeatureList<T>>, E>) - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory: Creates a new feature-list by flat-mapping an iterable to an optional feature
flatMapFromRange(int, int, Class<? extends Exception>, CheckedIntFunction<ObjectCollection, E>) - Static method in class org.anchoranalysis.image.voxel.object.ObjectCollectionFactory: Creates a new collection by flat-mapping integers (from a range) each to a ObjectCollection.
flatMapFromRange(int, int, IntFunction<ObjectCollection>) - Static method in class org.anchoranalysis.image.voxel.object.ObjectCollectionFactory: Creates a new collection by flat-mapping integers (from a range) each to a ObjectCollection.
flatMapFromStream(Stream<T>, Class<? extends Exception>, CheckedFunction<T, Stream<ObjectMask>, E>) - Static method in class org.anchoranalysis.image.voxel.object.ObjectCollectionFactory: Creates a new collection by flat-mapping an incoming stream to ObjectCollection and rethrowing any exception during mapping.
flatMapToList(Collection<S>, Class<? extends Exception>, CheckedFunction<S, Stream<? extends T>, E>) - Static method in class org.anchoranalysis.core.functional.FunctionalList: Flat-maps a collection to a list where in the original collection can produce many elements in the outgoing list.
flatMapToList(Collection<S>, Function<S, Stream<T>>) - Static method in class org.anchoranalysis.core.functional.FunctionalList: Flat-maps a collection to a list where in the original collection can produce many elements in the outgoing list.
Flatten - Class in org.anchoranalysis.image.io.bean.object.draw: Performs a flattening (maximum intensity projection in each channel) of the output of another writer
Flatten() - Constructor for class org.anchoranalysis.image.io.bean.object.draw.Flatten
Flatten(DrawObject) - Constructor for class org.anchoranalysis.image.io.bean.object.draw.Flatten
FlattenAsChannel - Class in org.anchoranalysis.plugin.io.bean.stack.reader: Combines all series and frames returned by a reader by converting them into multiple channels in the same image.
FlattenAsChannel() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.reader.FlattenAsChannel
flattenFrom(Voxels<FloatBuffer>) - Method in class org.anchoranalysis.image.voxel.projection.CountedProjectableBuffer: Flattens the accumulated voxels to the target type.
FlattenStackGenerator - Class in org.anchoranalysis.image.io.stack.output.generator: Like a StackGenerator but first applies a maximum-intensity-projection.
FlattenStackGenerator(boolean) - Constructor for class org.anchoranalysis.image.io.stack.output.generator.FlattenStackGenerator: Creates with possible padding.
flattenZ() - Method in class org.anchoranalysis.image.core.mask.Mask: Creates an otherwise identical Mask but a maximum-intensity-projection applied to the z-dimension.
flattenZ() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: A maximum-intensity projection.
flattenZ() - Method in class org.anchoranalysis.plugin.image.object.ColoredObject: A maximum-intensity projection.
flattenZ() - Method in class org.anchoranalysis.plugin.image.object.ColoredObjectCollection: A maximum-intensity projection.
flattenZ() - Method in class org.anchoranalysis.spatial.box.BoundingBox: Collapses the z-dimension of the box to a single voxel depth, and a corner at 0 voxels.
flattenZ() - Method in class org.anchoranalysis.spatial.box.Extent: Collapses the Z dimension.
FlattenZ - Class in org.anchoranalysis.plugin.image.bean.mask.provider.slice: Flattens a mask in the z-dimension, so it is 2D instead of 3D (like a maximum intensity projection).
FlattenZ - Class in org.anchoranalysis.plugin.image.bean.object.provider.slice: Flattens all object-masks in the z-dimension, so it is 2D instead of 3D (like a maximum intensity projection).
FlattenZ() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.slice.FlattenZ
FlattenZ() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.slice.FlattenZ
floatArray(float[]) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferWrap: Wraps an float-array into a voxel-buffer.
floatBuffer(FloatBuffer) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferWrap: Wraps a float buffer into a voxel-buffer.
floatFromDouble(Point2d) - Static method in class org.anchoranalysis.spatial.point.PointConverter: Convert a Point2d to a Point2f.
floatFromDouble(Point3d) - Static method in class org.anchoranalysis.spatial.point.PointConverter: Convert a Point3d to a Point3f.
floatFromInt(Point2i) - Static method in class org.anchoranalysis.spatial.point.PointConverter: Convert a Point2i to a Point3f using 0 as the value of the Z-axis component.
floatFromInt(ReadableTuple3i) - Static method in class org.anchoranalysis.spatial.point.PointConverter: Convert a ReadableTuple3i to a Point3f.
floatFromIntDropZ(ReadableTuple3i) - Static method in class org.anchoranalysis.spatial.point.PointConverter: Creates a ReadableTuple3i to a Point3f, preserving X- and Y-components but set setting the Z-component to be 0.
floatFromMat(Mat, Extent) - Static method in class org.anchoranalysis.plugin.opencv.convert.VoxelBufferFromMat: Converts a Mat to a VoxelBuffer with voxel data-type FloatBuffer.
FloatFromUnsignedByte - Class in org.anchoranalysis.io.bioformats.copyconvert.tofloat: Convert to a float buffer, given an unsigned-byte source buffer.
FloatFromUnsignedByte() - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.tofloat.FloatFromUnsignedByte
FloatFromUnsignedInt - Class in org.anchoranalysis.io.bioformats.copyconvert.tofloat: Convert to a float buffer, given an unsigned-int source buffer.
FloatFromUnsignedInt() - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.tofloat.FloatFromUnsignedInt
FloatUtilities - Class in org.anchoranalysis.math.arithmetic: Utilities for arithmetic operations involving type float.
FloatVoxelType - Class in org.anchoranalysis.image.voxel.datatype: A 32-bit voxel data-type representing floating-point numbers, as per the Java primitive float type.
FloodFillEachIntensityLevel - Class in org.anchoranalysis.plugin.imagej.bean.object.segment: Creates an object for each separate intensity-value (beginning at startingColor) by flood-filling.
FloodFillEachIntensityLevel() - Constructor for class org.anchoranalysis.plugin.imagej.bean.object.segment.FloodFillEachIntensityLevel
flushAndClose(Optional<NamedFeatureStore<FeatureInputResults>>, boolean, Function<InputOutputContext, FeatureCSVWriterFactory>, FeatureOutputMetadata, InputOutputContext) - Method in interface org.anchoranalysis.feature.io.results.LabelledResultsCollector: Writes any queued (but not yet written elements to the file-system), and closes open file-handles.
forBoxes(BoundingBox, BoundingBox) - Static method in class org.anchoranalysis.spatial.box.IntersectionOverUnion: Calculates the intersection-over-union score a pair of bounding-boxes.
ForceBitsPerPixel - Class in org.anchoranalysis.io.bioformats.bean.options: Forces the bits per pixel to be a specific-value, irrespective of what bioformats infers.
ForceBitsPerPixel() - Constructor for class org.anchoranalysis.io.bioformats.bean.options.ForceBitsPerPixel
ForceNumberChannels - Class in org.anchoranalysis.io.bioformats.bean.options: Forces the number of channels to be a specific-value, irrespective of what bioformats infers.
ForceNumberChannels() - Constructor for class org.anchoranalysis.io.bioformats.bean.options.ForceNumberChannels
ForceNumberFrames - Class in org.anchoranalysis.io.bioformats.bean.options: Forces the number of frames to be a specific-value, irrespective of what bioformats infers.
ForceNumberFrames() - Constructor for class org.anchoranalysis.io.bioformats.bean.options.ForceNumberFrames
ForceTimeSeriesToStack - Class in org.anchoranalysis.io.bioformats.bean.options: Treats a time-series as if it was a z-stack
ForceTimeSeriesToStack() - Constructor for class org.anchoranalysis.io.bioformats.bean.options.ForceTimeSeriesToStack
forChild() - Method in interface org.anchoranalysis.feature.calculate.FeatureCalculationInput: Performs calculations not on the main cache, but on a child cache.
forChild() - Method in class org.anchoranalysis.feature.session.SessionInputSequential
forEach(Consumer<RecordedExecutionTimes.RecordedOperation>) - Method in class org.anchoranalysis.core.time.RecordedExecutionTimes: For each unique operation with a recorded-time, call consumer.
forEach(Consumer<Feature<T>>) - Method in class org.anchoranalysis.feature.shared.SharedFeaturesSubset: Iterates over each feature in the instance.
forEach(Stream<T>, Class<? extends Exception>, CheckedConsumer<T, E>) - Static method in class org.anchoranalysis.core.functional.CheckedStream: Performs a Stream.forEach(java.util.function.Consumer<? super T>) but accepts a consumer that can throw a checked-exception.
forEach(CheckedBiConsumer<String, StoreSupplier<Stack>, E>) - Method in class org.anchoranalysis.image.core.stack.named.NamedStacks: Iterates over each entry in the map.
forEachProperty(BiConsumer<String, Object>) - Method in class org.anchoranalysis.image.core.object.properties.ObjectWithProperties: Executes a consumer on each property.
forgetAll() - Method in class org.anchoranalysis.plugin.mpp.shared.SharedStateRememberConverted: Forgets all converted inputs.
format() - Method in class org.anchoranalysis.plugin.io.bean.metadata.header.BMP
format() - Method in class org.anchoranalysis.plugin.io.bean.metadata.header.HeaderFormat: The associated ImageFileFormat with this header.
format() - Method in class org.anchoranalysis.plugin.io.bean.metadata.header.JPEG
format() - Method in class org.anchoranalysis.plugin.io.bean.metadata.header.PNG
FormatExtensions - Class in org.anchoranalysis.core.format: File extensions for various formats.
formatter() - Method in enum class org.anchoranalysis.plugin.io.naming.interval.DateStyle: Derives a formatter for the particular date-style.
ForSpecificAxis<T> - Class in org.anchoranalysis.plugin.image.feature.bean.dimensions: Dimensions-calculation for one specific axis only.
ForSpecificAxis() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.dimensions.ForSpecificAxis
Found<T> - Class in org.anchoranalysis.annotation.io.image.findable: A positive-result when an object is found at a particular location.
Found(T) - Constructor for class org.anchoranalysis.annotation.io.image.findable.Found: Creates a new Found instance.
FourChannelStackTester - Class in org.anchoranalysis.test.image.stackwriter: Helper methods to test a RasterWriter on stacks with between 1 and 4 channels.
FourChannelStackTester(StackTester, ImageComparer, boolean) - Constructor for class org.anchoranalysis.test.image.stackwriter.FourChannelStackTester: Creates for a tester and comparer.
FrequencyMap<T> - Class in org.anchoranalysis.plugin.io.shared: Counts the frequency of certain strings, and describes the contents in human language.
FrequencyMap() - Constructor for class org.anchoranalysis.plugin.io.shared.FrequencyMap
FriendlyExceptionCreator - Class in org.anchoranalysis.bean.xml.exception: Converts certain exceptions that occur from XML-Parsing into a friendly form to display to the user.
friendlyMessage() - Method in exception class org.anchoranalysis.core.exception.friendly.AnchorFriendlyCheckedException
friendlyMessage() - Method in exception class org.anchoranalysis.core.exception.friendly.AnchorFriendlyRuntimeException
friendlyMessage() - Method in interface org.anchoranalysis.core.exception.friendly.HasFriendlyErrorMessage: A friendly message to describe to the user what went wrong.
friendlyMessageHierarchy() - Method in exception class org.anchoranalysis.core.exception.friendly.AnchorFriendlyCheckedException
friendlyMessageHierarchy() - Method in exception class org.anchoranalysis.core.exception.friendly.AnchorFriendlyRuntimeException
friendlyMessageHierarchy() - Method in interface org.anchoranalysis.core.exception.friendly.HasFriendlyErrorMessage: A friendly message to describe to the user what went wrong, which doesn't impose a fixed-size, or showExceptionNames
friendlyMessageHierarchy(Writer, int, boolean) - Method in exception class org.anchoranalysis.core.exception.friendly.AnchorFriendlyCheckedException
friendlyMessageHierarchy(Writer, int, boolean) - Method in exception class org.anchoranalysis.core.exception.friendly.AnchorFriendlyRuntimeException
friendlyMessageHierarchy(Writer, int, boolean) - Method in interface org.anchoranalysis.core.exception.friendly.HasFriendlyErrorMessage: A friendly message to describe to the user what went wrong, including all nested exceptions that have a non-empty error message
from(Feature<T>...) - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory: Creates a list for one or more features
from(Channel) - Static method in class org.anchoranalysis.io.imagej.convert.ConvertToImagePlus: Creates an ImagePlus from a Channel.
from(Stack) - Static method in class org.anchoranalysis.image.io.stack.output.StackWriteAttributesFactory: The options that narrowly describe a stack as possible.
from(Stack, boolean) - Static method in class org.anchoranalysis.io.imagej.convert.ConvertToImagePlus: Creates an ImagePlus from a Stack.
from(VoxelsUntyped) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.ConvertToImg: Converts from a VoxelsUntyped (Anchor structure) to a Img (ImgLib2 structure).
from(VoxelsUntyped) - Static method in class org.anchoranalysis.io.imagej.convert.ConvertToImagePlus: Creates an ImagePlus from a VoxelsUntyped.
from(VoxelsUntyped, int) - Static method in class org.anchoranalysis.io.imagej.convert.ConvertToImageProcessor: Creates a ImageProcessor by extracting a slice from a VoxelsUntyped.
FromAnnotations<T> - Class in org.anchoranalysis.plugin.annotation.bean.file: Provides files associated with annotations.
FromAnnotations() - Constructor for class org.anchoranalysis.plugin.annotation.bean.file.FromAnnotations
fromByte(SliceBufferIndex<UnsignedByteBuffer>, int) - Static method in class org.anchoranalysis.io.imagej.convert.ConvertToImageProcessor: Creates a ImageProcessor by extracting a slice from a SliceBufferIndex of type UnsignedByteBuffer.
fromByte(VoxelBuffer<UnsignedByteBuffer>, Extent) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.ConvertToImg: Creates an Img from a VoxelBuffer with an unsigned byte data-type.
fromByte(VoxelBuffer<UnsignedByteBuffer>, Extent) - Static method in class org.anchoranalysis.io.imagej.convert.ConvertToImageProcessor: Creates a ImageProcessor from voxel-buffer (of type ByteBuffer) that is already a slice.
fromByte(Voxels<UnsignedByteBuffer>) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.ConvertToImg: Creates an Img from Voxels with an unsigned byte data-type.
fromByte(Voxels<UnsignedByteBuffer>) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.ConvertToNativeImg: Creates an NativeImg from Voxels with an unsigned byte data-type.
FromByte - Class in org.anchoranalysis.image.voxel.buffer.slice: Implementation of SliceBufferIndex with voxels of type unsigned byte.
FromChannel - Class in org.anchoranalysis.plugin.image.bean.dimensions.provider: Creates image-dimensions by referencing them from a ChannelProvider.
FromChannel - Class in org.anchoranalysis.plugin.image.bean.histogram.provider: Creates a Histogram from a Channel, optionally using a mask.
FromChannel - Class in org.anchoranalysis.plugin.image.bean.mask.provider.convert: Creates a mask from an existing channel, reusing the channel's buffer and considering all 0 values as off, and 255 values as on.
FromChannel() - Constructor for class org.anchoranalysis.plugin.image.bean.dimensions.provider.FromChannel
FromChannel() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.provider.FromChannel
FromChannel() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromChannel
FromChannelBase - Class in org.anchoranalysis.plugin.image.bean.mask.provider: Base-class for MaskProviders that accept a Channel as input.
FromChannelBase() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.FromChannelBase
FromChannelOrMask - Class in org.anchoranalysis.plugin.image.bean.stack.provider: Creates a Stack from a Channel or Mask (reusing the voxel buffers).
FromChannelOrMask() - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.FromChannelOrMask
FromChannelOrMask(ChannelProvider) - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.FromChannelOrMask: Creates a new instance with a specified channel provider.
FromDerivePath - Class in org.anchoranalysis.io.input.bean.grouper: Derives the grouping-key via a call to DerivePath.
FromDerivePath() - Constructor for class org.anchoranalysis.io.input.bean.grouper.FromDerivePath
FromDescriptiveName - Class in org.anchoranalysis.plugin.io.bean.file.path.prefixer: The prefixer uses a combination of a out-path-prefix and the descriptive-name of inputs to create an output prefix.
FromDescriptiveName() - Constructor for class org.anchoranalysis.plugin.io.bean.file.path.prefixer.FromDescriptiveName
FromDictionary<T> - Class in org.anchoranalysis.plugin.operator.feature.bean: Extracts a key-value from a Dictionary as a double.
FromDictionary() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.FromDictionary
FromDictionaryBase - Class in org.anchoranalysis.plugin.image.feature.bean.score: An abstract base class for features that require a Dictionary for initialization.
FromDictionaryBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.FromDictionaryBase
FromDimensionsBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider: An abstract base class for creating a channel from specified dimensions.
FromDimensionsBase - Class in org.anchoranalysis.plugin.image.bean.mask.provider: Base class for MaskProviders that create a mask based on given dimensions.
FromDimensionsBase<T> - Class in org.anchoranalysis.plugin.image.feature.bean.dimensions: Base class for features that are calculated from Dimensions.
FromDimensionsBase() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.FromDimensionsBase
FromDimensionsBase() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.FromDimensionsBase
FromDimensionsBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.dimensions.FromDimensionsBase
FromEntries - Class in org.anchoranalysis.plugin.io.bean.channel.map
FromEntries() - Constructor for class org.anchoranalysis.plugin.io.bean.channel.map.FromEntries
fromFiles(Collection<File>) - Static method in class org.anchoranalysis.core.system.path.CommonPath: Finds the common root directory of the paths to several Files.
FromFiles - Class in org.anchoranalysis.io.input.bean.path.provider: Extracts a path from a FilesProvider.
FromFiles() - Constructor for class org.anchoranalysis.io.input.bean.path.provider.FromFiles
fromFloat(VoxelBuffer<FloatBuffer>, Extent) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.ConvertToImg: Creates an Img from a VoxelBuffer with a float data-type.
fromFloat(VoxelBuffer<FloatBuffer>, Extent) - Static method in class org.anchoranalysis.io.imagej.convert.ConvertToImageProcessor: Creates a ImageProcessor from voxel-buffer (of type FloatBuffer) that is already a slice.
fromFloat(Voxels<FloatBuffer>) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.ConvertToImg: Creates an Img from Voxels with a float data-type.
fromFloat(Voxels<FloatBuffer>) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.ConvertToNativeImg: Creates an NativeImg from Voxels with a float data-type.
FromFloat - Class in org.anchoranalysis.image.voxel.buffer.slice: Implementation of SliceBufferIndex with voxels of type float.
FromHistogram - Class in org.anchoranalysis.plugin.image.task.bean.feature.source: Each input-file describes a histogram that produces one row of features.
FromHistogram() - Constructor for class org.anchoranalysis.plugin.image.task.bean.feature.source.FromHistogram: Creates a new FromHistogram instance.
FromImage - Class in org.anchoranalysis.plugin.image.task.bean.feature.source: Calculates features from a single image.
FromImage() - Constructor for class org.anchoranalysis.plugin.image.task.bean.feature.source.FromImage: Creates a new FromImage instance.
FromImageMetadata - Class in org.anchoranalysis.plugin.image.task.bean.feature.source: Calculates features from the metadata from single image.
FromImageMetadata() - Constructor for class org.anchoranalysis.plugin.image.task.bean.feature.source.FromImageMetadata: Creates a new FromImageMetadata instance.
FromInput - Class in org.anchoranalysis.plugin.image.bean.channel.provider: Finds the input-stack using a conventional name of input_image - and extracts the first channel
FromInput - Class in org.anchoranalysis.plugin.image.bean.stack.provider: Finds the input-stack using a conventional name of input_image
FromInput() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.FromInput
FromInput() - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.FromInput
FromInt - Class in org.anchoranalysis.image.voxel.buffer.slice: Implementation of SliceBufferIndex with voxels of type unsigned int.
fromIterable(Iterable<Feature<T>>) - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory: Creates a list of features from an iterable
FromList - Class in org.anchoranalysis.bean.shared.color.scheme: Specifies a list of colors by a list.
FromList() - Constructor for class org.anchoranalysis.bean.shared.color.scheme.FromList
FromMarks - Class in org.anchoranalysis.plugin.mpp.bean.object.provider: Creates object-masks from a MarkCollection where (a particular region of) each mark creates an object.
FromMarks() - Constructor for class org.anchoranalysis.plugin.mpp.bean.object.provider.FromMarks
FromMask - Class in org.anchoranalysis.plugin.image.bean.channel.provider.mask: Creates a Channel directly from a Mask without any modification.
FromMask - Class in org.anchoranalysis.plugin.image.bean.object.provider.mask: Converts a binary-mask to an object-collection (containing a single object)
FromMask() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.mask.FromMask
FromMask() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.mask.FromMask
FromMaskBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider.mask: A base class for a ChannelProvider which also uses a binary-mask, but which doesn't use any other ChannelProvider as an input.
FromMaskBase() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.mask.FromMaskBase
FromMetadata - Class in org.anchoranalysis.plugin.io.bean.channel.map
FromMetadata() - Constructor for class org.anchoranalysis.plugin.io.bean.channel.map.FromMetadata
fromObject(ObjectMask) - Static method in class org.anchoranalysis.plugin.opencv.convert.ConvertToMat: Convert a ObjectMask to a Mat.
FromObjects - Class in org.anchoranalysis.plugin.image.bean.mask.provider.convert: Creates a Mask from a collection of object-masks.
FromObjects() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromObjects
FromOutputName - Class in org.anchoranalysis.plugin.io.bean.file.namer
FromOutputName() - Constructor for class org.anchoranalysis.plugin.io.bean.file.namer.FromOutputName
fromPath(Path) - Static method in class org.anchoranalysis.image.core.stack.ImageFileAttributes: Reads ImageFileAttributes from a path.
fromPath(Path) - Static method in class org.anchoranalysis.io.bioformats.metadata.ImageTimestampsAttributesFactory: Reads ImageTimestampsAttributes from a path, trying to infer the acquisition-date from metadata headers.
fromPaths(Iterable<Path>) - Static method in class org.anchoranalysis.core.system.path.CommonPath: Finds the common root directory of several Paths.
fromPhysicalArea(double) - Method in class org.anchoranalysis.image.core.dimensions.UnitConverter: Converts from physical-area to pixels.
fromPhysicalArea(double, String) - Method in class org.anchoranalysis.image.core.dimensions.UnitConverter: Converts from physical-area to pixels.
fromPhysicalDistance(double) - Method in class org.anchoranalysis.image.core.dimensions.UnitConverter: Converts from physical-distance to voxels.
fromPhysicalDistance(double, DirectionVector) - Method in class org.anchoranalysis.image.core.dimensions.UnitConverter: Converts from physical-distance to voxels.
fromPhysicalVolume(double) - Method in class org.anchoranalysis.image.core.dimensions.UnitConverter: Converts from physical-volume to voxels.
fromPhysicalVolume(double, String) - Method in class org.anchoranalysis.image.core.dimensions.UnitConverter: Converts from physical-volume to voxels.
fromProvider(Provider<Feature<T>>) - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory: Creates a list for a single-feature created from a provider
fromProviders(Collection<FeatureProvider<T>>) - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory: Creates a list of features from a collection of feature-providers
fromRepeated(int, Supplier<ObjectMask>) - Static method in class org.anchoranalysis.image.voxel.object.ObjectCollectionFactory: Creates a new collection by repeatedly calling a function to create a single ObjectMask.
fromSet(Set<ObjectMask>) - Static method in class org.anchoranalysis.image.voxel.object.ObjectCollectionFactory: Creates a new collection from a set of ObjectMask.
fromShort(SliceBufferIndex<UnsignedShortBuffer>, int) - Static method in class org.anchoranalysis.io.imagej.convert.ConvertToImageProcessor: Creates a ImageProcessor by extracting a slice from a SliceBufferIndex of type UnsignedShortBuffer.
fromShort(VoxelBuffer<UnsignedShortBuffer>, Extent) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.ConvertToImg: Creates an Img from a VoxelBuffer with an unsigned short data-type.
fromShort(VoxelBuffer<UnsignedShortBuffer>, Extent) - Static method in class org.anchoranalysis.io.imagej.convert.ConvertToImageProcessor: Creates a ImageProcessor from voxel-buffer (of type ShortBuffer) that is already a slice.
fromShort(Voxels<UnsignedShortBuffer>) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.ConvertToImg: Creates an Img from Voxels with an unsigned short data-type.
fromShort(Voxels<UnsignedShortBuffer>) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.ConvertToNativeImg: Creates an NativeImg from Voxels with an unsigned short data-type.
FromShort - Class in org.anchoranalysis.image.voxel.buffer.slice: Implementation of SliceBufferIndex with voxels of type unsigned short.
FromSingle - Class in org.anchoranalysis.bean.shared.color.scheme: A single color repeated to meet the size.
FromSingle() - Constructor for class org.anchoranalysis.bean.shared.color.scheme.FromSingle
FromSingleMark - Class in org.anchoranalysis.plugin.mpp.bean.provider.collection: Creates a MarkCollection from a single mark provided by a SingleMarkProvider.
FromSingleMark() - Constructor for class org.anchoranalysis.plugin.mpp.bean.provider.collection.FromSingleMark
fromSlice(Voxels<UnsignedByteBuffer>, int, String) - Static method in class org.anchoranalysis.io.imagej.convert.ConvertToImagePlus: Creates an ImagePlus from one slice of a Voxels<UnsignedByteBuffer> voxels.
fromSlice(VoxelsUntyped, int) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.ConvertToImg: Creates an Img from a single z-slice of a VoxelsUntyped.
fromStack(Stack) - Static method in class org.anchoranalysis.plugin.opencv.convert.ConvertToMat: Converts a Stack to a Mat.
FromStack - Class in org.anchoranalysis.plugin.image.bean.channel.provider: Extracts a channel from a provider of a stack.
FromStack() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.FromStack
FromStack(ProviderAsStack) - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.FromStack: Creates a new instance with a specified stack provider.
FromStackChannel - Class in org.anchoranalysis.plugin.image.bean.mask.provider.convert: Creates a Mask from a specific channel in a stack.
FromStackChannel() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromStackChannel
FromStackReader - Class in org.anchoranalysis.image.io.bean.stack.metadata.reader: Uses a StackReader to read the image-metadata.
FromStackReader() - Constructor for class org.anchoranalysis.image.io.bean.stack.metadata.reader.FromStackReader
FromStackReader(StackReader) - Constructor for class org.anchoranalysis.image.io.bean.stack.metadata.reader.FromStackReader: Create from a StackReader.
FromStacks - Class in org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels: Selects a subset of channels from a set of stacks.
FromStacks() - Constructor for class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.FromStacks
fromStream(Stream<Feature<T>>) - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory: Creates a list of features from a stream
fromStream(Stream<Point3i>) - Static method in class org.anchoranalysis.image.core.points.BoundingBoxFromPoints: Create from a stream of Point3is.
fromStrings(Collection<String>) - Static method in class org.anchoranalysis.core.system.path.CommonPath: Finds the common root directory of several paths, encoded in Strings.
fromTwoPoints(Point3d, Point3d) - Static method in class org.anchoranalysis.image.core.points.BoundingBoxFromPoints: Creates a bounding-box for two unordered points.
fromVoxelBufferByte(VoxelBuffer<UnsignedByteBuffer>, Extent) - Static method in class org.anchoranalysis.plugin.opencv.convert.ConvertToMat: Converts a VoxelBuffer of type UnsignedByteBuffer to a Mat.
fromVoxelBufferFloat(VoxelBuffer<FloatBuffer>, Extent) - Static method in class org.anchoranalysis.plugin.opencv.convert.ConvertToMat: Converts a VoxelBuffer of type FloatBuffer to a Mat.
fromVoxelBufferShort(VoxelBuffer<UnsignedShortBuffer>, Extent) - Static method in class org.anchoranalysis.plugin.opencv.convert.ConvertToMat: Converts a VoxelBuffer of type UnsignedShortBuffer to a Mat.
fromVoxelsByte(Voxels<UnsignedByteBuffer>) - Static method in class org.anchoranalysis.plugin.opencv.convert.ConvertToMat: Converts a Voxels of type UnsignedByteBuffer to a Mat.
fromVoxelsFloat(Voxels<FloatBuffer>) - Static method in class org.anchoranalysis.plugin.opencv.convert.ConvertToMat: Converts a Voxels of type FloatBuffer to a Mat.
fromVoxelsShort(Voxels<UnsignedShortBuffer>) - Static method in class org.anchoranalysis.plugin.opencv.convert.ConvertToMat: Converts a Voxels of type UnsignedShortBuffer to a Mat.
FromXMLList - Class in org.anchoranalysis.bean.define.adder: Adds a list of Named-Items define in a XML file in the current directory.
FromXMLList() - Constructor for class org.anchoranalysis.bean.define.adder.FromXMLList
FunctionalIterate - Class in org.anchoranalysis.core.functional: Utilities for repeating operations a certain number of times.
FunctionalList - Class in org.anchoranalysis.core.functional: Utility functions for manipulating or creating List in a functional way.
FunctionalListParallel - Class in org.anchoranalysis.core.functional: Like FunctionalList but executes any operations in parallel where possible.
FunctionWithInt<S,V> - Interface in org.anchoranalysis.core.functional.unchecked: Like Function but also accepts an int parameter.

G

GaussianBlur2D - Class in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter: Applies a 2D Gaussian blur filter to each slice of a Channel independently.
GaussianBlur2D() - Constructor for class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.GaussianBlur2D
GaussianCumulative<T> - Class in org.anchoranalysis.plugin.operator.feature.bean.statistics: Calculates a score between 0 and 1 based on the Cumulative Distribution Function (CDF) of a Gaussian distribution.
GaussianCumulative() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.statistics.GaussianCumulative
generalWriteException(Class<T>, Path, Exception) - Static method in class org.anchoranalysis.image.io.bean.stack.writer.WriterErrorMessageHelper: Creates a ImageIOException with an error message that image-writing failed.
generateBackgroundRegion(ObjectCollectionWithProperties, Either<Dimensions, DisplayStack>) - Method in class org.anchoranalysis.image.io.object.output.rgb.DrawCroppedObjectsGenerator
generateBackgroundRegion(ObjectCollectionWithProperties, Either<Dimensions, DisplayStack>) - Method in class org.anchoranalysis.image.io.object.output.rgb.DrawObjectsGenerator
generateBackgroundRegion(ObjectCollectionWithProperties, Either<Dimensions, DisplayStack>) - Method in class org.anchoranalysis.image.io.object.output.rgb.ObjectsAsRGBGenerator: Creates a RGBStack containing the background, without objects being drawn upon it.
generateEdge(VoxelizedMarkMemo, VoxelizedMarkMemo, EnergyStack, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in interface org.anchoranalysis.mpp.feature.addcriteria.AddCriteria: Generates an edge between two marks based on the defined criteria.
generateEdge(VoxelizedMarkMemo, VoxelizedMarkMemo, EnergyStack, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaEnergyPair
generateEdge(VoxelizedMarkMemo, VoxelizedMarkMemo, EnergyStack, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaNever
generateEdge(VoxelizedMarkMemo, VoxelizedMarkMemo, EnergyStack, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaPair
generateIntersectingObjects(int, int, boolean) - Static method in class org.anchoranalysis.test.feature.plugins.objects.IntersectingCircleObjectsFixture: Generates a collection of circular objects, some intersecting and some not intersecting.
generateMasks(ObjectCollectionWithProperties) - Method in class org.anchoranalysis.image.io.object.output.rgb.DrawCroppedObjectsGenerator
generateMasks(ObjectCollectionWithProperties) - Method in class org.anchoranalysis.image.io.object.output.rgb.DrawObjectsGenerator
generateMasks(ObjectCollectionWithProperties) - Method in class org.anchoranalysis.image.io.object.output.rgb.ObjectsAsRGBGenerator: Creates a ObjectCollectionWithProperties indicative of the masks that will be imposed on top of the background-region.
generateNormal(double, double) - Method in interface org.anchoranalysis.core.random.RandomNumberGenerator: Generates a Gaussian (Normal) random variable with particular parameterization.
generateNormal(double, double) - Method in class org.anchoranalysis.core.random.RandomNumberGeneratorMersenne
generatePoisson(double) - Method in interface org.anchoranalysis.core.random.RandomNumberGenerator: Generates a Poisson random variable with particular parameterization.
generatePoisson(double) - Method in class org.anchoranalysis.core.random.RandomNumberGeneratorMersenne
GenerateToMatchObjects - Class in org.anchoranalysis.plugin.image.bean.color.provider: Generates colors to match the size of an object-collection.
GenerateToMatchObjects() - Constructor for class org.anchoranalysis.plugin.image.bean.color.provider.GenerateToMatchObjects
GenerateUniqueParameterization - Interface in org.anchoranalysis.bean: Objects that must implement well-defined equals() and hashCode() methods and also generate a name uniquely identifying the class and all parameterization.
generator() - Static method in class org.anchoranalysis.image.io.object.output.hdf5.ObjectCollectionWriter: A Generator which writes an ObjectCollection to the file-system.
Generator<T> - Interface in org.anchoranalysis.io.generator: A class that writes a particular type of object(s) to the filesystem.
GeneratorBridge<S,T> - Class in org.anchoranalysis.io.generator: Exposes a Generator<T> as if it was an Generator<S>.
GeneratorOutputter - Class in org.anchoranalysis.image.io.stack.output.generator: Settings and methods for writing to the filesystem from a generator.
get() - Method in interface org.anchoranalysis.bean.Provider: Gets or creates an object of type T.
get() - Method in class org.anchoranalysis.bean.shared.dictionary.DictionaryProviderReference
get() - Method in class org.anchoranalysis.core.cache.CachedSupplier
get() - Method in interface org.anchoranalysis.core.functional.checked.CheckedSupplier: Applies a supplier like with Supplier.get().
get() - Method in interface org.anchoranalysis.core.identifier.provider.store.StoreSupplier: Gets the object being supplied to the store.
get() - Method in class org.anchoranalysis.feature.bean.list.Define
get() - Method in class org.anchoranalysis.feature.bean.list.DefinedNamed
get() - Method in class org.anchoranalysis.feature.bean.list.DefineSingle
get() - Method in class org.anchoranalysis.feature.bean.list.PrependName
get() - Method in class org.anchoranalysis.feature.bean.provider.FeatureProviderDefine
get() - Method in class org.anchoranalysis.feature.bean.provider.FeatureProviderReference
get() - Method in interface org.anchoranalysis.feature.calculate.FeatureCalculationInput: The underlying feature-input.
get() - Method in interface org.anchoranalysis.feature.session.cache.finder.CacheSupplier: Gets the cache.
get() - Method in class org.anchoranalysis.feature.session.SessionInputSequential
get() - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderBinary
get() - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderTernary
get() - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderUnary
get() - Method in class org.anchoranalysis.image.bean.provider.HistogramProviderUnary
get() - Method in class org.anchoranalysis.image.bean.provider.MaskProviderUnary
get() - Method in class org.anchoranalysis.image.bean.provider.ObjectCollectionProviderUnary
get() - Method in class org.anchoranalysis.image.bean.provider.stack.Arrange
get() - Method in class org.anchoranalysis.image.bean.provider.stack.StackProviderUnary
get() - Method in interface org.anchoranalysis.image.core.stack.named.NamedStacksSupplier: Gets the NamedProvider of Stacks.
get() - Method in class org.anchoranalysis.image.io.bean.stack.combine.TileWithLabels
get() - Method in class org.anchoranalysis.image.io.bean.stack.combine.WriteText
get() - Method in class org.anchoranalysis.inference.concurrency.WithPriority: Gets the underlying element stored in the structure.
get() - Method in class org.anchoranalysis.io.input.bean.dictionary.ReadFromFile
get() - Method in class org.anchoranalysis.io.input.bean.path.provider.FilePathProviderReference
get() - Method in class org.anchoranalysis.io.input.bean.path.provider.FromFiles
get() - Method in interface org.anchoranalysis.io.input.path.PathSupplier: Supplies a Path.
get() - Method in interface org.anchoranalysis.io.output.writer.ElementSupplier: Gets/creates the element to be written.
get() - Method in interface org.anchoranalysis.io.output.writer.ElementWriterSupplier: Gets/creates the ElementWriter to be used for an output.
get() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromDimensionsBase
get() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromInput
get() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromStack
get() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.mask.FromMaskBase
get() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.Reference
get() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
get() - Method in class org.anchoranalysis.plugin.image.bean.color.provider.Concatenate
get() - Method in class org.anchoranalysis.plugin.image.bean.color.provider.GenerateToMatchObjects
get() - Method in class org.anchoranalysis.plugin.image.bean.dimensions.provider.FromChannel
get() - Method in class org.anchoranalysis.plugin.image.bean.dimensions.provider.GuessDimensions
get() - Method in class org.anchoranalysis.plugin.image.bean.dimensions.provider.SpecifyDimensions
get() - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.FromChannel
get() - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.Reference
get() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromStackChannel
get() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.FromChannelBase
get() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.FromDimensionsBase
get() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.Reference
get() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Concatenate
get() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.ConnectedComponentsFromMask
get() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Empty
get() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.IfParamEqual
get() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.mask.FromMask
get() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeTwoCollectionsItemwise
get() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Permute
get() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Reference
get() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.ReferenceOrElse
get() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentStack
get() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithChannelBase
get() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase
get() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeChannels
get() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.Concatenate
get() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.FromChannelOrMask
get() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.FromInput
get() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.Reference
get() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.IntensityMoments
get() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.DeriveFromPair
get() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.FeatureListProviderAggregatePair
get() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureBase
get() - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.PriorityQueueIndexRangeDownhill: Retrieves and removes the next item from the queue.
get() - Method in class org.anchoranalysis.plugin.mpp.bean.object.provider.FromMarks
get() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.CreateNew
get() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.FromSingleMark
get() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.PointsFromObjects
get() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.Reference
get() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.ReferenceOrEmpty
get() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.ScaleXY
get() - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGDescriptor
get() - Method in interface org.anchoranalysis.plugin.operator.feature.statistics.FeatureResultSupplier: Retrieves the result of a feature calculation.
get() - Method in class org.anchoranalysis.plugin.points.bean.FitPointsFromObjects
get(int) - Method in interface org.anchoranalysis.core.color.ColorIndex: The color for a particular index.
get(int) - Method in class org.anchoranalysis.core.color.ColorIndexModulo
get(int) - Method in class org.anchoranalysis.core.color.ColorList
get(int) - Method in class org.anchoranalysis.core.color.RGBColor: Gets a component from an index value.
get(int) - Method in class org.anchoranalysis.core.color.SingleColor
get(int) - Method in class org.anchoranalysis.feature.bean.list.FeatureList: Returns the element at the specified position in this list.
get(int) - Method in class org.anchoranalysis.feature.io.results.LabelledResultsVector: The result of a feature-calculation stored at a particular index.
get(int) - Method in class org.anchoranalysis.feature.name.FeatureNameList: Gets a name corresponding to a particular position.
get(int) - Method in class org.anchoranalysis.feature.results.ResultsVector: The result of a feature-calculation stored at a particular index.
get(int) - Method in class org.anchoranalysis.feature.results.ResultsVectorList: Gets a ResultsVector at a particular position i nthe list.
get(int) - Method in class org.anchoranalysis.feature.store.NamedFeatureStore: Gets a feature at a particular position.
get(int) - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.StackArrangement: Gets the BoundingBox corresponding to a particular index.
get(int) - Method in class org.anchoranalysis.image.core.object.properties.ObjectCollectionWithProperties: Get an item at a particular index.
get(int) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection: Get an ObjectMask at a particular position in the collection.
get(int) - Method in interface org.anchoranalysis.io.bioformats.DestinationChannelForIndex: Retrieves the channel corresponding to a particular index.
get(int) - Method in class org.anchoranalysis.math.arithmetic.RunningSumCollection: An individual item in the collection.
get(int) - Method in class org.anchoranalysis.math.statistics.moment.ImageMoments: Get an eigenvalue and corresponding eigenvector for a particular axis.
get(int) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy: Gets the mark at the specified index.
get(int) - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedIndividual: Gets the energy total at a specific index.
get(int) - Method in class org.anchoranalysis.mpp.feature.mark.MemoList: Returns the element at the specified position in this list.
get(int) - Method in class org.anchoranalysis.mpp.index.IndexByChannel: Gets the IndexByRegion for a specific channel.
get(int) - Method in class org.anchoranalysis.mpp.mark.MarkCollection: Gets a mark at a specific index.
get(int) - Method in class org.anchoranalysis.overlay.collection.OverlayCollection: Access a particular element in the collection by index.
get(int) - Method in class org.anchoranalysis.plugin.image.feature.object.ListWithThumbnails: Gets the item at the specified index in the list.
get(int) - Method in class org.anchoranalysis.spatial.box.BoundedList: Gets a particular element.
get(String) - Method in class org.anchoranalysis.feature.store.NamedFeatureStore: Gets a feature corresponding to a particular name.
get(String) - Method in class org.anchoranalysis.image.io.channel.input.ChannelMap: Gets the index corresponding to a particular channel-name.
get(String) - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergySchemeSet: Retrieves an EnergyScheme by its name.
get(String) - Method in interface org.anchoranalysis.mpp.io.input.MultiInputSubMap: Retrieves an entry from the map.
get(String) - Method in class org.anchoranalysis.mpp.io.input.OperationMap
get(String) - Method in class org.anchoranalysis.mpp.io.input.StackWithMap
get(String) - Method in class org.anchoranalysis.plugin.annotation.bean.label.GroupedAnnotationLabels: Gets the collection of AnnotationLabels for a specific group.
get(Optional<String>) - Method in class org.anchoranalysis.io.output.outputter.InputOutputContextSubdirectoryCache: Gets (from the cache if it's already there) a context for a subdirectory of given-name
get(K) - Method in class org.anchoranalysis.core.cache.LRUCache: Get a value, calculating if necessary, and caching the result.
get(K) - Method in class org.anchoranalysis.core.collection.MapCreate: Gets an existing element from the map, returning null if it is absent.
get(VoxelDataType) - Method in class org.anchoranalysis.image.voxel.datatype.VoxelDataTypeFactoryMultiplexer: Multiplexes one of the factories according to data-type
get(T) - Method in class org.anchoranalysis.plugin.image.task.labeller.FileLabelMap: Gets the label associated with a file identifier.
getAboveMaxValue() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareBase: Constant to return if outside the range (above the maximum allowed)
getAcquisitionTime() - Method in class org.anchoranalysis.image.core.stack.ImageMetadata: A timestamp, if available, of when the image was first physically created by the camera/device.
getAcqusitionTime() - Method in class org.anchoranalysis.image.io.stack.input.ImageTimestampsAttributes: A timestamp, if available, of when the image was first physically created by the camera/device.
getAdd() - Method in class org.anchoranalysis.plugin.mpp.bean.define.VisualizeOnBackground
getAddCriteria() - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria: The criteria used to determine which marks to add.
getAdditionalBackgrounds() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy: Additional background-stacks that are possible to use while annotating.
getAdditionalPropertyPaths() - Method in class org.anchoranalysis.bean.permute.property.PermuteProperty: Additional property paths that are also changed, together with propertyPath.
getAddSum() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientBaseAddSum: Added to all gradients (so we can store negative gradients).
getAfterPreoperation() - Method in class org.anchoranalysis.image.core.object.label.OverlappingObject: After pre-operation but before scaling
getAggregator() - Method in class org.anchoranalysis.plugin.image.task.bean.combine.AggregateChannelTask: How to aggregate the Channels.
getAlign() - Method in class org.anchoranalysis.image.bean.spatial.arrange.align.Grow: How to align the box after it is grown, as much as possible.
getAlign() - Method in class org.anchoranalysis.image.bean.spatial.arrange.overlay.Overlay: Indicates how to align the image across the three axes.
getAlign() - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImageCommonSize: How a smaller image (after scaling) is aligned to the larger image (with the common size).
getAligner() - Method in class org.anchoranalysis.image.bean.spatial.arrange.tile.Tile: How to align a smaller image inside a larger cell.
getAligner() - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage: When varyImageSize==false and varyImageLocation==false, how to align a smaller image inside a larger cell.
getAlignerLabel() - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage: When label==false and varyImageLocation==false, how to align the label with its associated image.
getAlignX() - Method in class org.anchoranalysis.image.bean.spatial.arrange.align.Align: Indicates how to align the image across the X-axis (i.e. horizontally): one of left, right, center.
getAlignY() - Method in class org.anchoranalysis.image.bean.spatial.arrange.align.Align: Indicates how to align the image across the Y-axis (i.e. vertically): one of top, bottom, center.
getAlignZ() - Method in class org.anchoranalysis.image.bean.spatial.arrange.align.Align: Indicates how to align the image across the Z-axis: one of top, bottom, center, repeat.
getAll() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown: Certain features are stored for every object, so that we can reference them in our calculations for the 'all' component.
getAll() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergyScheme: Features for all elements together.
getAllCacheNames() - Method in class org.anchoranalysis.feature.session.cache.finder.CacheTransferSourceCollection: The names of all child-caches that are made available.
getAngle() - Method in class org.anchoranalysis.spatial.orientation.OrientationAxisAngle: Angle part of axis-angle orientation (anti-clock in radians).
getAngleDegrees() - Method in class org.anchoranalysis.spatial.orientation.Orientation2D: The angle of the rotation in the 2D plane anti-clockwise, in degrees.
getAnnotations() - Method in class org.anchoranalysis.plugin.annotation.bean.file.FromAnnotations: The annotation input manager.
getAnnotatorStrategy() - Method in class org.anchoranalysis.annotation.io.bean.AnnotationInputManager: The strategy to be used for annotating.
getAppendDictionary() - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager: List of dictionaries to append.
getAppendFilePath() - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager: List of file paths to append.
getAppendHistogram() - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager: List of histograms to append.
getAppendMarks() - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager: List of marks to append.
getAppendMarksFromAnnotation() - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager: List of marks from annotations (both accepted and rejected) to append.
getAppendMarksFromAnnotationAcceptedOnly() - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager: List of marks from annotations (accepted only) to append.
getAppendMarksFromAnnotationRejectedOnly() - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager: List of marks from annotations (rejected only) to append.
getAppendObjects() - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager: List of object-collections to append to the MultiInput.
getAppendStack() - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager: List of additional stacks to append.
getArbitraryElement() - Method in interface org.anchoranalysis.core.identifier.provider.NamedProvider: Gets one element of the provider (arbitrarily).
getArrange() - Method in class org.anchoranalysis.image.bean.provider.stack.Arrange: Determines how the stacks in list are arranged.
getArrange() - Method in class org.anchoranalysis.image.bean.spatial.arrange.tile.Cell: How to arrange any RGBStacks in this particular cell.
getAsBoolean() - Method in interface org.anchoranalysis.core.functional.checked.CheckedBooleanSupplier: Applies a supplier like with BooleanSupplier.getAsBoolean().
getAsDouble(String) - Method in class org.anchoranalysis.core.value.Dictionary: Retrieves a value from the dictionary, and converts to a double.
getAspectRatio() - Method in class org.anchoranalysis.image.bean.spatial.arrange.fill.ExtentToArrange: The aspect-ratio: width of extent divided by height.
getAssigner() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations: The assigner used for annotation comparison.
getAssignmentCSV() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.ComparisonSharedState: The CSV assignment for the comparison.
getAsStack() - Method in class org.anchoranalysis.image.bean.provider.ChannelProvider
getAsStack() - Method in class org.anchoranalysis.image.bean.provider.MaskProvider
getAsStack() - Method in class org.anchoranalysis.image.bean.provider.stack.StackProvider
getAsStack() - Method in interface org.anchoranalysis.image.core.stack.ProviderAsStack: Retrieves or creates a Stack representation of an entity.
getAsString(String) - Method in class org.anchoranalysis.core.value.Dictionary: Retrieves a value from the dictionary as a String.
getAttributes() - Method in class org.anchoranalysis.image.io.stack.input.ImageTimestampsAttributes: Timestamps and other metadata associated with an image file-path, but not with the file's contents.
getAttributes() - Method in class org.anchoranalysis.image.io.stack.output.StackWriteOptions: The attributes of the particular stack to write.
getAxis() - Method in class org.anchoranalysis.image.bean.spatial.direction.AxisAlignedUnitVector: Which axis the unit-vector will align with.
getAxis() - Method in class org.anchoranalysis.image.feature.bean.object.single.CenterOfGravity: The axis along which to calculate the center of gravity.
getAxis() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientForAxis: Which axis?
getAxis() - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.ForSpecificAxis: The axis to perform the calculation on.
getAxis() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.ArbitraryInsidePoint: The axis to output.
getAxis() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxAlongAxisBase: The axis along which to calculate the feature value ("x", "y", or "z").
getAxis() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.GradientMeanForAxis
getAxis() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.PrincipalAxisOrientation: Which axis to read from (x,y,z)
getAxis() - Method in class org.anchoranalysis.spatial.orientation.OrientationAxisAngle: Axis part of axis-angle orientation (should be normalized).
getBackground() - Method in class org.anchoranalysis.annotation.io.bean.AnnotatorStrategy: The visual background to use while annotating.
getBackground() - Method in class org.anchoranalysis.image.inference.segment.SegmentedBackground: The background image to use for segmentation, when visualizing segmentations.
getBackground() - Method in class org.anchoranalysis.image.io.object.output.rgb.ObjectsAsRGBGenerator: A background image or dimensions to define an empty background.
getBackground() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations: The name of the stack to use as background to the annotations.
getBackground() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase: The background.
getBackgroundChannelIndex() - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize: Uses only this channel (identified by an index in the stack) as the background, -1 disables.
getBackgroundChannelProvider() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.MorphologicalOperatorBase: Optional provider for a background channel to use in intensity-based conditions.
getBackgroundID() - Method in class org.anchoranalysis.plugin.mpp.bean.define.VisualizeOnBackground
getBackgroundIntensity() - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImageCommonSize: The background intensity to use in each channel when the scaled image does not cover the entire canvas.
getBackgroundStackMap() - Method in class org.anchoranalysis.annotation.io.bean.AnnotationBackground: If non-null, maps underlying stack-name to a background.
getBaseName() - Method in class org.anchoranalysis.core.system.path.FilenameSplitExtension: The part of the filename without an extension.
getBeanName() - Method in class org.anchoranalysis.bean.AnchorBean: A short-name identifying a bean (by default the name of the class associated with the bean).
getBelowMinValue() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareBase: Constant to return if outside the range (below the minimum allowed)
getBinarySgmn() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.BinarySegmentByObject
getBitDepthPerChannel() - Method in class org.anchoranalysis.image.core.stack.ImageMetadata: The number of bits in memory to describe each voxel's intensity, per channel.
getBitsPerPixel() - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceBitsPerPixel: The assigned bits per pixels.
getBlockSize() - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters: The block-size as per OpenCV implementation (identical default-size).
getBlockStride() - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters: The block-stride as per OpenCV implementation (identical default-size).
getBlue() - Method in class org.anchoranalysis.bean.shared.color.RGBColorBean: The blue component value of the RGB color.
getBlue() - Method in class org.anchoranalysis.core.color.RGBColor: The blue component value of the RGB color.
getBlue() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeChannels: Provider for the blue channel.
getBorderWidth() - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices: Adds a border around each part of the montage.
getBoundRadius() - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
getBox() - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.BoundingBoxEnclosed: The BoundingBox in which the image should be placed.
getBridgeMatcher() - Method in class org.anchoranalysis.plugin.image.bean.object.match.Bridge: Used to match each input-object to an intermediary-object
getCache() - Method in interface org.anchoranalysis.feature.calculate.FeatureCalculationInput: Get the associated FeatureCalculationCache.
getCache() - Method in class org.anchoranalysis.feature.session.replace.CacheAndReuseStrategy: The cache mapping a particular input to a corresponding FeatureCalculationInput.
getCache() - Method in class org.anchoranalysis.feature.session.SessionInputSequential
getCacheNames() - Method in class org.anchoranalysis.feature.session.cache.finder.CacheTransferSource: The names of the child-caches that can be used as sources.
getCacheSize() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.collective.RelationWithMatches: Size of feature evaluation cache for featureEvaluatorMatch
getCalculateLevel() - Method in class org.anchoranalysis.image.bean.threshold.CalculateLevelUnary: The delegate CalculateLevel.
getCalculateLevel() - Method in class org.anchoranalysis.image.bean.threshold.ThresholderGlobal
getCalculateLevel() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectBase: Method to calculate the level for a particular object.
getCalculateLevel() - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.GreaterThanThreshold: Calculates the level for the threshold
getCalculateLevel() - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.LevelFromHistogram
getCalculateLevel() - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.ThresholdHistogram
getCalculateLevel() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevelBase: The method to calculate the threshold level.
getCalculateLevelElse() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelRelativeToThreshold: Alternative CalculateLevel to use when the condition in CalculateLevelRelativeToThreshold.useElseInstead(int, int) is met.
getCalculations() - Method in class org.anchoranalysis.mpp.feature.input.FeatureInputAllMemo: The list of memoized energy calculations for all marks.
getCalculator() - Method in class org.anchoranalysis.image.feature.calculator.NamedFeatureCalculatorMulti: The multi-feature calculator.
getCallUponDirectoryCreation() - Method in class org.anchoranalysis.experiment.arguments.InputArguments: When defined, this Consumer is called when an output directory is first created.
getCallUponDirectoryCreation() - Method in class org.anchoranalysis.io.output.outputter.DirectoryCreationParameters: When defined, this consumer is called when the directory is first created, as it is created lazily only when first needed.
getCellDefault() - Method in class org.anchoranalysis.image.bean.spatial.arrange.tile.Tile: Used to define an individual cell, when no specific entry is found in cells for a particular cell.
getCells() - Method in class org.anchoranalysis.image.bean.spatial.arrange.tile.Tile: Defines the corresponding StackArranger for an individual cell in table.
getCellSize() - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters: The cell-size as per OpenCV implementation (identical default-size).
getCenter() - Method in class org.anchoranalysis.image.voxel.buffer.SlidingBuffer: The buffer for the currently selected slice.
getCenterPoint() - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult: The center point of the fitted ellipsoid.
getCenterPointX() - Method in class org.anchoranalysis.plugin.points.bean.fitter.EllipseStandardFormConverter: Gets the x-coordinate of the ellipse's center point.
getCenterPointY() - Method in class org.anchoranalysis.plugin.points.bean.fitter.EllipseStandardFormConverter: Gets the y-coordinate of the ellipse's center point.
getChannel() - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderUnary: The delegate ChannelProvider that is called.
getChannel() - Method in class org.anchoranalysis.plugin.image.bean.dimensions.provider.FromChannel: The ChannelProvider to use for dimensions.
getChannel() - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.FromChannel: The provider for the channel from which to create the histogram.
getChannel() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.FromChannelBase: The provider for the channel from which to create the mask.
getChannel() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntensityGreaterEqualThan
getChannel() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.UnaryWithChannelBase: Provider for the channel to be used in object creation.
getChannel() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithChannelBase: Provider for the channel from which objects will be created.
getChannel() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.FromChannelOrMask: A channel that is provided to the stack.
getChannel() - Method in class org.anchoranalysis.plugin.image.task.grouped.NamedChannel: The Channel instance.
getChannel(int) - Method in class org.anchoranalysis.feature.energy.EnergyStack: Returns the channel at a particular position in the stack.
getChannel(int) - Method in class org.anchoranalysis.feature.energy.EnergyStackWithoutParameters: Returns the channel at a particular position in the stack.
getChannel(int) - Method in class org.anchoranalysis.image.core.stack.RGBStack: Returns the channel at a particular position in the stack.
getChannel(int) - Method in class org.anchoranalysis.image.core.stack.Stack: Returns the channel at a particular position in the stack.
getChannel(int) - Method in class org.anchoranalysis.image.core.stack.StackNotUniformSized: Returns the channel at a particular position in the stack.
getChannel(String, int, Logger) - Method in interface org.anchoranalysis.image.io.channel.input.ChannelGetter: Retrieve the Channel corresponding to channelName at a particular time-frame.
getChannel(String, int, Logger) - Method in class org.anchoranalysis.image.io.channel.map.NamedChannelsConcatenate
getChannel(String, int, Logger) - Method in class org.anchoranalysis.image.io.channel.map.OpenedNamedChannels
getChannel(String, Logger) - Method in class org.anchoranalysis.plugin.image.task.stack.ChannelGetterForTimepoint: Retrieves a channel with the given name for the specified timepoint.
getChannel1() - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderBinary: The first delegate ChannelProvider that is called.
getChannel1() - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderTernary: The first delegate ChannelProvider that is called.
getChannel2() - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderBinary: The second delegate ChannelProvider that is called.
getChannel2() - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderTernary: The second delegate ChannelProvider that is called.
getChannel3() - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderTernary: The third delegate ChannelProvider that is called.
getChannelAssignFrom() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromChannel: The channel provider from which pixels will be assigned.
getChannelChecker() - Method in class org.anchoranalysis.plugin.image.task.grouped.GroupedSharedState: Checks that Channels have a consistent voxel-data type.
getChannelConversionStyle() - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat: To convert as RGB or independently or in another way.
getChannelConverter() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.convert.Convert
getChannelConverter() - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat: Optionally, how to convert from one bit-depth to another (scaling, clamping etc.)
getChannelElse() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.IfParamEquals: The channel provider to use if the condition is false.
getChannelFirst() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Difference: Index of first channel
getChannelGroupID() - Method in class org.anchoranalysis.plugin.io.bean.file.group.parser.RegularExpression
getChannelID() - Method in class org.anchoranalysis.plugin.imagej.bean.define.AddEdgeFilters: The ID of the channel that provides the input to the filter.
getChannelIfVoxelZero() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.IfVoxelZero: If a pixel is zero in the input-channel, the output is formed from the corresponding pixel in this channel instead
getChannelIndex() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromStack: The index of the channel to extract from the stack.
getChannelIndex() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromStackChannel: The index of the channel to use from the stack.
getChannelIndex() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.One: The index of the channel to retrieve from stackName.
getChannelIndex() - Method in class org.anchoranalysis.plugin.io.multifile.FileDetails
getChannelLookup() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.NormalizeDifferenceToMedian
getChannelMap() - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannels
getChannelMask() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.histogram.ExportImageHistograms: If defined, this is the name of channel used as a mask over the values which are fed into the histogram
getChannelName() - Method in class org.anchoranalysis.plugin.io.bean.channel.map.SingleChannel
getChannelName() - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertNamedChannelsToStack: By default all channels are converted into a stack.
getChannelNames() - Method in class org.anchoranalysis.plugin.image.task.grouped.ConsistentChannelNamesChecker: The names of Channels that are consistent across all images.
getChannelNamesChecker() - Method in class org.anchoranalysis.plugin.image.task.grouped.GroupedSharedState: Checks that each image provides a consistent set of channels, and that they have the same RGB-state.
getChannelNum() - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetChannel
getChannelOptional(String, int, Logger) - Method in class org.anchoranalysis.image.io.channel.map.NamedChannelsConcatenate
getChannelOptional(String, int, Logger) - Method in interface org.anchoranalysis.image.io.channel.map.NamedChannelsMap: Gets a channel if it exists, returning empty if it doesn't.
getChannelOptional(String, int, Logger) - Method in class org.anchoranalysis.image.io.channel.map.OpenedNamedChannels
getChannelSecond() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Difference: Index of second channel
getChannelsExtra() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
getChannelThreshold() - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.ThresholdAgainstChannel
getChannelVoxelType() - Method in class org.anchoranalysis.test.image.stackwriter.ChannelSpecification: Default data-type for all channels in the stack if not otherwise specified.
getChecked() - Method in class org.anchoranalysis.io.output.outputter.Outputter: Gets the underlying delegate of Outputter that throws checked-exceptions instead of using a ErrorReporter.
getCheckParsedFilePathBag() - Method in class org.anchoranalysis.plugin.io.bean.file.group.GroupFiles: Imposes a condition on each parsed-file-path-bag which must be-fulfilled if a file is to be included.
getClassifierProvider() - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.BinaryClassifierImageLabeller: Provider for the classifier feature list.
getClassLabels() - Method in class org.anchoranalysis.image.inference.ImageInferenceContext: If available, labels of classes loaded from a text file at classLabelsPath.
getClassLabelsPath() - Method in class org.anchoranalysis.image.inference.bean.segment.instance.SegmentStackIntoObjectsScaleDecode: Relative-path to the class-labels file, a text file where each line specifies a class label in order, relative to the models/ directory in the Anchor distribution.
getCode(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedIntBuffer: Gets the encoded value at the given index.
getColor() - Method in class org.anchoranalysis.bean.shared.color.scheme.FromSingle: The single color to repeat.
getColor() - Method in class org.anchoranalysis.plugin.annotation.bean.label.AnnotationLabel: An optional color associated with the label when displayed via GUI.
getColor() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredMask
getColor() - Method in class org.anchoranalysis.plugin.image.object.ColoredObject: The RGB color.
getColor(int) - Method in class org.anchoranalysis.overlay.collection.ColoredOverlayCollection: Access a particular color in the collection by index.
getColorIDGetter() - Method in class org.anchoranalysis.overlay.writer.ObjectDrawAttributes: Gets a color ID associated with the object
getColorIndex() - Method in class org.anchoranalysis.overlay.writer.ObjectDrawAttributes: Colors for a given index
getColorList() - Method in class org.anchoranalysis.mpp.mark.ColoredMarks
getColors() - Method in class org.anchoranalysis.bean.shared.color.scheme.ColorSchemeUnary: The delegate that creates the color-list before subsequent processing.
getColors() - Method in class org.anchoranalysis.bean.shared.color.scheme.FromList: The list of colors to specify.
getColors() - Method in class org.anchoranalysis.overlay.collection.ColoredOverlayCollection: The list of colors, each element corresponding to overlays.
getColors() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBaseWithGenerator: Colors to use for drawing objects.
getColorScheme() - Method in class org.anchoranalysis.plugin.image.bean.color.provider.GenerateToMatchObjects
getColorsUnpaired() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations: The color scheme for unpaired objects.
getColorUnselectedObjects() - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize: Optionally outline the other (unselected for the thumbnail) objects in this particular color.
getColumn() - Method in class org.anchoranalysis.image.bean.spatial.arrange.tile.Cell: The column in the table that the cell refers to (zero-indexed).
getColumns() - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices: How many columns to use in the montage, or 0 to guess an approximately square output.
getCombined() - Method in interface org.anchoranalysis.mpp.index.VoxelPartition: Gets the combined voxel partition for all slices.
getCombined() - Method in class org.anchoranalysis.mpp.index.VoxelPartitionHistogram
getCommand() - Method in class org.anchoranalysis.plugin.imagej.bean.mask.provider.MorphologicalOperation: One of: open, close, fill, erode, dilate, skel, outline
getCommandName() - Method in class org.anchoranalysis.launcher.config.HelpConfig: The application command as described in the help message.
getComparerLeft() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager: The comparable source for the left side of the comparison.
getComparerMultiplex(boolean) - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationComparisonInput: Gets one of the two ComparableSources based on a boolean flag.
getComparerRight() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager: The comparable source for the right side of the comparison.
getComparers() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationComparisonInput: The two ComparableSources to compare.
getCondition() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.IfParamEquals: The condition to evaluate from the dictionary.
getCondition() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfKeyValueCondition
getConfidence() - Method in class org.anchoranalysis.image.inference.bean.reduce.ObjectForReduction: The associated confidence.
getConfidence() - Method in class org.anchoranalysis.image.inference.segment.LabelledWithConfidence: The confidence associated with element.
getConfidence() - Method in class org.anchoranalysis.image.inference.segment.WithConfidence: The confidence associated with element.
getContains() - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.DescriptiveNameContainsImageLabeller: The string to search for in the image's descriptive name.
getContains() - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterDescriptiveName: A descriptive-name must contain (case-sensitive) this string.
getContext() - Method in class org.anchoranalysis.core.identifier.provider.store.SharedObjects: Logger and other common configuration
getContext() - Method in class org.anchoranalysis.experiment.task.ParametersExperiment
getContext() - Method in class org.anchoranalysis.io.output.outputter.OutputterChecked: General settings for writing outputs.
getContext() - Method in class org.anchoranalysis.plugin.image.task.feature.FeatureCalculationContext: The input-output context for the operation.
getContext() - Method in class org.anchoranalysis.plugin.image.task.feature.FeatureExporterContext: Context for reading from or writing outputs to the file-system.
getContextExperiment() - Method in class org.anchoranalysis.experiment.task.InputBound: The input-output context associated with the current experiment.
getContextJob() - Method in class org.anchoranalysis.experiment.task.InputBound: The input-output context associated with the current job.
getContextParameters() - Method in class org.anchoranalysis.experiment.arguments.InputArguments: Context parameters that an influence determining inputs.
getConversion() - Method in class org.anchoranalysis.plugin.mpp.shared.ConvertedInput: The converted input.
getConvert() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.convert.ConvertWithHistogram
getConverters() - Method in class org.anchoranalysis.image.core.stack.DisplayStack: A list of optional converters that will be applied to the respective channel in stack if they exist.
getCopyFilesNaming() - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.CopyFilesNamingOne
getCost(int, int) - Method in class org.anchoranalysis.annotation.io.assignment.CostMatrix: Gets the cost from an element from the first-list to an element from the second-list.
getCosts() - Method in class org.anchoranalysis.annotation.io.assignment.AssignOverlappingObjects: A matrix linking the overlap between each ObjectMask to each other, respectively as rows and columns.
getCount() - Method in class org.anchoranalysis.core.time.RecordedExecutionTimes.RecordedOperation: How many times the operation occurred.
getCount() - Method in class org.anchoranalysis.math.arithmetic.Counter: The count, as per current state.
getCount() - Method in class org.anchoranalysis.math.arithmetic.RunningSum: The running count.
getCount() - Method in class org.anchoranalysis.math.statistics.VarianceCalculatorDouble: The running count of values.
getCount() - Method in class org.anchoranalysis.math.statistics.VarianceCalculatorLong: The running count of values.
getCount(int) - Method in class org.anchoranalysis.math.histogram.Histogram: The count corresponding to a particular value.
getCountThreshold() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerSplitMoreThan: If there are more than countThreshold elements, use summarizerGreaterThan, else summarizerElse.
getCreationTime() - Method in class org.anchoranalysis.image.core.stack.ImageFileAttributes: The creation timestamp on the file the image was loaded from.
getCsvFeaturesAggregated() - Method in class org.anchoranalysis.feature.io.results.FeatureOutputNames: The CSV of aggregated feature-results, if enabled.
getCsvFeaturesGroup() - Method in class org.anchoranalysis.feature.io.results.FeatureOutputNames: The CSV individually written for each group, if enabled.
getCsvFeaturesNonAggregated() - Method in class org.anchoranalysis.feature.io.results.FeatureOutputNames: The CSV of non-aggregated feature-results.
getCsvFilePath() - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterCSVColumn
getCustomName() - Method in class org.anchoranalysis.feature.bean.Feature: An optional additional name that be associated with the feature (defaults to an empty string).
getDebugModeParameters() - Method in class org.anchoranalysis.io.input.bean.InputManagerParameters: Parameters for debug-mode (only defined if we are in debug mode).
getDebugModeParameters() - Method in class org.anchoranalysis.io.input.InputContextParameters: Parameters for debug-mode (only defined if we are in debug mode).
getDecode() - Method in class org.anchoranalysis.image.inference.bean.segment.instance.SegmentStackIntoObjectsScaleDecode: Decodes inference output into segmented objects.
getDefault() - Static method in class org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte: Default values to use, if not otherwise specified.
getDefault() - Static method in class org.anchoranalysis.image.voxel.binary.values.BinaryValuesInt: Default values to use, if not otherwise specified.
getDefaultBeanClass() - Method in class org.anchoranalysis.bean.xml.factory.AnchorDefaultBeanFactory: Returns null as Optional is not supported by BeanFactory interface.
getDefaultColors() - Method in class org.anchoranalysis.io.output.bean.OutputWriteSettings: The default color-scheme used for outputs, if no other scheme is specified.
getDefaultExtension() - Method in interface org.anchoranalysis.core.format.FileFormat: The default extension to write associated with a particular format.
getDefaultExtension() - Method in enum class org.anchoranalysis.core.format.ImageFileFormat
getDefaultExtension() - Method in enum class org.anchoranalysis.core.format.NonImageFileFormat
getDefaultInstances() - Method in class org.anchoranalysis.bean.xml.factory.AnchorDefaultBeanFactory: Default bean-classes to use for particular family types of beans.
getDefaultInstances() - Static method in class org.anchoranalysis.bean.xml.RegisterBeanFactories: Default instances of different family-types of beans.
getDefaultStackReaderForMetadata() - Method in class org.anchoranalysis.plugin.mpp.bean.convert.ConvertNamedChannels: Supplies to the imageMetadataReader to use, if no other reader is specified.
getDefine() - Method in class org.anchoranalysis.mpp.feature.bean.mark.MarkEvaluator: Defines additional configuration for the evaluation process.
getDefine() - Method in class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputter: The Define to be applied on inputs.
getDefine() - Method in class org.anchoranalysis.plugin.mpp.bean.define.Develop: Defines entities (chanels, stacks etc.) that are derived from inputs and other entities.
getDelegate() - Method in class org.anchoranalysis.image.io.stack.output.generator.RasterGeneratorDelegateToRaster: The delegate.
getDelegate() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer: The underlying storage buffer, to which calls are delegated with our without conversion.
getDelegate() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer: The underlying storage buffer, to which calls are delegated with our without conversion.
getDelegate() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer: The underlying storage buffer, to which calls are delegated with our without conversion.
getDelegate() - Method in class org.anchoranalysis.io.input.InputFromManagerDelegate: The delegate.
getDelegate() - Method in class org.anchoranalysis.mpp.bean.bound.BoundMinMax
getDelegate() - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegate: Gets the delegate ResolvedPart.
getDelimiter() - Method in class org.anchoranalysis.plugin.io.bean.file.namer.SubsetRangeIfRequested: Character used to split the name into groups.
getDelimiter() - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.LastDirectoryAsPrefix
getDelta() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Mser
getDeltat() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.AnisotropicDiffusion: the integration constant for the numerical integration scheme.
getDepth() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ImposeResolution: Physical pixel size of a voxel in z-dimension.
getDerivePath() - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.MaskAsObject: Where to find the Mask to compare, as a function of the source file-path.
getDerivePath() - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.Objects: Where to find the objects to compare, as a function of the source file-path.
getDerivePath() - Method in class org.anchoranalysis.plugin.io.bean.path.derive.CollapseFileName: Called as a delegate to provide a source Path.
getDerivePath() - Method in class org.anchoranalysis.plugin.io.bean.path.derive.RemoveTrailingDirectory
getDescription() - Method in exception class org.anchoranalysis.core.exception.combinable.AnchorCombinableException: The (uncombined) description associated with the exception.
getDestination() - Method in class org.anchoranalysis.mpp.pair.MarkPair: Gets the destination mark of the pair (the one with the higher identifier).
getDestination() - Method in class org.anchoranalysis.mpp.pair.PairVoxelizedMarkMemo: Gets the destination VoxelizedMarkMemo.
getDestinationDirectory() - Method in class org.anchoranalysis.plugin.io.input.path.CopyContext: Destination directory for copying.
getDictionaries() - Method in class org.anchoranalysis.bean.shared.dictionary.DictionaryInitialization: Named-store of Dictionary objects.
getDictionary() - Method in class org.anchoranalysis.feature.initialization.FeatureInitialization: A dictionary of key-value pairs.
getDictionary() - Method in class org.anchoranalysis.feature.initialization.FeatureRelatedInitialization: The associated initialization for a DictionaryBean.
getDictionary() - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureEvaluator: Parameters to optionally associated with stackEnergy, and meaningless if stackEnergy is not specified.
getDictionary() - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement: Optional dictionary provider.
getDictionary() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByDictionary
getDictionary() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromDictionary: The dictionary from which an assignment will occur.
getDictionary() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
getDictionary() - Method in class org.anchoranalysis.plugin.image.bean.dictionary.DictionaryCondition: The dictionary to provide a value to check.
getDictionary() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.IfParamEqual
getDictionary() - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.ParamFromCollection: The name of the Dictionary that will be retrieved from SharedObjects.
getDictionary() - Method in class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputterWithEnergy: An optional dictionary provider.
getDictionary() - Method in class org.anchoranalysis.plugin.mpp.bean.define.Develop: If non-empty, the identifier for a dictionary that is treated as part of the energy-stack.
getDictionaryOptional() - Method in interface org.anchoranalysis.feature.input.FeatureInputDictionary: The associated dictionary, if it exists.
getDictionaryOptional() - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy
getDictionaryOptional() - Method in class org.anchoranalysis.mpp.feature.bean.mark.FeatureInputMark
getDictionaryRequired() - Method in interface org.anchoranalysis.feature.input.FeatureInputDictionary: The associated dictionary, or an exception if it doesn't exist.
getDimensions() - Method in class org.anchoranalysis.image.core.stack.ImageMetadata: The dimensions of the image.
getDimensions() - Method in class org.anchoranalysis.image.inference.ImageInferenceContext: The size of the image for which we wish to segment, before and after any scaling for model inference.
getDimensions() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromDimensionsBase: The provider for the dimensions of the channel to be created.
getDimensions() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.FromDimensionsBase: Provider for the dimensions used to create the mask.
getDimensions() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.slice.RepeatSlice: Dimensions to create new mask
getDimensions() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeBase: Provider for image dimensions.
getDimensions() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithDimensionsBase: Provider for the dimensions to be used.
getDimensions() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithOptionalDimensionsBase: Optional provider for dimensions.
getDimensions() - Method in class org.anchoranalysis.plugin.image.bean.scale.ToDimensions: The dimensions the source image/entity is desired to be scaled to.
getDimensions() - Method in class org.anchoranalysis.plugin.mpp.bean.object.provider.FromMarks
getDimensions() - Method in class org.anchoranalysis.plugin.points.bean.fitter.PointsFitterToMark: Provides the Dimensions for the fitting operation.
getDimensionsOptional() - Method in class org.anchoranalysis.mpp.feature.bean.mark.FeatureInputMark: Gets the optional dimensions associated with this feature input.
getDimensionsRequired() - Method in class org.anchoranalysis.mpp.feature.bean.mark.FeatureInputMark: Gets the dimensions associated with this feature input, throwing an exception if not present.
getDimensionsSourceFallback() - Method in class org.anchoranalysis.plugin.image.bean.scale.ToDimensions: Source dimensions used as a fallback, if they are not passed as parameter to ToDimensions.calculate(java.util.Optional<org.anchoranalysis.image.core.dimensions.Dimensions>, java.util.Optional<org.anchoranalysis.image.core.dimensions.size.suggestion.ImageSizeSuggestion>).
getDirection() - Method in class org.anchoranalysis.image.feature.bean.physical.ConvertToPhysicalDistance: Direction of the distance being converted, defaults to a unit vector along the X-axis.
getDirectionVector() - Method in class org.anchoranalysis.mpp.mark.points.LineSegment: Gets the direction vector of the line segment.
getDirectory() - Method in class org.anchoranalysis.core.system.path.PathDifference: The directory component of the difference, if it exists.
getDirectory() - Method in class org.anchoranalysis.io.input.bean.files.FilesProviderWithDirectoryString: A directory in which to look for files.
getDirectory() - Method in class org.anchoranalysis.io.input.file.FileWithDirectoryInput: A directory that must be a containing directory (at some hierarchical level) of file associated with this input.
getDirectory() - Method in class org.anchoranalysis.io.input.path.GlobExtractor.GlobWithDirectory: The directory part of the string, or null if it doesn't exist
getDirectory() - Method in class org.anchoranalysis.io.input.path.matcher.DualPathPredicates: Only accepts any containing directories where the predicate returns true
getDirectory() - Method in class org.anchoranalysis.io.output.outputter.directory.OutputterTarget: The directory into which outputting occurs.
getDirectory() - Method in class org.anchoranalysis.io.output.path.prefixer.DirectoryWithPrefix: The directory in which files can be written to.
getDirectory() - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.HomeSubdirectory: A relative-path (to the user home directory) which is used as an output directory
getDirectory() - Method in class org.anchoranalysis.test.image.WriteIntoDirectory: The directory in which stacks and other outputs are written.
getDirectoryAsPath(InputContextParameters) - Method in class org.anchoranalysis.io.input.bean.files.FilesProviderWithDirectory: The associated directory with the list of files.
getDirectoryAsPath(InputContextParameters) - Method in class org.anchoranalysis.io.input.bean.files.FilesProviderWithDirectoryString
getDirectoryAsPath(InputContextParameters) - Method in class org.anchoranalysis.io.input.bean.files.FilesProviderWithDirectoryUnary
getDirectoryAsPath(InputContextParameters) - Method in class org.anchoranalysis.io.input.bean.files.SingleFile
getDirectoryAsPathEnsureAbsolute(InputContextParameters) - Method in class org.anchoranalysis.io.input.bean.files.FilesProviderWithDirectory: Like FilesProviderWithDirectory.getDirectoryAsPath(org.anchoranalysis.io.input.InputContextParameters) but converts any relative path to absolute one.
getDirectoryPathToCopyMissingImagesTo() - Method in class org.anchoranalysis.test.image.rasterwriter.comparison.ComparisonPlan
getDisplayer() - Method in class org.anchoranalysis.image.inference.bean.segment.instance.SegmentStackIntoObjectsScaleDecode: How to convert an image to be displayed to the user.
getDisplayer() - Method in class org.anchoranalysis.image.inference.segment.SegmentedBackground: How to convert the background in an image suitable to be displayed.
getDisplayer() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations: How to convert an image to be displayed to the user.
getDisplayer() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase: How to convert an image to be displayed to the user.
getDisplayer() - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize: How to convert an image so that it can be displayed.
getDisplayer() - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.stack.ScaleToSize: How to convert an image to be displayed to the user.
getDisplayer() - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage: How to convert an image to be displayed to the user.
getDistance() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectNeighbors: How many neighbors to include by distance (distance==1 implies all directly touching neighbors, distance==2 implies those touching the directly touching etc.)
getDistanceMax() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevel: The maximum distance from the threshold level to consider.
getDistanceX() - Method in class org.anchoranalysis.plugin.points.bean.fitter.ReflectInAxesWithinDistance
getDistanceY() - Method in class org.anchoranalysis.plugin.points.bean.fitter.ReflectInAxesWithinDistance
getDistanceZ() - Method in class org.anchoranalysis.plugin.points.bean.fitter.ReflectInAxesWithinDistance
getDivideByZeroValue() - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.Divide: The value to return when division by zero occurs and Divide.avoidDivideByZero is true.
getDivisor() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequenceDouble: What to divide the integer-sequence by.
getDscr() - Method in class org.anchoranalysis.mpp.bean.bound.ResolvedBound: Gets a description of the bound.
getEigenvalue() - Method in class org.anchoranalysis.math.statistics.moment.EigenvalueAndVector: The eigenvalue.
getEigenvector() - Method in class org.anchoranalysis.math.statistics.moment.EigenvalueAndVector: The eigenvector corresponding to eigenvalue.
getElemAllCreator() - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement: Optional creator for features considering all elements.
getElemByCliqueSize(int) - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergyScheme: Gets the feature list for a specific clique size.
getElement() - Method in class org.anchoranalysis.image.inference.bean.reduce.ObjectForReduction: The underlying ObjectMask with whom a confidence and label is associated.
getElement() - Method in class org.anchoranalysis.image.inference.segment.LabelledWithConfidence: The underlying element with whom a confidence and label is associated.
getElement() - Method in class org.anchoranalysis.image.inference.segment.WithConfidence: The underlying element with whom a confidence is associated.
getElemIndCreator() - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement: Creates features for individual elements.
getElemPairCreator() - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement: Creates features for pairs of elements.
getEllipsoidCalculator() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid: Calculator for ellipsoid-related matrices.
getEllipsoidSum(double, double, double, DoubleMatrix2D) - Static method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid: Calculates the sum of squared coordinates relative to the ellipsoid's matrix.
getElseName() - Method in class org.anchoranalysis.io.input.file.FileNamerContext: A fallback name, if a failure occurs when naming.
getEmptyValue() - Method in class org.anchoranalysis.image.feature.bean.object.single.CenterOfGravity: The value to return if the center of gravity calculation results in NaN.
getEmptyValue() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.Intersection
getEmptyValue() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.ArbitraryInsidePoint: The value to return if no point is found inside the object-mask.
getEmptyValue() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanMaxSlice: The value to return when the object has no voxels in any slice.
getEmptyValue() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase: The value to return when the resulting object is empty.
getEmptyValue() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.DerivedObject: The value to return when the derived object is empty.
getEnclosing() - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.BoundingBoxEnclosed: An enclosing box (equal to or larger than box covering all screen-space used for this entity, including padding.
getEnd() - Method in class org.anchoranalysis.bean.permute.property.SequenceInteger: An index beyond which we cannot iterate (inclusive).
getEndIndex() - Method in class org.anchoranalysis.core.index.range.IndexRangeNegative: The index if the last element to use in the subsetting range, inclusive.
getEndPoint() - Method in class org.anchoranalysis.mpp.mark.points.LineSegment: Gets the end point of the line segment.
getEnergyChannelIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Identity: The index of the energy channel to use for calculations.
getEnergyChannelIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.RejectIfIntensityLessThan: The index of the energy channel to check for intensity.
getEnergyChannelIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.SingleChannel: The index of the energy channel to use for score calculation.
getEnergyChannelIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.QuantileAcrossConnectedComponents
getEnergyChannelIndexCheck() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram: The index of the energy channel to check.
getEnergyChannelIndexFail() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram: The index of the energy channel to use if the relation check fails.
getEnergyIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.NumberNeighboringVoxels: Index of which channel in the energy-stack to select
getEnergyIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.SpecificEnergyChannelBase: Index of which channel in the energy-stack to select. 0 represents the first channel, 1 the second, and so on.
getEnergyIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.FeatureEnergyChannel: Index of channel to use in the energy-stack (0 is the first channel, 1 is second etc.)
getEnergyIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.OutsideRange: The index of the energy channel to use for intensity values.
getEnergyIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.intensity.Intensity: The channel that that forms the histogram.
getEnergyIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.AsObjectMask: The channel that that forms an object-mask with the bounding-box set to entire channel's dimensions
getEnergyIndexGradient() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.TextureScore
getEnergyIndexMask() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase: A channel of the energyStack that is used as an additional mask using default byte values for on and off.
getEnergyIndexMask() - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.intensity.Intensity: Optionally, index of another channel that masks the histogram. -1 disables.
getEnergyIndexX() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.IntensityGradientBase: Index of the channel in the energy stack to use for the X-component of the gradient.
getEnergyIndexY() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.IntensityGradientBase: Index of the channel in the energy stack to use for the Y-component of the gradient.
getEnergyIndexZ() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.IntensityGradientBase: Index of the channel in the energy stack to use for the Z-component of the gradient.
getEnergyScheme() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown: Gets the energy scheme with shared features.
getEnergyScheme() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy: Associated Energy Scheme, which should include the EnergySavedPairs.
getEnergyScheme() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergySchemeWithSharedFeatures: The energy scheme used for calculations.
getEnergySchemeCreator() - Method in class org.anchoranalysis.mpp.feature.bean.mark.MarkEvaluator: Creator for the energy scheme used in mark evaluation.
getEnergyStack() - Method in class org.anchoranalysis.feature.initialization.FeatureInitialization: An energy-stack, which may form an input to the feature for calculation.
getEnergyStack() - Method in class org.anchoranalysis.mpp.proposer.ProposerContext: Energy stack for the current context.
getEnergyStack() - Method in class org.anchoranalysis.plugin.image.task.feature.calculator.FeatureCalculatorFromProvider: The energy stack used for feature calculations.
getEnergyStack() - Method in class org.anchoranalysis.plugin.image.task.feature.InitializationWithEnergyStack: The energy stack.
getEnergyStackOptional() - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy: The associated energy-stack.
getEnergyStackRequired() - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy: The associated energy-stack or throws an exception if it isn't present.
getEnergyTotal() - Method in class org.anchoranalysis.mpp.feature.energy.EnergyPair: The total energy associated with the pair of marks.
getEnergyTotal() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown: Gets the total energy of all marks.
getEnergyTotal() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy: The pre-annealed total energy.
getEnergyTotal() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedAll: Gets the total energy for all items.
getEnergyTotal() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedIndividual: The total energy of all individual marks.
getEnergyTotal() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedPairs: Pairwise energy total
getEquals() - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterDescriptiveName: A descriptive-name must be exactly equal to (case-sensitive) this string.
getError(int) - Method in class org.anchoranalysis.feature.results.ResultsVector: Gets an error state at a particular position.
getErrorNode() - Method in class org.anchoranalysis.mpp.proposer.ProposerContext: Error node for tracking and managing errors.
getErrorReporter() - Method in interface org.anchoranalysis.io.output.outputter.InputOutputContext: The associated error reporter.
getErrorReporter() - Method in class org.anchoranalysis.io.output.outputter.Outputter
getErrorReporter() - Method in class org.anchoranalysis.plugin.image.object.merge.GraphLogger: Gets the error reporter associated with the logger.
getExactDepth() - Method in class org.anchoranalysis.plugin.io.bean.input.files.provider.DirectoryDepth
getException() - Method in exception class org.anchoranalysis.core.functional.CheckedStream.ConvertedToRuntimeException
getException(String) - Method in interface org.anchoranalysis.core.identifier.provider.NamedProvider: Retrieves the item if it exists, or throws an exception if it doesn't exist.
getException(String) - Method in class org.anchoranalysis.core.identifier.provider.store.LazyEvaluationStore
getException(String) - Method in class org.anchoranalysis.feature.shared.SharedFeaturesSubset: Gets a feature by name, throwing an exception if it doesn't exist.
getException(String) - Method in class org.anchoranalysis.image.io.channel.input.ChannelMap: Like ChannelMap.get(java.lang.String) but throws an exception if a particular channel-name does not exist in the map.
getExecutionArguments() - Method in class org.anchoranalysis.experiment.task.InputOutputContextStateful: User-supplied arguments that can further specify an experiment's execution.
getExecutionArguments() - Method in class org.anchoranalysis.experiment.task.ParametersExperiment: User-supplied arguments that can further specify an experiment's execution.
getExecutionDuration() - Method in class org.anchoranalysis.experiment.task.processor.JobStateMonitor: How long the job took to execute in milliseconds.
getExecutionTimeRecorder() - Method in class org.anchoranalysis.core.time.OperationContext: Allows for the execution time of certain operations to be recorded.
getExecutionTimeRecorder() - Method in class org.anchoranalysis.experiment.task.ExperimentFeedbackContext: Allows execution-time for particular operations to be recorded.
getExecutionTimeRecorder() - Method in class org.anchoranalysis.experiment.task.InputOutputContextStateful
getExecutionTimeRecorder() - Method in class org.anchoranalysis.experiment.task.ParametersExperiment: Allows execution-time for particular operations to be recorded.
getExecutionTimeRecorder() - Method in class org.anchoranalysis.image.inference.ImageInferenceContext: Allows execution-time for particular operations to be recorded.
getExecutionTimeRecorder() - Method in class org.anchoranalysis.io.input.bean.InputManagerParameters: Allows for the execution time of certain operations to be recorded.
getExecutionTimeRecorder() - Method in interface org.anchoranalysis.io.output.outputter.InputOutputContext: Allows execution-times to be recorded for particular operations.
getExecutionTimeRecorder() - Method in class org.anchoranalysis.io.output.outputter.OutputWriteContext: Records the execution time of particular operations.
getExecutionTimeRecorder() - Method in class org.anchoranalysis.io.output.writer.ElementOutputter: Records the execution time of particular operations.
getExecutionTimeRecorder() - Method in class org.anchoranalysis.plugin.image.task.feature.FeatureCalculationContext: Records the execution-time of particular operations.
getExperimentIdentifier() - Method in class org.anchoranalysis.experiment.bean.io.OutputExperiment: A name for the experiment.
getExperimentIdentifier() - Method in class org.anchoranalysis.experiment.task.ParametersExperiment
getExpression() - Method in class org.anchoranalysis.bean.shared.regex.RegExSimple: A Java-style regular expression containing groups.
getExpression() - Method in class org.anchoranalysis.io.input.bean.path.matcher.MatchRegularExpression: The regular-expression, Java-style as described in Pattern.
getExpression() - Method in class org.anchoranalysis.plugin.io.bean.file.group.parser.RegularExpression
getExtension() - Method in class org.anchoranalysis.core.system.path.FilenameSplitExtension: The extension of the filename.
getExtension() - Method in class org.anchoranalysis.image.io.bean.stack.writer.OneOrThreeChannelsWriter: Which extension to use to write the image (without any leading period).
getExtensions() - Method in class org.anchoranalysis.io.input.bean.path.matcher.MatchExtensions: A set of file-extensions (without the period), one of which must match the end of a path.
getExtensions() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.BranchExtension: Any extensions to match (case insensitive) excluding any leading period.
getExtent() - Method in class org.anchoranalysis.image.bean.spatial.arrange.fill.ExtentToArrange: The Extent.
getExtent() - Method in class org.anchoranalysis.image.voxel.kernel.KernelPointCursor: The size of the image the kernel iterates over.
getExtent() - Method in class org.anchoranalysis.plugin.image.task.size.SizeMapping: The size.
getFactor() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreObjects: Factor to multiply the feature value by before assigning it to the output channel.
getFactorHigh() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Identity: The factor to apply for values above 0.5 when normalizing.
getFactorLow() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Identity: The factor to apply for values below 0.5 when normalizing.
getFallback() - Method in class org.anchoranalysis.io.input.bean.files.SpecificPathList: If no paths can be found either from listPaths or the input-context, then the fallback is called if exists, otherwise an error is thrown
getFallback() - Method in class org.anchoranalysis.plugin.image.bean.scale.ToSuggested: Used as a delegate to calculate the scale if suggestedSize is empty when passed to ToSuggested.calculate(java.util.Optional<org.anchoranalysis.image.core.dimensions.Dimensions>, java.util.Optional<org.anchoranalysis.image.core.dimensions.size.suggestion.ImageSizeSuggestion>).
getFallback() - Method in class org.anchoranalysis.plugin.image.task.bean.format.convertstyle.ExtractToRGB: If a channel doesn't match an RGB pattern, this conversion-style can be used instead.
getFallback() - Method in class org.anchoranalysis.plugin.image.task.bean.format.convertstyle.RGBIfNamesMatch: If a channel doesn't match an RGB pattern, this conversion-style can be used instead.
getFallback() - Method in class org.anchoranalysis.plugin.io.bean.metadata.reader.InferFromHeader: Fallback to use if EXIF information is non-existing or absent.
getFallbackName() - Method in class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierAuto: If there's no task-name, then this constant is used as a fallback name.
getFeature() - Method in class org.anchoranalysis.feature.bean.provider.FeatureProviderDefine: The feature to provide.
getFeature() - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureEvaluator: The single feature that will be calculated (possibly repeatedly) in the session.
getFeature() - Method in class org.anchoranalysis.image.io.bean.object.feature.OutputFeatureTable: A list of features to calculate in an evaluation context.
getFeature() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreObjects: Feature that calculates the score for an object.
getFeature() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureBase: The feature to be permuted.
getFeatureCondition() - Method in class org.anchoranalysis.plugin.operator.feature.bean.conditional.IfCondition
getFeatureCondition() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.IfConditionWithinRange: Calculates value for the condition - which is checked if it lies within a certain range
getFeatureElse() - Method in class org.anchoranalysis.plugin.operator.feature.bean.conditional.IfCondition
getFeatureEvaluator() - Method in class org.anchoranalysis.annotation.io.bean.comparer.MultipleComparer: Calculates the cost used when making assignments.
getFeatureEvaluator() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner
getFeatureEvaluator() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.collective.DiscardOutliers
getFeatureEvaluator() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.collective.RelationWithMatches
getFeatureEvaluator() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedFeature
getFeatureEvaluator() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.feature.ObjectCollectionProviderWithFeature: The feature evaluator used to calculate features for single objects.
getFeatureEvaluator() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeGreedyToIncreaseObjectFeature
getFeatureEvaluator() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeToIncreaseObjectFeature
getFeatureEvaluatorMatch() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.collective.RelationWithMatches
getFeatureEvaluatorMerge() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergePairs
getFeatureEvaluatorThreshold() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergePairs: Allows merge only if the feature-value satisfies a relation to this threshold
getFeatureLists() - Method in class org.anchoranalysis.feature.initialization.FeatureRelatedInitialization: Gets the underlying NamedProviderStore that provides shared-features.
getFeatureNameIndex() - Method in class org.anchoranalysis.feature.input.FeatureInputResults: A mapping from the name of the feature that produced a result, to its index position in results.
getFeatureNames() - Method in class org.anchoranalysis.plugin.image.task.feature.FeatureCalculationContext: The name of each feature being calculated, in identical order, as that is placed in the exported CSV.
getFeatureNames() - Method in class org.anchoranalysis.plugin.image.task.feature.FeatureExporter: The names of the features to be exported.
getFeatureProvider() - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureEvaluator: The single feature that will be calculated (possibly repeatedly) in the session
getFeatures() - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureListEvaluator: A list of providers, combined together to form a list of features, to be calculated in a session.
getFeatures() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures: The features to be exported (after possibly some manipulation or augmentation).
getFeatures() - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel: Features to calculate for objects in the features output.
getFeaturesAggregate() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures: Features applied to each group to aggregate values (accepting FeatureInputResults).
getFeaturesImage() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors: Additional features that only depend on the image, so do not need to be replicated for every object.
getFeatureSource() - Method in class org.anchoranalysis.plugin.image.task.feature.FeatureCalculationContext: The features that are calculated, encapsulated in some object.
getFeaturesPair() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors: Additional features that are processed on the pair of images (i.e.
getFeatureTables() - Method in class org.anchoranalysis.plugin.mpp.bean.define.Develop: Specifies a feature-table that can also be outputted.
getFile() - Method in class org.anchoranalysis.io.input.file.NamedFile: The file.
getFile() - Method in class org.anchoranalysis.io.input.file.SingleFileInputBase: The associated single file.
getFileAttributes() - Method in class org.anchoranalysis.image.core.stack.ImageMetadata: Attributes associated with the file on the filesystem.
getFileInput() - Method in class org.anchoranalysis.plugin.io.bean.file.group.GroupFiles
getFileInput() - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannels
getFileInput() - Method in class org.anchoranalysis.plugin.io.bean.input.stack.Stacks
getFilename() - Method in class org.anchoranalysis.core.system.path.PathDifference: The file-name component of the difference, if it exists.
getFilePath() - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetSlice
getFilePathParser() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader
getFilePaths() - Method in class org.anchoranalysis.bean.shared.path.FilePathInitialization: Named-store of file-paths.
getFilePaths() - Method in class org.anchoranalysis.feature.initialization.FeatureRelatedInitialization: A named-set of file-paths.
getFiles() - Method in class org.anchoranalysis.io.input.bean.dictionary.ReadFromFile: Provides a single file containing a dictionary.
getFiles() - Method in class org.anchoranalysis.io.input.bean.files.FilesProviderUnary
getFiles() - Method in class org.anchoranalysis.io.input.bean.files.FilesProviderWithDirectoryUnary
getFiles() - Method in class org.anchoranalysis.io.input.bean.path.provider.FromFiles: A provider that should return exactly one File whose path is employed.
getFiles() - Method in class org.anchoranalysis.plugin.io.bean.file.provider.Rooted
getFiles() - Method in class org.anchoranalysis.plugin.io.bean.input.files.NamedFiles: The files to use as inputs.
getFiles() - Method in class org.anchoranalysis.plugin.io.bean.input.files.NamedFilesWithDirectory: The files to use as inputs.
getFilter() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfObjectFilter
getFilter() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.ObjectCollectionProviderFilterBase: The filter to apply to the object collection.
getFilter() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Filter
getFilter() - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageLabellerStringMap
getFilterInitialization(Path) - Method in class org.anchoranalysis.plugin.image.task.labeller.SharedStateFilteredImageOutput: Gets the filter initialization, initializing it if necessary.
getFirst() - Method in class org.anchoranalysis.annotation.io.assignment.CostMatrix: The first set of elements.
getFirst() - Method in class org.anchoranalysis.image.feature.input.FeatureInputPairObjects: Gets the first ObjectMask.
getFirst() - Method in class org.anchoranalysis.io.output.bean.rules.OutputEnableRulesSpecify: Output-names in the first-level.
getFirstArgument() - Method in class org.anchoranalysis.launcher.config.HelpConfig: The application's first argument as described in the help message.
getFirstBinaryValues() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection: The BinaryValuesInt associated with the first object in the collection.
getFirstBinaryValuesByte() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection: The BinaryValuesByte associated with the first object in the collection.
getFixedSizeScaler() - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage: How to calculate the size of each image, when varyImageSize==false.
getFloat() - Static method in class org.anchoranalysis.image.voxel.factory.VoxelsFactory: A factory that creates voxels of type float.
getFontColor() - Method in class org.anchoranalysis.image.io.bean.stack.combine.TextStyle: Font-color of drawn text
getFontName() - Method in class org.anchoranalysis.image.io.bean.stack.combine.TextStyle: Font-name of drawn text
getFontSize() - Method in class org.anchoranalysis.image.io.bean.stack.combine.TextStyle: Font-size of drawn text
getForAllSlices(int) - Method in class org.anchoranalysis.mpp.index.IndexByRegion: Gets the combined voxel partition for all slices in a region.
getFormats() - Method in class org.anchoranalysis.plugin.io.bean.metadata.reader.InferFromHeader: The formats whose headers will be searched, to find sufficient metadata to populate ImageMetadata.
getFormatVoxelwiseCompare() - Method in class org.anchoranalysis.test.image.rasterwriter.comparison.ComparisonPlan: The file-format to use for the voxel-wise comparison (if it's activated).
getForSlice(int, int) - Method in class org.anchoranalysis.mpp.index.IndexByRegion: Gets the voxel partition for a specific slice in a region.
getFrame(int) - Method in class org.anchoranalysis.image.io.stack.time.TimeSeries: Gets a frame in the time-series.
getFriendlyName() - Method in class org.anchoranalysis.feature.bean.Feature: A user-friendly human-readable name for the Feature.
getFrom() - Method in class org.anchoranalysis.core.graph.TypedEdge: The vertex the edge joins from.
getGaussianSigmaMeters() - Method in class org.anchoranalysis.plugin.imagej.bean.define.AddEdgeFilters: The sigma value for the Gaussian filter in meters.
getGenerator() - Method in class org.anchoranalysis.io.generator.sequence.BoundOutputter: The generator to be (repeatedly) used to write elements in the sequence.
getGlob() - Method in class org.anchoranalysis.io.input.bean.path.matcher.MatchGlob: The string describing a glob e.g. "*.jpg".
getGlob() - Method in class org.anchoranalysis.io.input.path.GlobExtractor.GlobWithDirectory: A glob with Java's getPathMatcher syntax.
getGradient() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
getGrayscaleReconstruction() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.MinimaImpositionGrayscaleReconstruction: The grayscale reconstruction algorithm to be used.
getGreen() - Method in class org.anchoranalysis.bean.shared.color.RGBColorBean: The green component value of the RGB color.
getGreen() - Method in class org.anchoranalysis.core.color.RGBColor: The green component value of the RGB color.
getGreen() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeChannels: Provider for the green channel.
getGroup() - Method in class org.anchoranalysis.feature.io.csv.metadata.RowLabels: An identifier for a higher-level group which the row belongs to (foreign key)
getGroup() - Method in class org.anchoranalysis.plugin.annotation.bean.label.AnnotationLabel: Specifies a group for the label (similar labels that are displayed together).
getGroup() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures: Includes an additional group column in CSVs, and creates group-specific feature files.
getGroup() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase: How to partition the inputs into groups.
getGroup() - Method in class org.anchoranalysis.plugin.io.bean.grouper.IfGroupIndexRange: Fallback to use when no group-index-range is specified.
getGrouper() - Method in class org.anchoranalysis.plugin.image.task.feature.FeatureExporter: When defined, assigns each input to a group.
getGrouper() - Method in class org.anchoranalysis.plugin.image.task.grouped.GroupedSharedState: How to group the inputs.
getGroupGeneratorName() - Method in class org.anchoranalysis.plugin.image.task.feature.FeatureCalculationContext: The optional name of the group generator.
getGroupHeaders() - Method in class org.anchoranalysis.feature.io.csv.metadata.LabelHeaders: Headers describing the non-feature columns outputted in the CSV related to identifying the group of a row
getGroupIndexRange() - Method in class org.anchoranalysis.experiment.arguments.TaskArguments: An index-range to use for grouping, by subsetting components from each input's identifier.
getGroupMap() - Method in class org.anchoranalysis.plugin.image.task.grouped.GroupedSharedState: Gets the group map, creating it if it doesn't exist yet.
getHeaders() - Method in class org.anchoranalysis.feature.io.csv.metadata.FeatureCSVMetadata: Headers for the CSV file.
getHeaders() - Method in class org.anchoranalysis.io.input.csv.CSVReader.OpenedCSVFile: The header-names of the CSV file if available.
getHeight() - Method in class org.anchoranalysis.image.bean.spatial.SizeXY: Size in Y dimension.
getHeight() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ImposeResolution: Physical pixel size of a voxel in y-dimension.
getHistogram() - Method in class org.anchoranalysis.image.bean.provider.HistogramProviderUnary: The delegate HistogramProvider that is called.
getHistogram() - Method in class org.anchoranalysis.image.feature.input.FeatureInputHistogram: The histogram associated with this feature input.
getHistogram() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.convert.ConvertWithHistogram: If set, a histogram used in conversion to describe input intensities (across perhaps multiple images).
getHistogram() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.segment.SegmentChannel: An optional histogram of voxel intensity values which can be used by segment
getHistogram() - Method in class org.anchoranalysis.plugin.image.intensity.level.LevelResult: The Histogram of intensity values for this level.
getHistogram() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromHistogram: If non-null, a histogram is extracted from this provider rather than the histogram from the inputted CSV.
getHistogramChannelIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevelBase: The index of the histogram channel to use for calculations.
getHistogramIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram: The index of the histogram to use for comparison.
getHistogramsExtra() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
getId() - Method in class org.anchoranalysis.bean.shared.dictionary.DictionaryProviderReference: Unique identifier for the Dictionary to retrieve.
getId() - Method in class org.anchoranalysis.feature.bean.operator.Reference: The identifier that uniquely determines the other feature to reference.
getId() - Method in class org.anchoranalysis.feature.bean.provider.FeatureProviderReference: The name of the feature to reference.
getId() - Method in class org.anchoranalysis.feature.bean.results.FeatureResultsStatistic: The name of the feature, whose results will provide the statistic.
getId() - Method in class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationReference: The identifier of the existing BinarySegmentation to use.
getId() - Method in class org.anchoranalysis.io.input.bean.path.provider.FilePathProviderReference: A unique identifer for another FilePathProvider that is referenced.
getId() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.Reference: The ID of the channel to retrieve from the named-provider.
getId() - Method in class org.anchoranalysis.plugin.image.bean.dimensions.provider.FromChannel: An shared-objects identifier for a ChannelProvider to use for dimensions.
getId() - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.Reference: The identifier of the histogram to reference.
getId() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.Reference: The identifier of the mask to reference.
getId() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Reference: The identifier of the object collection to reference.
getId() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.ReferenceOrElse
getId() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.Reference: The identifier of the stack to retrieve.
getId() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjects: ID for the particular object-collection
getId() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures: Translates an input file name to a unique ID.
getId() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.Reference: The ID of the MarkCollection to retrieve from the initialization context.
getId() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.ReferenceOrEmpty
getId() - Method in class org.anchoranalysis.plugin.points.bean.fitter.Reference: The ID of the referenced PointsFitter.
getIdentifier() - Method in class org.anchoranalysis.io.input.file.NamedFile: Unique identifier associated with the file.
getIdentifier() - Method in class org.anchoranalysis.mpp.mark.Mark: Gets the identifier of the mark.
getIdentifier() - Method in class org.anchoranalysis.mpp.overlay.OverlayMark: Gets the identifier of the mark.
getIdentifier(T, int) - Method in interface org.anchoranalysis.core.identifier.getter.IdentifierGetter: Gets the unique identifier.
getIdentifier(T, int) - Method in class org.anchoranalysis.core.identifier.getter.IdentifyFromIteration
getIdentifierSubrange() - Method in class org.anchoranalysis.io.input.InputContextParameters: If defined, this indicates and specifies only a subset of the naming-elements to use.
getIdGetter() - Method in class org.anchoranalysis.overlay.writer.ObjectDrawAttributes: Gets a unique ID associated with the object
getIfPresent(K) - Method in class org.anchoranalysis.core.cache.LRUCache: Gets an value, if present, but doesn't create any new entry if it's absent.
getIgnoreContains() - Method in class org.anchoranalysis.annotation.io.bean.AnnotationBackground: If non-empty, to not display any stacks in backgroundStackMap whose name contains this string.
getImage() - Method in class org.anchoranalysis.image.feature.calculator.merged.MergedPairsFeatures
getImage() - Method in class org.anchoranalysis.mpp.init.PointsInitialization: The image initialization associated with this points initialization.
getImage() - Method in class org.anchoranalysis.plugin.image.task.feature.InitializationWithEnergyStack: The image initialization.
getImageDimensions() - Method in class org.anchoranalysis.io.bioformats.copyconvert.ImageFileShape
getImageLabeller() - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageAssignLabel: Maps a label to an image
getImageMetadataReader() - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage: How to read the ImageMetadata from the file-system.
getImageMetadataReader() - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImageCommonSize: How to read the ImageMetadata from the file-system.
getImageMetadataReader() - Method in class org.anchoranalysis.plugin.mpp.bean.convert.ConvertNamedChannels: How to read the ImageMetadata from the file-system.
getImgChannelMapCreator() - Method in class org.anchoranalysis.plugin.io.bean.file.group.GroupFiles
getIncrement() - Method in class org.anchoranalysis.bean.permute.property.SequenceInteger: Size of step to use when incrementing.
getIndex() - Method in interface org.anchoranalysis.core.index.AssociatedIndex: The associated index.
getIndex() - Method in class org.anchoranalysis.core.index.Indexable
getIndex() - Method in class org.anchoranalysis.image.bean.spatial.arrange.fill.ExtentToArrange: Index position.
getIndex() - Method in class org.anchoranalysis.image.inference.bean.reduce.ObjectForReduction: The index of the element in the original list for reduction, or ObjectForReduction.NEWLY_ADDED if newly added.
getIndex() - Method in class org.anchoranalysis.image.io.bean.channel.IndexedChannel: The index (starting at zero) of this Channel relative to others.
getIndex() - Method in class org.anchoranalysis.image.voxel.kernel.KernelPointCursor: The index in the buffer that the kernel currently is focussed on.
getIndex() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.AtIndex
getIndex() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.slice.SliceAt: Index in z-dimension of slice to extract.
getIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.SpecificAxisBase: Specifies which principal-axis to use for calculations (0=largest eigenvalue, 1=second-largest eigenvalue etc.)
getIndex() - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGFeature: Which index to return from the HOG descriptor.
getIndexDay() - Method in class org.anchoranalysis.plugin.io.bean.file.pattern.TimestampPattern: The index of the group in regularExpression that encodes the day, starting from 0 for the first group.
getIndexEnd() - Method in class org.anchoranalysis.io.input.bean.path.NameElementRange: The index of the last element (inclusive) for the range.
getIndexEnd() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.slice.ExtractSliceRange: Slice index to end extracting from (inclusive).
getIndexForMemo(VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.mark.EnergyMemoList: Gets the index for a specific memo.
getIndexHours() - Method in class org.anchoranalysis.plugin.io.bean.file.pattern.TimestampPattern: The index of the group in regularExpression that encodes the hours, starting from 0 for the first group.
getIndexMinutes() - Method in class org.anchoranalysis.plugin.io.bean.file.pattern.TimestampPattern: The index of the group in regularExpression that encodes the minutes, starting from 0 for the first group.
getIndexMonth() - Method in class org.anchoranalysis.plugin.io.bean.file.pattern.TimestampPattern: The index of the group in regularExpression that encodes the month, starting from 0 for the first group.
getIndexSeconds() - Method in class org.anchoranalysis.plugin.io.bean.file.pattern.TimestampPattern: The index of the group in regularExpression that encodes the seconds, starting from 0 for the first group.
getIndexStart() - Method in class org.anchoranalysis.io.input.bean.path.NameElementRange: The index of the first element (inclusive) for the range.
getIndexStart() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.slice.ExtractSliceRange: Slice index to start extracting from (inclusive).
getIndexYear() - Method in class org.anchoranalysis.plugin.io.bean.file.pattern.TimestampPattern: The index of the group in regularExpression that encodes the year, starting from 0 for the first group.
getIndividual() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown: Energy saved for individual marks.
getIndividual() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergyScheme: Features for individual elements (clique-size==1).
getInitialization() - Method in class org.anchoranalysis.bean.initializable.InitializableBean: The parameters used for initialization.
getInitialization() - Method in class org.anchoranalysis.plugin.image.task.labeller.ImageLabellerStringMapInitialization
getInitializationType() - Method in class org.anchoranalysis.bean.initializable.property.BeanInitializer: Type of parameters to be propagated, corresponding to P.
getInnerCoreDistance() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid: The distance to the inner core, expressed as a ratio of the radii.
getInput() - Method in class org.anchoranalysis.annotation.io.bean.AnnotationInputManager: The inputs to be annotated.
getInput() - Method in class org.anchoranalysis.experiment.bean.io.InputOutputExperiment: The input-manager to specify where/which/how necessary inputs for the experiment occur.
getInput() - Method in class org.anchoranalysis.experiment.task.InputBound: The input is bound
getInput() - Method in class org.anchoranalysis.experiment.task.ParametersUnbound
getInput() - Method in class org.anchoranalysis.io.input.bean.InputManagerUnary: The delegate input-manager which will be circumstantially called by the current input-manager.
getInput() - Method in class org.anchoranalysis.launcher.executor.ExperimentExecutor: The input selection parameter.
getInput() - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager: The input manager for the main stack.
getInput() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager: The input manager for the base input type T.
getInput() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationComparisonInput: Gets the input from manager.
getInput() - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
getInput() - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertNamedChannelsToStack
getInputContext() - Method in class org.anchoranalysis.io.input.bean.InputManagerParameters: Additional parameters that offer context for many beans that provide input-functions.
getInputDebug() - Method in class org.anchoranalysis.plugin.io.bean.input.BranchIfDebug: If defined, this provides an input to the manager when in debug-mode, rather than than otherwise inputs.
getInputDirectory() - Method in class org.anchoranalysis.io.input.file.FileNamerContext: A directory associated with the inputs, which if defined, is guaranteed to be a parent of them all.
getInputDirectory() - Method in class org.anchoranalysis.io.input.InputContextParameters: If defined, a directory which can be used by beans to find input.
getInputFilterExtensions() - Method in class org.anchoranalysis.io.input.InputContextParameters: A trie of extensions that can be used filter inputs.
getInputFilterGlob() - Method in class org.anchoranalysis.io.input.InputContextParameters: A glob that can be used by beans to filter input.
getInputIfPresent(T) - Method in class org.anchoranalysis.feature.session.cache.finder.CacheTransferSource: Gets corresponding FeatureCalculationInput for an input, if present, but doesn't create any new entry if it's absent.
getInputName() - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager: The name of the input to be used in the MultiInput.
getInputName() - Method in class org.anchoranalysis.plugin.onnx.bean.object.segment.stack.SegmentObjectsFromONNXModel: The name of the input in the ONNX model.
getInputOutput() - Method in class org.anchoranalysis.experiment.io.InitializationContext: The input-output context.
getInputPaths() - Method in class org.anchoranalysis.io.input.InputContextParameters: A list of paths referring to specific inputs.
getInputPointShift() - Method in class org.anchoranalysis.plugin.points.bean.fitter.ConicFitterBase: The shift to apply to input points before fitting.
getInputScale() - Method in class org.anchoranalysis.image.inference.segment.MultiScaleObject: Gets the ObjectMask at the scale associated with the input-image.
getInstance() - Static method in class org.anchoranalysis.image.voxel.resizer.VoxelsResizerFactory: Singleton instance of VoxelsResizerFactory.
getInstanceFor(Class<? extends T>) - Method in class org.anchoranalysis.bean.BeanInstanceMap: Gets an instance from the map for a particular family-type.
getInt(int) - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer: Gets an element from the buffer at a particular position, converting, if necessary, to an int.
getInt(int) - Method in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsoluteWithSlidingBuffer: Get a value from the buffer at a particular absolute position.
getInt(int, int) - Method in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsoluteWithSlidingBuffer: Get a value from the buffer at a particular relative position.
getIntensity() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
getIntensityHistogram() - Method in class org.anchoranalysis.image.bean.nonbean.segment.BinarySegmentationParameters: A histogram of the intensity values of the voxels that are being segmented.
getInterpolator() - Method in class org.anchoranalysis.image.bean.provider.stack.Arrange: The interpolator to use for scaling images, if needed.
getInterpolator() - Method in class org.anchoranalysis.image.inference.bean.segment.instance.SegmentStackIntoObjectsScaleDecode: The interpolator to use for scaling images.
getInterpolator() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.ScaleXY: The interpolator to use for scaling images.
getInterpolator() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.AtScale: The interpolator to use.
getInterpolator() - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize: Interpolator used when scaling the background
getInterpolator() - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.stack.ScaleToSize
getInterpolator() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.CombineObjectsForFeatures: Interpolator used to resize images in thumbnail generation.
getInterpolator() - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage: How to resize images.
getInterpolator() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase: The interpolator to use for scaling images.
getInterpolator() - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage: The interpolator to use for scaling images.
getInterpolator() - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel: The interpolator to use for scaling images.
getInterpolator() - Method in class org.anchoranalysis.plugin.onnx.bean.object.segment.decode.instance.maskrcnn.DecodeMaskRCNN: The interpolator to use for scaling images.
getInterpolator() - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters: The interpolator to use for scaling images.
getItem() - Method in class org.anchoranalysis.bean.NamedBean: The item that is to be named, the underlying bean.
getItem() - Method in class org.anchoranalysis.feature.bean.list.DefineSingle: The sole feature that forms the list.
getItem() - Method in class org.anchoranalysis.feature.bean.list.PrependName: Provides the features and names before any prepending.
getItem() - Method in class org.anchoranalysis.feature.bean.operator.FeatureUnary
getItem() - Method in class org.anchoranalysis.image.feature.bean.object.pair.FeatureDeriveFromPair: The feature to be applied to individual objects.
getItem() - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.ThresholdHistogram
getItem() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.DeriveFromPair
getItem() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.FeatureListProviderAggregatePair: For each feature in the list, a corresponding aggregate feature is created in the output list.
getItem() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.Intensity: Feature to apply to the histogram
getItem() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.DerivedObject: The feature to calculate on the derived object.
getItem() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjectsSingleElement: The feature to calculate for each intersecting object pair.
getItem() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.PairedWithMask
getItem() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.RejectIfIntensityLessThan: The VoxelScore to use for calculating the score if the intensity is not rejected.
getItem() - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.FeatureSingleObjectFromShared: The feature to be calculated on a single object.
getItem() - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.intensity.Intensity: Feature to apply to the histogram.
getItem() - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.AsObjectMask
getItem() - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.QuantileAcrossConnectedComponents
getItem() - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Rooted
getItem1() - Method in class org.anchoranalysis.feature.bean.operator.FeatureBinary: Provides the first value for the binary-function.
getItem2() - Method in class org.anchoranalysis.feature.bean.operator.FeatureBinary: Provides the second value for the binary-function.
getItemMean() - Method in class org.anchoranalysis.plugin.operator.feature.bean.statistics.StatisticalBase: The Feature used to calculate the mean.
getItemStdDev() - Method in class org.anchoranalysis.plugin.operator.feature.bean.statistics.StatisticalBase: The Feature used to calculate the standard deviation.
getIterations() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.AnisotropicDiffusion: How many iterations to perform diffusion.
getIterations() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.MorphologicalOperatorBase: Number of iterations to apply the morphological operation.
getIterations() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.ObjectCollectionProviderMorphological: The number of iterations to apply the morphological operation.
getIterations() - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.Repeat: The maximum number of iterations.
getIterations() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.Intersection: The number of dilations and erosions to apply to determine if two objects intersect
getIterations() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase: The number of dilations and erosions to apply and whether to do in the Z dimension.
getIterations() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.Erode: The number of iterations to perform the erosion operation.
getIterations() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.NumberRemovedVoxelsAfterClosing
getIterations() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.Shell: The number of dilations and erosions to apply and whether to do so in the Z dimension.
getIterations() - Method in class org.anchoranalysis.plugin.imagej.bean.mask.provider.MorphologicalOperation: iterations for erode, dilate, open, close
getIterationsDilation() - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations: Number of times to perform morphological dilation.
getIterationsErosion() - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations: Number of times to perform morphological erosion.
getJobDescription() - Method in class org.anchoranalysis.experiment.task.processor.SubmittedJob: A unique description for the job.
getJobState() - Method in class org.anchoranalysis.experiment.task.processor.SubmittedJob: The current execution-state of the job.
getKappa() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.AnisotropicDiffusion: A parameter kappa associated with the diffusion functions.
getKeepProcessorsFree() - Method in class org.anchoranalysis.experiment.bean.processor.DebugDependentProcessor: How many processors to avoid using for the tasks.
getKeepProcessorsFree() - Method in class org.anchoranalysis.experiment.bean.processor.ParallelProcessor: How many processors to avoid using for the tasks.
getKernelApplication() - Method in class org.anchoranalysis.image.voxel.kernel.morphological.DilationContext: How the kernel is applied to the scene.
getKernelHalfWidth() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.Median: Kernel will be a square kernel of size (2*kernelHalfWidth+1)x(2*kernelHalfWidth+1)
getKey() - Method in exception class org.anchoranalysis.core.index.GetOperationFailedException: The key that was used in the operation that created this exception.
getKey() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromDictionary: The key of the value in the dictionary that will be assigned.
getKey() - Method in class org.anchoranalysis.plugin.image.bean.dictionary.DictionaryCondition: The key in the dictionary whose value is checked.
getKey() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.IfParamEqual
getKey() - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.ParamFromCollection: The name of the key in the dictionary, whose corresponding value will be returned.
getKey() - Method in class org.anchoranalysis.plugin.io.bean.file.group.parser.FilePathParser
getKey() - Method in class org.anchoranalysis.plugin.io.bean.file.group.parser.RegularExpression
getKey() - Method in class org.anchoranalysis.plugin.operator.feature.bean.FromDictionary
getKeyGroupID() - Method in class org.anchoranalysis.plugin.io.bean.file.group.parser.RegularExpression
getKeyLower() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByDictionary
getKeyPrefix() - Method in class org.anchoranalysis.plugin.operator.feature.bean.FromDictionary: Prefix prepended to key
getKeySuffix() - Method in class org.anchoranalysis.plugin.operator.feature.bean.FromDictionary
getKeyUpper() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByDictionary
getLabel() - Method in class org.anchoranalysis.annotation.image.ImageLabelAnnotation: The label that applies to the image.
getLabel() - Method in class org.anchoranalysis.image.inference.bean.reduce.ObjectForReduction: The label associated with the element.
getLabel() - Method in class org.anchoranalysis.image.inference.segment.LabelledWithConfidence: The label associated with the element.
getLabel() - Method in class org.anchoranalysis.image.io.bean.stack.combine.StackProviderWithLabel: The label associated with stack.
getLabelled() - Method in class org.anchoranalysis.image.inference.bean.reduce.ObjectForReduction: The underlying labelled ObjectMask for input to a reduction algorithm.
getLabelMap() - Method in class org.anchoranalysis.plugin.image.task.labeller.ImageCSVLabellerInitialization: The map associating file identifiers with labels.
getLabels() - Method in class org.anchoranalysis.feature.io.results.LabelledResultsVector: The labels.
getLabels() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.ImageLabelStrategy: List of AnnotationLabels available for annotation.
getLabels() - Method in class org.anchoranalysis.plugin.image.task.feature.LabelledResultsVectorWithThumbnail: The labels describing the results.
getLastPoints1() - Method in class org.anchoranalysis.mpp.bean.proposer.MarkMergeProposer: Gets the points associated with the first mark from the last proposal.
getLastPoints2() - Method in class org.anchoranalysis.mpp.bean.proposer.MarkMergeProposer: Gets the points associated with the second mark from the last proposal.
getLeft() - Method in class org.anchoranalysis.plugin.annotation.comparison.ObjectsToCompare: Objects on left-side of the comparison.
getLeftUnassigned() - Method in class org.anchoranalysis.annotation.io.assignment.OverlappingObjects: The unassigned objects in the left set.
getLevel() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Constant
getLevel() - Method in class org.anchoranalysis.plugin.image.intensity.level.LevelResult: The level value.
getLimitUpper() - Method in class org.anchoranalysis.io.input.InputContextParameters: If defined, an upper limit that is imposed on the number of inputs.
getList() - Method in class org.anchoranalysis.bean.define.adder.Concatenate
getList() - Method in class org.anchoranalysis.bean.shared.regex.RegExList: The list of RegExes that are successively tried to be matched.
getList() - Method in class org.anchoranalysis.bean.shared.StringMap: A list of mappings between a single-items in the respective sets.
getList() - Method in class org.anchoranalysis.experiment.bean.log.ToMultiple: The list of loggers to log to
getList() - Method in class org.anchoranalysis.feature.bean.list.Define: The list that specifies features.
getList() - Method in class org.anchoranalysis.feature.bean.list.DefinedNamed: A list of FeatureListProviders with an associated name.
getList() - Method in class org.anchoranalysis.feature.bean.list.FeatureList: The list of features.
getList() - Method in class org.anchoranalysis.feature.bean.operator.FeatureFromList: The features whose results will be somehow combined, to form the result of this class.
getList() - Method in class org.anchoranalysis.image.bean.provider.stack.Arrange: The stacks that are passed in respect order into arrange.
getList() - Method in class org.anchoranalysis.image.io.bean.stack.combine.TileWithLabels: The list of StackProviderWithLabels that are tiled.
getList() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMap: List of region memberships.
getList() - Method in class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaOr: List of AddCriteriaPair to be combined with OR operation.
getList() - Method in class org.anchoranalysis.plugin.image.bean.color.provider.Concatenate: A list of ColorProvider to be concatenated.
getList() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelListBase: List of CalculateLevel objects to be used in the calculation.
getList() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.combine.ObjectFilterCombine: A list of other filters from which the sub-classes implement filtering behaviour.
getList() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Concatenate: List of ObjectCollectionProviders whose ObjectCollections will be concatenated.
getList() - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.Sequence: A list of binary-segmentations that are applied successively (the output of the predecessor becomes the input of the sucecssor)
getList() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.Concatenate
getList() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.SpecificAndRename
getList() - Method in class org.anchoranalysis.plugin.io.bean.channel.map.FromEntries
getList() - Method in class org.anchoranalysis.plugin.io.bean.file.provider.Combine
getList() - Method in class org.anchoranalysis.plugin.io.bean.input.Concatenate: The list of InputManagers that will be concatenated.
getList() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerAggregate
getListAdditionalChannelProviders() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreObjects: Additional channels to be included in the EnergyStack for feature calculation.
getListAppend() - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
getListFeatures() - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.BinaryClassifierImageLabeller: List of named feature list providers for additional features.
getListImageFeatures() - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement: List of named feature providers for image-based features.
getListImageFeatures() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergyScheme: A list of features of the image that are calculated first, and exposed to the other features as parameters.
getListPaths() - Method in class org.anchoranalysis.io.input.bean.files.SpecificPathList: If specified, this forms the list of paths which is provided as input.
getLoader() - Method in class org.anchoranalysis.test.image.io.TestLoaderImage: Delegate loader (for non image-related loading)
getLoader1() - Method in class org.anchoranalysis.test.image.DualComparer: The first loader.
getLoader2() - Method in class org.anchoranalysis.test.image.DualComparer: The second loader.
getLocal(int) - Method in interface org.anchoranalysis.image.voxel.kernel.BufferRetriever: Get a buffer at a particular index in the z-dimension.
getLocal(int) - Method in class org.anchoranalysis.image.voxel.kernel.LocalSlices
getLocalPath() - Method in class org.anchoranalysis.bean.AnchorBean: A local path on the file-system, optionally associated with this bean.
getLog() - Method in class org.anchoranalysis.experiment.bean.log.OnlyIf: The logger to use if conditions are fulfilled
getLogExperiment() - Method in class org.anchoranalysis.experiment.bean.io.OutputExperiment: Where log messages that do not pertain to a specific job (input) appear.
getLogger() - Method in class org.anchoranalysis.bean.initializable.InitializableBean: The logger.
getLogger() - Method in class org.anchoranalysis.core.log.CommonContext: The logger.
getLogger() - Method in class org.anchoranalysis.core.time.OperationContext: Where to write informative messages to, and and any non-fatal errors (fatal errors are throw as exceptions).
getLogger() - Method in class org.anchoranalysis.experiment.io.InitializationContext: The associated logger.
getLogger() - Method in class org.anchoranalysis.experiment.task.InputBound: The Logger associated with this input, as it is being processed as a job.
getLogger() - Method in class org.anchoranalysis.experiment.task.InputOutputContextStateful
getLogger() - Method in class org.anchoranalysis.image.inference.ImageInferenceContext: Where to log information messages during inference.
getLogger() - Method in class org.anchoranalysis.io.input.bean.InputManagerParameters: Where to write informative messages to, and and any non-fatal errors (fatal errors are throw as exceptions).
getLogger() - Method in class org.anchoranalysis.io.input.file.FileNamerContext: Logs information messages.
getLogger() - Method in interface org.anchoranalysis.io.output.outputter.InputOutputContext: The associated logger.
getLogger() - Method in class org.anchoranalysis.plugin.image.task.feature.FeatureCalculationContext: Gets the logger for the context.
getLogger() - Method in class org.anchoranalysis.plugin.points.bean.FitPoints: The logger for recording errors.
getLoggerExperiment() - Method in class org.anchoranalysis.experiment.task.ExperimentFeedbackContext: The logger associated with the experiment.
getLoggerExperiment() - Method in class org.anchoranalysis.experiment.task.ParametersExperiment: The message-logger used for experiment-wide messages.
getLoggerTaskCreator() - Method in class org.anchoranalysis.experiment.task.ParametersExperiment: This is a means to create new log-reporters for each task.
getLogReporterJob() - Method in class org.anchoranalysis.experiment.task.InputBound: The StatefulMessageLogger associated with the job thati s being processed.
getLogTask() - Method in class org.anchoranalysis.experiment.bean.io.InputOutputExperiment: Where log messages that do pertain to a specific job (input) appear.
getMainObjectName() - Method in class org.anchoranalysis.mpp.io.input.MultiInput: Gets the name of the main input object.
getMainObjectName() - Method in class org.anchoranalysis.mpp.io.input.StackWithMap: Gets the name of the main object.
getMajorAxisAngle() - Method in class org.anchoranalysis.plugin.points.bean.fitter.EllipseStandardFormConverter: Gets the angle of the major axis in radians.
getMajorAxisSlope() - Method in class org.anchoranalysis.plugin.points.bean.fitter.EllipseStandardFormConverter: Gets the slope of the major axis.
getMap() - Method in class org.anchoranalysis.mpp.io.input.OperationMap: Retrieves the internal map storing the operations.
getMap() - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageLabellerStringMap
getMap() - Method in class org.anchoranalysis.plugin.image.task.labeller.ImageLabellerStringMapInitialization
getMapping() - Method in class org.anchoranalysis.plugin.io.shared.AnonymizeSharedState
getMark() - Method in class org.anchoranalysis.mpp.feature.bean.mark.FeatureInputMark: The mark associated with this feature input.
getMark() - Method in class org.anchoranalysis.mpp.mark.voxelized.memo.VoxelizedMarkMemo: The associated mark.
getMark() - Method in class org.anchoranalysis.mpp.overlay.OverlayMark: The Mark to overlay.
getMark() - Method in class org.anchoranalysis.plugin.points.calculate.ellipse.ObjectWithEllipse: The best-fit ellipse for the object.
getMarkEvaluator() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy: A mark-evaluator that is added to the GUI to support this annotation
getMarkFactory() - Method in class org.anchoranalysis.mpp.feature.bean.mark.MarkEvaluator: Factory for creating marks with identifiers.
getMarkFactory() - Method in class org.anchoranalysis.plugin.points.bean.FitPointsFromObjects: The MarkFactory used to create new marks.
getMarkProposer() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy: Name of the MarkProposer to use.
getMarkProvider() - Method in class org.anchoranalysis.mpp.bean.points.CreateMarkFromPoints: Provides the mark to be fitted.
getMarkProvider() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.FromSingleMark: The provider for a single mark.
getMarks() - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria: Gets all marks in the collection.
getMarks() - Method in class org.anchoranalysis.mpp.feature.bean.mark.collection.FeatureInputMarkCollection: The collection of marks.
getMarks() - Method in class org.anchoranalysis.mpp.feature.energy.IndexableMarksWithEnergy: The marks with their energy breakdown.
getMarks() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown: Gets the collection of marks.
getMarks() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy: The marks in the collection.
getMarks() - Method in class org.anchoranalysis.mpp.mark.ColoredMarks
getMarks() - Method in class org.anchoranalysis.mpp.mark.MarkCollection: The underlying List that stores the Marks in the collection.
getMarks() - Method in class org.anchoranalysis.plugin.mpp.bean.object.provider.FromMarks
getMarks() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.ScaleXY: The provider for the MarkCollection to be scaled.
getMarks() - Method in class org.anchoranalysis.plugin.mpp.bean.stack.provider.ColoredMarks
getMarksReject() - Method in class org.anchoranalysis.annotation.mark.DualMarksAnnotation: Marks covering area that should be rejected, can be null
getMarksWithTotalEnergy() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown: Gets the marks with their total energy.
getMask() - Method in class org.anchoranalysis.image.bean.provider.MaskProviderUnary: The delegate Provider<Mask> that is called.
getMask() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.mask.FromMaskBase: The MaskProvider used to create the binary mask.
getMask() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.mask.UnaryWithMaskBase: The MaskProvider used to create the binary mask.
getMask() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
getMask() - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.FromChannel: An optional mask provider to restrict the histogram creation to specific areas.
getMask() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.segment.SegmentChannel: An optional mask which restricts the algorithm to only parts of the channel where the mask has an on voxel
getMask() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.ConnectedComponentsFromMask
getMask() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.mask.AndObjectsWithMasks
getMask() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.mask.FromMask
getMask() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentChannel: Optional mask to restrict the segmentation area.
getMask() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredMask
getMask() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.FromChannelOrMask: A mask that is provided to the stack.
getMask() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.PairedWithMask
getMask() - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.MaskAsSingleObject: The provider for the mask to be treated as a single object.
getMask() - Method in class org.anchoranalysis.plugin.imagej.bean.object.provider.FillHoles
getMaskElse() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfPredicateBase: Returned instead of mask if the predicate is not satisfied.
getMaskValue() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.histogram.ExportImageHistograms: What voxel value to read as "On" in the mask above.
getMatch() - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterCSVColumn
getMatcher() - Method in class org.anchoranalysis.io.input.bean.files.SearchDirectory
getMatcher() - Method in class org.anchoranalysis.io.input.bean.path.matcher.MatchExtensions: A secondary matcher, which is required additionally match (as well as the extension).
getMatcher() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.collective.RelationWithMatches
getMatcher() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.feature.ObjectWithMaximumFeatureFromEachMatchedCollection
getMatcher() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.Match: The ObjectMatcher used to find matches in the input object collection.
getMatches() - Method in class org.anchoranalysis.image.core.object.MatchedObject: The matches associated with the source-object
getMatrix() - Method in class org.anchoranalysis.annotation.io.assignment.CostMatrix: A two-dimensional array mapping the costs from first to second.
getMatrix() - Method in class org.anchoranalysis.spatial.orientation.RotationMatrix: The underlying matrix used internally in the rotation-matrix.
getMax() - Method in class org.anchoranalysis.image.voxel.iterator.MinMaxRange: The maximum value.
getMax() - Method in class org.anchoranalysis.mpp.bean.bound.BoundMinMax: Gets the maximum value of the bound.
getMax() - Method in class org.anchoranalysis.mpp.bean.bound.ResolvedBound
getMax() - Method in class org.anchoranalysis.mpp.mark.points.PointListBase: The maximum x, y, z coordinates of all the points in the list.
getMax() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByMinMaxValue
getMax() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.ClampHistogramMax
getMax() - Method in class org.anchoranalysis.plugin.image.feature.bean.physical.UnitsWithinRange: Maximum-boundary for acceptable range
getMax() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.OutsideRange: The maximum value of the range (exclusive).
getMax() - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.InvertedMax
getMax() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.CompareWithRangeFeature: Calculates maximally-allowed range boundary
getMax() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareFromScalars: Boundary value indicating the maximally-allowed range value.
getMaxCost() - Method in class org.anchoranalysis.annotation.io.bean.comparer.MultipleComparer: The maximum cost (as calculated by featureEvaluator) to accept when creating an assignment between objects.
getMaxCost() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner
getMaxDirectoryDepth() - Method in class org.anchoranalysis.io.input.bean.files.SearchDirectory: If non-negative the max depth of directories.
getMaxDistance() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithOptionalDistanceConstraint: An optional maximum distance between objects that can be merged.
getMaxDistance() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.CostOverlapWithinMidpointDistance
getMaximumIndex() - Method in interface org.anchoranalysis.core.index.range.IndexRange: The maximum index in the range.
getMaximumNumberChannels() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.IntensityMoments: An upper limit on the number of channels in the energy-stack for which we create features.
getMaxInstant() - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster.ClusterIdentifier: Maximum timestamp in cluster.
getMaxNumberItems() - Method in class org.anchoranalysis.plugin.io.bean.file.provider.Limit
getMaxNumberItems() - Method in class org.anchoranalysis.plugin.io.bean.input.Limit
getMaxNumberProcessors() - Method in class org.anchoranalysis.experiment.arguments.TaskArguments: Suggests a maximum number of processors (CPUs) for a task.
getMaxNumberProcessors() - Method in class org.anchoranalysis.experiment.bean.processor.DebugDependentProcessor: An upper limit on the number of the processors that can be simultaneously used in parallel, if they are available.
getMaxNumberProcessors() - Method in class org.anchoranalysis.experiment.bean.processor.ParallelProcessor: Theoretical maximum number of (CPU) processors to use in parallel.
getMaxNumItems() - Method in class org.anchoranalysis.plugin.io.bean.file.provider.LimitWithDirectory
getMaxPathWidth() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.input.ExtractIdentifierAndPath: The maximum width permitted for an identifier, so that it is printed as one line.
getMaxResolved(Optional<Resolution>, boolean) - Method in class org.anchoranalysis.mpp.bean.bound.BoundDegrees
getMaxResolved(Optional<Resolution>, boolean) - Method in class org.anchoranalysis.mpp.bean.bound.BoundPhysicalExtent
getMaxResolved(Optional<Resolution>, boolean) - Method in class org.anchoranalysis.mpp.bean.bound.BoundUnitless
getMaxResolved(Optional<Resolution>, boolean) - Method in class org.anchoranalysis.mpp.bean.bound.MarkBounds: Gets the resolved maximum value of the bound, considering resolution and dimensionality.
getMaxSize() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Mser
getMaxSplitGroups() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations: The maximum number of groups to split the identifier into.
getMaxTime() - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster.ClusterIdentifier: Gets the latest date-time in the cluster.
getMaxValue() - Method in class org.anchoranalysis.math.histogram.Histogram: Maximum possible value in the histogram (inclusive).
getMaxVar() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Mser
getMaxVolume() - Method in class org.anchoranalysis.plugin.imagej.bean.mask.provider.FillHoles: The maximum volume of a hole to be filled.
getMaxX() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Box: Maximum X coordinate inclusive.
getMaxY() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Box: Maximum Y coordinate inclusive.
getMaxZ() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Box: Maximum Z coordinate inclusive.
getMean() - Method in class org.anchoranalysis.math.statistics.MeanScale: The mean.
getMean(int) - Method in class org.anchoranalysis.math.statistics.moment.ImageMoments: Get the mean-value for a particular axis.
getMedianRadiusMeters() - Method in class org.anchoranalysis.plugin.imagej.bean.define.AddEdgeFilters: The radius of the median filter in meters.
getMemo() - Method in class org.anchoranalysis.mpp.feature.input.FeatureInputSingleMemo: The memoized voxelized mark.
getMemoForIndex(int) - Method in class org.anchoranalysis.mpp.feature.mark.EnergyMemoList: Gets the memo for a specific index.
getMemoForIndex(int) - Method in class org.anchoranalysis.mpp.feature.mark.MemoList
getMemoForIndex(int) - Method in interface org.anchoranalysis.mpp.mark.voxelized.memo.MemoForIndex: Retrieves the VoxelizedMarkMemo for the specified index.
getMemoForMark(MarkCollection, Mark) - Method in class org.anchoranalysis.mpp.feature.mark.EnergyMemoList: Gets the memo for a specific mark in the collection.
getMerged() - Method in class org.anchoranalysis.image.feature.input.FeatureInputPairObjects: Returns a merged version of the two objects.
getMergedOptional() - Method in class org.anchoranalysis.image.feature.input.FeatureInputPairObjects: Gets the optional merged ObjectMask.
getMessage() - Method in exception class org.anchoranalysis.core.index.GetOperationFailedException: A message describing the failure.
getMessageLogger() - Method in class org.anchoranalysis.experiment.task.InputOutputContextStateful: Exposed as StatefulMessageLogger rather than as MessageLogger that is found in Logger
getMessageNoInputs() - Method in class org.anchoranalysis.experiment.bean.io.InputOutputExperiment: A message written to the logger if no inputs exist for the experiment, and it thus ends early.
getMessageReporter() - Method in interface org.anchoranalysis.io.output.outputter.InputOutputContext: The associated message reporter.
getMessages() - Method in class org.anchoranalysis.plugin.mpp.shared.ConvertedInput: Any messages written to the log during conversion.
getMetadata() - Method in class org.anchoranalysis.image.feature.input.FeatureInputImageMetadata: The image metadata.
getMethod() - Method in class org.anchoranalysis.plugin.fiji.bean.mask.provider.AutoLocalThreshold
getMethod() - Method in class org.anchoranalysis.plugin.fiji.bean.threshold.ThresholderAutoIJ: The thresholding method to use.
getMethod() - Method in class org.anchoranalysis.plugin.io.bean.task.CopyFiles: How the copying occurs from source to destination file.
getMin() - Method in class org.anchoranalysis.image.voxel.iterator.MinMaxRange: The minimum value.
getMin() - Method in class org.anchoranalysis.mpp.bean.bound.BoundMinMax: Gets the minimum value of the bound.
getMin() - Method in class org.anchoranalysis.mpp.bean.bound.ResolvedBound
getMin() - Method in class org.anchoranalysis.mpp.mark.points.PointListBase: The minimum x, y, z coordinates of all the points in the list.
getMin() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByMinMaxValue
getMin() - Method in class org.anchoranalysis.plugin.image.feature.bean.physical.UnitsWithinRange: Minimum-boundary for acceptable range
getMin() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.OutsideRange: The minimum value of the range (inclusive).
getMin() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.CompareWithRangeFeature: Calculates minimally-allowed range boundary
getMin() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareFromScalars: Boundary value indicating the minimally-allowed range value.
getMin(Function<FileDetails, Optional<Integer>>) - Method in class org.anchoranalysis.plugin.io.multifile.ParsedFilePathBag: Gets the minimum value obtained by applying a function to all FileDetails.
getMinConfidence() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ThresholdConfidence: The minimum confidence of an element for its object-mask to be initially included for consideration (before merging).
getMinConfidence() - Method in class org.anchoranalysis.plugin.onnx.bean.object.segment.decode.instance.maskrcnn.DecodeMaskRCNN: Only proposals outputted from the model with a score greater or equal to this threshold are considered.
getMinConfidence() - Method in class org.anchoranalysis.plugin.onnx.bean.object.segment.decode.instance.text.DecodeEAST: Proposed bounding boxes below this confidence interval are removed from consideration.
getMinDifference() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Difference: A minimum difference, below which 0.0 is returned
getMinDifference() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.DifferenceCalculateLevelStandardDeviation
getMinDiversity() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Mser
getMinimaImposition() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.ImposeMinima
getMinimumBoundingBoxVolume() - Method in class org.anchoranalysis.plugin.imagej.bean.object.segment.FloodFillEachIntensityLevel: Only objects whose bounding-box volume is greater or equal to this threshold are included.
getMinimumIndex() - Method in interface org.anchoranalysis.core.index.range.IndexRange: The minimum index in the range.
getMinimumPerCluster() - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster.ClusterByTimestamp: The minimum number of files that must exist for a cluster.
getMinInstant() - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster.ClusterIdentifier: Minimum timestamp in cluster.
getMinIntensity() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.RejectIfIntensityLessThan: The minimum intensity threshold.
getMinIntensity() - Method in class org.anchoranalysis.plugin.imagej.bean.threshold.ThresholderSimpleFillHoles2D: The minimum intensity value for thresholding.
getMinIntensityValue() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.MorphologicalOperatorBase: Minimum intensity value for voxels to be considered in the operation.
getMinMaskValue() - Method in class org.anchoranalysis.plugin.onnx.bean.object.segment.decode.instance.maskrcnn.DecodeMaskRCNN: Only voxels with a value greater or equal to this threshold are considered as part of the mask.
getMinNumberObjects() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.collective.DiscardOutliers
getMinNumberPoints() - Method in class org.anchoranalysis.plugin.points.bean.SplitContourAtSaddlePoints: If a contour has less than this number of points, we don't split it, and return it as-is
getMinNumberVoxels() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.split.SplitIntoSquares: Only includes squares that have at least this number of voxels.
getMinNumberVoxels() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.ConnectedComponentsFromBinarySegmentation
getMinNumberVoxels() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ThresholdConfidence: The minimum number of voxels that must exist in a connected-component to be included.
getMinNumPoints() - Method in class org.anchoranalysis.mpp.bean.points.CreateMarkFromPoints: Minimum number of points required to create a mark.
getMinNumPoints() - Method in class org.anchoranalysis.plugin.points.bean.fitter.PointsFitterToMark: The minimum number of points required for fitting.
getMinNumZSlices() - Method in class org.anchoranalysis.plugin.io.bean.file.group.check.AtLeastZSlices
getMinorAxisAngle() - Method in class org.anchoranalysis.plugin.points.bean.fitter.EllipseStandardFormConverter: Gets the angle of the minor axis in radians.
getMinorAxisSlope() - Method in class org.anchoranalysis.plugin.points.bean.fitter.EllipseStandardFormConverter: Gets the slope of the minor axis.
getMinOverlap() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.CostOverlapWithinMidpointDistance
getMinRadius() - Method in class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresEllipseFitter
getMinRadius() - Method in class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresEllipsoidFitter
getMinRatio() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.collective.DiscardOutliers
getMinResolution() - Method in class org.anchoranalysis.plugin.image.bean.scale.MinimumXYResolution: The minimum resolution to achieve in meters.
getMinResolved(Optional<Resolution>, boolean) - Method in class org.anchoranalysis.mpp.bean.bound.BoundDegrees
getMinResolved(Optional<Resolution>, boolean) - Method in class org.anchoranalysis.mpp.bean.bound.BoundPhysicalExtent
getMinResolved(Optional<Resolution>, boolean) - Method in class org.anchoranalysis.mpp.bean.bound.BoundUnitless
getMinResolved(Optional<Resolution>, boolean) - Method in class org.anchoranalysis.mpp.bean.bound.MarkBounds: Gets the resolved minimum value of the bound, considering resolution and dimensionality.
getMinSize() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Mser
getMinTime() - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster.ClusterIdentifier: Gets the earliest date-time in the cluster.
getMinusOne() - Method in class org.anchoranalysis.image.voxel.buffer.SlidingBuffer: The voxel-buffer for the slice with the currently selected slice's index -1 or null if it's the first slice.
getMinVolume() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.ConnectedComponentsFromMask
getMinX() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Box: Minimum X coordinate inclusive.
getMinY() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Box: Minimum Y coordinate inclusive.
getMinZ() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Box: Minimum Z coordinate inclusive.
getModel() - Method in class org.anchoranalysis.inference.concurrency.ConcurrentModel: The underlying model.
getModelBinaryPath() - Method in class org.anchoranalysis.plugin.opencv.bean.object.segment.stack.SegmentObjectsFromTensorFlowModel: Relative-path to the TensorFlow model file, likely with .pb extension, relative to the models/ directory in the Anchor distribution.
getModelDirectory() - Method in class org.anchoranalysis.core.log.CommonContext: Directory where machine-learning models can be found.
getModelDirectory() - Method in class org.anchoranalysis.experiment.arguments.InputArguments: A directory indicating where models can be located.
getModelDirectory() - Method in class org.anchoranalysis.experiment.task.InputOutputContextStateful
getModelDirectory() - Method in interface org.anchoranalysis.io.output.outputter.InputOutputContext: An input-directory in which models are stored.
getModelDirectory() - Method in class org.anchoranalysis.plugin.image.task.feature.FeatureCalculationContext: Gets the model directory path.
getModelPath() - Method in class org.anchoranalysis.plugin.onnx.bean.object.segment.stack.SegmentObjectsFromONNXModel: Relative-path to the model file in ONNX form, relative to the models/ directory in the Anchor distribution.
getModelPool() - Method in class org.anchoranalysis.plugin.image.task.segment.SharedStateSegmentInstance: The concurrent model pool for inference.
getModelScale() - Method in class org.anchoranalysis.image.inference.segment.MultiScaleObject: Gets the ObjectMask at the scale associated with the segmentation.
getModelTextGraphPath() - Method in class org.anchoranalysis.plugin.opencv.bean.object.segment.stack.SegmentObjectsFromTensorFlowModel: Relative-path to the TensorFlow model file, likely with .pb.txt extension, relative to the models/ directory in the Anchor distribution.
getModificationTime() - Method in class org.anchoranalysis.image.core.stack.ImageFileAttributes: The last modified timestamp on the file the image was loaded from.
getMultipleComparer() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy: Multiple comparer for comparing annotations.
getMultipleOf() - Method in class org.anchoranalysis.plugin.image.bean.scale.FitTo: The eventual width and height of the image must be a multiple of this number.
getMultiplyBy() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D: A factor to multiply the distance values by.
getName() - Method in class org.anchoranalysis.bean.define.adder.FromXMLList: The name of the file in the current working directory WITHOUT THE .xml EXTENSION
getName() - Method in class org.anchoranalysis.bean.NamedBean: The name associated with item.
getName() - Method in class org.anchoranalysis.bean.shared.path.RootPath: The name of the root-path, which need not be unique in itself.
getName() - Method in interface org.anchoranalysis.core.identifier.name.NameValue: The associated name.
getName() - Method in class org.anchoranalysis.core.identifier.name.SimpleNameValue
getName() - Method in class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierConstant
getName() - Method in class org.anchoranalysis.image.io.bean.channel.IndexedChannel: The name of the Channel this entry represents.
getName() - Method in class org.anchoranalysis.io.generator.combined.OptionalNameValue: An optional-name.
getName() - Method in class org.anchoranalysis.io.output.path.prefixer.NamedPath: A unique name associated with the path
getName() - Method in class org.anchoranalysis.mpp.mark.conic.Circle
getName() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
getName() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
getName() - Method in class org.anchoranalysis.mpp.mark.conic.Sphere
getName() - Method in class org.anchoranalysis.mpp.mark.Mark: Returns the name of this mark type.
getName() - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
getName() - Method in class org.anchoranalysis.mpp.mark.points.PointList
getName() - Method in class org.anchoranalysis.mpp.mark.points.Polygon
getName() - Method in class org.anchoranalysis.mpp.mark.points.PolygonCurve
getName() - Method in class org.anchoranalysis.mpp.mark.points.RotatableBoundingBox
getName() - Method in class org.anchoranalysis.plugin.image.task.grouped.NamedChannel: The name associated with the channel.
getNameLeft() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager: The name of the left side in the comparison.
getNamer() - Method in class org.anchoranalysis.plugin.io.bean.file.group.GroupFiles
getNamer() - Method in class org.anchoranalysis.plugin.io.bean.file.namer.RemoveExtension
getNamer() - Method in class org.anchoranalysis.plugin.io.bean.file.namer.SubsetRangeIfRequested: The namer that is called to provide names that are subsetted.
getNamer() - Method in class org.anchoranalysis.plugin.io.bean.input.files.NamedFilesBase
getNameRight() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager: The name of the right side in the comparison.
getNames() - Method in class org.anchoranalysis.annotation.io.comparer.StatisticsToExport: The names of statistics describing the annotation-comparison, as produced by StatisticsToExport.getValues().
getNames() - Method in class org.anchoranalysis.image.feature.calculator.NamedFeatureCalculatorMulti: The list of feature names associated with the calculator.
getNames() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationComparisonInput: Names associated with the two sources being compared.
getNameSubrange() - Method in class org.anchoranalysis.io.input.file.FileNamerContext: If defined, this indicates and specifies only a subset of the naming-elements to use.
getNaming() - Method in class org.anchoranalysis.plugin.io.bean.task.CopyFiles: How an output name (and path) is selected for an input file.
getNamingSharedState() - Method in class org.anchoranalysis.plugin.io.shared.RecordingCounter
getNavigateHigherDirectories() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader: Search x number directories higher than file.
getNumber() - Method in class org.anchoranalysis.experiment.task.processor.JobDescription
getNumberBins() - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters: The number of bins in each histogram for a cell.
getNumberChannels() - Method in class org.anchoranalysis.feature.energy.EnergyStack: The number of channels in the stack.
getNumberChannels() - Method in class org.anchoranalysis.feature.energy.EnergyStackWithoutParameters: The number of channels in the stack.
getNumberChannels() - Method in class org.anchoranalysis.image.core.stack.DisplayStack: The number of channels in the stack.
getNumberChannels() - Method in class org.anchoranalysis.image.core.stack.ImageMetadata: The number of channels in the image.
getNumberChannels() - Method in class org.anchoranalysis.image.core.stack.Stack: The number of channels in the stack.
getNumberChannels() - Method in class org.anchoranalysis.image.core.stack.StackNotUniformSized: The number of channels in the Stack.
getNumberChannels() - Method in class org.anchoranalysis.image.io.stack.output.box.ScaleableBackground: Number of channels in the background.
getNumberChannels() - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceNumberChannels: The assigned number of channels.
getNumberChannels() - Method in class org.anchoranalysis.io.bioformats.copyconvert.ImageFileShape
getNumberChannels() - Method in class org.anchoranalysis.test.image.stackwriter.ChannelSpecification: How many channels in the stack?
getNumberChannelsPerArray() - Method in class org.anchoranalysis.io.bioformats.copyconvert.ImageFileEncoding: The total number of channels found in any one buffer.
getNumberColumns() - Method in class org.anchoranalysis.image.bean.spatial.arrange.tile.Tile: The number of columns to use in the table produced when tiling.
getNumberConverter() - Method in class org.anchoranalysis.plugin.io.shared.AnonymizeSharedState
getNumberDecimalPlaces() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner
getNumberDigits() - Method in class org.anchoranalysis.io.output.bean.path.prefixer.IncrementingNumber: Number of digits in the number, with leading zeros as necessary.
getNumberDilations() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectIndependently
getNumberDimensions() - Method in class org.anchoranalysis.spatial.orientation.RotationMatrix: The number of dimensions in the rotation-matrix.
getNumberFrames() - Method in class org.anchoranalysis.image.core.stack.ImageMetadata: The number of frames (separate images representing different points in a time-series) in the image.
getNumberFrames() - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceNumberFrames: The assigned number of frames.
getNumberFrames() - Method in class org.anchoranalysis.io.bioformats.copyconvert.ImageFileShape
getNumberGPUProcessors() - Method in class org.anchoranalysis.experiment.bean.processor.ParallelProcessor: How many GPU processors to use when this is possible as a substitute for a CPU processor
getNumberLevelsGrouping() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations: The number of levels for grouping.
getNumberLoopPoints() - Method in class org.anchoranalysis.plugin.points.bean.SplitContourAtSaddlePoints
getNumberParentOperations() - Method in class org.anchoranalysis.core.time.RecordedExecutionTimes.RecordedOperation: The number of parent operations.
getNumberParentOperations() - Method in class org.anchoranalysis.experiment.time.RunningSumParented: The number of parent operations.
getNumberRows() - Method in class org.anchoranalysis.image.bean.spatial.arrange.fill.Fill: The number of rows to use the montage, when sufficient images are available.
getNumberRows() - Method in class org.anchoranalysis.image.bean.spatial.arrange.tile.Tile: The number of rows to use in the table produced when tiling.
getNumberSeries() - Method in class org.anchoranalysis.image.core.stack.ImageMetadata: The number of separate images stored in the file.
getNumberSlices() - Method in class org.anchoranalysis.io.bioformats.copyconvert.ImageFileShape: The number of z-slices for a specific channel and frame.
getNumberSubdirectories() - Method in class org.anchoranalysis.plugin.io.bean.file.namer.LastDirectories: How many directories to include in the name.
getNumColumns() - Method in class org.anchoranalysis.image.io.bean.stack.combine.TileWithLabels: How many columns when tiling, so long as there are sufficient StackProviderWithLabels.
getObject() - Method in class org.anchoranalysis.annotation.io.image.findable.Found: The found object.
getObject() - Method in class org.anchoranalysis.image.feature.input.FeatureInputSingleObject: The object mask associated with this input.
getObject() - Method in class org.anchoranalysis.overlay.object.OverlayObjectMask: The ObjectMask to draw.
getObject() - Method in class org.anchoranalysis.plugin.image.intensity.level.LevelResult: The ObjectMask associated with this level.
getObject() - Method in class org.anchoranalysis.plugin.image.object.ColoredObject: The object-mask.
getObject() - Method in class org.anchoranalysis.plugin.image.object.merge.ObjectVertex: The ObjectMask represented by this vertex.
getObject() - Method in class org.anchoranalysis.plugin.points.calculate.ellipse.ObjectWithEllipse: The object mask.
getObject1() - Method in class org.anchoranalysis.mpp.feature.input.FeatureInputPairMemo: The first memoized voxelized mark.
getObject2() - Method in class org.anchoranalysis.mpp.feature.input.FeatureInputPairMemo: The second memoized voxelized mark.
getObjectMatcher() - Method in class org.anchoranalysis.plugin.image.bean.object.match.Bridge: Used to match each intermediary-object to a final-object
getObjects() - Method in class org.anchoranalysis.image.bean.provider.ObjectCollectionProviderUnary: The delegate Provider<ObjectCollection> that is called.
getObjects() - Method in class org.anchoranalysis.image.feature.input.FeatureInputObjectCollection: The collection of objects associated with this feature input.
getObjects() - Method in class org.anchoranalysis.image.inference.segment.SegmentedObjects: The segmented-objects, at two different scales.
getObjects() - Method in class org.anchoranalysis.image.io.bean.object.feature.OutputFeatureTable: The objects for which features are calculated.
getObjects() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransformForEachObject3D
getObjects() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectBase: The objects for whom a level is calculated.
getObjects() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.UnaryWithObjectsBase: The provider for the collection of objects to be used in channel creation.
getObjects() - Method in class org.anchoranalysis.plugin.image.bean.color.provider.GenerateToMatchObjects
getObjects() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromObjects
getObjects() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntersectsWith
getObjects() - Method in class org.anchoranalysis.plugin.image.bean.object.match.Always
getObjects() - Method in class org.anchoranalysis.plugin.image.bean.object.match.Intersection: Provider for the objects to intersect with the source objects.
getObjects() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Permute
getObjects() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredObjects: Objects to draw on a background
getObjects() - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.ObjectAggregationBase: The provider for the collection of objects to calculate features on.
getObjects() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.PointsFromObjects: Provider for the object collection from which to create point marks.
getObjects() - Method in class org.anchoranalysis.plugin.points.bean.fitter.PointsFitterToMark: Provides the ObjectCollection to be used in the fitting process.
getObjects1() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeTwoCollectionsItemwise: First collection with items to be merged
getObjects2() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeTwoCollectionsItemwise: Second collection with items to be merged
getObjectsBlue() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeColoredObjects
getObjectsContainer() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithContainerBase: Optional provider for a container of objects.
getObjectsElse() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.ReferenceOrElse
getObjectsGreater() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.GreaterIntersectionWith
getObjectsGreen() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeColoredObjects
getObjectsGrouped() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.FilterByGroup: Provides the ObjectCollection used for grouping the objects to be filtered.
getObjectsLesser() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.GreaterIntersectionWith
getObjectsRed() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeColoredObjects
getObjectsSeeds() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentChannel: Optional provider for seed objects to guide the segmentation.
getObjectsSeeds() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentWithSeeds
getObjectsSource() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromIntersectingObjects
getObjectsSource() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentWithSeeds
getObjectsSplitBy() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.split.SplitByObjects: Provider for the collection of objects used to split the input objects.
getObjectsTarget() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromIntersectingObjects
getOff() - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte: The byte representation of the value for off.
getOff() - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValuesInt: The integer representation of the value for off.
getOffset() - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster.ClusterIdentifier: The offset to assume the time-stamp belongs in.
getOn() - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte: The byte representation of the value for on.
getOn() - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValuesInt: The integer representation of the value for on.
getOperationContext() - Method in class org.anchoranalysis.io.input.bean.InputManagerParameters: Allows for logging and recording the execution-time of particular operations.
getOperationContext() - Method in class org.anchoranalysis.mpp.proposer.ProposerContext: Operation context for the current operation.
getOperationContext() - Method in class org.anchoranalysis.plugin.image.task.feature.FeatureCalculationContext: Gets the operation context.
GetOperationFailedException - Exception Class in org.anchoranalysis.core.index: When a get operation fails for a particular key.
GetOperationFailedException(int, String) - Constructor for exception class org.anchoranalysis.core.index.GetOperationFailedException: Creates with a message, but no cause - with an integer key.
GetOperationFailedException(int, Throwable) - Constructor for exception class org.anchoranalysis.core.index.GetOperationFailedException: Creates with a cause, but no message - with an integer key.
GetOperationFailedException(Exception) - Constructor for exception class org.anchoranalysis.core.index.GetOperationFailedException: Creates with only a cause, omitting a key and a message.
GetOperationFailedException(String, String) - Constructor for exception class org.anchoranalysis.core.index.GetOperationFailedException: Creates with a message, but no cause - with a String key.
GetOperationFailedException(String, Throwable) - Constructor for exception class org.anchoranalysis.core.index.GetOperationFailedException: Creates with a cause, but no message - with a String key.
getOperationIdentifier() - Method in class org.anchoranalysis.core.time.RecordedExecutionTimes.RecordedOperation: An (unique) identifier for the operation.
getOptional(String) - Method in interface org.anchoranalysis.core.identifier.provider.NamedProvider: Retrieves the item if it exists, or returns Optional.empty() if it doesn't exist.
getOptional(String) - Method in class org.anchoranalysis.core.identifier.provider.NamedProviderBridge
getOptional(String) - Method in class org.anchoranalysis.core.identifier.provider.NamedProviderCombine
getOptional(String) - Method in class org.anchoranalysis.core.identifier.provider.NameValueMap
getOptional(String) - Method in class org.anchoranalysis.core.identifier.provider.store.EagerEvaluationStore
getOptional(String) - Method in class org.anchoranalysis.core.identifier.provider.store.LazyEvaluationStore
getOptional(String) - Method in class org.anchoranalysis.feature.shared.SharedFeatures
getOptional(String) - Method in class org.anchoranalysis.image.core.stack.named.NamedStacks
getOptional(String) - Method in class org.anchoranalysis.image.io.stack.time.ExtractFrameStore
getOptions() - Method in class org.anchoranalysis.io.bioformats.bean.BioformatsReader: Options that influence how stack is read.
getOptions() - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptionsDelegate: Options can be specified to alter how an image file is read.
getOrCalculate(T) - Method in class org.anchoranalysis.feature.calculate.cache.part.ResolvedPart: Executes the operation and returns a result, either by doing the calculation, or retrieving a cached-result from previously.
getOrCalculate(T) - Method in class org.anchoranalysis.feature.calculate.part.CalculationPart: Executes the operation and returns a result, either by doing the calculation, or retrieving a cached-result from previously.
getOrCalculate(T, U) - Method in class org.anchoranalysis.feature.calculate.cache.part.ResolvedPartMap: Executes the operation and returns a result, either by doing the calculation, or retrieving a cached-result from a previous execution.
getOrCalculate(T, U) - Method in class org.anchoranalysis.feature.calculate.part.CalculationPartMap: Executes the operation and returns a result, either by doing the calculation, or retrieving a cached-result from a previous execution.
getOrCreate(Class<?>) - Method in class org.anchoranalysis.core.identifier.provider.store.SharedObjects: Gets an existing store, or creates a new one
getOrientation() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
getOrientation() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid: The orientation of the ellipsoid.
getOriginal() - Method in class org.anchoranalysis.image.core.object.label.OverlappingObject: Original unscaled element before any operations
getOrLog(String, Logger) - Method in interface org.anchoranalysis.annotation.io.image.findable.Findable: Gets an object or otherwise logs a message describing what went wrong.
getOrLog(String, Logger) - Method in class org.anchoranalysis.annotation.io.image.findable.Found
getOrLog(String, Logger) - Method in class org.anchoranalysis.annotation.io.image.findable.NotFound
getOrNull(U) - Method in class org.anchoranalysis.feature.calculate.part.CalculationPartMap: Gets an existing result for the current input from the cache.
getOtherwise() - Method in class org.anchoranalysis.plugin.io.bean.file.namer.IfRelativeToDirectory: The namer to use if the relative-to-directory option is not selected.
getOutlineColor() - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel: The color of the outline.
getOutlineWidth() - Method in class org.anchoranalysis.image.io.bean.object.draw.Outline: The size of the outline, in terms of the number of voxels.
getOutlineWidth() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations: How many pixels should the outline be around objects.
getOutlineWidth() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.AtScale
getOutlineWidth() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase: The width of the outline (only relevant if outline==true).
getOutlineWidth() - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize: The width of the outline.
getOutlineWidth() - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel: The width of the outline.
getOutlineWidth() - Method in class org.anchoranalysis.plugin.mpp.bean.define.VisualizeOnBackground
getOutPath() - Method in class org.anchoranalysis.plugin.io.bean.path.derive.InsertRegExGroups: Constructs a path as an output, replacing $1, $2 etc. with the respective group from the matched regular-expression.
getOutput() - Method in class org.anchoranalysis.experiment.bean.io.OutputExperiment: The output-manager that specifies how/where/which elements occur duing outputting.
getOutput() - Method in class org.anchoranalysis.launcher.executor.ExperimentExecutor: The output selection parameter.
getOutputDirectory() - Method in class org.anchoranalysis.io.output.outputter.Outputter: The directory into which outputting occurs.
getOutputDirectory() - Method in class org.anchoranalysis.io.output.outputter.OutputterChecked: The directory into which outputting occurs.
getOutputDirectory() - Method in class org.anchoranalysis.io.output.path.prefixer.OutputPrefixerSettings: A directory indicating where inputs can be located.
getOutputEnabledDelta() - Method in class org.anchoranalysis.experiment.arguments.OutputArguments: Additions/subtractions of outputs for the experiment supplied by the user.
getOutputName() - Method in class org.anchoranalysis.experiment.bean.log.ToTextFileBase: The name to use (without extension) for the text-file log
getOutputName() - Method in class org.anchoranalysis.feature.io.csv.metadata.FeatureCSVMetadata: The output name for the features CSV.
getOutputName() - Method in class org.anchoranalysis.io.output.namestyle.OutputNameStyle: An identifier used in rules to determine if an output is enabled or not.
getOutputName() - Method in class org.anchoranalysis.plugin.image.task.bean.combine.AggregateChannelTask: How to name the aggregated channel in the output.
getOutputNameStyle() - Method in class org.anchoranalysis.io.generator.sequence.pattern.OutputPattern
getOutputNameStyle() - Method in class org.anchoranalysis.plugin.io.bean.file.namer.FromOutputName
getOutputPattern() - Method in class org.anchoranalysis.io.generator.sequence.BoundOutputter
getOutputsDisabled() - Method in class org.anchoranalysis.io.output.bean.enabled.SpecificDisabled: The names of the outputs that are disbled.
getOutputsEnabled() - Method in class org.anchoranalysis.io.output.bean.enabled.SpecificEnabled: The names of the outputs that are enabled.
getOutputsEnabled() - Method in class org.anchoranalysis.io.output.bean.OutputManager: Which outputs are enabled or not enabled.
getOutputsEnabled() - Method in class org.anchoranalysis.io.output.outputter.OutputterChecked: Which outputs are enabled or not enabled.
getOutputsEnabled() - Method in class org.anchoranalysis.io.output.writer.ElementOutputter: Which outputs are enabled or not enabled.
getOutputStackProvider() - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageAssignLabel: If it's set, a stack is generated that is outputted into subdirectory corresponding to the groupIdentifier.
getOutputter() - Method in class org.anchoranalysis.experiment.io.InitializationContext: An outputter that writes to the particular output-directory.
getOutputter() - Method in class org.anchoranalysis.experiment.task.InputBound: The Outputter associated with this input, as it is being processed as a job.
getOutputter() - Method in class org.anchoranalysis.experiment.task.InputOutputContextStateful
getOutputter() - Method in class org.anchoranalysis.experiment.task.ParametersExperiment: An outputter that writes to the particular output-directory.
getOutputter() - Method in class org.anchoranalysis.io.generator.sequence.BoundOutputter: The outputter to be used for the sequence.
getOutputter() - Method in interface org.anchoranalysis.io.output.outputter.InputOutputContext: An outputter that writes to the particular output-directory.
getOutputter() - Method in class org.anchoranalysis.io.output.writer.ElementOutputter: The outputter for writing the element.
getOutputterFor(String) - Method in class org.anchoranalysis.plugin.image.task.labeller.SharedStateFilteredImageOutput: Gets the outputter for a specific group identifier.
getOutputWriteSettings() - Method in class org.anchoranalysis.io.output.bean.OutputManager: General settings (default file extensions, colors etc.) for outputting files.
getOutside() - Method in class org.anchoranalysis.plugin.image.feature.bean.physical.UnitsWithinRange: Returned as a constant if a value lies otside the range
getOutsideKernelPolicy() - Method in class org.anchoranalysis.image.voxel.kernel.KernelApplicationParameters: How to handle voxels that appear in a neighborhood that lies outside the scene boundaries.
getOverlay(int) - Method in class org.anchoranalysis.overlay.collection.ColoredOverlayCollection: Access a particular Overlay in the collection by index.
getOverlays() - Method in class org.anchoranalysis.overlay.collection.ColoredOverlayCollection: The collection of overlays, each element corresponding to colors.
getPaddingXY() - Method in class org.anchoranalysis.image.bean.spatial.Padding: Padding placed on each side of the outputted image (if it's within the image) in XY directions
getPaddingZ() - Method in class org.anchoranalysis.image.bean.spatial.Padding: Padding placed on each side of the outputted image (if it's within the image) in Z direction
getPair() - Method in class org.anchoranalysis.image.feature.calculator.merged.MergedPairsFeatures
getPair() - Method in class org.anchoranalysis.mpp.feature.energy.EnergyPair: The pair of marks.
getPair() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown: Every combination of interactions between marks and the associated energy.
getPair() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergyScheme: Features for pairs of elements (clique-size==2).
getPairAddCriteria() - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement: Criteria for adding pairs of elements.
getPairAddCriteria() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergyScheme: Criteria for adding pairs to the energy calculation.
getPairsFor(Mark) - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria: Gets all pairs associated with a specific mark.
getPairTypeClass() - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria: The class type of the pair.
getParameters() - Method in class org.anchoranalysis.feature.energy.EnergyStack: The associated parameters.
getParameters() - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGDescriptor: Parameters used for calculating HOG
getParameters() - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGFeature: Parameters used for calculating HOG.
getParametersExperiment() - Method in class org.anchoranalysis.experiment.task.ParametersUnbound
getParamPrefix() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureSequenceInteger: Prefix for the parameter key.
getParentDirectoryCreator() - Method in class org.anchoranalysis.io.output.outputter.directory.OutputterTarget: Parent directory creator to be executed before any derived sub-directories.
getPath() - Method in class org.anchoranalysis.annotation.io.AnnotationWithStrategy: Path to annotation.
getPath() - Method in class org.anchoranalysis.annotation.io.image.findable.NotFound: The path an object was not found at.
getPath() - Method in class org.anchoranalysis.bean.shared.path.RootPath: A path on a file-system to the directory, that defines the root.
getPath() - Method in class org.anchoranalysis.io.input.bean.files.SingleFile: The path of the single-file.
getPath() - Method in class org.anchoranalysis.io.input.file.NamedFile: The path of NamedFile.getFile().
getPath() - Method in class org.anchoranalysis.io.output.path.prefixer.NamedPath: The path
getPath() - Method in class org.anchoranalysis.plugin.image.task.size.SizeMapping: The path.
getPath() - Method in class org.anchoranalysis.plugin.io.bean.file.path.RootedFilePath
getPath() - Method in class org.anchoranalysis.plugin.io.bean.file.path.StaticFilePath
getPath() - Method in class org.anchoranalysis.plugin.io.multifile.FileDetails
getPathAnnotation() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.SinglePathStrategy: Derives the path to the corresponding annotation files, given a path to the image to be annotated.
getPathDefaultMarks() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy: Path to derive default marks from.
getPathDictionary() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy: Path to derive dictionary from.
getPathLabel() - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageCSVLabeller: Path to a CSV label file (comma-separated, with header, no quotes).
getPathParser() - Method in class org.anchoranalysis.plugin.io.bean.file.group.GroupFiles
getPaths() - Method in class org.anchoranalysis.plugin.io.bean.file.provider.FileSetFromStringSet
getPaths() - Method in class org.anchoranalysis.plugin.io.bean.input.files.provider.FilterForExistingFiles: All files need to be present
getPayload() - Method in class org.anchoranalysis.core.graph.TypedEdge: The edge.
getPayload() - Method in class org.anchoranalysis.plugin.image.object.merge.ObjectVertex: The payload associated with this vertex.
getPermutation() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeature: A permutation to apply.
getPermutations() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeature: A list of permutations to apply.
getPermuteProperty() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Permute
getPermuteProperty() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureSequenceInteger: Defines how to permute the property with a sequence of integers.
getPixelsForPlane(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels: Gets the encoded int buffer for a specific plane.
getPlusOne() - Method in class org.anchoranalysis.image.voxel.buffer.SlidingBuffer: The voxel-buffer for the slice with the currently selected slice's index +1 or null if it's the final slice.
getPoint() - Method in class org.anchoranalysis.image.voxel.kernel.KernelPointCursor: The point around which the cursor may iterate.
getPointFitters() - Method in class org.anchoranalysis.mpp.init.PointsInitialization: Store for point fitters.
getPoints() - Method in class org.anchoranalysis.mpp.mark.points.PointListBase: The list of 3D points that make up this mark.
getPoints() - Method in class org.anchoranalysis.spatial.point.Contour: An ordered list of points in the contour.
getPointsFitter() - Method in class org.anchoranalysis.mpp.bean.points.CreateMarkFromPoints: Fits the provided mark to the extracted points.
getPointsFitter() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy: Name of the PointsFitter to use.
getPointsFitter() - Method in class org.anchoranalysis.plugin.points.bean.FitPoints: The PointsFitter used to fit points to a mark.
getPointsFitter() - Method in class org.anchoranalysis.plugin.points.bean.FitPointsFromObjects: The PointsFitterToMark used to fit points to marks.
getPointsFitter() - Method in class org.anchoranalysis.plugin.points.bean.fitter.PointsFitterToMark: The PointsFitter used to fit points to a mark.
getPointsFitter() - Method in class org.anchoranalysis.plugin.points.bean.fitter.ReflectInAxesWithinDistance
getPointsProposer() - Method in class org.anchoranalysis.plugin.points.bean.FitPoints: The PointsProposer used to generate points.
getPosition() - Method in class org.anchoranalysis.mpp.mark.MarkWithPosition: The position of the mark in 3D space.
getPostcondition() - Method in class org.anchoranalysis.image.voxel.kernel.morphological.DilationContext: If defined, a condition which must be satisfied after an iteration occurs, otherwise no more iterations occur.
getPower() - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.MeanRaisedToPower: The power to which the mean value is raised.
getPrefix() - Method in class org.anchoranalysis.bean.define.adder.DefineAdderWithPrefixBean: A prefix that is placed before the name of every bean created.
getPrefix() - Method in class org.anchoranalysis.feature.bean.list.PrependName: The string to prepend to the custom-name of each feature.
getPrefix() - Method in class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixerAvoidResolve: A string prefixed to each output-path.
getPrefix() - Method in class org.anchoranalysis.io.output.outputter.directory.OutputterTarget: The directory and prefix into which outputting occurs.
getPrefix() - Method in class org.anchoranalysis.io.output.outputter.Outputter: The directory and prefix into which outputting occurs.
getPrefix() - Method in class org.anchoranalysis.io.output.outputter.OutputterChecked: The directory and prefix into which outputting occurs.
getPrefix() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.DeriveFromPair
getPrefix() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.FeatureListProviderAggregatePair: The string to prepend.
getPrefixer() - Method in class org.anchoranalysis.experiment.arguments.OutputArguments: Where outputs are written, and how identifiers are styled.
getPrefixer() - Method in class org.anchoranalysis.experiment.task.ParametersExperiment: Determines prefixes used in the paths for outputted files.
getPrefixer() - Method in class org.anchoranalysis.io.output.bean.OutputManager: Determines a prefix to use when outputting a file based upon an input-path.
getPrefixer() - Method in class org.anchoranalysis.io.output.path.prefixer.PathPrefixerContext: Settings for where and how outputs should be prefixed.
getPrefixer() - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.LastDirectoryAsPrefix
getPrefixer() - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.Rooted
getPrefixerElse() - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.IfIncrementingNumberRequested: Called if the requested condition is not true.
getPrefixerIf() - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.IfIncrementingNumberRequested: Called if the requested condition is true.
getPrefixToRemove() - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.DirectoryStructure
getPrependColor() - Method in class org.anchoranalysis.bean.shared.color.scheme.Prepend: The color to prepend.
getPriority() - Method in class org.anchoranalysis.plugin.image.object.merge.priority.PrioritisedVertex
getProperties() - Method in class org.anchoranalysis.image.core.object.properties.ObjectWithProperties: A mapping between keys and corresponding values.
getProperty(String) - Method in class org.anchoranalysis.image.core.object.properties.ObjectWithProperties: Retrieves the value of a property corresponding to a particular name.
getPropertyInitializer() - Method in class org.anchoranalysis.bean.initializable.InitializableBean: Assigns a parameter, if possible, to a bean - as used by bean initializer.
getPropertyPath() - Method in class org.anchoranalysis.bean.permute.property.PermuteProperty: Either a direct property of a bean or a nested-property with the children separated by full-stops.
getPyramid() - Method in class org.anchoranalysis.image.core.stack.ImageMetadata: Metadata to describe an image pyramid, if it exists.
getQuantile() - Method in class org.anchoranalysis.feature.bean.results.Quantile: The quantile.
getQuantile() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.QuantileStretch
getQuantile() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Quantile
getQuantile() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.collective.DiscardOutliers
getQuantile() - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Quantile: The quantile to calculate from the histogram.
getQuantile() - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.QuantileAcrossObjects
getQuantile() - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.QuantileAcrossConnectedComponents
getQuantileHigh() - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Range
getQuantileLow() - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Range
getQuantileLower() - Method in class org.anchoranalysis.image.bean.displayer.IntensityQuantiles: The lower quantile to use as the lower-limit for the intensity range to display.
getQuantileLower() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ToByteUpperLowerQuantileIntensity: The lower quantile value for intensity scaling.
getQuantileUpper() - Method in class org.anchoranalysis.image.bean.displayer.IntensityQuantiles: The lower quantile to use as the upper-limit for the intensity range to display.
getQuantileUpper() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ToByteUpperLowerQuantileIntensity: The upper quantile value for intensity scaling.
getRadii() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
getRadii() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid: The radii of the ellipsoid in 3D.
getRadius() - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
getRadius() - Method in class org.anchoranalysis.plugin.fiji.bean.mask.provider.AutoLocalThreshold
getRadius() - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.WithRadiusBase: The radius of the operation.
getRadiusX() - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult: The radius of the ellipsoid along the X-axis.
getRadiusY() - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult: The radius of the ellipsoid along the Y-axis.
getRadiusZ() - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult: The radius of the ellipsoid along the Z-axis.
getRandomNumberGenerator() - Method in class org.anchoranalysis.mpp.proposer.ProposerContext: Random number generator for sampling operations.
getRangeC() - Method in class org.anchoranalysis.plugin.io.multifile.SizeExtents
getRangeT() - Method in class org.anchoranalysis.plugin.io.multifile.SizeExtents
getRangeZ() - Method in class org.anchoranalysis.plugin.io.multifile.SizeExtents
getRatioHeightForLabel() - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage: When label==true, this determines the height of the label.
getRatioRowsToColumns() - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage: An ideal approximate ratio of the number of rows to the number of columns.
getRaw() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer: Gets an unsigned-byte (represented as a byte) at the current buffer position.
getRaw() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer: Gets an unsigned-int (represented as an int) at the current buffer position.
getRaw() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer: Gets an unsigned-short (represented as a short) at the current buffer position.
getRaw(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer: Gets an unsigned-byte (represented as a byte) at a particular buffer position.
getRaw(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer: Gets an unsigned-int (represented as a int) at a particular buffer position.
getRaw(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer: Gets an unsigned-short (represented as a short) at a particular buffer position.
getReader() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.RotateImageToMatchEXIFOrientation: Reads the image that is subsequently flattened.
getReaderMatching() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.BranchExtension: The reader to use if the extension matches.
getReaderNotMatching() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.BranchExtension: The reader to use if the extension does not match.
getReason() - Method in class org.anchoranalysis.annotation.io.image.findable.NotFound: The reason an object could not be found.
getReceive() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.combine.CombineBase: The MaskProvider for the second mask to be combined.
getRecordedOutputs() - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputsWithRules: If defined, records output-names that are written / not-written during the experiment.
getRed() - Method in class org.anchoranalysis.bean.shared.color.RGBColorBean: The red component value of the RGB color.
getRed() - Method in class org.anchoranalysis.core.color.RGBColor: The red component value of the RGB color.
getRed() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeChannels: Provider for the red channel.
getReduce() - Method in class org.anchoranalysis.image.inference.bean.segment.instance.SuppressNonMaximum: The algorithm for reducing the number of object-masks.
getReduce() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.FeatureListProviderAggregatePair: Method for reducing all pairs into a single value e.g.
getReferencePoissonIntensity() - Method in class org.anchoranalysis.mpp.bean.mark.factory.MarkWithIdentifierFactory: The reference Poisson intensity for mark creation.
getReferences() - Method in class org.anchoranalysis.feature.bean.list.ReferencingFeatureListProvider: The names of other feature-lists, whose features may be referenced by this feature.
getReferencesFeatureListCreator() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeature: Makes sure a particular feature list creator is evaluated
getReferencesList() - Method in class org.anchoranalysis.feature.bean.provider.FeatureProviderReference: The name of the list in which the feature referenced by id resides.
getRegex() - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.RegularExpressionBase
getRegex() - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Replace: Regular expression to match against string
getRegEx() - Method in class org.anchoranalysis.plugin.io.bean.file.namer.RegExMatcher
getRegEx() - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.PathRegEx: Regular expression to use to match path with at least one group in it.
getRegEx() - Method in class org.anchoranalysis.plugin.io.bean.file.provider.RemoveMatching: If a path matches a regular expression it is removed.
getRegEx() - Method in class org.anchoranalysis.plugin.io.bean.input.Exclude: A regular-expression to be matched against the identifiers of inputs.
getRegEx() - Method in class org.anchoranalysis.plugin.io.bean.path.derive.InsertRegExGroups: The regular-expression to use for matching groups.
getRegEx() - Method in class org.anchoranalysis.plugin.io.bean.path.derive.JoinRegExGroups
getRegExDirectory() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader: If non-empty a regular-expression is applied to directories.
getRegExFile() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader: If non-empty a regular-expression is applied to files.
getRegionID() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipWithFlags: Gets the ID of the region.
getRegionID() - Method in class org.anchoranalysis.plugin.mpp.bean.object.provider.FromMarks
getRegionID() - Method in class org.anchoranalysis.plugin.mpp.bean.stack.provider.ColoredMarks
getRegionMap() - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement: Mapping of regions.
getRegionMap() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergyScheme: The region map used in the energy scheme.
getRegionMap() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergySchemeWithSharedFeatures: Gets the region map from the energy scheme.
getRegionMap() - Method in class org.anchoranalysis.mpp.feature.mark.EnergyMemoList: Gets the region map associated with this energy memo list.
getRegionMap() - Method in class org.anchoranalysis.mpp.mark.voxelized.memo.VoxelizedMarkMemo: The region map.
getRegionMap() - Method in class org.anchoranalysis.mpp.proposer.ProposerContext: Region map for the current context.
getRegionMap() - Method in class org.anchoranalysis.plugin.mpp.bean.object.provider.FromMarks
getRegionMembership() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipWithFlags: Gets the underlying region membership.
getRegularExpression() - Method in class org.anchoranalysis.plugin.io.bean.file.pattern.TimestampPattern: The regular-expression that checks a match and specifies groups for the encoded date-time.
getRejectionReason() - Method in class org.anchoranalysis.annotation.mark.DualMarksAnnotation: A reason for rejection, if the annotation was rejected by the annotator.
getRelation() - Method in class org.anchoranalysis.bean.shared.relation.threshold.RelationToConstant: The relation to the threshold, where the threshold forms the second operand.
getRelation() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterRelation: The relation to be used in the filter predicate.
getRelation() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergePairs: Relation to threshold
getRelation() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram: The relation to test between the voxel value and the histogram value.
getRelation() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.RejectIfConditionXYResolution: A predicate defined by the relationship of the XY-resolution to a constant threshold.
getRemainder() - Method in class org.anchoranalysis.core.system.path.SplitPath: The second component, what remains in the path.
getRepeatZProvider() - Method in class org.anchoranalysis.image.io.bean.stack.combine.WriteText: Repeats the generated (2D) string in z, so it's the same z-size as intensityProvider
getReplacement() - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.SubstituteRegularExpression
getReplacement() - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Replace: What to replace in the path
getRequireArguments() - Method in class org.anchoranalysis.experiment.bean.log.OnlyIf: The conditions that must be fulfilled
getResizer() - Method in class org.anchoranalysis.image.inference.ImageInferenceContext: How to resize images or voxel-buffers.
getResizeTo() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase: If set, each channel is scaled to a specific size before aggregation (useful for combining different sized images).
getResizeTo() - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGDescriptor: The input-image is rescaled to this width/height before calculating HOG descriptors
getResizeTo() - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGFeature: The input is rescaled to this width/height before calculating HOG descriptors.
getResolution() - Method in class org.anchoranalysis.image.bean.nonbean.segment.BinarySegmentationParameters: A Resolution associated with the image being segmented.
getResolutionCount() - Method in class org.anchoranalysis.image.core.stack.ImagePyramidMetadata: The number of distinct resolution-levels that exist in the pyramid.
getResolutionOptional() - Method in class org.anchoranalysis.feature.input.FeatureInputDimensions
getResolutionOptional() - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy
getResolutionOptional() - Method in interface org.anchoranalysis.feature.input.FeatureInputWithResolution: The resolution of the associated image, if it is available.
getResolutionOptional() - Method in class org.anchoranalysis.image.feature.input.FeatureInputHistogram: Gets the optional resolution information.
getResolutionOptional() - Method in class org.anchoranalysis.mpp.feature.bean.mark.collection.FeatureInputMarkCollection
getResolutionOptional() - Method in class org.anchoranalysis.mpp.feature.bean.mark.FeatureInputMark
getResolutionRequired() - Method in interface org.anchoranalysis.feature.input.FeatureInputWithResolution: The resolution of the associated image, or an exception if it is not available.
getRestrictTo() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.Invert: If set, the inversion only occurs on a particular region of the mask, as determined by this mask
getResult(int) - Method in class org.anchoranalysis.feature.results.ResultsVector: Gets a result value at a particular position.
getResults() - Method in class org.anchoranalysis.feature.input.FeatureInputResults: The results of a prior feature-calculation, corresponding to a list of features.
getResults() - Method in class org.anchoranalysis.feature.io.results.LabelledResultsVector: The results.
getResults() - Method in class org.anchoranalysis.plugin.image.task.feature.FeatureCalculationContext: The stored results and thumbnail writer.
getResults() - Method in class org.anchoranalysis.plugin.image.task.feature.FeatureExporter: Saved store feature calculation results, and writes associated thumbnails.
getResults() - Method in class org.anchoranalysis.plugin.image.task.feature.LabelledResultsVectorWithThumbnail: The results vector with an optional thumbnail.
getResultsVector() - Method in class org.anchoranalysis.plugin.image.task.feature.ResultsVectorWithThumbnail: Supplier for the ResultsVector.
getRgb() - Method in class org.anchoranalysis.image.io.stack.output.StackWriteAttributes: Whether it's an RGB or RGBA image when it has three/four channels respectively.
getRGB() - Method in class org.anchoranalysis.bean.shared.color.RGBColorBean: Returns the RGB value encoded as an int as in Color.getRGB().
getRGB() - Method in class org.anchoranalysis.core.color.RGBColor: Returns the RGB value encoded as an int as in Color.getRGB().
getRight() - Method in class org.anchoranalysis.plugin.annotation.comparison.ObjectsToCompare: Objects on right-side of the comparison.
getRightUnassigned() - Method in class org.anchoranalysis.annotation.io.assignment.OverlappingObjects: The unassigned objects in the right set.
getRoot() - Method in class org.anchoranalysis.core.system.path.SplitPath: The first component, the root of the path.
getRoot() - Method in class org.anchoranalysis.test.TestLoader: Path to where the test-data is stored.
getRoot1() - Method in class org.anchoranalysis.math.equation.QuadraticEquationSolver.QuadraticRoots: The first root.
getRoot2() - Method in class org.anchoranalysis.math.equation.QuadraticEquationSolver.QuadraticRoots: The second root.
getRootName() - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.Rooted: The name of the root-path to associate with this fileset.
getRootName() - Method in class org.anchoranalysis.plugin.io.bean.file.path.RootedFilePath
getRootName() - Method in class org.anchoranalysis.plugin.io.bean.file.provider.Rooted
getRootName() - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Rooted
getRotationAngle() - Method in class org.anchoranalysis.mpp.bean.bound.rotation.BoundRotation2D
getRotationMatrix() - Method in class org.anchoranalysis.spatial.orientation.Orientation: Derives a RotationMatrix that can be applied to rotate an entity anti-clockwise to the current orientation.
getRotationMatrix() - Method in class org.anchoranalysis.spatial.orientation.OrientationRotationMatrix: The rotation-matrix.
getRotationX() - Method in class org.anchoranalysis.mpp.bean.bound.rotation.BoundRotation3D
getRotationY() - Method in class org.anchoranalysis.mpp.bean.bound.rotation.BoundRotation3D
getRotationZ() - Method in class org.anchoranalysis.mpp.bean.bound.rotation.BoundRotation3D
getRotMatrix() - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult: The rotation matrix, which must be considered immutable to be used here.
getRow() - Method in class org.anchoranalysis.image.bean.spatial.arrange.tile.Cell: The row in the table that the cell refers to (zero-indexed).
getRunningSum() - Method in class org.anchoranalysis.experiment.time.RunningSumParented
getSampleEvery() - Method in class org.anchoranalysis.plugin.io.bean.file.provider.SampleWithDirectory
getScale() - Method in class org.anchoranalysis.math.statistics.MeanScale: The scale, typically the standard-deviation.
getScale() - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices: Whether to increase or reduce the size of the images.
getScaleCalculator() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.ScaleXY
getScaleCalculator() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.ScaleXY: Determines how much to scale by.
getScaleCalculator() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Scale
getScaleCalculator() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.AtScale
getScaleCalculator() - Method in class org.anchoranalysis.plugin.image.bean.scale.Invert: The delegate ScaleCalculator whose calculation will be inverted.
getScaleCalculator() - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage: Calculates what scale-factor to apply on the image.
getScaleCalculator() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.ScaleXY: The ScaleCalculator used to determine the scaling factor.
getScaleFactor() - Method in class org.anchoranalysis.image.inference.ImageInferenceContext: The inverse of the scaling-factor applied to reduce unscaledDimensions to the input-matrix used for inference.
getScaleFactor() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientBase: Scale factor applied to the gradient values.
getScaleInput() - Method in class org.anchoranalysis.image.inference.bean.segment.instance.SegmentStackIntoObjectsScaleDecode: Any scaling to be applied to the input-image before being input to the model for inference.
getScaleLower() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByDictionary
getScaleLower() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ToByteUpperLowerQuantileIntensity: Sets the min by multiplying the quantileLower by this constant.
getScaleRadii() - Method in class org.anchoranalysis.plugin.points.bean.fitter.ConicFitterBase: The scale factor to apply to the radii of the conic.
getScaleRoundingError() - Method in class org.anchoranalysis.image.bean.spatial.arrange.fill.ExtentToArrange: Stores the difference that occurs between a discretized scaled width and what it should ideally be.
getScaleUpper() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByDictionary
getScaleUpper() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ToByteUpperLowerQuantileIntensity: Sets the max by multiplying the quantileUpper by this constant.
getScore() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
getScoreProvider() - Method in class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice
getScoreThreshold() - Method in class org.anchoranalysis.image.inference.bean.reduce.RemoveOverlappingObjects: Bounding boxes with scores above this threshold are removed.
getSearchObjects() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjects: Gets the collection of objects to search for intersections.
getSecond() - Method in class org.anchoranalysis.annotation.io.assignment.CostMatrix: The second set of elements.
getSecond() - Method in class org.anchoranalysis.image.feature.input.FeatureInputPairObjects: Gets the second ObjectMask.
getSecond() - Method in class org.anchoranalysis.io.output.bean.rules.OutputEnableRulesSpecify: Output-names in the second-level (for all first level output-names).
getSegment() - Method in class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationUnary: The delegate BinarySegmentation that may be called.
getSegment() - Method in class org.anchoranalysis.image.bean.segment.object.SegmentChannelIntoObjectsUnary: The delegate SegmentChannelIntoObjects that is called.
getSegment() - Method in class org.anchoranalysis.image.inference.bean.segment.instance.SuppressNonMaximum: The segmentation algorithm that is applied as an input to non-maximum suppression.
getSegment() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.segment.SegmentChannel: Segmentation algorithm
getSegment() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentChannel: The segmentation algorithm to use.
getSegment() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentChannelByObject
getSegment() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentStack: The segmentation procedure.
getSegment() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentWithSeeds
getSegment() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.ConnectedComponentsFromBinarySegmentation
getSegment() - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel: The segmentation algorithm.
getSegmentStack() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.SegmentOnMaximumIntensityAndExpandInZ
getSelect() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.DeriveFromPair: Either "merged" or "first" or "second" indicating which feature to delegate from
getSelectChannels() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase: Selects which channels are included, optionally renaming.
getSemiMajorAxis() - Method in class org.anchoranalysis.plugin.points.bean.fitter.EllipseStandardFormConverter: Gets the length of the semi-major axis.
getSemiMinorAxis() - Method in class org.anchoranalysis.plugin.points.bean.fitter.EllipseStandardFormConverter: Gets the length of the semi-minor axis.
getSeperator() - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
getSequence() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequence: A sequence of integers, with each element assigned assigned directly during the permutation, or after further manipulation.
getSequence() - Method in class org.anchoranalysis.plugin.image.task.bean.format.ChangeableOutputSequence: The current output sequence.
getSeriesIndex() - Method in class org.anchoranalysis.image.io.bean.stack.metadata.reader.FromStackReader: The series to open to the read the metadata (zero-indexed).
getSettings() - Method in class org.anchoranalysis.io.output.outputter.Outputter: General settings for outputting.
getSettings() - Method in class org.anchoranalysis.io.output.outputter.OutputterChecked: General settings for outputting.
getSettings() - Method in class org.anchoranalysis.io.output.outputter.OutputWriteContext: User-define settings for outputting in output-manager.
getSettings() - Method in class org.anchoranalysis.io.output.writer.ElementOutputter: General settings for outputting.
getSharedFeatures() - Method in class org.anchoranalysis.feature.initialization.FeatureRelatedInitialization: Shared features available for reference during calculation.
getSharedFeatures() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergySchemeSet: Shared features associated with all energy schemes in the set.
getSharedFeatures() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergySchemeWithSharedFeatures: Shared features used across calculations.
getSharedObjects() - Method in class org.anchoranalysis.feature.initialization.FeatureInitialization: Shared-objects, which can be referenced by the feature to influence calculation.
getSharedState() - Method in class org.anchoranalysis.experiment.task.InputBound: The state shared between inputs.
getSharedState() - Method in class org.anchoranalysis.experiment.task.ParametersUnbound
getSharedState() - Method in class org.anchoranalysis.plugin.io.input.path.CopyContext: State shared across all inputs when copying.
getSharedState() - Method in class org.anchoranalysis.plugin.mpp.shared.SharedStateRememberConverted: The shared state.
getShell() - Method in class org.anchoranalysis.mpp.bean.mark.factory.MarkEllipseFactory: The shell thickness of the ellipse.
getShell() - Method in class org.anchoranalysis.mpp.bean.mark.factory.MarkEllipsoidFactory: The shell thickness of the ellipsoid.
getShell() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse: The size of the shell, expressed as a ratio of the radius.
getShell() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid: The size of the shell, expressed as a ratio of the radii.
getShell() - Method in class org.anchoranalysis.plugin.points.bean.fitter.ConicFitterBase: The shell thickness of the conic.
getShortName() - Method in class org.anchoranalysis.experiment.task.processor.JobDescription
getShowOngoingJobsLessThan() - Method in class org.anchoranalysis.experiment.bean.processor.ParallelProcessor: When the number of ongoing jobs is less than this threshold, they are shown in event logs. 0 disables.
getSigma() - Method in class org.anchoranalysis.plugin.image.bean.blur.BlurStrategy: The sigma value for the blur operation.
getSigma() - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.GaussianBlur2D: The standard deviation of the Gaussian distribution used for blurring.
getSingle() - Method in class org.anchoranalysis.image.feature.calculator.merged.MergedPairsFeatures
getSize() - Method in class org.anchoranalysis.experiment.arguments.TaskArguments: Suggests dimensions or a scaling-factor to resize an image to.
getSize() - Method in class org.anchoranalysis.image.io.bean.stack.combine.WriteText: Explicit size of the image the string is draw on.
getSize() - Method in class org.anchoranalysis.image.voxel.kernel.Kernel: The size of the kernel-matrix in one dimension, either X or Y.
getSize() - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize: Size of all created thumbnails
getSize() - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.stack.ScaleToSize
getSize() - Method in class org.anchoranalysis.plugin.io.multifile.IntegerRange
getSizeXY() - Method in class org.anchoranalysis.plugin.image.bean.dimensions.provider.SpecifyDimensions: Length of X and Y dimensions.
getSizeZ() - Method in class org.anchoranalysis.plugin.image.bean.dimensions.provider.SpecifyDimensions: Length of Z dimension.
getSkipFirstTrim() - Method in class org.anchoranalysis.plugin.io.bean.path.derive.RemoveTrailingDirectory
getSkipNumberSubdirectories() - Method in class org.anchoranalysis.plugin.io.bean.file.namer.LastDirectories: Initially skip this number of directories before including them in the description.
getSlice() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.slice.RepeatSlice
getSlice(int) - Method in interface org.anchoranalysis.mpp.index.VoxelPartition: Gets the voxel partition for a specific slice.
getSlice(int) - Method in class org.anchoranalysis.mpp.index.VoxelPartitionHistogram
getSliceFirst() - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices: First slice to include in the montage.
getSliceIndex() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.slice.RepeatSlice: Which slice to use from mask
getSliceIndex() - Method in class org.anchoranalysis.plugin.io.multifile.FileDetails
getSliceLast() - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices: Last slice to include in the montage.
getSmoothingFactor() - Method in class org.anchoranalysis.plugin.points.bean.SplitContourAtSaddlePoints
getSource() - Method in class org.anchoranalysis.bean.shared.StringMapItem: The origin of the mapping.
getSource() - Method in class org.anchoranalysis.image.core.object.MatchedObject: The source object (which is matched against others)
getSource() - Method in class org.anchoranalysis.mpp.pair.MarkPair: Gets the source mark of the pair (the one with the lower identifier).
getSource() - Method in class org.anchoranalysis.mpp.pair.PairVoxelizedMarkMemo: Gets the source VoxelizedMarkMemo.
getSource() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures: Source of feature-values to be exported.
getSourceDirectory() - Method in class org.anchoranalysis.plugin.io.input.path.CopyContext: Source directory of copying.
getSources() - Method in class org.anchoranalysis.annotation.io.bean.comparer.MultipleComparer: The other entities to compare with the annotation.
getSplitIdentifierRegex() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations: If non-empty, the string (a regular-expression) is used to split the file's identifier into groups.
getSquareSize() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.split.SplitIntoSquares
getStack() - Method in class org.anchoranalysis.image.bean.provider.stack.StackProviderUnary: The delegate Provider<Stack> that is called.
getStack() - Method in class org.anchoranalysis.image.core.stack.DisplayStack: The underlying stack that will be displayed, possibly after conversion.
getStack() - Method in class org.anchoranalysis.image.io.bean.stack.combine.StackProviderWithLabel: Provides the stack.
getStack() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromStack: Provides a stack.
getStack() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentStack: The stack to segment
getStack() - Method in class org.anchoranalysis.plugin.image.task.slice.MontageSharedState: The stack into which individual images are written.
getStackEnergy() - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureEvaluator: Optionally specifies an energy-stack to be associated with every calculation input.
getStackEnergy() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromImage: Optionally defines an energy-stack for feature calculation (if not set, the energy-stack is considered to be the input stacks).
getStackEnergy() - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.BinaryClassifierImageLabeller: Provider for the energy stack.
getStackEnergy() - Method in class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice
getStackEnergy() - Method in class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputterWithEnergy: The stack provider for the energy stack.
getStackID() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfStackExists
getStackName() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.One: If defined, processing only occurs the stack with this specific name and index.
getStackNameDefault() - Method in class org.anchoranalysis.annotation.io.bean.AnnotationBackground: The name of the default stack from backgroundStackMap to display as background when annotating.
getStackProviderID() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromStack: Specifies the ID of an existing stack.
getStackProviderID() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromStackChannel: The identifier of the stack provider to retrieve the stack from.
getStackReader() - Method in class org.anchoranalysis.annotation.io.bean.AnnotatorStrategy: How to read raster Stacks from the file-system.
getStackReader() - Method in class org.anchoranalysis.image.io.bean.stack.metadata.reader.FromStackReader: The StackReader to use to read the image metadata.
getStackReader() - Method in class org.anchoranalysis.image.io.bean.stack.reader.InputManagerWithStackReader: How to read an image from the file-system.
getStackReader() - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.MaskAsObject: How to read the Mask from the file-system.
getStackReader() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationComparisonInput: The StackReader to use for reading image stacks.
getStackReader() - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage: Fallback for imageMetadataReader to read image files without a directy metadata reader.
getStackReader() - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImageCommonSize: Fallback for imageMetadataReader to read image files without a direct metadata reader.
getStackReader() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.FlattenAsChannel: Reads the image that is subsequently flattened.
getStackReader() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ImposeResolution: Reads an image before a resolution is imposed.
getStackReader() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader
getStackReader() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ReadVoxelExtentXml: Reads an image before a resolution is imposed.
getStackReader() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.RejectIfConditionXYResolution: Reads an image before a resolution is imposed.
getStackStore() - Method in class org.anchoranalysis.plugin.image.task.grouped.ChannelSource: A named set of Stacks from which Channels may be extracted.
getStart() - Method in class org.anchoranalysis.bean.permute.property.SequenceInteger: The index to begin iteration from.
getStartIndex() - Method in class org.anchoranalysis.core.index.range.IndexRangeNegative: The index if the first element to use in the subsetting range, zero-indexed.
getStartingIntensity() - Method in class org.anchoranalysis.plugin.imagej.bean.object.segment.FloodFillEachIntensityLevel: The first intensity-value to consider as a valid object (e.g. usually 0 is ignored as background).
getStartPoint() - Method in class org.anchoranalysis.mpp.mark.points.LineSegment: Gets the start point of the line segment.
getStrategy() - Method in class org.anchoranalysis.annotation.io.AnnotationWithStrategy: The strategy on how annotation occurs.
getStrategy() - Method in class org.anchoranalysis.feature.session.replace.BoundReplaceStrategy: The strategy that has been bound (if it exists).
getStrategy() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.Blur
getStyle() - Method in class org.anchoranalysis.image.io.bean.stack.combine.WriteText
getStyle() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures: Visual style for how feature export occurs.
getStyle() - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel: Visual style for how feature export occurs.
getSubdirectoryName() - Method in class org.anchoranalysis.io.generator.sequence.pattern.OutputPattern: The name of a subdirectory in the current context to write to, or if empty, files are written into the current directory context.
getSubtractConstant() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.IntensityGradientBase: A constant value to subtract from each voxel intensity before calculating the gradient.
getSubtractMean() - Method in class org.anchoranalysis.image.inference.bean.segment.instance.SegmentStackIntoObjectsScaleDecode: A constant intensity for each respective channel to be subtracted before performing inference.
getSubtractRadii() - Method in class org.anchoranalysis.plugin.points.bean.fitter.ConicFitterBase: The value to subtract from the radii of the conic.
getSuggestedFormatToWrite() - Method in class org.anchoranalysis.image.io.stack.output.StackWriteOptions: A suggestion on what file-format to write.
getSuggestedFormatToWrite() - Method in class org.anchoranalysis.io.output.outputter.OutputWriteContext: A suggestion on what file-format to write.
getSuggestedFormatToWrite() - Method in class org.anchoranalysis.io.output.writer.ElementOutputter: A suggestion on what file-format to write.
getSuggestedImageOutputFormat() - Method in class org.anchoranalysis.io.output.path.prefixer.OutputPrefixerSettings: A file format suggested for writing images to the file system.
getSuggestedSize() - Method in class org.anchoranalysis.experiment.io.InitializationContext: A suggested input on how to resize an image, if one is provided.
getSum() - Method in class org.anchoranalysis.math.arithmetic.RunningSum: The running sum.
getSummarizer() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.input.SummarizerInputFromManager
getSummarizer() - Method in class org.anchoranalysis.plugin.io.bean.task.SummarizeBase
getSummarizerElse() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerSplitMoreThan: Used for summary if count(elements) <= countThreshold
getSummarizerGreaterThan() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerSplitMoreThan: Used for summary if count(elements) > countThreshold
getTarget() - Method in class org.anchoranalysis.bean.shared.StringMapItem: The destination of the mapping.
getTargetClass() - Method in class org.anchoranalysis.bean.initializable.property.ExtractDerivedParameter: The class of the target type T.
getTargetSize() - Method in class org.anchoranalysis.plugin.image.bean.scale.FitTo: The target size.
getTask() - Method in class org.anchoranalysis.experiment.bean.processor.JobProcessor: The task to be applied to inputs.
getTask() - Method in class org.anchoranalysis.launcher.executor.ExperimentExecutor: The task selection parameter.
getTask() - Method in class org.anchoranalysis.plugin.mpp.bean.convert.ConvertNamedChannels: The underlying task that will be called, perhaps with a different input-type.
getTaskArguments() - Method in class org.anchoranalysis.experiment.task.InputBound: The arguments for the task that is being processed.
getTaskName() - Method in class org.anchoranalysis.experiment.arguments.TaskArguments: A name to describe the ongoing task.
getTaskProcessor() - Method in class org.anchoranalysis.experiment.bean.io.InputOutputExperiment: What task is associated with the experiment, and how it is processed.
getTemplateMark() - Method in class org.anchoranalysis.mpp.bean.mark.factory.MarkWithIdentifierFactory: A template mark factory from which all new marks are created.
getTemporary() - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels: Gets a list of points with temporary encoded values.
getText() - Method in class org.anchoranalysis.image.io.bean.stack.combine.WriteText: Text to draw on an image.
getThreshold() - Method in class org.anchoranalysis.bean.shared.relation.threshold.RelationToConstant: The constant threshold.
getThreshold() - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.CutBelowThreshold
getThreshold() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelRelativeToThreshold: Threshold value to compare against when deciding whether to use the alternative calculation.
getThreshold() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntensityGreaterEqualThan
getThreshold() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedFeature
getThreshold() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedVolume
getThreshold() - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Count
getThreshold() - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.RatioThreshold: The threshold condition to be applied to the histogram values.
getThreshold() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjectsThreshold: The threshold value for considering intersecting objects.
getThreshold() - Method in class org.anchoranalysis.plugin.operator.feature.bean.conditional.IfCondition
getThresholder() - Method in class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationThreshold: Performs the global thresholding.
getThresholder() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.segment.Threshold: The thresholder that will convert a channel into a binary-channel
getThresholdHours() - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster.ClusterByTimestamp: Files whose creation-time differs <= this parameter are joined into the same cluster.
getThresholdNumberObjectsGlobal() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ThresholdConfidence: When the number of objects is greater or equal than this, they are reduced globally, without separation.
getThumbnail() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.CombineObjectsForFeatures: Generates a thumbnail representation of one or more combined objects, as form a single input.
getThumbnail() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromImage: Method to generate a thumbnail for images.
getThumbnail() - Method in class org.anchoranalysis.plugin.image.task.feature.ResultsVectorWithThumbnail: Supplier for the optional thumbnail DisplayStack.
getThumbnailBatch() - Method in class org.anchoranalysis.plugin.image.feature.object.ListWithThumbnails: The optional thumbnail batch associated with the list.
getTimeAnnotationLastUpdated() - Method in class org.anchoranalysis.annotation.mark.DualMarksAnnotation: Number of seconds since the UNIX epoch
getTimeIndex() - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertNamedChannelsToStack
getTimeIndex() - Method in class org.anchoranalysis.plugin.io.multifile.FileDetails
getTimeIndexGroupID() - Method in class org.anchoranalysis.plugin.io.bean.file.group.parser.RegularExpression
getTimes() - Method in class org.anchoranalysis.bean.shared.color.scheme.Repeat: How many times to duplicate the list.
getTimestampPatterns() - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster.ClusterByTimestamp: The patterns which can be used to extract a date-time from a filename.
getTimeZoneOffset() - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster.ClusterByTimestamp: If >= 0, sets a specific time-offset in hours.
getTo() - Method in class org.anchoranalysis.core.graph.TypedEdge: The vertex the edge joins to.
getTotal() - Method in class org.anchoranalysis.mpp.feature.energy.EnergyTotal: Gets the current total energy value.
getTotalCount() - Method in class org.anchoranalysis.math.histogram.Histogram: The total count across values in the histogram.
getTotalNumberJobs() - Method in class org.anchoranalysis.experiment.task.processor.ConcurrentJobMonitor: The total number of submitted jobs to be executed.
getTrimTrailingDirectory() - Method in class org.anchoranalysis.plugin.io.bean.path.derive.RemoveTrailingDirectory
getUnconvertedVoxelAt(int, Point3i) - Method in class org.anchoranalysis.image.core.stack.DisplayStack: Retrieve the intensity of a voxel at a particular point, before any conversion is applied.
getUniqueLabel() - Method in class org.anchoranalysis.plugin.annotation.bean.label.AnnotationLabel: Label that uniquely identifies the ID (for machine purposes).
getUnitConverterOptional() - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy: Converts voxelized measurements to/from physical units.
getUnitType() - Method in class org.anchoranalysis.image.bean.unitvalue.distance.DistancePhysical: A string indicating type of units to use, as per SpatialUnits.
getUnitType() - Method in class org.anchoranalysis.image.bean.unitvalue.extent.area.AreaPhysical: How much each value represents e.g. square nanometers, squares millimeters etc.
getUnitType() - Method in class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumePhysical: How much each value represents e.g. cubic nanometers, cubic millimeters etc.
getUnitType() - Method in class org.anchoranalysis.image.feature.bean.physical.FeatureConvertUnits: The type of unit to convert to, represented as a string (e.g., "um" for micrometers).
getUnitTypeFrom() - Method in class org.anchoranalysis.plugin.operator.feature.physical.ConvertUnits: The unit type to convert from.
getUnitTypeTo() - Method in class org.anchoranalysis.plugin.operator.feature.physical.ConvertUnits: The unit type to convert to.
getUnsigned() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBufferAsInt: Gets an unsigned-byte (represented as a int) at the current buffer position.
getUnsigned() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
getUnsigned() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer: Gets an unsigned-int (represented as a long) at the current buffer position.
getUnsigned() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
getUnsigned(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBufferAsInt: Gets an unsigned-byte (represented as a int) at a particular buffer position.
getUnsigned(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
getUnsigned(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer: Gets an unsigned-int (represented as a long) at a particular buffer position.
getUnsigned(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
getUnsignedByte() - Static method in class org.anchoranalysis.image.voxel.factory.VoxelsFactory: A factory that creates voxels of type unsigned byte.
getUnsignedInt() - Static method in class org.anchoranalysis.image.voxel.factory.VoxelsFactory: A factory that creates voxels of type unsigned int.
getUnsignedShort() - Static method in class org.anchoranalysis.image.voxel.factory.VoxelsFactory: A factory that creates voxels of type unsigned short.
getUserFriendlyLabel() - Method in class org.anchoranalysis.plugin.annotation.bean.label.AnnotationLabel: Descriptive user-friendly label displayed via GUI.
getValue() - Method in class org.anchoranalysis.bean.NamedBean
getValue() - Method in interface org.anchoranalysis.core.identifier.name.NameValue: The associated value.
getValue() - Method in class org.anchoranalysis.core.identifier.name.SimpleNameValue
getValue() - Method in class org.anchoranalysis.core.value.TypedValue: The value.
getValue() - Method in class org.anchoranalysis.feature.bean.operator.Constant: The constant value.
getValue() - Method in class org.anchoranalysis.image.bean.unitvalue.distance.DistancePhysical: The value in units of type unitType.
getValue() - Method in class org.anchoranalysis.image.bean.unitvalue.distance.DistanceVoxels: The distance in units of voxels.
getValue() - Method in class org.anchoranalysis.image.bean.unitvalue.extent.area.AreaPhysical: The volume in units of meters, with the unit described by unitType.
getValue() - Method in class org.anchoranalysis.image.bean.unitvalue.extent.area.AreaPixels: The volume in pixels.
getValue() - Method in class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumePhysical: The volume in units of meters, with the unit described by unitType.
getValue() - Method in class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumeVoxels: The volume in voxels.
getValue() - Method in class org.anchoranalysis.io.generator.combined.OptionalNameValue: The value.
getValue() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignValue
getValue() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.CreateNew
getValue() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.UnaryWithValueBase: The scalar value to be used in channel creation.
getValue() - Method in class org.anchoranalysis.plugin.image.bean.dictionary.DictionaryCondition: The value the key should have in the dictionary, in order for the condition to be fulfilled.
getValue() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.EmptyHistogramConstant
getValue() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.IfParamEqual
getValue() - Method in class org.anchoranalysis.plugin.image.bean.scale.ConstantScaleFactor: The constant floating-point value to scale each dimension by.
getValue() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.CountEqual: The intensity value to count.
getValue() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram: The value to return if the relation test passes.
getValue() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.NormalizeByConstant: The constant value to divide the voxel intensity by.
getValue() - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Constant
getValue() - Method in class org.anchoranalysis.plugin.operator.feature.bean.WithValueBase: The constant value to be used in the operation.
getValueIfEmpty() - Method in class org.anchoranalysis.image.feature.bean.histogram.FeatureHistogramStatistic: The value to return iff exceptionifEmpty is false.
getValueIfTooFewVoxels() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.ImageMomentsBase: A value to return if there are too few voxels (less than MIN_NUM_VOXELS) to calculate moments.
getValueNoObject() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreObjects: The value assigned to voxels that do not belong to any object.
getValueNoObjects() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjects: The value to return when there are no objects in the search collection.
getValues() - Method in class org.anchoranalysis.annotation.io.comparer.StatisticsToExport: The values of statistics describing the annotation-comparison, corresponding exactly to the names in StatisticsToExport.getNames().
getValues() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyDoubleSet: The respect double values to assign during the permutation.
getValues() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyStringSet: The respect string values to assign during the permutation.
getVaryingSizeWidth() - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage: If no specific width or scaling-factor is suggested, this determines the default width that the combined-montage should have, when varyImageSize==true.
getVaryingSizeWidthRatio() - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage: If no specific width or scaling-factor is suggested, this determines the default percentage of the existing size, the combined-montage should have, when varyImageSize==true.
getVersion() - Method in class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierConstant
getVertex() - Method in class org.anchoranalysis.plugin.image.object.merge.priority.PrioritisedVertex
getVoxelDataType() - Method in class org.anchoranalysis.image.bean.nonbean.ConsistentChannelChecker: The voxel-data-type that is consistent across all channels.
getVoxelDataType() - Method in class org.anchoranalysis.image.core.channel.Channel: The underlying data-type of the voxels in the channel, represented by a VoxelDataType instance.
getVoxelDataType() - Method in class org.anchoranalysis.image.voxel.VoxelsUntyped: The underlying data-type of the voxels, represented by a VoxelDataType instance.
getVoxels() - Method in class org.anchoranalysis.image.voxel.buffer.SlidingBuffer: The voxels from which buffers corresponding to slices are extracted.
getVoxelsConverter() - Method in class org.anchoranalysis.image.core.channel.convert.attached.channel.QuantileIntensity
getVoxelsConverter() - Method in class org.anchoranalysis.image.core.channel.convert.attached.channel.UpperLowerQuantileIntensity
getVoxelsConverter() - Method in class org.anchoranalysis.image.core.channel.convert.attached.channel.IntensityRange
getVoxelsConverter() - Method in class org.anchoranalysis.image.core.channel.convert.attached.channel.MaxIntensity
getVoxelsConverter() - Method in interface org.anchoranalysis.image.core.channel.convert.attached.ChannelConverterAttached: Converts voxels to have type voxel-type T.
getVoxelsConverter() - Method in class org.anchoranalysis.image.core.channel.convert.attached.histogram.MaxIntensityFromHistogram
getVoxelsConverter() - Method in class org.anchoranalysis.image.core.channel.convert.attached.histogram.QuantileIntensityFromHistogram
getVoxelsConverter() - Method in class org.anchoranalysis.image.core.channel.convert.attached.histogram.UpperLowerQuantileIntensityFromHistogram
getVoxelsConverter() - Method in class org.anchoranalysis.image.core.channel.convert.ChannelConverter: A converter used to change the Voxels to targetDataType.
getWeightBackground() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.OtsuWeighted
getWeightForeground() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.OtsuWeighted
getWeightItem1Greater() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.Range: Weight applied when the first item's value is greater than the second.
getWeightItem2Greater() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.Range: Weight applied when the second item's value is greater than the first.
getWeightWidthDescription() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.ImageLabelStrategy: The weight to use for the width of the description.
getWhenBinaryChannel() - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchChannels: Writer employed if a stack is a single-channeled binary image.
getWhenDetailed() - Method in class org.anchoranalysis.experiment.bean.log.SwitchDetailedLogging: Logger to use when detailed-logging is on
getWhenEqual() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.IfParamEqual
getWhenFalse() - Method in class org.anchoranalysis.image.io.bean.object.draw.IfElse: The DrawObject that is used when condition==false.
getWhenNot() - Method in class org.anchoranalysis.experiment.bean.log.SwitchDetailedLogging: Logger to use when detailed-logging is off
getWhenNotEightBit() - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchChannels: Writer employed if a stack contains channels that are not 8-bit.
getWhenNotEqual() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.IfParamEqual
getWhenRelative() - Method in class org.anchoranalysis.plugin.io.bean.file.namer.IfRelativeToDirectory: The namer to use if the relative-to-directory option is selected.
getWhenRGB() - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchChannels: Writer employed if a stack is a three-channeled RGB image.
getWhenRGBAlpha() - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchChannels: Writer employed if a stack is a four-channeled RGBA image.
getWhenSingleChannel() - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchChannels: Writer employed if a stack is a single-channeled image, not guaranteed to be binary.
getWhenThreeChannels() - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchChannels: Writer employed if a stack is a three-channeled non-RGB image.
getWhenTrue() - Method in class org.anchoranalysis.image.io.bean.object.draw.IfElse: The DrawObject that is used when condition==true.
getWidth() - Method in class org.anchoranalysis.image.bean.spatial.arrange.fill.Fill: The width of the combined image in pixels.
getWidth() - Method in class org.anchoranalysis.image.bean.spatial.SizeXY: Size in X dimension.
getWidth() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Difference: Width (what the difference is divided by)
getWidth() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ImposeResolution: Physical pixel size of a voxel in x-dimension.
getWidthFactor() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.DifferenceCalculateLevelStandardDeviation
getWidthRatio() - Method in class org.anchoranalysis.image.bean.spatial.arrange.fill.Fill: What fraction of the natural width of the elements should be used to determine the final width.
getWindowSize() - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters: The window-size as per OpenCV implementation.
getWithConfidence() - Method in class org.anchoranalysis.image.inference.segment.LabelledWithConfidence: The element with associated confidence.
getWithin() - Method in class org.anchoranalysis.plugin.image.feature.bean.physical.UnitsWithinRange: Returned as a constant if a value lies within the range
getWithinValue() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.CompareWithRange: Constant to return if value lies within the range
getWithinValue() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.CompareWithRangeFeature: Constant to return if value lies within the range
getWriter() - Method in class org.anchoranalysis.image.io.bean.object.draw.Flatten
getWriter() - Method in class org.anchoranalysis.io.generator.text.TextFileOutput: The PrintWriter used for writing the text file.
getWriter() - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchChannels: Default writer, if a more specific writer is not specified for a condition.
getWriter() - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.WriteResolutionXml
getWriterAlways2D() - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchStack: Writer to use if it is guaranteed that the image will always be 2D.
getWriterElse() - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchStack: Otherwise the writer to use.
getWriterIfNoSuggestion() - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchSuggestedFormat: The writer to use if there is no suggested file-format.
getWriterInstance(Class<? extends T>) - Method in class org.anchoranalysis.io.output.bean.OutputWriteSettings: Gets a writer-instance for a particular writerParentClass.
getWriters() - Method in class org.anchoranalysis.io.output.bean.OutputWriteSettings: Specifies a writer bean instance for a particular type of writer (identified by the writer bean class)
getWriters() - Method in class org.anchoranalysis.io.output.outputter.OutputterChecked: The writers associated with this output-manager.
getWritersIfSuggested() - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchSuggestedFormat: A list of writers to select if a given format is used
getX() - Method in class org.anchoranalysis.image.bean.spatial.direction.SpecifyVector: Component of the vector along the x-axis.
getXmlAggregatedGroup() - Method in class org.anchoranalysis.feature.io.results.FeatureOutputNames: The name of the XML file outputted with aggregated values for each group, if enabled.
getXMLConfiguration() - Method in class org.anchoranalysis.experiment.bean.Experiment: The configuration of experiment serialized into XML form.
getY() - Method in class org.anchoranalysis.image.bean.spatial.direction.SpecifyVector: Component of the vector along the y-axis.
getZ() - Method in class org.anchoranalysis.image.bean.spatial.direction.SpecifyVector: Component of the vector along the z-axis.
getZSliceGroupID() - Method in class org.anchoranalysis.plugin.io.bean.file.group.parser.RegularExpression
getZSliceNum() - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetSlice
GIF - Enum constant in enum class org.anchoranalysis.core.format.ImageFileFormat: GIF
GlobalRegionIdentifiers - Class in org.anchoranalysis.mpp.mark: Defines global identifiers for different regions of a mark.
GlobExtractor - Class in org.anchoranalysis.io.input.path: Extracts a glob from a string describing it, and a direcory which gives it context.
GlobExtractor.GlobWithDirectory - Class in org.anchoranalysis.io.input.path: A string describing a glob, associated with a directory onto which it will be applied.
GlobWithDirectory(Optional<String>, String) - Constructor for class org.anchoranalysis.io.input.path.GlobExtractor.GlobWithDirectory: Creates a new GlobWithDirectory instance.
GradientBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider.gradient: Base class to calculate the gradient of the voxels in a Channel.
GradientBase() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientBase
GradientBaseAddSum - Class in org.anchoranalysis.plugin.image.bean.channel.provider.gradient: Like GradientBase but allows an arbitrary constant to be added to voxels storing the gradient.
GradientBaseAddSum() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientBaseAddSum
gradientCalculation() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.IntensityGradientBase: Creates a CalculationPart for calculating the gradient from the specified channels.
GradientForAxis - Class in org.anchoranalysis.plugin.image.bean.channel.provider.gradient: Extracts the gradient in the direction of a particular axis (identified by an index)
GradientForAxis() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientForAxis
GradientMagnitude - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient: Calculates the mean of the intensity-gradient defined by multiple Energy channels in a particular direction
GradientMagnitude() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.GradientMagnitude
GradientMeanForAxis - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient: Calculates the mean of the intensity-gradient defined by multiple Energy channels in a particular direction
GradientMeanForAxis() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.GradientMeanForAxis
GradientXY - Class in org.anchoranalysis.plugin.image.bean.channel.provider.gradient: Calculates a Channel's gradient along the x and y axes.
GradientXY() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientXY
GraphLogger - Class in org.anchoranalysis.plugin.image.object.merge: A logger for graph operations, using a DescribeGraph to generate descriptions.
GraphLogger(DescribeGraph, Logger) - Constructor for class org.anchoranalysis.plugin.image.object.merge.GraphLogger: Creates a new GraphLogger instance.
GraphWithoutPayload<V> - Class in org.anchoranalysis.core.graph: A graph, either directed or undirected, where edges contain no payload.
GraphWithoutPayload(boolean) - Constructor for class org.anchoranalysis.core.graph.GraphWithoutPayload: Creates the graph.
GraphWithPayload<V,P> - Class in org.anchoranalysis.core.graph: A graph, either directed or undirected, with edges containing a payload of type E.
GraphWithPayload(boolean) - Constructor for class org.anchoranalysis.core.graph.GraphWithPayload: Creates the graph.
GrayscaleReconstruction2DIJ - Class in org.anchoranalysis.plugin.fiji.bean.channel.grayscalereconstruction: Performs 2D grayscale reconstruction using ImageJ's implementation.
GrayscaleReconstruction2DIJ() - Constructor for class org.anchoranalysis.plugin.fiji.bean.channel.grayscalereconstruction.GrayscaleReconstruction2DIJ
GrayscaleReconstructionByErosion - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction: Abstract base class for performing grayscale reconstruction by erosion.
GrayscaleReconstructionByErosion() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction.GrayscaleReconstructionByErosion
GrayscaleReconstructionRobinson - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction: Implements grayscale reconstruction using Robinson's algorithm.
GrayscaleReconstructionRobinson() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction.GrayscaleReconstructionRobinson
GreaterIntersectionWith - Class in org.anchoranalysis.plugin.image.bean.object.filter.independent: Only accepts an object if it has greater (or EQUAL) intersection with objectsGreater than objectsLesser
GreaterIntersectionWith() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.independent.GreaterIntersectionWith
GreaterThan - Class in org.anchoranalysis.math.relation: Returns true iff valueFirst is greater than valueSecond.
GreaterThan() - Constructor for class org.anchoranalysis.math.relation.GreaterThan
GreaterThanBean - Class in org.anchoranalysis.bean.shared.relation: A relation double1 > double2.
GreaterThanBean() - Constructor for class org.anchoranalysis.bean.shared.relation.GreaterThanBean
GreaterThanEqualTo - Class in org.anchoranalysis.math.relation: Returns true iff valueFirst is greater than or equal to valueSecond.
GreaterThanEqualTo() - Constructor for class org.anchoranalysis.math.relation.GreaterThanEqualTo
GreaterThanEqualToBean - Class in org.anchoranalysis.bean.shared.relation: A relation double1 >= double2.
GreaterThanEqualToBean() - Constructor for class org.anchoranalysis.bean.shared.relation.GreaterThanEqualToBean
GreaterThanThreshold - Class in org.anchoranalysis.plugin.image.bean.histogram.provider: Thresholds a histogram using a CalculateLevel keeping only the values greater equal than the threshold
GreaterThanThreshold() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.provider.GreaterThanThreshold
greedyMatch() - Method in class org.anchoranalysis.math.optimization.HungarianAlgorithm: Find a valid matching by greedily selecting among zero-cost matchings.
green() - Method in class org.anchoranalysis.image.core.stack.RGBStack: The green channel.
GREEN - Static variable in class org.anchoranalysis.image.core.stack.RGBChannelNames: Name for the green channel.
GroupedAnnotationLabels - Class in org.anchoranalysis.plugin.annotation.bean.label: A set of AnnotationLabels partitioned into their unique groups.
GroupedAnnotationLabels(Collection<AnnotationLabel>) - Constructor for class org.anchoranalysis.plugin.annotation.bean.label.GroupedAnnotationLabels: Creates a new instance of GroupedAnnotationLabels.
groupedLabels() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.ImageLabelStrategy: Creates a GroupedAnnotationLabels from the current labels.
GroupedResults - Class in org.anchoranalysis.feature.io.results.group: Stores feature-calculation results, indexing by their group.
GroupedResults() - Constructor for class org.anchoranalysis.feature.io.results.group.GroupedResults
GroupedSharedState<S,T> - Class in org.anchoranalysis.plugin.image.task.grouped: Commonality between shared state for grouped export tasks.
GroupedSharedState(Optional<InputGrouper>, Function<ConsistentChannelChecker, GroupMapByName<S, T>>) - Constructor for class org.anchoranalysis.plugin.image.task.grouped.GroupedSharedState: Creates a new GroupedSharedState instance.
GroupedStackBase<S,T> - Class in org.anchoranalysis.plugin.image.task.bean.grouped: Base class for stacks (usually each channel from an image) that are somehow grouped-together.
GroupedStackBase() - Constructor for class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase
Grouper - Class in org.anchoranalysis.io.input.bean.grouper: Determines how partition inputs into groups.
Grouper() - Constructor for class org.anchoranalysis.io.input.bean.grouper.Grouper
GroupFiles - Class in org.anchoranalysis.plugin.io.bean.file.group: An InputManagerWithStackReader that can unify separate images in separate files to form a single Stack.
GroupFiles() - Constructor for class org.anchoranalysis.plugin.io.bean.file.group.GroupFiles
groupForKey(String) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.AnnotationComparisonAssigner: Gets the ImageCounterWithStatistics for a specific key.
groupForKey(String) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner
groupForKey(String) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.MaskIntersectionAssigner
GroupingRoot - Annotation Interface in org.anchoranalysis.bean.annotation: Indicates that a set of definitions of classes can be collectively grouped using this class.
GroupMapByName<S,T> - Class in org.anchoranalysis.plugin.image.task.grouped: Adds items to aggregate structures identified uniquely by a name, and allows these items to be later outputted.
GroupMapByName(String, Optional<Stream<String>>, Optional<InputOutputContext>, Supplier<T>, CheckedBiConsumer<S, T, OperationFailedException>) - Constructor for class org.anchoranalysis.plugin.image.task.grouped.GroupMapByName: Creates a group-map.
groupsForImage(SplitString) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.ComparisonSharedState: Retrieves the groups for a given image based on its descriptive split.
Grow - Class in org.anchoranalysis.image.bean.spatial.arrange.align: Grow the bounding-box to fill larger as much as possible.
Grow() - Constructor for class org.anchoranalysis.image.bean.spatial.arrange.align.Grow
Grow(boolean) - Constructor for class org.anchoranalysis.image.bean.spatial.arrange.align.Grow: Create to preserve the aspect-ratio or not.
Grow(boolean, Align) - Constructor for class org.anchoranalysis.image.bean.spatial.arrange.align.Grow: Creates a new Grow instance.
growBuffer(Point3i, Point3i, Optional<Extent>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Grows the object-mask's voxel buffers in the positive and negative directions by a certain amount.
growBuffer(Point3i, Point3i, Optional<Extent>, VoxelsFactoryTypeBound<T>) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: Grows the voxel buffer in the positive and negative directions by a certain amount.
growBy(int) - Method in class org.anchoranalysis.spatial.box.Extent: Creates a new Extent with toAdd size added to each dimension.
growBy(ReadableTuple3i) - Method in class org.anchoranalysis.spatial.box.Extent: Creates a new Extent with toAdd size added to each respective dimension.
growBy(Tuple3i, Extent) - Method in class org.anchoranalysis.spatial.box.BoundingBox: Grow the bounding-box by toAdd amount in each dimension in both positive and negative directions.
growToZ(int) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Grows a single z-sliced ObjectMask by duplicating the slice across the z-dimension sizeZ number of times.
growToZ(int, VoxelsFactoryTypeBound<T>) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: Grows a single z-sliced BoundedVoxels by duplicating the slice across the z-dimension sizeZ number of times.
growWidth(int) - Method in class org.anchoranalysis.image.bean.spatial.arrange.fill.ExtentToArrange: Changes the width of the underlying Extent by adding growBy pixels.
guaranteedImageAttributes() - Method in class org.anchoranalysis.annotation.io.assignment.generator.AssignmentGenerator
guaranteedImageAttributes() - Method in class org.anchoranalysis.image.io.channel.output.ChannelGenerator
guaranteedImageAttributes() - Method in class org.anchoranalysis.image.io.object.output.grayscale.ObjectsAsGrayscaleGenerator
guaranteedImageAttributes() - Method in class org.anchoranalysis.image.io.object.output.mask.ObjectAsMaskGenerator
guaranteedImageAttributes() - Method in class org.anchoranalysis.image.io.object.output.rgb.ObjectsAsRGBGenerator
guaranteedImageAttributes() - Method in class org.anchoranalysis.image.io.stack.output.box.DrawObjectOnStackGenerator
guaranteedImageAttributes() - Method in class org.anchoranalysis.image.io.stack.output.box.ExtractBoundingBoxAreaFromStackGenerator
guaranteedImageAttributes() - Method in class org.anchoranalysis.image.io.stack.output.generator.DisplayStackGenerator
guaranteedImageAttributes() - Method in class org.anchoranalysis.image.io.stack.output.generator.FlattenStackGenerator
guaranteedImageAttributes() - Method in class org.anchoranalysis.image.io.stack.output.generator.RasterGenerator: Guarantees on the attributes of all images created by the generator.
guaranteedImageAttributes() - Method in class org.anchoranalysis.image.io.stack.output.generator.RasterGeneratorDelegateToDisplayStack
guaranteedImageAttributes() - Method in class org.anchoranalysis.image.io.stack.output.generator.RasterGeneratorDelegateToRaster
guaranteedImageAttributes() - Method in class org.anchoranalysis.image.io.stack.output.generator.StackGenerator
GuessDimensions - Class in org.anchoranalysis.plugin.image.bean.dimensions.provider: Guesses dimensions from an input-image if it exists.
GuessDimensions() - Constructor for class org.anchoranalysis.plugin.image.bean.dimensions.provider.GuessDimensions

H

has(K) - Method in class org.anchoranalysis.core.cache.LRUCache: Is a particular key present already in the cache?
hasAllRequiredArguments(boolean) - Method in class org.anchoranalysis.experiment.bean.require.RequireArguments: Do all necessary arguments exist?
hasAllRequiredArguments(boolean) - Method in class org.anchoranalysis.experiment.bean.require.RequireDebugMode
hasArray() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer: Whether the buffer has an array?
hasAtLeastOneDisabled() - Method in class org.anchoranalysis.io.output.recorded.MultiLevelRecordedOutputs: If there is at least one disabled output.
hasAtLeastOneDisabled() - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputs: If there is at least one disabled output.
hasAtLeastOneEnabled() - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputs: If there is at least one enabled output.
hasAtLeastOneMultiplex(boolean) - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputs: Multiplex between RecordedOutputs.hasAtLeastOneEnabled() and RecordedOutputs.hasAtLeastOneDisabled().
hasBeenInitialized() - Method in class org.anchoranalysis.io.output.bean.OutputWriteSettings: Whether the method OutputWriteSettings.initialize(org.anchoranalysis.bean.BeanInstanceMap) has been called yet?
hasCachedResult() - Method in class org.anchoranalysis.feature.calculate.part.CalculationPart: Has the calculation already been executed, with a cached result existing?
hasChannel(String) - Method in interface org.anchoranalysis.image.io.channel.input.ChannelGetter: Does a particular channel-name exist?
hasChannel(String) - Method in class org.anchoranalysis.image.io.channel.map.NamedChannelsConcatenate
hasChannel(String) - Method in class org.anchoranalysis.image.io.channel.map.OpenedNamedChannels
hasChannel(String) - Method in class org.anchoranalysis.plugin.image.task.stack.ChannelGetterForTimepoint: Checks if a channel with the given name exists.
HasFriendlyErrorMessage - Interface in org.anchoranalysis.core.exception.friendly: Methods for extracting a user-friendly error description.
hashCode() - Method in class org.anchoranalysis.annotation.image.ImageLabelAnnotation
hashCode() - Method in class org.anchoranalysis.annotation.io.assignment.CostMatrix
hashCode() - Method in class org.anchoranalysis.annotation.io.image.findable.Found
hashCode() - Method in class org.anchoranalysis.annotation.io.image.findable.NotFound
hashCode() - Method in interface org.anchoranalysis.bean.GenerateUniqueParameterization
hashCode() - Method in class org.anchoranalysis.bean.primitive.DoubleList
hashCode() - Method in class org.anchoranalysis.bean.primitive.DoubleSet
hashCode() - Method in class org.anchoranalysis.bean.primitive.IntegerList
hashCode() - Method in class org.anchoranalysis.bean.primitive.IntegerSet
hashCode() - Method in class org.anchoranalysis.bean.primitive.StringList
hashCode() - Method in class org.anchoranalysis.bean.primitive.StringSet
hashCode() - Method in class org.anchoranalysis.bean.shared.path.RootPath
hashCode() - Method in class org.anchoranalysis.bean.shared.relation.EqualToBean
hashCode() - Method in class org.anchoranalysis.bean.shared.relation.GreaterThanBean
hashCode() - Method in class org.anchoranalysis.bean.shared.relation.GreaterThanEqualToBean
hashCode() - Method in class org.anchoranalysis.bean.shared.relation.LessThanBean
hashCode() - Method in class org.anchoranalysis.bean.shared.relation.LessThanEqualToBean
hashCode() - Method in class org.anchoranalysis.bean.shared.relation.RelationBean
hashCode() - Method in class org.anchoranalysis.bean.shared.relation.threshold.RelationToConstant
hashCode() - Method in class org.anchoranalysis.core.color.RGBColor
hashCode() - Method in class org.anchoranalysis.core.graph.TypedEdge
hashCode() - Method in class org.anchoranalysis.core.index.Indexable
hashCode() - Method in class org.anchoranalysis.core.index.range.IndexRangeNegative
hashCode() - Method in class org.anchoranalysis.core.log.CommonContext
hashCode() - Method in class org.anchoranalysis.core.system.path.FilenameSplitExtension
hashCode() - Method in class org.anchoranalysis.core.system.path.SplitPath
hashCode() - Method in class org.anchoranalysis.core.time.OperationContext
hashCode() - Method in class org.anchoranalysis.core.value.TypedValue
hashCode() - Method in class org.anchoranalysis.experiment.task.ParametersUnbound
hashCode() - Method in class org.anchoranalysis.experiment.task.processor.JobDescription
hashCode() - Method in class org.anchoranalysis.experiment.task.processor.SubmittedJob
hashCode() - Method in class org.anchoranalysis.experiment.time.RunningSumParented
hashCode() - Method in class org.anchoranalysis.feature.calculate.cache.ChildCacheName
hashCode() - Method in class org.anchoranalysis.feature.calculate.cache.part.ResolvedPart
hashCode() - Method in class org.anchoranalysis.feature.calculate.cache.part.ResolvedPartMap
hashCode() - Method in class org.anchoranalysis.feature.calculate.part.CalculationPart
hashCode() - Method in class org.anchoranalysis.feature.calculate.part.CalculationPartMap
hashCode() - Method in class org.anchoranalysis.feature.initialization.FeatureInitialization
hashCode() - Method in class org.anchoranalysis.feature.input.FeatureInputDimensions
hashCode() - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy
hashCode() - Method in class org.anchoranalysis.feature.input.FeatureInputNull
hashCode() - Method in class org.anchoranalysis.feature.input.FeatureInputResults
hashCode() - Method in class org.anchoranalysis.feature.io.csv.metadata.FeatureCSVMetadata
hashCode() - Method in class org.anchoranalysis.feature.io.name.CombinedName
hashCode() - Method in class org.anchoranalysis.feature.io.name.SimpleName
hashCode() - Method in class org.anchoranalysis.feature.io.results.LabelledResultsVector
hashCode() - Method in class org.anchoranalysis.feature.results.ResultsVector
hashCode() - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.StackArrangement
hashCode() - Method in class org.anchoranalysis.image.bean.spatial.arrange.fill.ExtentToArrange: To correspond to ExtentToArrange.equals(Object).
hashCode() - Method in class org.anchoranalysis.image.bean.spatial.SizeXY
hashCode() - Method in class org.anchoranalysis.image.bean.threshold.CalculateLevel
hashCode() - Method in class org.anchoranalysis.image.bean.threshold.CalculateLevelUnary
hashCode() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryNotOffVoxels
hashCode() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryNotOnVoxels
hashCode() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryOffVoxels
hashCode() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryOnVoxels
hashCode() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryVoxelsBase
hashCode() - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
hashCode() - Method in class org.anchoranalysis.image.core.dimensions.Resolution
hashCode() - Method in class org.anchoranalysis.image.core.mask.Mask
hashCode() - Method in class org.anchoranalysis.image.core.object.label.OverlappingObject
hashCode() - Method in class org.anchoranalysis.image.core.object.MatchedObject
hashCode() - Method in class org.anchoranalysis.image.core.object.properties.ObjectWithProperties
hashCode() - Method in class org.anchoranalysis.image.core.stack.ImagePyramidMetadata
hashCode() - Method in class org.anchoranalysis.image.core.stack.Stack
hashCode() - Method in class org.anchoranalysis.image.feature.calculation.CalculateInputFromPair
hashCode() - Method in class org.anchoranalysis.image.feature.calculation.CalculateNumberVoxels
hashCode() - Method in class org.anchoranalysis.image.feature.calculator.NamedFeatureCalculatorMulti
hashCode() - Method in class org.anchoranalysis.image.feature.input.FeatureInputImageMetadata
hashCode() - Method in class org.anchoranalysis.image.feature.input.FeatureInputObjectCollection
hashCode() - Method in class org.anchoranalysis.image.feature.input.FeatureInputPairObjects
hashCode() - Method in class org.anchoranalysis.image.feature.input.FeatureInputSingleObject
hashCode() - Method in class org.anchoranalysis.image.feature.input.FeatureInputStack
hashCode() - Method in class org.anchoranalysis.image.inference.bean.reduce.ObjectForReduction
hashCode() - Method in class org.anchoranalysis.image.inference.ImageInferenceContext
hashCode() - Method in class org.anchoranalysis.image.inference.segment.LabelledWithConfidence
hashCode() - Method in class org.anchoranalysis.image.inference.segment.WithConfidence
hashCode() - Method in class org.anchoranalysis.image.io.stack.input.ImageTimestampsAttributes
hashCode() - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte
hashCode() - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValuesInt
hashCode() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer
hashCode() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBufferAsInt
hashCode() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
hashCode() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer
hashCode() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
hashCode() - Method in class org.anchoranalysis.image.voxel.datatype.VoxelDataType
hashCode() - Method in class org.anchoranalysis.image.voxel.iterator.MinMaxRange
hashCode() - Method in class org.anchoranalysis.image.voxel.kernel.KernelApplicationParameters
hashCode() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
hashCode() - Method in class org.anchoranalysis.inference.concurrency.ConcurrentModel
hashCode() - Method in class org.anchoranalysis.inference.concurrency.WithPriority
hashCode() - Method in class org.anchoranalysis.io.bioformats.copyconvert.ImageFileEncoding
hashCode() - Method in class org.anchoranalysis.io.bioformats.copyconvert.ImageFileShape
hashCode() - Method in class org.anchoranalysis.io.generator.combined.OptionalNameValue
hashCode() - Method in class org.anchoranalysis.io.generator.sequence.BoundOutputter
hashCode() - Method in class org.anchoranalysis.io.input.file.FileNamerContext
hashCode() - Method in class org.anchoranalysis.io.input.file.NamedFile
hashCode() - Method in class org.anchoranalysis.io.input.InputsWithDirectory
hashCode() - Method in class org.anchoranalysis.io.input.path.GlobExtractor.GlobWithDirectory
hashCode() - Method in class org.anchoranalysis.io.output.outputter.directory.OutputterTarget
hashCode() - Method in class org.anchoranalysis.io.output.outputter.DirectoryCreationParameters
hashCode() - Method in class org.anchoranalysis.io.output.outputter.Outputter
hashCode() - Method in class org.anchoranalysis.io.output.path.prefixer.NamedPath
hashCode() - Method in class org.anchoranalysis.launcher.config.HelpConfig
hashCode() - Method in class org.anchoranalysis.math.equation.QuadraticEquationSolver.QuadraticRoots
hashCode() - Method in class org.anchoranalysis.math.statistics.MeanScale
hashCode() - Method in class org.anchoranalysis.math.statistics.moment.EigenvalueAndVector
hashCode() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMap
hashCode() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
hashCode() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipWithFlags
hashCode() - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.CalculateDeriveSingleMemoFromPair
hashCode() - Method in class org.anchoranalysis.mpp.feature.bean.mark.FeatureInputMark
hashCode() - Method in class org.anchoranalysis.mpp.feature.energy.EnergyPair
hashCode() - Method in class org.anchoranalysis.mpp.feature.energy.IndexableMarksWithEnergy
hashCode() - Method in class org.anchoranalysis.mpp.feature.input.FeatureInputAllMemo
hashCode() - Method in class org.anchoranalysis.mpp.feature.input.FeatureInputPairMemo
hashCode() - Method in class org.anchoranalysis.mpp.feature.input.FeatureInputSingleMemo
hashCode() - Method in class org.anchoranalysis.mpp.feature.mark.MemoList
hashCode() - Method in class org.anchoranalysis.mpp.overlay.OverlayMark
hashCode() - Method in class org.anchoranalysis.mpp.pair.MarkPair
hashCode() - Method in class org.anchoranalysis.mpp.pair.PairVoxelizedMarkMemo
hashCode() - Method in class org.anchoranalysis.mpp.proposer.ProposerContext
hashCode() - Method in class org.anchoranalysis.overlay.object.OverlayObjectMask
hashCode() - Method in class org.anchoranalysis.overlay.Overlay
hashCode() - Method in class org.anchoranalysis.overlay.writer.ObjectDrawAttributes
hashCode() - Method in class org.anchoranalysis.plugin.annotation.comparison.ObjectsToCompare
hashCode() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelListBase
hashCode() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelRelativeToThreshold
hashCode() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.ClampHistogramMax
hashCode() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Constant
hashCode() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.EmptyHistogramConstant
hashCode() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.IfGreaterThan
hashCode() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.IfLessThan
hashCode() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Maximum
hashCode() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Minimum
hashCode() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Otsu
hashCode() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.OtsuWeighted
hashCode() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Quantile
hashCode() - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations
hashCode() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.CalculateIntersecting
hashCode() - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.CalculateDeriveObjectInput
hashCode() - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegate
hashCode() - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegateOption
hashCode() - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateIncrementalOperationMap
hashCode() - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateObjectMask
hashCode() - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateShellObjectMask
hashCode() - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateDilation
hashCode() - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateDilationMap
hashCode() - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateErosion
hashCode() - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateErosionMap
hashCode() - Method in class org.anchoranalysis.plugin.image.feature.stack.calculation.CalculateHistogram
hashCode() - Method in class org.anchoranalysis.plugin.image.feature.stack.calculation.CalculateHistogramMasked
hashCode() - Method in class org.anchoranalysis.plugin.image.object.ColoredObject
hashCode() - Method in class org.anchoranalysis.plugin.image.task.bean.format.ChangeableOutputSequence
hashCode() - Method in class org.anchoranalysis.plugin.image.task.feature.FeatureExporterContext
hashCode() - Method in class org.anchoranalysis.plugin.image.task.feature.InitializationWithEnergyStack
hashCode() - Method in class org.anchoranalysis.plugin.image.task.feature.LabelledResultsVectorWithThumbnail
hashCode() - Method in class org.anchoranalysis.plugin.image.task.feature.ResultsVectorWithThumbnail
hashCode() - Method in class org.anchoranalysis.plugin.image.task.grouped.NamedChannel
hashCode() - Method in class org.anchoranalysis.plugin.image.task.labeller.ImageCSVLabellerInitialization
hashCode() - Method in class org.anchoranalysis.plugin.image.task.labeller.ImageLabellerStringMapInitialization
hashCode() - Method in class org.anchoranalysis.plugin.io.input.path.CopyContext
hashCode() - Method in class org.anchoranalysis.plugin.io.multifile.FileDetails
hashCode() - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetChannel
hashCode() - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetSlice
hashCode() - Method in class org.anchoranalysis.plugin.io.shared.AnonymizeSharedState
hashCode() - Method in class org.anchoranalysis.plugin.mpp.shared.ConvertedInput
hashCode() - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters
hashCode() - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult
hashCode() - Method in class org.anchoranalysis.plugin.points.calculate.ellipse.CalculateEllipseLeastSquares
hashCode() - Method in class org.anchoranalysis.plugin.points.calculate.ellipse.ObjectWithEllipse
hashCode() - Method in class org.anchoranalysis.plugin.points.calculate.ellipsoid.CalculateEllipsoidLeastSquares
hashCode() - Method in class org.anchoranalysis.spatial.box.BoundingBox
hashCode() - Method in class org.anchoranalysis.spatial.box.Extent
hashCode() - Method in class org.anchoranalysis.spatial.orientation.Orientation
hashCode() - Method in class org.anchoranalysis.spatial.orientation.Orientation2D
hashCode() - Method in class org.anchoranalysis.spatial.orientation.Orientation3DEulerAngles
hashCode() - Method in class org.anchoranalysis.spatial.orientation.OrientationAxisAngle
hashCode() - Method in class org.anchoranalysis.spatial.orientation.OrientationRotationMatrix
hashCode() - Method in class org.anchoranalysis.spatial.point.Point2d
hashCode() - Method in class org.anchoranalysis.spatial.point.Point2f
hashCode() - Method in class org.anchoranalysis.spatial.point.Point2i
hashCode() - Method in class org.anchoranalysis.spatial.point.Point3d
hashCode() - Method in class org.anchoranalysis.spatial.point.Point3f
hashCode() - Method in class org.anchoranalysis.spatial.point.Point3i
hashCode() - Method in class org.anchoranalysis.spatial.point.Tuple3d
hashCode() - Method in class org.anchoranalysis.spatial.point.Tuple3f
hashCode() - Method in class org.anchoranalysis.spatial.point.Tuple3i
hashCode() - Method in class org.anchoranalysis.spatial.point.Vector3d
hashCode() - Method in class org.anchoranalysis.spatial.scale.ScaleFactor
hashCode() - Method in class org.anchoranalysis.test.image.rasterwriter.comparison.ComparisonPlan
hashCode() - Method in class org.anchoranalysis.test.image.stackwriter.ChannelSpecification
hasHdf5Extension(Path) - Static method in class org.anchoranalysis.image.io.object.input.ObjectCollectionReader: Whether a path has a suitable extension to be considered a HDF5 file?
hasHeaders() - Method in class org.anchoranalysis.io.input.csv.CSVReader.OpenedCSVFile: Does the first line of the CSV file specify headers rather than values?
hasIdenticalXY() - Method in class org.anchoranalysis.spatial.scale.ScaleFactor: Is the scale-factor identical in X and Y dimensions?
hasIntersectingVoxels(ObjectMask) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Determines whether there are any intersecting voxels on two object-masks.
hasIntersectingVoxels(ObjectMask, ObjectMask) - Static method in class org.anchoranalysis.image.voxel.iterator.intersecting.CountVoxelsIntersectingObjects: Determines whether there are any intersecting voxels on two object-masks.
hasKey(U) - Method in class org.anchoranalysis.feature.calculate.part.CalculationPartMap: Does a result exist for the current input, and a particular key?
hasMatch(String) - Method in class org.anchoranalysis.bean.shared.regex.RegEx: Returns a boolean whether the regular-expression successfully matches a string or not.
hasMoreThanOneSlice() - Method in class org.anchoranalysis.image.core.stack.Stack: Does the stack have more than one slice in the z-dimension?
hasNecessaryExtents() - Method in class org.anchoranalysis.plugin.io.multifile.SizeExtents
hasNext() - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.PriorityQueueIndexRangeDownhill: Checks if there are any items left in the queue.
hasNoCombinableNestedExceptions() - Method in exception class org.anchoranalysis.core.exception.combinable.AnchorCombinableException: Are there nested-exceptions (according to our traversal rules) that are combinable?
hasNonZeroCount(int) - Method in class org.anchoranalysis.math.histogram.Histogram: Whether at least one value, greater or equal to startMin has non-zero count?
hasNoPadding() - Method in class org.anchoranalysis.image.bean.spatial.Padding: Whether no padding exists.
hasOffVoxel() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels: At least one voxel exists with an off value.
hasOneSlice() - Method in class org.anchoranalysis.feature.energy.EnergyStack: Does exactly one z-slice exist in the energy stack?
hasOnVoxel() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels: At least one voxel exists with an on value.
hasOption(String) - Method in class org.anchoranalysis.launcher.options.CommandLineExtracter: Identical to CommandLine.hasOption(java.lang.String).
hasOptionWithoutArgument(String) - Method in class org.anchoranalysis.launcher.options.CommandLineExtracter: Checks if an option exists, but without any argument(s) specified.
hasProperty(String) - Method in class org.anchoranalysis.image.core.object.properties.ObjectWithProperties: Whether a particular property exists with a particular name.
hasRemaining() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer: Whether there are elements between the current position and the limit Buffer.hasRemaining().
hasRemaining() - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer: Are there voxels remaining in a buffer?
hasRemaining() - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferUnsigned
hasTemporary() - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels: Checks if there are any temporary encoded values in the voxels.
HasTouchingVoxels - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.touching: A simple scheme for counting the touching voxels.
HasTouchingVoxels() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.HasTouchingVoxels
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.experiment.bean.processor.JobProcessor: Is the execution-time of the task per-input expected to be very quick to execute?
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.experiment.bean.task.Task: Is the execution-time of the task per-input expected to be very quick to execute?
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.launcher.run.tasks.HelloWorld
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.annotation.bean.aggregate.AggregateAnnotations
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageAssignLabel
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.io.bean.task.CopyFiles
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.io.bean.task.SummarizeBase
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.mpp.bean.convert.ConvertNamedChannels
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.mpp.bean.define.Develop
hasWarningOccurred() - Method in interface org.anchoranalysis.core.log.error.ErrorReporter: Checks if at least one warning has been outputted.
hasWarningOccurred() - Method in class org.anchoranalysis.core.log.error.ErrorReporterBase
hasWarningOccurred() - Method in class org.anchoranalysis.experiment.task.ErrorReporterForTask
hasWrittenHeaders() - Method in class org.anchoranalysis.io.generator.tabular.CSVWriter: Whether the CSV file writes header-names as the first line.
HDF5 - Enum constant in enum class org.anchoranalysis.core.format.NonImageFileFormat: HDF5
HDF5ObjectsGenerator - Class in org.anchoranalysis.image.io.object.output.hdf5: A generator that writes a ObjectCollection to a HDF5 file.
HDF5ObjectsGenerator() - Constructor for class org.anchoranalysis.image.io.object.output.hdf5.HDF5ObjectsGenerator: Creates with compression activated.
HDF5ObjectsGenerator(boolean) - Constructor for class org.anchoranalysis.image.io.object.output.hdf5.HDF5ObjectsGenerator: Creates a new HDF5ObjectsGenerator instance.
HDF5PathHelper - Class in org.anchoranalysis.image.io.object: Paths to identify objects in the HDF5 for object-masks.
HeaderFormat - Class in org.anchoranalysis.plugin.io.bean.metadata.header: Populates ImageMetadata from the header of an image-file.
HeaderFormat() - Constructor for class org.anchoranalysis.plugin.io.bean.metadata.header.HeaderFormat
headers() - Method in class org.anchoranalysis.io.input.csv.ReadByLine: The headers of the CSV file.
headers(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FeatureSource: Generates label-headers for the non-feature-result columns in the CSV.
headers(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.SingleRowPerInput
height() - Static method in class org.anchoranalysis.test.image.MaskFixture: The **height** of the mask that will be created.
HelloWorld<S> - Class in org.anchoranalysis.launcher.run.tasks: A dummy task that simply writes a message to all log files, specifically: 1. log file for experiment 2. log file for each input-object
HelloWorld() - Constructor for class org.anchoranalysis.launcher.run.tasks.HelloWorld
help() - Method in class org.anchoranalysis.launcher.config.LauncherConfig
HelpConfig - Class in org.anchoranalysis.launcher.config: Configuration for help messages in the launcher.
HelpConfig(String, String) - Constructor for class org.anchoranalysis.launcher.config.HelpConfig: Creates a new HelpConfig instance.
hexString() - Method in class org.anchoranalysis.core.color.RGBColor: Converts the red-blue-green values as a hex-string.
higherCountExistsThan(int) - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateAtCorner
higherCountExistsThan(int) - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateImplementation
higherCountExistsThan(int) - Method in interface org.anchoranalysis.image.voxel.extracter.predicate.VoxelsPredicate: Whether the count is greater than a particular threshold.
highestConfidence() - Method in class org.anchoranalysis.image.inference.segment.SegmentedObjects: The object-mask with the highest confidence.
histogram() - Method in interface org.anchoranalysis.image.voxel.statistics.VoxelStatistics: A Histogram of all voxel values.
histogram() - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsCombined
histogram() - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsFromHistogram
histogram() - Method in class org.anchoranalysis.mpp.io.input.MultiInput: Gets the map of Histograms.
histogram(String) - Static method in class org.anchoranalysis.plugin.image.provider.ReferenceFactory: Creates a reference to a histogram.
Histogram - Class in org.anchoranalysis.math.histogram: A histogram of integer values.
Histogram(int) - Constructor for class org.anchoranalysis.math.histogram.Histogram: Constructs with a maximum value, and assuming a minimum value of 0.
Histogram(int, int) - Constructor for class org.anchoranalysis.math.histogram.Histogram: Constructs with a minimum and maximum value.
Histogram.BinConsumer - Interface in org.anchoranalysis.math.histogram: Consumes a bin and corresponding count.
HistogramCSVGenerator - Class in org.anchoranalysis.image.io.histogram.output: Writes a histogram to a CSV file.
HistogramCSVGenerator() - Constructor for class org.anchoranalysis.image.io.histogram.output.HistogramCSVGenerator
HistogramCSVReader - Class in org.anchoranalysis.image.io.histogram.input: Reads a CSV file from the file-system that describes a histogram of voxel values.
HistogramFactory - Class in org.anchoranalysis.image.voxel.statistics: Creates a Histogram to describe the intensity values of voxels in aggregate.
HistogramFixture - Class in org.anchoranalysis.test.feature.plugins: A fixture for creating predefined histograms for testing purposes.
HistogramFromObjectsFactory - Class in org.anchoranalysis.image.core.object: Create a Histogram of the voxel intensity values in an image, pertaining to a region defined by a ObjectMask or a Mask.
HistogramProvider - Class in org.anchoranalysis.image.bean.provider: Base class for beans that implement Provider to provide a Histogram.
HistogramProvider() - Constructor for class org.anchoranalysis.image.bean.provider.HistogramProvider
HistogramProviderUnary - Class in org.anchoranalysis.image.bean.provider: Implementation of HistogramProvider that calls a single delegate HistogramProvider.
HistogramProviderUnary() - Constructor for class org.anchoranalysis.image.bean.provider.HistogramProviderUnary
histograms() - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitialization: A collection of Histograms, indexed by name.
HistogramStatistics - Class in org.anchoranalysis.math.histogram: Further statistics that can be derived from a histogram in addition to those existing as direct methods of Histogram.
HistogramThresholder - Class in org.anchoranalysis.plugin.image.intensity: Utility class for thresholding histograms.
HOGDescriptor - Class in org.anchoranalysis.plugin.opencv.bean.feature: Creates the entire HOG descriptor for an image.
HOGDescriptor() - Constructor for class org.anchoranalysis.plugin.opencv.bean.feature.HOGDescriptor
HOGFeature - Class in org.anchoranalysis.plugin.opencv.bean.feature: One part of a Histogram of Oriented Gradients descriptor, as applied to an image stack.
HOGFeature() - Constructor for class org.anchoranalysis.plugin.opencv.bean.feature.HOGFeature
HOGFeature(SizeXY, int) - Constructor for class org.anchoranalysis.plugin.opencv.bean.feature.HOGFeature: Create with a specific size to resize to, and index.
HOGParameters - Class in org.anchoranalysis.plugin.opencv.bean.feature: Parameters for calculating a HOG Descriptor covering window-size, block-size etc.
HOGParameters() - Constructor for class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters
HOGParameters(Interpolator) - Constructor for class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters: Creates with a particular Interpolator.
HomeSubdirectory - Class in org.anchoranalysis.plugin.io.bean.file.path.prefixer
HomeSubdirectory() - Constructor for class org.anchoranalysis.plugin.io.bean.file.path.prefixer.HomeSubdirectory
HorizontalCacheCreator - Class in org.anchoranalysis.feature.session.cache: Creates a FeatureCalculationCache which caches the results of calls to features, even if the same feature appears multiple times, directly or indirectly.
HorizontalCacheCreator(FeatureList<? extends FeatureInput>, SharedFeatures, FeatureInitialization, Logger) - Constructor for class org.anchoranalysis.feature.session.cache.HorizontalCacheCreator: Creates a new HorizontalCacheCreator instance.
HSB - Class in org.anchoranalysis.bean.shared.color.scheme: Creates a sequence of colors by varying the hue-component in a HSB color model.
HSB() - Constructor for class org.anchoranalysis.bean.shared.color.scheme.HSB
HungarianAlgorithm - Class in org.anchoranalysis.math.optimization: An implementation of the Hungarian algorithm for solving the assignment problem.
HungarianAlgorithm(double[][]) - Constructor for class org.anchoranalysis.math.optimization.HungarianAlgorithm: Construct an instance of the algorithm.

I

idAndIncrement() - Method in class org.anchoranalysis.mpp.bean.mark.factory.MarkWithIdentifierFactory: Generates a new unique identifier and increments the counter.
identiferFor(ChannelSpecification, boolean, String, boolean) - Static method in class org.anchoranalysis.test.image.stackwriter.IdentifierHelper: Builds an identifier for particular properties.
identifier() - Method in class org.anchoranalysis.io.input.file.SingleFileInputBase
identifier() - Method in interface org.anchoranalysis.io.input.InputFromManager: A unique name associated with the input.
identifier() - Method in class org.anchoranalysis.io.input.InputFromManagerDelegate
identifier() - Method in class org.anchoranalysis.mpp.io.input.MultiInput
identifier() - Method in class org.anchoranalysis.mpp.mark.Mark: Returns a string identifier for the mark.
identifier(Optional<String>) - Method in class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifier: Creates an identifier for the experiment.
identifier(Optional<String>) - Method in class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierAuto
identifier(Optional<String>) - Method in class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierConstant
identifierAsPath() - Method in interface org.anchoranalysis.io.input.InputFromManager: Like InputFromManager.identifier() but converts the identifier to a path.
IdentifierGetter<T> - Interface in org.anchoranalysis.core.identifier.getter: Gets a unique identifier for a particular element at a particular iteration point.
IdentifierHelper - Class in org.anchoranalysis.test.image.stackwriter: Builds an identifier (a filename without extension) for a saved-raster corresponding to certain properties.
IdentifyFromIteration<T> - Class in org.anchoranalysis.core.identifier.getter: Identify an element uniquely only by its iteration timepoint.
IdentifyFromIteration() - Constructor for class org.anchoranalysis.core.identifier.getter.IdentifyFromIteration
IdentifyObjects - Class in org.anchoranalysis.plugin.image.bean.channel.provider.score: Assigns a unique id number to each object.
IdentifyObjects() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.score.IdentifyObjects
Identity - Class in org.anchoranalysis.io.input.bean.path: Returns the same Path as the argument passed in.
Identity - Class in org.anchoranalysis.plugin.image.feature.bean.score: A voxel score that can optionally normalize and adjust the intensity values.
Identity() - Constructor for class org.anchoranalysis.io.input.bean.path.Identity
Identity() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.Identity
IdentityImposeValueRelationToHistogram - Class in org.anchoranalysis.plugin.image.feature.bean.score: A voxel score that imposes a value relation to a histogram.
IdentityImposeValueRelationToHistogram() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram
idFor(ObjectWithProperties, int) - Method in class org.anchoranalysis.overlay.writer.ObjectDrawAttributes: ID for a particular object
IfCondition<T> - Class in org.anchoranalysis.plugin.operator.feature.bean.conditional: The result of featureCondition is compared to a threshold, and then either the underlying feature is calculated (positive case), or featureElse is (negative case)
IfCondition() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.conditional.IfCondition
IfConditionWithinRange<T> - Class in org.anchoranalysis.plugin.operator.feature.bean.range: Calculates a value if a condition lies within a certain range, otherwise returns constants
IfConditionWithinRange() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.range.IfConditionWithinRange
IfElse - Class in org.anchoranalysis.image.io.bean.object.draw: Branches to two different DrawObject depending on a predicate.
IfElse() - Constructor for class org.anchoranalysis.image.io.bean.object.draw.IfElse
IfElse(IfElse.Predicate, DrawObject, DrawObject) - Constructor for class org.anchoranalysis.image.io.bean.object.draw.IfElse: Creates for a particular condition.
IfElse.Predicate - Interface in org.anchoranalysis.image.io.bean.object.draw: Interface for the condition that is tested, to determine which DrawObject to use.
IfGreaterThan - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold: Calculates a level from the first delegate and if greater than a threshold, recalculates from a second delegate.
IfGreaterThan() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.IfGreaterThan
IfGroupIndexRange - Class in org.anchoranalysis.plugin.io.bean.grouper: When a IndexRangeNegative is passed as an argument, an InputGrouper is constructed that extracts elements from a Path.
IfGroupIndexRange() - Constructor for class org.anchoranalysis.plugin.io.bean.grouper.IfGroupIndexRange
IfHighLow - Class in org.anchoranalysis.plugin.image.bean.mask.provider.combine: Outputs the logical operation iff first==HIGH and second==LOW then LOW voxelwise on both masks, modifying {mask} with the result.
IfHighLow() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.combine.IfHighLow
IfIncrementingNumberRequested - Class in org.anchoranalysis.plugin.io.bean.file.path.prefixer: Multiplexes between two PathPrefixers depending on whether an incrementing number sequence was output was requested.
IfIncrementingNumberRequested() - Constructor for class org.anchoranalysis.plugin.io.bean.file.path.prefixer.IfIncrementingNumberRequested
IfKeyValueCondition - Class in org.anchoranalysis.plugin.image.bean.mask.provider.predicate: The current mask is returned if a condition on key-values is satisfied otherwise maskElse is returned.
IfKeyValueCondition() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfKeyValueCondition
IfLessThan - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold: Calculates a level from the first delegate and if less than a threshold, recalculates from a second delegate.
IfLessThan() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.IfLessThan
IfNotEmpty - Class in org.anchoranalysis.plugin.image.bean.mask.provider.predicate: The current mask is returned if it's non-empty (at least one on voxel) otherwise maskElse is returned.
IfNotEmpty() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfNotEmpty
IfObjectFilter - Class in org.anchoranalysis.plugin.image.bean.mask.provider.predicate: The current mask is returned if the mask (treated as an object) passed an object-filter, otherwise maskElse is returned.
IfObjectFilter() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfObjectFilter
ifOptionWithoutArgument(String, Consumer<T>) - Method in class org.anchoranalysis.launcher.options.process.AddOptionsFromCommandLine: Executes consumer if an option exists without any argument.
IfOutsideRange<T> - Class in org.anchoranalysis.plugin.operator.feature.bean.range: Clamps a feature value if it lies outside a specified range.
IfOutsideRange() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.range.IfOutsideRange
IfParamEqual - Class in org.anchoranalysis.plugin.image.bean.object.provider: Multiplexes between two object-collection-providers depending on whether a parameter value equals a particular string
IfParamEqual() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.IfParamEqual
IfParamEquals - Class in org.anchoranalysis.plugin.image.bean.channel.provider: Provides a channel based on a condition from a dictionary.
IfParamEquals() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.IfParamEquals
IfPredicateBase - Class in org.anchoranalysis.plugin.image.bean.mask.provider.predicate: Base class which multiplexes between the current mask and an alternative depending if a condition is met.
IfPredicateBase() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfPredicateBase
ifPresent(Optional<S>, CheckedConsumer<S, E>) - Static method in class org.anchoranalysis.core.functional.OptionalUtilities: Like Optional.map(java.util.function.Function<? super T, ? extends U>) but tolerates an exception in the mapping function, which is immediately thrown.
ifPresentMultiple(String, CheckedConsumer<String[], ExperimentExecutionException>) - Method in class org.anchoranalysis.launcher.options.CommandLineExtracter: Executes a Consumer if an option is present - allowing that option to occur multiple times.
ifPresentMultiple(String, CheckedConsumer<String[], ExperimentExecutionException>) - Method in class org.anchoranalysis.launcher.options.process.AddOptionsFromCommandLine: Executes consumer if one or more options exists with a single argument.
ifPresentSingle(String, CheckedConsumer<String, ExperimentExecutionException>) - Method in class org.anchoranalysis.launcher.options.CommandLineExtracter: Executes a Consumer if an option is present - allowing that option to occur only once.
ifPresentSingle(String, CheckedConsumer<String, ExperimentExecutionException>) - Method in class org.anchoranalysis.launcher.options.process.AddOptionsFromCommandLine: Executes consumer if maximally one option exists with a single argument - without passing associated.
ifPresentSingleAssociated(String, CheckedBiConsumer<T, String, ExperimentExecutionException>) - Method in class org.anchoranalysis.launcher.options.process.AddOptionsFromCommandLine: Executes consumer if maximally one option exists with a single argument - passing associated.
IfRelativeToDirectory - Class in org.anchoranalysis.plugin.io.bean.file.namer: Multiplexes between two namers depending on if the relative-to-directory option is selected.
IfRelativeToDirectory() - Constructor for class org.anchoranalysis.plugin.io.bean.file.namer.IfRelativeToDirectory
IfStackExists - Class in org.anchoranalysis.plugin.image.bean.mask.provider.predicate: The current mask is a particular stack exists (at least one on voxel) otherwise maskElse is returned.
IfStackExists() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfStackExists
IfVoxelZero - Class in org.anchoranalysis.plugin.image.bean.channel.provider.intensity: Creates a new channel which is a merged version of two input channels according to rules.
IfVoxelZero() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.IfVoxelZero
IGNORE_OUTSIDE - Enum constant in enum class org.anchoranalysis.image.voxel.kernel.OutsideKernelPolicy: Ignore any parts of the neighborhood that lie outside the scene.
IGNORE_SECONDS - Enum constant in enum class org.anchoranalysis.plugin.io.naming.interval.TimeStyle: The time is included in the name, but without seconds: hh.mm
IGNORE_YEAR - Enum constant in enum class org.anchoranalysis.plugin.io.naming.interval.DateStyle: The date is included in the name, but without the year: mmm-dd
IgnoreUnderscorePrefix - Class in org.anchoranalysis.io.output.bean.enabled: All outputs are allowed unless the name's first character is an underscore.
IgnoreUnderscorePrefix() - Constructor for class org.anchoranalysis.io.output.bean.enabled.IgnoreUnderscorePrefix
IgnoreUnderscorePrefixUnless - Class in org.anchoranalysis.io.output.bean.rules: Like IgnoreUnderscorePrefix for all first and level-outputs unless a particular outputs are explicitly specified.
IgnoreUnderscorePrefixUnless() - Constructor for class org.anchoranalysis.io.output.bean.rules.IgnoreUnderscorePrefixUnless
IgnoreUnderscorePrefixUnless(StringSet) - Constructor for class org.anchoranalysis.io.output.bean.rules.IgnoreUnderscorePrefixUnless: Create with first-level output names
image() - Method in class org.anchoranalysis.mpp.init.MarksInitialization: The image initialization associated with this marks initialization.
ImageAssignLabel<T> - Class in org.anchoranalysis.plugin.image.task.bean.labeller: Assigns a label to each image and copies into subdirectories for each label, and creates a labelling CSV.
ImageAssignLabel() - Constructor for class org.anchoranalysis.plugin.image.task.bean.labeller.ImageAssignLabel
ImageBean<T> - Class in org.anchoranalysis.image.bean: A bean that must be initialized with ImageInitialization before usage.
ImageBean() - Constructor for class org.anchoranalysis.image.bean.ImageBean: Create with default initializer and assigner.
ImageComparer - Interface in org.anchoranalysis.test.image.rasterwriter.comparison: Base class for a method comparing two image files.
ImageCounter<T> - Interface in org.anchoranalysis.plugin.annotation.counter: Counts images on aggregate, some with associated annotations, others without.
ImageCounterList<T> - Class in org.anchoranalysis.plugin.annotation.counter: Allows operations to be applied to several ImageCounters collectively.
ImageCounterList() - Constructor for class org.anchoranalysis.plugin.annotation.counter.ImageCounterList
ImageCounterWithStatistics<T> - Interface in org.anchoranalysis.plugin.annotation.counter: Like ImageCounter but also exports statistics.
ImageCSVLabeller - Class in org.anchoranalysis.plugin.image.task.bean.labeller: Labels images based on a CSV file containing image identifiers and corresponding labels.
ImageCSVLabeller() - Constructor for class org.anchoranalysis.plugin.image.task.bean.labeller.ImageCSVLabeller
ImageCSVLabellerInitialization - Class in org.anchoranalysis.plugin.image.task.labeller: Initialization data for an image CSV labeller.
ImageCSVLabellerInitialization(FileLabelMap<String>) - Constructor for class org.anchoranalysis.plugin.image.task.labeller.ImageCSVLabellerInitialization: Creates a new ImageCSVLabellerInitialization instance.
ImageFileAttributes - Class in org.anchoranalysis.image.core.stack: Timestamps and other metadata associated with an image file-path, but not with the file's contents.
ImageFileAttributes(Path, ZonedDateTime, ZonedDateTime) - Constructor for class org.anchoranalysis.image.core.stack.ImageFileAttributes: Creates a new ImageFileAttributes instance.
ImageFileEncoding - Class in org.anchoranalysis.io.bioformats.copyconvert: How values are encoded into an image-file.
ImageFileEncoding(boolean, boolean, int) - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.ImageFileEncoding: Creates a new ImageFileEncoding instance.
ImageFileFormat - Enum Class in org.anchoranalysis.core.format: A type of image format that are read/written to the filesystem, together with the extensions it may use.
ImageFileShape - Class in org.anchoranalysis.io.bioformats.copyconvert: How to shape the image (across various dimensions) after the copying
ImageFileShape(Dimensions, int, int) - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.ImageFileShape
ImageInferenceContext - Class in org.anchoranalysis.image.inference: Attributes describing the situation in which inference on images is occurring.
ImageInferenceContext(DualScale<Dimensions>, ScaleFactor, Optional<List<String>>, VoxelsResizer, ExecutionTimeRecorder, Logger) - Constructor for class org.anchoranalysis.image.inference.ImageInferenceContext: Creates a new ImageInferenceContext instance.
ImageInferenceModel<T> - Interface in org.anchoranalysis.image.inference: A model used for inference that accepts an image as an input.
ImageInitialization - Class in org.anchoranalysis.image.bean.nonbean.init: The state used to initialize a ImageBean.
ImageInitialization(SharedObjects) - Constructor for class org.anchoranalysis.image.bean.nonbean.init.ImageInitialization: Create with shared-objects.
ImageInitialization(SharedObjects, Optional<ImageSizeSuggestion>) - Constructor for class org.anchoranalysis.image.bean.nonbean.init.ImageInitialization: Create with shared-objects and a resizing suggestion.
ImageInitializationFactory - Class in org.anchoranalysis.image.io: Creates instances of ImageInitialization based upon an InputOutputContext.
ImageIOException - Exception Class in org.anchoranalysis.image.io: When an error occurs reading or writing an image to/from the file-system.
ImageIOException(String) - Constructor for exception class org.anchoranalysis.image.io.ImageIOException: Create with a message only.
ImageIOException(String, Throwable) - Constructor for exception class org.anchoranalysis.image.io.ImageIOException: Create with a message and cause.
ImageIOException(Throwable) - Constructor for exception class org.anchoranalysis.image.io.ImageIOException: Create with a cause only.
ImageIOWriter - Class in org.anchoranalysis.plugin.io.bean.stack.writer
ImageIOWriter() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.writer.ImageIOWriter
ImageJ - Class in org.anchoranalysis.io.imagej.bean.interpolator: Resizes with linear interpolation as implemented in ImageJ.
ImageJ() - Constructor for class org.anchoranalysis.io.imagej.bean.interpolator.ImageJ
ImageJConversionException - Exception Class in org.anchoranalysis.io.imagej.convert: When conversion to ImageJ data/type is not possible, or an error occurs during conversion.
ImageJConversionException(Exception) - Constructor for exception class org.anchoranalysis.io.imagej.convert.ImageJConversionException: Creates with a message.
ImageJConversionException(String) - Constructor for exception class org.anchoranalysis.io.imagej.convert.ImageJConversionException: Creates with a message.
ImageJRasterWriter - Class in org.anchoranalysis.io.imagej.bean.stack.writer: Base class for writing a raster using ImageJ.
ImageJRasterWriter() - Constructor for class org.anchoranalysis.io.imagej.bean.stack.writer.ImageJRasterWriter
ImageLabelAnnotation - Class in org.anchoranalysis.annotation.image: A single label that is associated with an image.
ImageLabelAnnotation(String) - Constructor for class org.anchoranalysis.annotation.image.ImageLabelAnnotation: Creates a new ImageLabelAnnotation instance.
ImageLabelAnnotationReader - Class in org.anchoranalysis.annotation.io.image: Reads an ImageLabelAnnotation from the file-system.
ImageLabelAnnotationReader() - Constructor for class org.anchoranalysis.annotation.io.image.ImageLabelAnnotationReader
ImageLabelAnnotationWriter - Class in org.anchoranalysis.annotation.io.image: Writes an ImageLabelAnnotation to the file-system.
ImageLabelAnnotationWriter() - Constructor for class org.anchoranalysis.annotation.io.image.ImageLabelAnnotationWriter
ImageLabeller<T> - Class in org.anchoranalysis.plugin.image.task.bean.labeller: Associates a label with an image.
ImageLabeller() - Constructor for class org.anchoranalysis.plugin.image.task.bean.labeller.ImageLabeller
ImageLabellerStringMap<T> - Class in org.anchoranalysis.plugin.image.task.bean.labeller: Maps one set of labels to another
ImageLabellerStringMap() - Constructor for class org.anchoranalysis.plugin.image.task.bean.labeller.ImageLabellerStringMap
ImageLabellerStringMapInitialization<T> - Class in org.anchoranalysis.plugin.image.task.labeller
ImageLabellerStringMapInitialization(Map<String, String>, T) - Constructor for class org.anchoranalysis.plugin.image.task.labeller.ImageLabellerStringMapInitialization
ImageLabelStrategy - Class in org.anchoranalysis.plugin.annotation.bean.strategy: Assigns a single label per image, as a whole.
ImageLabelStrategy() - Constructor for class org.anchoranalysis.plugin.annotation.bean.strategy.ImageLabelStrategy
ImageMetadata - Class in org.anchoranalysis.image.core.stack: Information about an image, but not about the intensity or content of image voxels.
ImageMetadata(Dimensions, int, int, int, boolean, int, ImageFileAttributes, Optional<ZonedDateTime>, Optional<ImagePyramidMetadata>) - Constructor for class org.anchoranalysis.image.core.stack.ImageMetadata: Creates a new ImageMetadata instance.
ImageMetadataInput - Class in org.anchoranalysis.image.io.stack.input: An input that provides a ImageMetadata but only lazily when first called.
ImageMetadataInput(NamedFile, CheckedSupplier<ImageMetadata, ImageIOException>) - Constructor for class org.anchoranalysis.image.io.stack.input.ImageMetadataInput: Create for a particular file and metadata.
ImageMetadataReader - Class in org.anchoranalysis.image.io.bean.stack.metadata.reader: Reads an ImageMetadata from the file-system.
ImageMetadataReader() - Constructor for class org.anchoranalysis.image.io.bean.stack.metadata.reader.ImageMetadataReader
ImageMoments - Class in org.anchoranalysis.math.statistics.moment: The first moment (mean) and eigenvalues of the second moments (covariance) from a matrix of points.
ImageMoments(DoubleMatrix2D, boolean, boolean) - Constructor for class org.anchoranalysis.math.statistics.moment.ImageMoments: Calculates the second-moments from the covariance of a matrix of points.
ImageMomentsBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.moments: A base class for features that are calculated using image-moments.
ImageMomentsBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.ImageMomentsBase
ImagePyramidMetadata - Class in org.anchoranalysis.image.core.stack: Metadata to describe a pyramid-representation of images, if at least one exists in a file.
ImagePyramidMetadata(int) - Constructor for class org.anchoranalysis.image.core.stack.ImagePyramidMetadata: Creates a new ImagePyramidMetadata instance.
ImageSize - Class in org.anchoranalysis.plugin.io.bean.summarizer.image: Summarizes the size of images.
ImageSize() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.image.ImageSize
ImageSizePrereader - Class in org.anchoranalysis.plugin.image.task.stack: Reads the size of each image initially, before normal (parallel) task execution.
ImageSizePrereader(ImageMetadataReader, StackReader, OperationContext) - Constructor for class org.anchoranalysis.plugin.image.task.stack.ImageSizePrereader: Creates a new ImageSizePrereader instance.
imageSizesFor(List<StackSequenceInput>) - Method in class org.anchoranalysis.plugin.image.task.stack.ImageSizePrereader: Extract the image-size for each StackSequenceInput.
ImageSizeSuggestion - Interface in org.anchoranalysis.image.core.dimensions.size.suggestion: A suggestion on a size for an image.
ImageSizeSuggestionFactory - Class in org.anchoranalysis.image.core.dimensions.size.suggestion: Creates a ImageSizeSuggestion.
ImageTimestampsAttributes - Class in org.anchoranalysis.image.io.stack.input: This combines ImageFileAttributes plus a timestamp for image-acqusition.
ImageTimestampsAttributes(ImageFileAttributes, Optional<ZonedDateTime>) - Constructor for class org.anchoranalysis.image.io.stack.input.ImageTimestampsAttributes: Creates a new ImageTimestampsAttributes instance.
ImageTimestampsAttributesFactory - Class in org.anchoranalysis.io.bioformats.metadata: Derives ImageTimestampsAttributes from a file, additionally checking for EXIF metadata.
ImgLib2Lanczos - Class in org.anchoranalysis.image.bean.interpolator: Resizes with an interpolator that uses Lanczos resampling as implemented in Imglib2.
ImgLib2Lanczos() - Constructor for class org.anchoranalysis.image.bean.interpolator.ImgLib2Lanczos
ImgLib2Linear - Class in org.anchoranalysis.image.bean.interpolator: Resizes with an interpolator that uses linear interpolation as implemented in Imglib2.
ImgLib2Linear() - Constructor for class org.anchoranalysis.image.bean.interpolator.ImgLib2Linear
immutableAdd(Point2i, Point2i) - Static method in class org.anchoranalysis.spatial.point.Point2i: Adds two points immutably.
immutableAdd(Point3d, int, int, int) - Static method in class org.anchoranalysis.spatial.point.Point3d: Adds values to a point immutably.
immutableAdd(ReadableTuple3i, int, int, int) - Static method in class org.anchoranalysis.spatial.point.Point3i: Adds values to a tuple immutably.
immutableAdd(ReadableTuple3i, ReadableTuple3i) - Static method in class org.anchoranalysis.spatial.point.Point3i: Adds two tuples immutably.
immutableAdd(ReadableTuple3i, ReadableTuple3i, ReadableTuple3i) - Static method in class org.anchoranalysis.spatial.point.Point3i: Adds three tuples immutably.
immutableAdd(Tuple3d, Tuple3d) - Static method in class org.anchoranalysis.spatial.point.Point3d: Adds two tuples immutably.
immutableScale(ReadableTuple3i, int) - Static method in class org.anchoranalysis.spatial.point.Point3i: Multiplies each component by factor without changing any values in an existing point.
immutableScale(Tuple3d, int) - Static method in class org.anchoranalysis.spatial.point.Point3d: Scales a tuple immutably.
immutableSubtract(ReadableTuple3i, ReadableTuple3i) - Static method in class org.anchoranalysis.spatial.point.Point3i: Subtracts two tuples immutably.
immutableSubtract(Tuple3d, Tuple3d) - Static method in class org.anchoranalysis.spatial.point.Point3d: Subtracts a Tuple3d from a Tuple3d immutably.
immutableSubtract(Tuple3i, Tuple3d) - Static method in class org.anchoranalysis.spatial.point.Point3d: Subtracts a Tuple3d from a Tuple3i immutably.
imposeMinima(Channel, ObjectCollection, Optional<ObjectMask>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.MinimaImposition: Imposes minima on a channel based on seed objects and an optional containing mask.
imposeMinima(Channel, ObjectCollection, Optional<ObjectMask>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.MinimaImpositionGrayscaleReconstruction
ImposeMinima - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel: Imposes minima in seed locations on the input-channel before performing the segmentation
ImposeMinima() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.channel.ImposeMinima
imposeMinimumRadius(double) - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult: Imposes a minimum radius on all axes of the ellipsoid.
ImposeResolution - Class in org.anchoranalysis.plugin.io.bean.stack.reader: Adds an explicit Resolution to an image after it has been read.
ImposeResolution() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.reader.ImposeResolution
INCLUDE_ENTIRELY - Enum constant in enum class org.anchoranalysis.plugin.io.naming.interval.DateStyle: The entire date is included in the name: yyyy-mm-dd
INCLUDE_ENTIRELY - Enum constant in enum class org.anchoranalysis.plugin.io.naming.interval.TimeStyle: The entire time is included in the name: hh.mm.ss
IncludeBeanFactory - Class in org.anchoranalysis.bean.xml.factory: Defines an AnchorBean in a separate file on the file-system.
IncludeBeanFactory() - Constructor for class org.anchoranalysis.bean.xml.factory.IncludeBeanFactory
includeFirst() - Method in class org.anchoranalysis.image.feature.calculator.merged.MergedPairsInclude: Checks if the first object should be included.
includeFirstOrSecond() - Method in class org.anchoranalysis.image.feature.calculator.merged.MergedPairsInclude: Checks if either the first or second object should be included.
includeGroupInExperiment(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FeatureSource: Determines if group columns should be added to the CSV exports and other group exports may occur in sub-directories.
includeGroupInExperiment(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromHistogram
includeGroupInExperiment(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromImage
includeGroupInExperiment(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromImageMetadata
IncludeListBeanFactory<T> - Class in org.anchoranalysis.bean.xml.factory: Like ListBeanFactory but also includes elements in other lists defined in the include tag. as elements.
IncludeListBeanFactory() - Constructor for class org.anchoranalysis.bean.xml.factory.IncludeListBeanFactory: Default constructor.
includeMarks(VoxelizedMarkMemo, VoxelizedMarkMemo, Dimensions, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaOr
includeMarks(VoxelizedMarkMemo, VoxelizedMarkMemo, Dimensions, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaPair: Determines whether to include a pair of marks based on specific criteria.
includeMarks(VoxelizedMarkMemo, VoxelizedMarkMemo, Dimensions, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class org.anchoranalysis.mpp.feature.addcriteria.ArbitraryPointCommon
includeMarks(VoxelizedMarkMemo, VoxelizedMarkMemo, Dimensions, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class org.anchoranalysis.mpp.feature.addcriteria.BoundingBoxIntersection
IncludeMarksFailureException - Exception Class in org.anchoranalysis.mpp.feature.addcriteria: Exception thrown when there's a failure in including marks during the add criteria process.
IncludeMarksFailureException(Exception) - Constructor for exception class org.anchoranalysis.mpp.feature.addcriteria.IncludeMarksFailureException: Constructs a new exception with the specified cause.
IncludeMarksFailureException(String) - Constructor for exception class org.anchoranalysis.mpp.feature.addcriteria.IncludeMarksFailureException: Constructs a new exception with the specified detail message.
includeMerged() - Method in class org.anchoranalysis.image.feature.calculator.merged.MergedPairsInclude: Checks if the merged object should be included.
includeSecond() - Method in class org.anchoranalysis.image.feature.calculator.merged.MergedPairsInclude: Checks if the second object should be included.
IncorrectImageSizeException - Exception Class in org.anchoranalysis.image.core.dimensions: When an image has incompatible image-size with expectations.
IncorrectImageSizeException(String) - Constructor for exception class org.anchoranalysis.image.core.dimensions.IncorrectImageSizeException: Create with a message.
IncorrectVoxelTypeException - Exception Class in org.anchoranalysis.image.voxel.datatype: When an unexpected VoxelDataType is encountered.
IncorrectVoxelTypeException(String) - Constructor for exception class org.anchoranalysis.image.voxel.datatype.IncorrectVoxelTypeException: Create with only a message.
IncorrectVoxelTypeException(Throwable) - Constructor for exception class org.anchoranalysis.image.voxel.datatype.IncorrectVoxelTypeException: Create with only a cause.
IncreaseFeatureCondition - Class in org.anchoranalysis.plugin.image.object.merge.condition: An AfterCondition that checks if merging two ObjectMasks increases a specific feature value.
IncreaseFeatureCondition(FeatureEvaluator<FeatureInputSingleObject>) - Constructor for class org.anchoranalysis.plugin.image.object.merge.condition.IncreaseFeatureCondition: Creates a new IncreaseFeatureCondition instance.
increment() - Method in class org.anchoranalysis.math.arithmetic.Counter: Increases the counter by one.
increment(double) - Method in class org.anchoranalysis.math.arithmetic.RunningSum: Adds a new item to the sum, and increments the count by 1.
increment(double, long) - Method in class org.anchoranalysis.math.arithmetic.RunningSum: Increments both the sum and count by particular values.
increment(K) - Method in class org.anchoranalysis.core.collection.MapCreateCountdown: Increments the entry associated with key, creating a counter for it if none already exists.
increment(RunningSum) - Method in class org.anchoranalysis.math.arithmetic.RunningSum: Increments (adds) an existing RunningSum to the current.
increment(Point2d) - Method in class org.anchoranalysis.spatial.point.RunningSumPoint: Increments the running-sum by a Point2d.
increment(Point2i) - Method in class org.anchoranalysis.spatial.point.RunningSumPoint: Increments the running-sum by a Point2i.
increment(Point3d) - Method in class org.anchoranalysis.spatial.point.RunningSumPoint: Increments the running-sum by a Point3d.
increment(Point3i) - Method in class org.anchoranalysis.spatial.point.RunningSumPoint: Increments the running-sum by a Point3i.
increment(Tuple3d) - Method in class org.anchoranalysis.spatial.point.Tuple3d: Increments each component's value by the corresponding value in a Tuple3d.
incrementBy(int) - Method in class org.anchoranalysis.math.arithmetic.Counter: Increases the counter by a specific value.
incrementCount(T) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.image.SummarizerImageMetadata
incrementCount(T) - Method in class org.anchoranalysis.plugin.io.shared.FrequencyMap: Increments the count for a given key.
incrementCounter() - Method in class org.anchoranalysis.plugin.io.shared.RecordingCounter: Increments the counter.
incrementIndexOnly() - Method in class org.anchoranalysis.image.voxel.kernel.KernelPointCursor: Increments the current index state by one, without changing the current point state.
incrementingByOne(String, OutputterChecked) - Method in class org.anchoranalysis.image.io.stack.output.OutputSequenceStackFactory: Creates an sequence of stacks in a subdirectory with a number in the outputted file name that increments each time by one.
incrementingByOne(OutputPatternIntegerSuffix) - Method in class org.anchoranalysis.io.generator.sequence.OutputSequenceFactory: Writes elements to directory, with an incrementing integer in the filename.
incrementingByOneCurrentDirectory(String, String, int) - Method in class org.anchoranalysis.io.generator.sequence.OutputSequenceFactory: Writes elements to the current directory, with an incrementing integer in the filename.
incrementingByOneStream(OutputPatternIntegerSuffix, Stream<T>) - Method in class org.anchoranalysis.io.generator.sequence.OutputSequenceFactory: Writes file for each element in a stream with an incrementing integer sequence in the outputted file-name.
IncrementingNumber - Class in org.anchoranalysis.io.output.bean.path.prefixer: Outputs an incrementing number for each output that occurs.
IncrementingNumber() - Constructor for class org.anchoranalysis.io.output.bean.path.prefixer.IncrementingNumber
IncrementingNumber(String) - Constructor for class org.anchoranalysis.io.output.bean.path.prefixer.IncrementingNumber: Creates with a prefix.
incrementReturn() - Method in class org.anchoranalysis.math.arithmetic.Counter: Increases the counter by one, returning the previous value.
incrementValue(int) - Method in class org.anchoranalysis.math.histogram.Histogram: Increments the count for a particular value by one.
incrementValueBy(int, int) - Method in class org.anchoranalysis.math.histogram.Histogram: Increments the count for a particular value.
incrementValueBy(int, long) - Method in class org.anchoranalysis.math.histogram.Histogram: Like Histogram.incrementValueBy(int, int) but accepts a long as the increase argument.
incrementX() - Method in class org.anchoranalysis.image.voxel.kernel.KernelPointCursor: Increments the point and associated index by one in the X dimension.
incrementX() - Method in class org.anchoranalysis.spatial.point.Point2i: Increments the X component's value by one.
incrementX() - Method in class org.anchoranalysis.spatial.point.Tuple3i: Increments the X component's value by one.
incrementX(double) - Method in class org.anchoranalysis.spatial.point.Tuple3d: Increments the X component's value by a shift.
incrementX(int) - Method in class org.anchoranalysis.spatial.point.Point2i: Increments the X component's value by a shift.
incrementX(int) - Method in class org.anchoranalysis.spatial.point.Tuple3i: Increments the X component's value by a shift.
incrementXTwice() - Method in class org.anchoranalysis.image.voxel.kernel.KernelPointCursor: Increments the point and associated index by two in the X dimension.
incrementY() - Method in class org.anchoranalysis.image.voxel.kernel.KernelPointCursor: Increments the point and associated index by one in the Y dimension.
incrementY() - Method in class org.anchoranalysis.spatial.point.Point2i: Increments the Y component's value by one.
incrementY() - Method in class org.anchoranalysis.spatial.point.Tuple3i: Increments the Y component's value by one.
incrementY(double) - Method in class org.anchoranalysis.spatial.point.Tuple3d: Increments the Y component's value by a shift.
incrementY(int) - Method in class org.anchoranalysis.spatial.point.Point2i: Increments the Y component's value by a shift.
incrementY(int) - Method in class org.anchoranalysis.spatial.point.Tuple3i: Increments the Y component's value by a shift.
incrementYTwice() - Method in class org.anchoranalysis.image.voxel.kernel.KernelPointCursor: Increments the point and associated index by two in the Y dimension.
incrementZ() - Method in class org.anchoranalysis.image.voxel.kernel.KernelPointCursor: Increments the point by one in the Z dimension.
incrementZ() - Method in class org.anchoranalysis.spatial.point.Tuple3i: Increments the Z component's value by one.
incrementZ(double) - Method in class org.anchoranalysis.spatial.point.Tuple3d: Increments the Z component's value by a shift.
incrementZ(int) - Method in class org.anchoranalysis.spatial.point.Tuple3i: Increments the Z component's value by a shift.
incrementZTwice() - Method in class org.anchoranalysis.image.voxel.kernel.KernelPointCursor: Increments the point by two in the Z dimension.
IndependentChannels - Class in org.anchoranalysis.plugin.image.task.bean.format.convertstyle: Converts each channel independently and creates a single-channeled stack from the conversion.
IndependentChannels() - Constructor for class org.anchoranalysis.plugin.image.task.bean.format.convertstyle.IndependentChannels
index(int) - Method in class org.anchoranalysis.plugin.io.multifile.IntegerRange: Maps an original integer to it's index from (0..size]
index(int, int, int, Extent) - Method in enum class org.anchoranalysis.image.core.dimensions.OrientationChange: Like {#link determineOutputIndex(int,int,Extent)} but also accepts an index.
index(int, int, Extent) - Method in enum class org.anchoranalysis.image.core.dimensions.OrientationChange: Determines the index in a output-array to put an element after applying the orientation-change.
Indexable - Class in org.anchoranalysis.core.index: Holds a single-index which is hashable and comparable.
Indexable(int) - Constructor for class org.anchoranalysis.core.index.Indexable
IndexableMarksWithEnergy - Class in org.anchoranalysis.mpp.feature.energy: An Indexable object that contains MarksWithEnergyBreakdown.
IndexableMarksWithEnergy(int, MarksWithEnergyBreakdown) - Constructor for class org.anchoranalysis.mpp.feature.energy.IndexableMarksWithEnergy: Creates a new IndexableMarksWithEnergy.
IndexableOutputNameStyle - Class in org.anchoranalysis.io.output.namestyle: An output-name with an index somehow appended or prepended in a particular style.
IndexableOutputNameStyle() - Constructor for class org.anchoranalysis.io.output.namestyle.IndexableOutputNameStyle: Empty constructor, as needed for deserialization.
IndexableOutputNameStyle(String) - Constructor for class org.anchoranalysis.io.output.namestyle.IndexableOutputNameStyle: Creates with an output-name.
IndexableOutputNameStyle(IndexableOutputNameStyle) - Constructor for class org.anchoranalysis.io.output.namestyle.IndexableOutputNameStyle: Copy constructor.
IndexByChannel<T> - Class in org.anchoranalysis.mpp.index: An index structure that organizes voxel partitions by channel.
IndexByChannel() - Constructor for class org.anchoranalysis.mpp.index.IndexByChannel
IndexByRegion<T> - Class in org.anchoranalysis.mpp.index: An index structure that organizes voxel partitions by region and slice.
IndexByRegion(VoxelPartitionFactory<T>, int, int) - Constructor for class org.anchoranalysis.mpp.index.IndexByRegion: Constructs an IndexByRegion with a specified number of regions and slices.
IndexedChannel - Class in org.anchoranalysis.image.io.bean.channel: A particular Channel to be read from a file, identified by its position (index) in the file.
IndexedChannel(String, int) - Constructor for class org.anchoranalysis.image.io.bean.channel.IndexedChannel: Creates a new IndexedChannel instance.
indexedWithInteger(OutputPatternIntegerSuffix) - Method in class org.anchoranalysis.io.generator.sequence.OutputSequenceFactory: Writes elements (indexed by integers) to directory, without any order in the sequence.
indexOf(String) - Method in class org.anchoranalysis.feature.name.FeatureNameMapToIndex: The index for a particular featureName
indexOf(Mark) - Method in class org.anchoranalysis.mpp.mark.MarkCollection: Finds the index of a specific mark in the collection.
IndexRange - Interface in org.anchoranalysis.core.index.range: A range of discrete integers with a minimum and a maximum.
IndexRangeNegative - Class in org.anchoranalysis.core.index.range: Specifying a sub-range of indices, tolerating also negative indices.
IndexRangeNegative(int, int) - Constructor for class org.anchoranalysis.core.index.range.IndexRangeNegative: Create with a start and end index.
IndexRangeNegativeFactory - Class in org.anchoranalysis.core.index.range: Creates IndexRangeNegative.
IndexRangeSeek - Interface in org.anchoranalysis.core.index.range: A range of discrete integers, where one can always find the succeeding or preceding index.
InferenceModel - Interface in org.anchoranalysis.inference: A model used for inference.
InferFromHeader - Class in org.anchoranalysis.plugin.io.bean.metadata.reader: Tries to construct the ImageMetadata from EXIF and other metadata, if available, or otherwise falls back to another reader.
InferFromHeader() - Constructor for class org.anchoranalysis.plugin.io.bean.metadata.reader.InferFromHeader
InferFromHeader(ImageMetadataReader, List<HeaderFormat>) - Constructor for class org.anchoranalysis.plugin.io.bean.metadata.reader.InferFromHeader: Creates a new InferFromHeader instance.
InitializableBean<B,P> - Class in org.anchoranalysis.bean.initializable: A bean that must be initialized with some parameters before being used.
InitializableBean(BeanInitializer, InitializationParameterAssigner) - Constructor for class org.anchoranalysis.bean.initializable.InitializableBean: Creates a new InitializableBean instance.
InitializationContext - Class in org.anchoranalysis.experiment.io: Context for creating initialization-parameters.
InitializationContext(InputOutputContext) - Constructor for class org.anchoranalysis.experiment.io.InitializationContext: Create with an InputOutputContext.
InitializationContext(InputOutputContext, Optional<ImageSizeSuggestion>) - Constructor for class org.anchoranalysis.experiment.io.InitializationContext: Creates a new InitializationContext instance.
InitializationFactory - Class in org.anchoranalysis.image.feature.calculator: A factory for creating FeatureInitialization objects.
InitializationFactory - Class in org.anchoranalysis.plugin.image.task.stack: Factory for creating ImageInitialization instances.
InitializationParameterAssigner - Interface in org.anchoranalysis.bean.initializable.property: Assigns a parameter to a bean, if the bean accepts it.
InitializationWithEnergyStack - Class in org.anchoranalysis.plugin.image.task.feature: Combines ImageInitialization with an EnergyStack.
InitializationWithEnergyStack(EnergyStack, InitializationContext) - Constructor for class org.anchoranalysis.plugin.image.task.feature.InitializationWithEnergyStack: Creates a new instance with a given energy stack and initialization context.
InitializationWithEnergyStack(ImageInitialization, EnergyStack) - Constructor for class org.anchoranalysis.plugin.image.task.feature.InitializationWithEnergyStack: Creates a new InitializationWithEnergyStack instance.
initialize() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown: Initializes the energy calculations.
initialize(Path) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.BinaryOutcomeImageLabeller
initialize(Path) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageCSVLabeller
initialize(Path) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageLabeller: Initializes the labeller.
initialize(Path) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageLabellerStringMap
initialize(List<Histogram>, Optional<Dictionary>) - Method in class org.anchoranalysis.image.feature.bean.VoxelScore: Initializes the voxels-score.
initialize(List<Histogram>, Optional<Dictionary>) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevelBase
initialize(List<Histogram>, Optional<Dictionary>) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.FromDictionaryBase: Initializes the feature with histograms and a dictionary.
initialize(List<Histogram>, Optional<Dictionary>) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram
initialize(List<Histogram>, Optional<Dictionary>) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.NormalizeByMax
initialize(BeanInstanceMap) - Method in class org.anchoranalysis.io.output.bean.OutputWriteSettings: This method should be called once on this object before further calling OutputWriteSettings.getWriterInstance(java.lang.Class<? extends T>).
initialize(Logger) - Method in interface org.anchoranalysis.plugin.image.object.merge.condition.AfterCondition: Initializes the condition with a logger.
initialize(Logger) - Method in class org.anchoranalysis.plugin.image.object.merge.condition.IncreaseFeatureCondition
initialize(FeatureInitialization, Logger) - Method in interface org.anchoranalysis.feature.calculate.cache.FeatureCalculationCache: Initializes the cache.
initialize(VoxelPartitionFactory<T>, int, int, int) - Method in class org.anchoranalysis.mpp.index.IndexByChannel: Initializes the channel index with a specified number of channels, regions, and slices.
initialize(P, Logger) - Method in class org.anchoranalysis.bean.initializable.InitializableBean: Initializes the bean with the necessary parameters.
InitializeException - Exception Class in org.anchoranalysis.core.exception: An exception that occurs when initializing something, and it doesn't succeed
InitializeException(String) - Constructor for exception class org.anchoranalysis.core.exception.InitializeException: Creates with a message, but without a cause.
InitializeException(String, Throwable) - Constructor for exception class org.anchoranalysis.core.exception.InitializeException: Creates with message and cause.
InitializeException(Throwable) - Constructor for exception class org.anchoranalysis.core.exception.InitializeException: Creates with a cause, but without a message.
initializePhase(int) - Method in class org.anchoranalysis.math.optimization.HungarianAlgorithm: Initialize the next phase of the algorithm by clearing the committed workers and jobs sets and by initializing the slack arrays to the values corresponding to the specified root worker.
initializeRecursive(Logger) - Method in class org.anchoranalysis.bean.NullParametersBean: Initialize this bean and any suitable child beans.
initializeRecursive(FeatureInitialization, Logger) - Method in class org.anchoranalysis.feature.bean.list.FeatureList: Initializes all features in the list, and recursively any features they contain.
initializeRecursive(FeatureInitialization, Logger) - Method in class org.anchoranalysis.feature.shared.SharedFeaturesSubset: Initialize all features in this instance, recursively also initializating any child-features.
initializeRecursive(P, Logger) - Method in class org.anchoranalysis.bean.initializable.InitializableBean: Initializes this object, and all children objects, so long as they have P once a Bean doesn't have P, the children are not evaluated.
initializerForMarksBeans() - Static method in class org.anchoranalysis.mpp.bean.MarksBean: Creates a property-initializer for MPP-Beans.
initRecursiveWithInitializer(BeanInitializer<?>, Logger) - Method in class org.anchoranalysis.bean.initializable.InitializableBean: Initializes the bean and recursively all contained beans (who have compatible initialization requirements)
initSource(int, int) - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.ProcessChangedPointAbsoluteMasked: The value and offset for the source point (around which we process neighbors).
initSource(int, int) - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsolute: The value and offset for the source point (around which we process neighbors).
initSource(int, int) - Method in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsoluteWithSlidingBuffer
initSource(Point3i, int, int) - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighbor: Specify the source-point (of which all the processed points are neighbors).
initUpdatableMarks(MemoForIndex, EnergyStack, Logger, SharedFeatures) - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
initUpdatableMarks(MemoForIndex, EnergyStack, Logger, SharedFeatures) - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedPairs
initUpdatableMarks(MemoForIndex, EnergyStack, Logger, SharedFeatures) - Method in interface org.anchoranalysis.mpp.mark.UpdatableMarks: Initializes the updatable marks with necessary context.
input() - Method in class org.anchoranalysis.experiment.arguments.ExecutionArguments: Arguments to help determine the input to the experiment.
INPUT_IMAGE - Static variable in class org.anchoranalysis.image.io.stack.StackIdentifiers: The image used as the primary input for a task.
InputArguments - Class in org.anchoranalysis.experiment.arguments: Arguments that can further specify an experiment's input in addition to its bean specification.
InputArguments() - Constructor for class org.anchoranalysis.experiment.arguments.InputArguments
InputBound<T,S> - Class in org.anchoranalysis.experiment.task: Input for executing a task, associated with shared-state and other parameters.
InputBound(T, S, boolean, InputOutputContextStateful, InputOutputContextStateful) - Constructor for class org.anchoranalysis.experiment.task.InputBound: Creates a new InputBound instance.
inputContextParameters() - Method in class org.anchoranalysis.experiment.arguments.ExecutionArguments: Additional parameters that offer context for many beans that provide input-functions.
InputContextParameters - Class in org.anchoranalysis.io.input: Additional parameters that offer context for many beans that provide input-functions.
InputContextParameters() - Constructor for class org.anchoranalysis.io.input.InputContextParameters
InputFactory - Class in org.anchoranalysis.launcher.executor.selectparam.path: SelectParam<Path> factory for inputs.
InputFromManager - Interface in org.anchoranalysis.io.input: One particular input for processing.
InputFromManagerDelegate<T> - Class in org.anchoranalysis.io.input: A base class for InputFromManager-implementing classes that delegate to another.
InputFromManagerDelegate(T) - Constructor for class org.anchoranalysis.io.input.InputFromManagerDelegate
InputGrouper - Interface in org.anchoranalysis.io.input.grouper: Derives a grouping key from an input.
InputManager<T> - Class in org.anchoranalysis.io.input.bean: Base class for describing the inputs.
InputManager() - Constructor for class org.anchoranalysis.io.input.bean.InputManager
InputManagerParameters - Class in org.anchoranalysis.io.input.bean: Parameters passed to an InputManager to generate input-objects.
InputManagerParameters(Logger) - Constructor for class org.anchoranalysis.io.input.bean.InputManagerParameters: Create with only a logger, and using sensible default values for the other fields.
InputManagerParameters(OperationContext) - Constructor for class org.anchoranalysis.io.input.bean.InputManagerParameters: Create with only a OperationContext, and using sensible default values for the other fields.
InputManagerParameters(InputContextParameters, OperationContext) - Constructor for class org.anchoranalysis.io.input.bean.InputManagerParameters: Creates a new InputManagerParameters instance.
InputManagerUnary<T> - Class in org.anchoranalysis.io.input.bean: Base class for an InputManager that delegates to another InputManager with the same input-type.
InputManagerUnary() - Constructor for class org.anchoranalysis.io.input.bean.InputManagerUnary
InputManagerWithStackReader<T> - Class in org.anchoranalysis.image.io.bean.stack.reader: Extends an InputManager to add a StackReader bean property.
InputManagerWithStackReader() - Constructor for class org.anchoranalysis.image.io.bean.stack.reader.InputManagerWithStackReader
inputName() - Method in class org.anchoranalysis.image.inference.bean.segment.instance.SegmentStackIntoObjectsScaleDecode: The name of the tensor in the model which the input-image is mapped to.
inputName() - Method in class org.anchoranalysis.mpp.io.input.StackWithMap: Gets the input name.
inputName() - Method in class org.anchoranalysis.plugin.onnx.bean.object.segment.stack.SegmentObjectsFromONNXModel
inputName() - Method in class org.anchoranalysis.plugin.opencv.bean.object.segment.stack.SegmentObjectsFromTensorFlowModel
inputOutput(ExecutionArguments, OutputterChecked) - Method in class org.anchoranalysis.experiment.task.ExperimentFeedbackContext: Derive an InputOutputContextStateful from the current context.
InputOutputContext - Interface in org.anchoranalysis.io.output.outputter: A context for performing input generally and outputting to a particular output-directory.
InputOutputContextFixture - Class in org.anchoranalysis.test.image: A fixture for creating InputOutputContext instances for testing purposes.
InputOutputContextStateful - Class in org.anchoranalysis.experiment.task: This exists as an implementation of InputOutputContext that exposes a StatefulMessageLogger.
InputOutputContextStateful(ExecutionArguments, Outputter, ExecutionTimeRecorder, StatefulMessageLogger, ErrorReporter) - Constructor for class org.anchoranalysis.experiment.task.InputOutputContextStateful: Creates with initialization arguments.
InputOutputContextSubdirectoryCache - Class in org.anchoranalysis.io.output.outputter: Caches a InputOutputContext for each subdirectory as they are created.
InputOutputContextSubdirectoryCache(InputOutputContext, boolean) - Constructor for class org.anchoranalysis.io.output.outputter.InputOutputContextSubdirectoryCache: Creates a new InputOutputContextSubdirectoryCache instance.
InputOutputExperiment<T,S> - Class in org.anchoranalysis.experiment.bean.io: An experiment that uses both an InputManager to specify inputs and a OutputManager to specify outputting.
InputOutputExperiment() - Constructor for class org.anchoranalysis.experiment.bean.io.InputOutputExperiment
InputReadFailedException - Exception Class in org.anchoranalysis.io.input: When an error occurs reading an input.
InputReadFailedException(String) - Constructor for exception class org.anchoranalysis.io.input.InputReadFailedException: Create with a message only.
InputReadFailedException(String, Throwable) - Constructor for exception class org.anchoranalysis.io.input.InputReadFailedException: Create with a message and cause.
InputReadFailedException(Throwable) - Constructor for exception class org.anchoranalysis.io.input.InputReadFailedException: Create with a cause only.
inputs() - Method in class org.anchoranalysis.io.input.InputsWithDirectory: The inputs.
inputs(InputManagerParameters) - Method in class org.anchoranalysis.annotation.io.bean.AnnotationInputManager
inputs(InputManagerParameters) - Method in class org.anchoranalysis.io.input.bean.InputManager: Creates a list of inputs given particular parameters.
inputs(InputManagerParameters) - Method in class org.anchoranalysis.io.input.bean.InputManagerUnary
inputs(InputManagerParameters) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
inputs(InputManagerParameters) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager
inputs(InputManagerParameters) - Method in class org.anchoranalysis.plugin.io.bean.file.group.GroupFiles
inputs(InputManagerParameters) - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannels
inputs(InputManagerParameters) - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
inputs(InputManagerParameters) - Method in class org.anchoranalysis.plugin.io.bean.input.Concatenate
inputs(InputManagerParameters) - Method in class org.anchoranalysis.plugin.io.bean.input.files.NamedFiles
inputs(InputManagerParameters) - Method in class org.anchoranalysis.plugin.io.bean.input.files.NamedFilesWithDirectory
inputs(InputManagerParameters) - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertNamedChannelsToStack
inputs(InputManagerParameters) - Method in class org.anchoranalysis.plugin.io.bean.input.stack.Stacks
inputSelectParam(CommandLine) - Static method in class org.anchoranalysis.launcher.executor.selectparam.SelectParamFactory: Creates a SelectParam for input selection.
inputsFromDelegate(InputsWithDirectory<T>, InputManagerParameters) - Method in class org.anchoranalysis.io.input.bean.InputManagerUnary: Calculates the inputs to return given the inputs from the delegate.
inputsFromDelegate(InputsWithDirectory<T>, InputManagerParameters) - Method in class org.anchoranalysis.plugin.io.bean.input.BranchIfDebug
inputsFromDelegate(InputsWithDirectory<T>, InputManagerParameters) - Method in class org.anchoranalysis.plugin.io.bean.input.Exclude
inputsFromDelegate(InputsWithDirectory<T>, InputManagerParameters) - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterCSVColumn
inputsFromDelegate(InputsWithDirectory<T>, InputManagerParameters) - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterDescriptiveName
inputsFromDelegate(InputsWithDirectory<T>, InputManagerParameters) - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterIfDebug
inputsFromDelegate(InputsWithDirectory<T>, InputManagerParameters) - Method in class org.anchoranalysis.plugin.io.bean.input.Limit
inputsFromDelegate(InputsWithDirectory<T>, InputManagerParameters) - Method in class org.anchoranalysis.plugin.io.bean.input.LimitIfRequested
inputsFromDelegate(InputsWithDirectory<T>, InputManagerParameters) - Method in class org.anchoranalysis.plugin.io.bean.input.Shuffle
inputsFromDelegate(InputsWithDirectory<T>, InputManagerParameters) - Method in class org.anchoranalysis.plugin.io.bean.input.ShuffleIfRequested
inputsFromDelegate(InputsWithDirectory<T>, InputManagerParameters) - Method in class org.anchoranalysis.plugin.io.bean.input.SortAlphabetically
InputsWithDirectory<T> - Class in org.anchoranalysis.io.input: All inputs for an experiment, together with any parent directory which is specified as a parent for these inputs.
InputsWithDirectory(List<T>) - Constructor for class org.anchoranalysis.io.input.InputsWithDirectory: Creates without any parent directory.
InputsWithDirectory(List<T>, Optional<Path>) - Constructor for class org.anchoranalysis.io.input.InputsWithDirectory: Creates a new InputsWithDirectory instance.
inputType() - Method in class org.anchoranalysis.feature.bean.Feature: The class corresponding to feature input-type.
inputType() - Method in class org.anchoranalysis.feature.bean.operator.FeatureBinary
inputType() - Method in class org.anchoranalysis.feature.bean.operator.FeatureFromList
inputType() - Method in class org.anchoranalysis.feature.bean.operator.FeatureGeneric
inputType() - Method in class org.anchoranalysis.feature.bean.operator.FeatureUnary
inputType() - Method in class org.anchoranalysis.feature.bean.results.FeatureResults
inputType() - Method in class org.anchoranalysis.image.feature.bean.FeatureEnergy
inputType() - Method in class org.anchoranalysis.image.feature.bean.FeatureHistogram
inputType() - Method in class org.anchoranalysis.image.feature.bean.FeatureImageMetadata
inputType() - Method in class org.anchoranalysis.image.feature.bean.FeatureStack
inputType() - Method in class org.anchoranalysis.image.feature.bean.object.collection.FeatureObjectCollection
inputType() - Method in class org.anchoranalysis.image.feature.bean.object.pair.FeaturePairObjects
inputType() - Method in class org.anchoranalysis.image.feature.bean.object.single.FeatureSingleObject
inputType() - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.AsSingle
inputType() - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.FeatureAllMemo
inputType() - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.FeaturePairMemo
inputType() - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.FeatureSingleMemo
inputType() - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.FromDimensionsBase
inputType() - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.FeatureSingleObjectFromShared
inputTypesExpected() - Method in class org.anchoranalysis.experiment.bean.task.Task: Highest class(es) that will function as a valid input.
inputTypesExpected() - Method in class org.anchoranalysis.launcher.run.tasks.HelloWorld
inputTypesExpected() - Method in class org.anchoranalysis.plugin.annotation.bean.aggregate.AggregateAnnotations
inputTypesExpected() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
inputTypesExpected() - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage
inputTypesExpected() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures
inputTypesExpected() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FeatureSource: Specifies the highest class(es) that will function as a valid input.
inputTypesExpected() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromHistogram
inputTypesExpected() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromImage
inputTypesExpected() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromImageMetadata
inputTypesExpected() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase
inputTypesExpected() - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageAssignLabel
inputTypesExpected() - Method in class org.anchoranalysis.plugin.image.task.bean.RasterTask
inputTypesExpected() - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage
inputTypesExpected() - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel
inputTypesExpected() - Method in class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice
inputTypesExpected() - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
inputTypesExpected() - Method in class org.anchoranalysis.plugin.io.bean.task.CopyFiles
inputTypesExpected() - Method in class org.anchoranalysis.plugin.io.bean.task.SummarizeInputs
inputTypesExpected() - Method in class org.anchoranalysis.plugin.mpp.bean.convert.ConvertNamedChannels
inputTypesExpected() - Method in class org.anchoranalysis.plugin.mpp.bean.define.Develop
InputTypesExpected - Class in org.anchoranalysis.experiment.task: A list of base (parent) classes for input-types that a task expects.
InputTypesExpected(Class<? extends InputFromManager>) - Constructor for class org.anchoranalysis.experiment.task.InputTypesExpected: Creates with the class of the input-type.
insertBeginning(String) - Method in class org.anchoranalysis.feature.name.FeatureNameList: Inserts a new feature-name at the beginning of the list.
insertBeginning(String[]) - Method in class org.anchoranalysis.feature.name.FeatureNameList: Inserts new feature-names at the beginning of the list.
InsertRegExGroups - Class in org.anchoranalysis.plugin.io.bean.path.derive: Generates an out string where $digit$ is replaced with the #digit group from a regex
InsertRegExGroups() - Constructor for class org.anchoranalysis.plugin.io.bean.path.derive.InsertRegExGroups
InsertRegExGroups(RegEx, String) - Constructor for class org.anchoranalysis.plugin.io.bean.path.derive.InsertRegExGroups: Creates a new InsertRegExGroups instance.
instance() - Static method in class org.anchoranalysis.bean.initializable.parameters.NullInitialization: Singleton instance of NullInitialization.
instance() - Static method in class org.anchoranalysis.core.time.ExecutionTimeRecorderIgnore: Singleton instance.
instance() - Static method in class org.anchoranalysis.feature.input.FeatureInputNull: A singleton instance.
instance() - Static method in class org.anchoranalysis.feature.session.cache.finder.DefaultChildCacheFinder: Singleton instance of DefaultChildCacheFinder.
instance() - Static method in class org.anchoranalysis.image.core.channel.factory.ChannelFactory: Singleton instance of ChannelFactory.
instance() - Static method in class org.anchoranalysis.image.voxel.factory.VoxelsFactory: Singleton instance.
instance() - Static method in class org.anchoranalysis.io.bioformats.ConfigureBioformatsLogging: A singleton instance.
instance() - Static method in class org.anchoranalysis.mpp.bean.regionmap.RegionMapSingleton: Gets the singleton instance of RegionMap.
instance() - Static method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeNull: Gets the singleton instance of ErrorNodeNull.
instance() - Static method in class org.anchoranalysis.plugin.io.input.path.RootPathMap
INSTANCE - Static variable in class org.anchoranalysis.experiment.task.NoSharedState: A singleton instance.
INSTANCE - Static variable in class org.anchoranalysis.image.voxel.datatype.FloatVoxelType: A singleton instance of the type.
INSTANCE - Static variable in class org.anchoranalysis.image.voxel.datatype.SignedShortVoxelType: A singleton instance of the type.
INSTANCE - Static variable in class org.anchoranalysis.image.voxel.datatype.UnsignedByteVoxelType: A singleton instance of the type.
INSTANCE - Static variable in class org.anchoranalysis.image.voxel.datatype.UnsignedIntVoxelType: A singleton instance of the type.
INSTANCE - Static variable in class org.anchoranalysis.image.voxel.datatype.UnsignedShortVoxelType: A singleton instance of the type.
INSTANCE - Static variable in class org.anchoranalysis.io.output.bean.enabled.All: A singleton instance of All.
INSTANCE - Static variable in class org.anchoranalysis.io.output.bean.enabled.IgnoreUnderscorePrefix: A singleton instance of IgnoreUnderscorePrefix.
INSTANCE - Static variable in class org.anchoranalysis.io.output.bean.enabled.None: A singleton instance of None.
INSTANCE - Static variable in class org.anchoranalysis.io.output.bean.rules.Permissive: A singleton instance of Permissive.
INSTANCE - Static variable in class org.anchoranalysis.test.image.ResolutionFixture: A pre-created Resolution instance for use in tests.
InstanceSegmentationTestBase - Class in org.anchoranalysis.test.image.segment: Base class for testing implementations of SegmentStackIntoObjectsPooled.
InstanceSegmentationTestBase() - Constructor for class org.anchoranalysis.test.image.segment.InstanceSegmentationTestBase
InsufficientPointsException - Exception Class in org.anchoranalysis.mpp.bean.points.fitter: Exception thrown when there are not enough points to perform a fitting operation.
InsufficientPointsException() - Constructor for exception class org.anchoranalysis.mpp.bean.points.fitter.InsufficientPointsException: Constructs an InsufficientPointsException with a default error message.
InsufficientPointsException(String) - Constructor for exception class org.anchoranalysis.mpp.bean.points.fitter.InsufficientPointsException: Constructs an InsufficientPointsException with a specified error message.
InsufficientPointsException(String, Throwable) - Constructor for exception class org.anchoranalysis.mpp.bean.points.fitter.InsufficientPointsException: Constructs an InsufficientPointsException with a specified error message and cause.
InsufficientPointsException(Throwable) - Constructor for exception class org.anchoranalysis.mpp.bean.points.fitter.InsufficientPointsException: Constructs an InsufficientPointsException with a specified cause.
IntBinaryPredicate - Interface in org.anchoranalysis.core.functional.unchecked: Like IntPredicate but accepts two arguments.
IntegerList - Class in org.anchoranalysis.bean.primitive: A bean defining a list of Integers.
IntegerList(Integer...) - Constructor for class org.anchoranalysis.bean.primitive.IntegerList: Constructs with one or more values added to the list.
IntegerListFactory - Class in org.anchoranalysis.bean.xml.factory.primitive: Creates a IntegerList from a XML element.
IntegerListFactory() - Constructor for class org.anchoranalysis.bean.xml.factory.primitive.IntegerListFactory
IntegerRange - Class in org.anchoranalysis.plugin.io.multifile
IntegerRange(int) - Constructor for class org.anchoranalysis.plugin.io.multifile.IntegerRange
IntegerRange(int, int) - Constructor for class org.anchoranalysis.plugin.io.multifile.IntegerRange
IntegerSet - Class in org.anchoranalysis.bean.primitive: A bean defining a set of Integers.
IntegerSet() - Constructor for class org.anchoranalysis.bean.primitive.IntegerSet
IntegerSet(Integer...) - Constructor for class org.anchoranalysis.bean.primitive.IntegerSet: Constructs with one or more values added to the list.
IntegerSetFactory - Class in org.anchoranalysis.bean.xml.factory.primitive: Creates a IntegerSet from a XML element.
IntegerSetFactory() - Constructor for class org.anchoranalysis.bean.xml.factory.primitive.IntegerSetFactory
IntegerSuffixOutputNameStyle - Class in org.anchoranalysis.io.output.namestyle: Outputs a file-name involving an integer suffix of length numberDigits with leading zeros.
IntegerSuffixOutputNameStyle() - Constructor for class org.anchoranalysis.io.output.namestyle.IntegerSuffixOutputNameStyle: Empty constructor, as needed for deserialization.
IntegerSuffixOutputNameStyle(String, int) - Constructor for class org.anchoranalysis.io.output.namestyle.IntegerSuffixOutputNameStyle: Creates with an output-name and a number of digits.
IntegerSuffixOutputNameStyle(String, String, int) - Constructor for class org.anchoranalysis.io.output.namestyle.IntegerSuffixOutputNameStyle: Creates with an output-name, a prefix, and a number of digits.
Intensity - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity: Calculates a statistic from the intensity values covered by a single object-mask in a channel.
Intensity - Class in org.anchoranalysis.plugin.image.feature.bean.stack.intensity: The intensity of a particular channel of the stack, by default the mean-intensity.
Intensity() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.Intensity
Intensity() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.stack.intensity.Intensity
IntensityGradientBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient: Base class for features that calculate intensity gradients from multiple channels.
IntensityGradientBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.IntensityGradientBase
IntensityGreaterEqualThan - Class in org.anchoranalysis.plugin.image.bean.object.filter.independent: Only keep objects where at least one voxel (on a particular channel) has intensity greater or equal to a threshold.
IntensityGreaterEqualThan() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntensityGreaterEqualThan
intensityMax(Voxels<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll: Finds the maximum intensity-value (as an int) among all voxels.
IntensityMeanCalculator - Class in org.anchoranalysis.plugin.image.intensity: Utility class for calculating mean intensity of objects in a channel.
IntensityMeanMaxSlice - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity: Calculates the maximum mean intensity across all slices of an object in a channel.
IntensityMeanMaxSlice() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanMaxSlice
IntensityMeanShell - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity: Constructs a 'shell' around an object by a number of dilation/erosion operations (not including the original object-mask) and measures the mean intensity of this shell
IntensityMeanShell() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShell
IntensityMeanShellBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity: Constructs a shell around an object-mask using a standard dilation and erosion process.
IntensityMeanShellBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase
IntensityMeanShellMaxSlice - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity: Constructs a 'shell' around an object by a number of dilation/erosion operations (not including the original object-mask) and measures the mean intensity of this shell
IntensityMeanShellMaxSlice() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellMaxSlice
intensityMin(Voxels<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll: Finds the minimum intensity-value (as an int) among all voxels.
intensityMinMax(Voxels<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll: Finds the maximum intensity-value (as an int) among all voxels.
IntensityMoments - Class in org.anchoranalysis.plugin.image.feature.bean.list: Calculate various moment-related statistics about the intensity of each channel of an image.
IntensityMoments() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.IntensityMoments
IntensityQuantiles - Class in org.anchoranalysis.image.bean.displayer: Implementation of StackDisplayer that converts to unsigned-8bit by taking the upper and lower quantiles of the intensity range.
IntensityQuantiles() - Constructor for class org.anchoranalysis.image.bean.displayer.IntensityQuantiles
IntensityRange - Class in org.anchoranalysis.image.core.channel.convert.attached.channel: Converts a Channel to UnsignedByteBuffer by scaling against the maximum intensity value that appears in it.
IntensityRange() - Constructor for class org.anchoranalysis.image.core.channel.convert.attached.channel.IntensityRange: Default constructor.
Interpolator - Class in org.anchoranalysis.image.bean.interpolator: Defines a particular type of interpolation method that can be used for resizing images.
Interpolator() - Constructor for class org.anchoranalysis.image.bean.interpolator.Interpolator
intersect(ObjectMask, Extent) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Intersects this object-mask with another
IntersectingCircleObjectsFixture - Class in org.anchoranalysis.test.feature.plugins.objects: A fixture for generating collections of intersecting and non-intersecting circular objects.
IntersectingObjects<T> - Class in org.anchoranalysis.image.voxel.object: A data-structure to efficiently determine which object-masks intersect in a collection.
IntersectingObjects(Collection<T>, Function<T, ObjectMask>) - Constructor for class org.anchoranalysis.image.voxel.object.IntersectingObjects: Creates an r-tree for particular objects, as extracted from elements.
intersection() - Method in class org.anchoranalysis.spatial.box.BoundingBox: For evaluating the intersection between this bounding-box and others.
Intersection - Class in org.anchoranalysis.plugin.image.bean.object.match: An ObjectMatcher that matches objects based on their intersection with a provided set of objects.
Intersection - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair: Finds the intersection of two objects and calculates a feature on it
Intersection() - Constructor for class org.anchoranalysis.plugin.image.bean.object.match.Intersection
Intersection() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.pair.Intersection
IntersectionOverUnion - Class in org.anchoranalysis.spatial.box: Calculates the intersection-over-union score for a pair of bounding-boxes.
intersectsWith(double, double) - Method in class org.anchoranalysis.spatial.rtree.IntervalRTree: Which bounding-boxes intersect with another specific bounding box?
intersectsWith(ObjectMask) - Method in class org.anchoranalysis.image.voxel.object.IntersectingObjects: All elements that intersect with a particular object.
intersectsWith(BoundingBox) - Method in class org.anchoranalysis.image.voxel.object.IntersectingObjects: All elements that intersect with a particular bounding box.
intersectsWith(BoundingBox) - Method in class org.anchoranalysis.spatial.rtree.BoundingBoxRTree: Which bounding-boxes intersect with another specific bounding box?
IntersectsWith - Class in org.anchoranalysis.plugin.image.bean.object.filter.independent: Keeps objects which intersects with ANY ONE of a collection of other objects.
IntersectsWith() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntersectsWith
IntersectsWithContainer - Class in org.anchoranalysis.plugin.image.bean.object.provider.filter: Returns only the objects that intersect with at least one object in the container
IntersectsWithContainer() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.filter.IntersectsWithContainer
intersectsWithStream(double, double) - Method in class org.anchoranalysis.spatial.rtree.IntervalRTree: Like IntervalRTree.intersectsWith(double, double) but returns a Stream instead of a Set.
intersectsWithStream(Rectangle) - Method in class org.anchoranalysis.spatial.rtree.RTree: A stream of the elements that a rectangle intersects with.
intersectsWithStream(ObjectMask) - Method in class org.anchoranalysis.image.voxel.object.IntersectingObjects: Like IntersectingObjects.intersectsWith(ObjectMask) but returns the objects as a Stream rather than a Set.
intersectsWithStream(BoundingBox) - Method in class org.anchoranalysis.spatial.rtree.BoundingBoxRTree: Like BoundingBoxRTree.intersectsWith(BoundingBox) but returns a Stream instead of a Set.
intersectWith(Extent) - Method in class org.anchoranalysis.spatial.box.Extent: Intersects this extent with another (i.e. takes the smaller value in each dimension).
IntervalRTree<T> - Class in org.anchoranalysis.spatial.rtree: An R-Tree that contains items, each with an associated one-dimensional interval.
IntervalRTree() - Constructor for class org.anchoranalysis.spatial.rtree.IntervalRTree: Creates an empty R-Tree.
IntervalRTree(int) - Constructor for class org.anchoranalysis.spatial.rtree.IntervalRTree: Creates an empty R-Tree with a specified number of children.
intFromDouble(Point3d, boolean) - Static method in class org.anchoranalysis.spatial.point.PointConverter: Convert a Point3d to a Point3i, optionally rounding values.
intFromDoubleCeil(Point3d) - Static method in class org.anchoranalysis.spatial.point.PointConverter: Convert a Point3d to a Point3i using the ceiling operation.
intFromDoubleFloor(Point2d) - Static method in class org.anchoranalysis.spatial.point.PointConverter: Convert a Point2d to a Point2i using the floor operation.
intFromDoubleFloor(Point3d) - Static method in class org.anchoranalysis.spatial.point.PointConverter: Convert a Point3d to a Point3i using the floor operation.
intFromFloat(Point3f, boolean) - Static method in class org.anchoranalysis.spatial.point.PointConverter: Convert a Point3f to a Point3i, optionally rounding values.
IntToFloatFunction - Interface in org.anchoranalysis.core.functional.unchecked: Represents a function that accepts an int-valued argument and produces a float-valued result.
INVALID_AXIS_INDEX - Static variable in class org.anchoranalysis.spatial.axis.AxisConverter: Human-readable error message used when an invalid int-value for axis is passed.
INVALID_AXIS_STRING - Static variable in class org.anchoranalysis.spatial.axis.AxisConverter: Human-readable error message used when an invalid String-value for axis is passed.
invalidate() - Method in interface org.anchoranalysis.feature.calculate.cache.FeatureCalculationCache: Invalidates existing caches so the next calculation occurs freshly.
invalidate() - Method in interface org.anchoranalysis.feature.calculate.cache.ResettableCalculation: Resets the cached-calculation, so the next call to doOperationWithParameters() is guaranteed to calculation the operation, and store the value in the cache.
invalidate() - Method in class org.anchoranalysis.feature.calculate.part.CalculationPart
invalidate() - Method in class org.anchoranalysis.feature.calculate.part.CalculationPartMap: Invalidates the cache, removing any items already stored.
invalidateExcept(Set<ChildCacheName>) - Method in interface org.anchoranalysis.feature.calculate.cache.FeatureCalculationCache: Invalidates existing caches so the next calculations occur freshly - except some particular child-caches who are not invalidated.
InvalidPathArgumentException - Exception Class in org.anchoranalysis.launcher.executor.selectparam.path.convert: An exception thrown if an invalid path is inputted as an argument.
InvalidPathArgumentException(String) - Constructor for exception class org.anchoranalysis.launcher.executor.selectparam.path.convert.InvalidPathArgumentException: Creates an exception with a custom message.
InvalidPathArgumentException(String, InvalidPathException) - Constructor for exception class org.anchoranalysis.launcher.executor.selectparam.path.convert.InvalidPathArgumentException: Creates an exception for an invalid path argument.
invert() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels: Changes the off state to be the on state and vice-versa.
invert() - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte: Inverts the values so off becomes on, and vice-versa.
invert() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Produces a new object-mask that uses the same voxel-buffer but switches the off and on mapping.
invert() - Method in class org.anchoranalysis.spatial.scale.ScaleFactor: Build a new scale factor where each dimension is set to the reciprocal of its current value.
invert(Mask) - Static method in class org.anchoranalysis.image.core.mask.MaskInverter: Modifies a mask so that off voxels become on voxels and vice versa.
Invert - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic: Inverts the intensity values of a Channel by subtracting each voxel from the maximum value for the channel's data type.
Invert - Class in org.anchoranalysis.plugin.image.bean.mask.provider: Switches on voxels to off and vice-versa.
Invert - Class in org.anchoranalysis.plugin.image.bean.scale: Invert the ScaleFactor calculated by the scaleCalculator delegate.
Invert - Class in org.anchoranalysis.plugin.image.bean.segment.binary: Performs a segmentation and inverts and on and off bytes
Invert() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.Invert
Invert() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.Invert
Invert() - Constructor for class org.anchoranalysis.plugin.image.bean.scale.Invert
Invert() - Constructor for class org.anchoranalysis.plugin.image.bean.segment.binary.Invert
InvertedMax<T> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic: Finds the repciprocal (multiplicate inverse), but imposes a maximum ceiling via a constant.
InvertedMax() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.InvertedMax
invertObjectDuplicate(ObjectMask) - Static method in class org.anchoranalysis.image.core.mask.MaskInverter: Creates a new object-mask where off voxels become on voxels and vice versa.
isAcceptDirectoryErrors() - Method in class org.anchoranalysis.io.input.bean.files.SearchDirectory: If true, continues when a directory-access-error occurs (logging it), otherwise throws an exception.
isAccepted() - Method in class org.anchoranalysis.annotation.mark.DualMarksAnnotation: Whether the the annotation was marked as accepted by the annotator?
isAcceptMissingResolution() - Method in class org.anchoranalysis.image.feature.bean.physical.WithResolutionBase: Whether to return Double.NaN (if true) or throw an exception (if false) when image resolution is missing.
isAcceptMissingResolution() - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.VoxelPhysicalSize: Whether to throw an exception (if true) if image-resolution is missing, or return Double.Nan (if false).
isAcceptNoResolution() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ReadVoxelExtentXml: If false, an exception is thrown if the resolution file is missing for a particular image.
isAddName() - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
isAddOne() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Quantile
isAlways2D() - Method in class org.anchoranalysis.image.io.stack.output.StackWriteAttributes: Whether the output is guaranteed to only ever 2D i.e. maximally one z-slice?
isAnyChannel3D() - Method in class org.anchoranalysis.image.core.stack.Stack: Is at least one channel 3D?
isAnyChannel3D() - Method in class org.anchoranalysis.image.core.stack.StackNotUniformSized: Is at least one channel 3D?
isApplyResolution() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D: If true, multiplies the values by the x-resolution, if it exists.
isApplyToPath() - Method in class org.anchoranalysis.io.input.bean.path.matcher.MatchRegularExpression: If true, the filter is applied to the path, not just the filename (using forward slashes as directory separators)
isAsPercentage() - Method in class org.anchoranalysis.feature.bean.results.Quantile: If true, the quantile is interpreted as a percentage rather than a decimal.
isAtLeastOnePositive() - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations: Checks if at least one of iterationsDilation and iterationsErosion is more than 0.
isAvoidBulletOnFirst() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerAggregate: Iff true no bullet is added for the very first-item in the list
isAvoidDivideByZero() - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.Divide: If true, returns a predefined value when division by zero occurs instead of throwing an exception.
isAvoidOverlappingObjects() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors: If true, no overlapping objects are treated as pairs
isBigNeighborhood() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Dilate
isBigNeighborhood() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.ConnectedComponentsFromMask: If true uses 8 neighborhood rather than 4 neighborhood etc. in 2D, and similar in 3D
isBigNeighborhood() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.DecomposeIntoConnectedComponents: if true, uses 8 neighborhood instead of 4, and similarly in 3d
isBigNeighborhood() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Dilate
isBinary() - Method in class org.anchoranalysis.image.io.stack.output.StackWriteAttributes: Whether all channels represent a binary image.
isBinary() - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage: Iff true the image to be scaled is treated as a binary-mask, and interpolation during scaling ensures only two binary-values are outputted.
isBit0() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership: Flag for region 0.
isBit1() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership: Flag for region 1.
isBit2() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership: Flag for region 2.
isBit3() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership: Flag for region 3.
isBit4() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership: Flag for region 4.
isBit5() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership: Flag for region 5.
isBit6() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership: Flag for region 6.
isBit7() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership: Flag for region 7.
isBold() - Method in class org.anchoranalysis.image.io.bean.stack.combine.TextStyle: Whether to bold the drawn text
isBoundingBoxAtBorder(BoundingBox, Extent) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.border.AtBorderBase: Checks if the bounding box of an object is at the border of the image.
isBoundingBoxAtBorder(BoundingBox, Extent) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.border.AtBorderXY
isBoundingBoxAtBorder(BoundingBox, Extent) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.border.AtBorderZ
isBufferOff(UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.kernel.KernelPointCursor: Is the value at the current index in this buffer corresponding to an off state?
isBufferOn(UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.kernel.KernelPointCursor: Is the value at the current index in this buffer corresponding to an on state?
isBySlices() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.ConnectedComponentsFromMask
isBytewiseCompare() - Method in class org.anchoranalysis.test.image.rasterwriter.comparison.ComparisonPlan
isCalledRegisterAllPackage() - Static method in class org.anchoranalysis.bean.xml.RegisterBeanFactories: Has the method RegisterBeanFactories.registerAllPackageBeanFactories() already been called?
isCaseSensitive() - Method in class org.anchoranalysis.plugin.io.bean.file.namer.patternspan.PatternSpan: Iff true, a case sensitive search is used to match patterns.
isChangeExisting() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.convert.ConvertBase: If true, the existing channel can be changed.
isClearOutsideMask() - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.ThresholdAgainstChannel
isCompatibleWith(Class<? extends FeatureInput>, Class<? extends FeatureInput>) - Static method in class org.anchoranalysis.feature.input.FeatureInputType: Can these parameters be used with a particular feature?
isCompatibleWith(Mark) - Method in interface org.anchoranalysis.mpp.mark.CompatibleWithMark: Tests if the implementing object is compatible with a mark of a particular type.
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.points.bean.FitPoints
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresEllipseFitter
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresEllipsoidFitter
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.points.bean.fitter.Reference
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.points.bean.fitter.ReflectInAxesWithinDistance
isCompleted() - Method in class org.anchoranalysis.experiment.task.processor.JobStateMonitor: Is a job completed?
isCompletedFailure() - Method in class org.anchoranalysis.experiment.task.processor.JobStateMonitor: Has a job completed with a failure?
isCompletedSuccessfully() - Method in class org.anchoranalysis.experiment.task.processor.JobStateMonitor: Has a job completed with a successful outcome?
isConditionTrue() - Method in class org.anchoranalysis.plugin.image.bean.dictionary.DictionaryCondition: Checks if the condition is true by comparing the value in the dictionary with the expected value.
isConnectedComponentID(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedIntBuffer: Checks if the value at the given offset is a connected component ID.
isConnectedComponentIDCode(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels: Checks if the given code represents a connected component ID.
isConnectedComponentIDCode(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.WatershedEncoding: Checks if the given code represents a connected component ID.
isConsiderForMerge() - Method in class org.anchoranalysis.plugin.image.object.merge.priority.PrioritisedVertex
isConvexHull() - Method in class org.anchoranalysis.plugin.points.bean.FitPointsFromObjects: If true, reduces the set of points by applying a convex-hull operation.
isCopyNonInputs() - Method in class org.anchoranalysis.experiment.arguments.InputArguments: When true, any files in the input directory that are unused as inputs, are copied to the output directory.
isCov() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shape.ObjectRadiusStandardDeviation: If true, returns the coefficient of variation (stdDev/mean) instead of standard deviation.
isCreateShort() - Method in class org.anchoranalysis.image.bean.provider.stack.Arrange: If true, the created raster has unsigned short voxel data type.
isCreateShort() - Method in class org.anchoranalysis.image.io.bean.stack.combine.TileWithLabels: When true, the voxel-data-type of the created image is unsigned short, otherwise unsigned byte.
isCreateShort() - Method in class org.anchoranalysis.image.io.bean.stack.combine.WriteText: When true, text is drawn across all z-slices in the stack. when false, it appears on only one z-slice.
isCreateShort() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D: If true, creates a short (16-bit) output instead of byte (8-bit).
isCreateShort() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransformForEachObject3D
isCreateShort() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.CreateNew: If True creates an unsigned short-image
isCsvIgnoreZeros() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.histogram.ExportImageHistograms: Iff true, bins with zero-counts are not written as a row in the CSV file.
isDay() - Method in class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierAuto: If true, the current day (yyyy.MM.dd) is included in the output.
isDebug() - Method in class org.anchoranalysis.bean.shared.path.RootPath: If true this root is preferred, when executing a job in debugging mode.
isDebug() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedFeature
isDebugEnabled() - Method in class org.anchoranalysis.experiment.task.InputOutputContextStateful
isDebugEnabled() - Method in interface org.anchoranalysis.io.output.outputter.InputOutputContext: Is debug-mode enabled?
isDebugMode() - Method in class org.anchoranalysis.io.output.path.prefixer.PathPrefixerContext: Whether debug-mode is activated.
isDebugModeActivated() - Method in class org.anchoranalysis.io.input.bean.InputManagerParameters: Whether debug-mode has been activated.
isDebugModeEnabled() - Method in class org.anchoranalysis.experiment.arguments.ExecutionArguments: Has debug mode been enabled when executing an experiment?
isDefault() - Method in interface org.anchoranalysis.launcher.executor.selectparam.SelectParam: Checks if this is the default option that occurs without any additional user effort.
isDefault() - Method in class org.anchoranalysis.launcher.executor.selectparam.UseDefaultManager
isDeleteExistingDirectory() - Method in class org.anchoranalysis.io.output.outputter.DirectoryCreationParameters: When true, this will delete any existing directory with the same path, and then create it anew.
isDetailedLogging() - Method in class org.anchoranalysis.experiment.task.ExperimentFeedbackContext: Iff true, additional log messages are written to describe each job in terms of its unique name, output folder, average execution time etc.
isDetailedLogging() - Method in class org.anchoranalysis.experiment.task.InputBound: Whether logging is more detailed (true) or less detailed (false).
isDetailedLogging() - Method in class org.anchoranalysis.experiment.task.ParametersExperiment: Iff true, additional log messages are written to describe each job in terms of its unique name, output folder, average execution time etc.
isDifferentColorsForPairs() - Method in class org.anchoranalysis.annotation.io.assignment.generator.AssignmentColorPool: If true, different colors are used for paired objects, otherwise always the same color is used.
isDirect() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer: Is this buffer direct or non-direct?
isDirect() - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer: Is this buffer direct or non-direct?
isDirect() - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferUnsigned
isDirectionChainCode(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels: Checks if the given code represents a direction chain code.
isDirectionChainCode(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.WatershedEncoding: Checks if the given code represents a direction chain code.
isDisableDebugMode() - Method in class org.anchoranalysis.plugin.io.bean.file.path.RootedFilePath
isDisableDebugMode() - Method in class org.anchoranalysis.plugin.io.bean.file.provider.Rooted
isDo3D() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.AnisotropicDiffusion: Whether to perform the diffusion in 3D direction, or rather only in the 2D plane.
isDo3D() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.ObjectCollectionProviderMorphological: Whether to perform the operation in 3D (true) or 2D (false).
isDo3D() - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations: Whether to perform the morphological dimensions in 3D or 2D.
isDo3D() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
isDo3D() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.TouchingVoxels: Whether to perform calculations in 3D (true) or 2D (false).
isDo3D() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.Erode: If true, performs 3D erosion; if false, performs 2D erosion on each z-slice separately.
isDo3D() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.NumberRemovedVoxelsAfterClosing
isDo3D() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.OutlineKernelBase: If true, applies the kernel in 3D; otherwise, applies it in 2D.
isDuplicate() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.Reference: If true, the channel is duplicated after it is retrieved, to prevent overwriting existing data.
isDuplicate() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.Reference: If true, the mask is duplicated after it is retrieved, to prevent overwriting existing data.
isEightBitChannels() - Method in class org.anchoranalysis.image.io.stack.output.StackWriteAttributes: Whether each channel is 8 bits.
isEmpty() - Method in class org.anchoranalysis.bean.primitive.DoubleList
isEmpty() - Method in class org.anchoranalysis.bean.primitive.DoubleSet
isEmpty() - Method in class org.anchoranalysis.bean.primitive.IntegerList
isEmpty() - Method in class org.anchoranalysis.bean.primitive.IntegerSet
isEmpty() - Method in interface org.anchoranalysis.bean.primitive.PrimitiveBeanCollection: Whether the collection is empty or not.
isEmpty() - Method in class org.anchoranalysis.bean.primitive.StringList
isEmpty() - Method in class org.anchoranalysis.bean.primitive.StringSet
isEmpty() - Method in class org.anchoranalysis.core.collection.MapCreate: Whether the map is empty or not.
isEmpty() - Method in class org.anchoranalysis.core.collection.StringSetTrie: Does the set contain no elements?
isEmpty() - Method in interface org.anchoranalysis.core.identifier.provider.NamedProvider: Are there any items in the provider?
isEmpty() - Method in class org.anchoranalysis.core.time.RecordedExecutionTimes: Are there no recorded operations?
isEmpty() - Method in class org.anchoranalysis.feature.bean.list.FeatureList: Returns true if this list contains no elements.
isEmpty() - Method in class org.anchoranalysis.feature.results.ResultsVectorList: Returns true if the list contains no elements.
isEmpty() - Method in class org.anchoranalysis.image.core.object.properties.ObjectCollectionWithProperties: Whether the number of objects is zero.
isEmpty() - Method in class org.anchoranalysis.image.inference.bean.reduce.ReduceObjectsGraph: Do no elements exist?
isEmpty() - Method in class org.anchoranalysis.image.inference.segment.SegmentedObjects: Whether no segmented objects exist.
isEmpty() - Method in class org.anchoranalysis.image.io.stack.time.TimeSeries: Whether the series contains no frames?
isEmpty() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection: Whether the collection contains no objects.
isEmpty() - Method in class org.anchoranalysis.io.input.InputsWithDirectory: Whether no inputs exist.
isEmpty() - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputs: If no output-names exist.
isEmpty() - Method in class org.anchoranalysis.math.histogram.Histogram: If no value exists in the histogram with a count greater than zero.
isEmpty() - Method in class org.anchoranalysis.mpp.mark.MarkCollection: Checks if the collection is empty.
isEmpty() - Method in class org.anchoranalysis.spatial.box.Extent: Does the extent contain zero voxels?
isEmpty() - Method in class org.anchoranalysis.spatial.box.PointRange: Has a valid min and max defined?
isEmpty() - Method in class org.anchoranalysis.spatial.rtree.RTree: Returns true if and only if the R-tree is empty of entries.
isEnabled() - Method in class org.anchoranalysis.io.generator.text.TextFileOutput: Whether the writer is enabled to write to the file-system.
isErodeAtBoundary() - Method in class org.anchoranalysis.plugin.points.bean.convexhull.ConvexHullBase: Whether to erode the mask at the boundary before finding the contour.
isErrorDisconnectedObjects() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.split.RemoveIntersectingVoxels: If true, throws an error if there is a disconnected object after the erosion
isEvaluated() - Method in class org.anchoranalysis.core.cache.CachedSupplierBase: Has the function already been evaluated?
isExceptionIfEmpty() - Method in class org.anchoranalysis.image.feature.bean.histogram.FeatureHistogramStatistic: If true, then an exception is thrown if the histogram is empty, otherwise FeatureHistogramStatistic.valueIfEmpty is returned.
isExcludeZero() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.Intensity: Iff true, zero-valued voxels are excluded from the histogram
isExcludeZero() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanMaxSlice: If true, zero-valued voxels are excluded from the mean intensity calculation.
isExecuting() - Method in class org.anchoranalysis.experiment.task.processor.JobStateMonitor: Is a job currently executing?
isExitWithMinima() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong.WatershedYeong: If true, exits early and just returns the minima, without any further segmentation
isExpandLabelZ() - Method in class org.anchoranalysis.image.io.bean.stack.combine.TileWithLabels: When true, the label is repeated across all z-slices in the stack. when false, it appears on only one z-slice.
isFieldAnnotatedAsOptional(Field) - Static method in class org.anchoranalysis.bean.FieldAccessor: Is a particular Field on a AnchorBean marked as optional?
isFindMaxima() - Method in class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice: If true, the maxima of the score is searched for.
isFinished() - Method in class org.anchoranalysis.annotation.mark.DualMarksAnnotation
isFirst() - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.AsSingle: Iff true, first object is used, otherwise the second
isFirstDefined() - Method in class org.anchoranalysis.io.output.bean.rules.OutputEnableRulesSpecify: Are output-names in the first-level defined?
isFirstLineHeaders() - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
isFlatten() - Method in class org.anchoranalysis.annotation.io.bean.comparer.MultipleComparer: If true, a maximum-intensity-projection is first applied to any 3D objects into a 2D plane, before comparison.
isFlatten() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations: If true, a maximum-intensity-projection is first applied to any 3D objects into a 2D plane, before comparison.
isFlatten() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.ExteriorContour: If true, any 3D mask is flattened in the z-dimension (maximum intensity projection) to make it 2D
isFlatten() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase: If true, objects and the background are flattened in the z dimension (via maximum intensity projection), so that a 2D image is produced.
isForceChangeBytes() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.Invert: If true, rather than modifying the binary-values (an index) bytes are modified in the buffer to reflect the existing binary-values.
isForceDetailedLogging() - Method in class org.anchoranalysis.experiment.bean.io.OutputExperiment: Whether more detailed log-messages around each experiment occur.
isForceEagerEvaluation() - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
isForceRGB() - Method in class org.anchoranalysis.image.bean.provider.stack.Arrange: Iff true, ensures every stack is converted into 3 channels.
isGaussian() - Method in class org.anchoranalysis.plugin.imagej.bean.define.AddEdgeFilters: If true, the Gaussian filter is included.
isGpu() - Method in class org.anchoranalysis.inference.concurrency.ConcurrentModel: Whether model is using the GPU or not.
isGPU() - Method in class org.anchoranalysis.inference.concurrency.WithPriority: Is the element returned by WithPriority.get() associated with a GPU?
isIgnoreAtThreshold() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.OutlineKernelBase: If true, ignores voxels at the threshold when applying the kernel.
isIgnoreCase() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.path.FilePathPattern: if true, case is ignored in the pattern matching.
isIgnoreFileNotFoundAppend() - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
isIgnoreFittingFailure() - Method in class org.anchoranalysis.plugin.points.bean.FitPointsFromObjects: If true, ignores fitting failures and continues processing.
isIgnoreHidden() - Method in class org.anchoranalysis.io.input.bean.files.SearchDirectory: If true, case is ignored in the pattern matching.
isIgnoreHidden() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.path.FilePathPattern: Iff true, any hidden-path is not considered, and simply ignored
isIgnoreHigherSide() - Method in class org.anchoranalysis.plugin.operator.feature.bean.statistics.GaussianCumulative: If true, always returns 1.0 for values higher than the mean.
isIgnoreLowerSide() - Method in class org.anchoranalysis.plugin.operator.feature.bean.statistics.GaussianCumulative: If true, always returns 1.0 for values lower than the mean.
isIgnoreMissingChannel() - Method in class org.anchoranalysis.plugin.image.task.bean.format.convertstyle.IndependentChannels: Iff true and we cannot find a channel in the file, we ignore it and carry on
isIgnoreNaN() - Method in class org.anchoranalysis.feature.bean.operator.Sum: If true, we ignore any NaN values.
isIgnoreNoObjects() - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel: When true, then the outputs (outline, mask, image etc.) are not written for images that produce no objects.
isIgnoreOutside() - Method in class org.anchoranalysis.image.voxel.kernel.KernelApplicationParameters: When true, any parts of the neighborhood that lie outside the scene are not considered in kernel neighborhoods.
isIgnoreOutside() - Method in enum class org.anchoranalysis.image.voxel.kernel.OutsideKernelPolicy: When true, any parts of the neighborhood that lie outside the scene are not considered in kernel neighborhoods.
isIgnoreZero() - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.RatioNonMode: Whether to ignore the zero value when calculating the ratio.
isIgnoreZeros() - Method in class org.anchoranalysis.image.io.histogram.output.HistogramCSVGenerator: Iff true bins in the histogram with a zero count are not written
isIgnoreZIfNaN() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D: If true and the z-resolution is undefined, the z dimension is ignored.
isIncludeBatchDimension() - Method in class org.anchoranalysis.plugin.onnx.bean.object.segment.stack.SegmentObjectsFromONNXModel: If true, a 4-dimensional tensor is created (with the first dimension describing a batch-size of 1), instead of the usual 3-dimensional tensor describing channel, height, width.
isIncludeDirectories() - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.DirectoryStructure: If false, the folders are ignored, and only the file-name is used in the output
isIncludeFeatureNames() - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement: If true, the names of the imageFeatures are taken as a combination of the namedItem and the actual features.
isIncludeFirst() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors: Include features for the First-object of the pair
isIncludeMerged() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors: Include features for the Merged-object of the pair
isIncludeSecond() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors: Include features for the Second-object of the pair
isIncludeZ() - Method in class org.anchoranalysis.image.io.bean.object.draw.Outline: If true the outline is also applied in the z-dimension, otherwise this is ignored as possible boundary
isIncludeZ() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.NotTouchingSceneBorder
isInitialized() - Method in class org.anchoranalysis.bean.initializable.InitializableBean: Has the been already been initialized via a call to InitializableBean.initialize(BeanInitialization, Logger) or similar.
isInputCompatibleWith(Class<? extends InputFromManager>) - Method in class org.anchoranalysis.experiment.bean.processor.JobProcessor: Is an input-type compatible with this particular task?
isInputCompatibleWith(Class<? extends InputFromManager>) - Method in class org.anchoranalysis.experiment.bean.task.Task: Is an input-object type compatible with this particular task?
isInteger() - Method in class org.anchoranalysis.image.voxel.datatype.FloatVoxelType
isInteger() - Method in class org.anchoranalysis.image.voxel.datatype.SignedVoxelType
isInteger() - Method in class org.anchoranalysis.image.voxel.datatype.UnsignedVoxelType
isInteger() - Method in class org.anchoranalysis.image.voxel.datatype.VoxelDataType: Whether the data-type represents an integer or floating-point?
isInterleaveChannels() - Method in class org.anchoranalysis.plugin.onnx.bean.object.segment.stack.SegmentObjectsFromONNXModel: If true, the channels are placed as the final position of the tensor (**after** width/height) instead of **before** width/height.
isInterleaved() - Method in class org.anchoranalysis.io.bioformats.copyconvert.ImageFileEncoding: Whether the channels are interleaved
isInverse() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.IntersectsWithContainer
isInverse() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase: If true, calculates instead on the inverse of the object-mask (what's left when the shell is removed).
isInverseMask() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase: If true, uses the inverse of the passed mask.
isInvert() - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.MaskAsObject: If true the Mask is inverted before conversion into an ObjectCollection.
isInvert() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromObjects
isInvert() - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.FilterWithRegularExpression: Iff true, then a file is rejected if the regular-expression matches and vice-versa.
isKeepExtension() - Method in class org.anchoranalysis.plugin.io.bean.path.derive.CollapseFileName: When true, the extension is appended to the directory.
isKeepExtremes() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Identity: Whether to keep extreme values (0 and 1) unchanged when normalizing.
isKeepZ() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ImposeResolution: Keep the z-resolution if it is already defined
isKeyRequired() - Method in class org.anchoranalysis.plugin.io.bean.file.group.parser.RegularExpression
isLabel() - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices: If true, a label is added beside every image showing the slice index.
isLocalized() - Method in class org.anchoranalysis.io.input.bean.files.FilesProviderWithDirectoryString: When true paths are resolved against the location of the associated BeanXML file.
isLogPath() - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Rooted: if true, the pathIn and pathOut are logged.
isMakeRGB() - Method in class org.anchoranalysis.test.image.stackwriter.ChannelSpecification: If true, the the RGB-flag is set on the created stack, if false it is not.
isMarksSpan(MarkCollection) - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria: Checks if the given MarkCollection spans all marks in this collection.
isMarksSpan(MarkCollection) - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedPairs: Checks if the pair collection only contains items from a particular mark configuration.
isMax() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram: Whether to use the maximum (true) or minimum (false) value from the histogram.
isMedian() - Method in class org.anchoranalysis.plugin.imagej.bean.define.AddEdgeFilters: If true, the median filter is included.
isMemberFlag(byte) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipWithFlags: Checks if the given membership flag is set for this region.
isMemberFlag(byte, byte) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership: Checks if a given membership flag is set for a specific region.
isMemberFlag(byte, byte) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipAnd
isMemberFlag(byte, byte) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipOr
isMemberFlagAnd(byte, byte) - Static method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipUtilities: Checks if a membership flag is set using an AND operation.
isMemberFlagOr(byte, byte) - Static method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipUtilities: Checks if a membership flag is set using an OR operation.
isMerge() - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.CutBelowThreshold
isMinima(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedIntBuffer: Checks if the value at the given offset is a minima.
isMinima(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels: Checks if the given code represents a minima.
isMip() - Method in class org.anchoranalysis.image.feature.bean.object.single.NumberVoxels: If true, calculates the number of voxels in the maximum intensity projection (MIP) of the object.
isMip() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.surface.SurfaceNumberVoxelsBase: If true, calculates the surface on a maximum intensity projection rather than the 3D object.
isNoBlack() - Method in class org.anchoranalysis.plugin.fiji.bean.threshold.ThresholderAutoIJ: If true, the thresholding algorithm will not consider black pixels (value 0) in its calculations.
isNormalize() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Identity: Whether to normalize the voxel intensity values.
isNoScale() - Method in class org.anchoranalysis.spatial.scale.ScaleFactor: Does the scale-factor involve no scaling at all?
isNumeric() - Method in class org.anchoranalysis.core.value.TypedValue: Whether the value is numeric or not.
isOff(byte) - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte: Does a particular value correspond to the off state?
isOff(int, int, int) - Method in interface org.anchoranalysis.image.voxel.binary.BinaryOnOffSetter: Does the voxel at this point have an off state?
isOff(Point3i) - Method in interface org.anchoranalysis.image.voxel.binary.BinaryOnOffSetter: Does the voxel at this point have an off state?
isOmitExperimentIdentifier() - Method in class org.anchoranalysis.experiment.arguments.OutputArguments: Has a request occurred that the experiment-identifier is omitted?
isOmitExperimentIdentifier() - Method in class org.anchoranalysis.io.output.path.prefixer.OutputPrefixerSettings: When true, Requests that the experiment-identifier (name and index) is not included in the output-directory path.
isOn(byte) - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte: Does a particular value correspond to the on state?
isOn(int, int, int) - Method in interface org.anchoranalysis.image.voxel.binary.BinaryOnOffSetter: Does the voxel at this point have an on state?
isOn(Point3i) - Method in interface org.anchoranalysis.image.voxel.binary.BinaryOnOffSetter: Does the voxel at this point have an on state?
isOpenInDesktop() - Method in class org.anchoranalysis.launcher.executor.ExperimentExecutor: Whether to open the output directory in the desktop GUI after execution (if supported on the O/S).
isOperationAlreadyRecorded(String) - Method in class org.anchoranalysis.core.time.ExecutionTimeRecorder: Has a particular operation already been recorded?
isOperationAlreadyRecorded(String) - Method in class org.anchoranalysis.core.time.ExecutionTimeRecorderIgnore
isOutline() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase: If true, an outline is drawn around the entries.
isOutlineAtBoundary() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.ExteriorContour
isOutputEnabled() - Method in class org.anchoranalysis.io.generator.tabular.CSVWriter: Whether the output is enabled or not?
isOutputEnabled(String) - Method in class org.anchoranalysis.io.output.bean.enabled.All
isOutputEnabled(String) - Method in class org.anchoranalysis.io.output.bean.enabled.IgnoreUnderscorePrefix
isOutputEnabled(String) - Method in class org.anchoranalysis.io.output.bean.enabled.None
isOutputEnabled(String) - Method in class org.anchoranalysis.io.output.bean.enabled.SpecificDisabled
isOutputEnabled(String) - Method in class org.anchoranalysis.io.output.bean.enabled.SpecificEnabled
isOutputEnabled(String) - Method in class org.anchoranalysis.io.output.enabled.multi.MultiLevelBinary
isOutputEnabled(String) - Method in class org.anchoranalysis.io.output.enabled.multi.MultiLevelNot
isOutputEnabled(String) - Method in class org.anchoranalysis.io.output.enabled.OutputEnabledMutable
isOutputEnabled(String) - Method in class org.anchoranalysis.io.output.enabled.single.SingleLevelBinary
isOutputEnabled(String) - Method in class org.anchoranalysis.io.output.enabled.single.SingleLevelInSet
isOutputEnabled(String) - Method in class org.anchoranalysis.io.output.enabled.single.SingleLevelNot
isOutputEnabled(String) - Method in interface org.anchoranalysis.io.output.enabled.single.SingleLevelOutputEnabled: Is a particular a particular output-enabled?
isOutputIncrementingNumberSequence() - Method in class org.anchoranalysis.io.output.path.prefixer.OutputPrefixerSettings: When true, requests outputting with an incrementing number sequence, rather than the usual outputter (normally based upon input filenames).
isOutputShort() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientBase: If true, outputs a short channel, otherwise byte channel.
isOutsideAtThreshold() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.OutlineKernelBase: If true, considers voxels outside the object at the threshold as part of the object.
isOutsideOffUnignored() - Method in class org.anchoranalysis.image.voxel.kernel.KernelApplicationParameters: True only when voxels outside the scene should not be ignored and considered as off.
isOutsideOffUnignored() - Method in class org.anchoranalysis.image.voxel.kernel.KernelPointCursor: True only when voxels outside the scene should not be ignored and considered as off.
isOutsideOn() - Method in class org.anchoranalysis.image.voxel.kernel.KernelApplicationParameters: In cases where KernelApplicationParameters.isIgnoreOutside() is false, then whether to treat voxels that lie outside the scene as on (if true) or off (if false).
isOutsideOn() - Method in class org.anchoranalysis.image.voxel.kernel.KernelPointCursor: Whether to treat voxels that lie outside the scene as on (if true) or off (if false).
isOutsideOn() - Method in enum class org.anchoranalysis.image.voxel.kernel.OutsideKernelPolicy: In cases where OutsideKernelPolicy.isIgnoreOutside() is false, then whether to treat voxels that lie outside the scene as on (if true) or off (if false).
isOutsideOnUnignored() - Method in class org.anchoranalysis.image.voxel.kernel.KernelApplicationParameters: True only when voxels outside the scene should not be ignored and considered as on.
isOverlappingObjects() - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize: Whether objects may overlap or not when unscaled.
isParamPrefixAppendNumber() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFirstSecondOrder: If true, the constant is appended to the param prefix (a dot and a number).
isPixelOn(int, int, int) - Method in class org.anchoranalysis.test.image.object.CutOffCorners
isPixelOn(int, int, int) - Method in interface org.anchoranalysis.test.image.object.VoxelPattern: Determines if a voxel at the given coordinates is "on" according to the pattern.
isPlateau(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels: Checks if the given code represents a plateau.
isPlayloadUsed() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergePairs
isPlayloadUsed() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeToIncreaseObjectFeature
isPlayloadUsed() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithFeature: Checks if the payload is considered in making decisions.
isPointInside(Point3i) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
isPointInside(Point3i) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
isPointInside(Point3i) - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
isPointInside(Point3i) - Method in class org.anchoranalysis.mpp.mark.Mark: Determines if a point is inside the mark.
isPointInside(Point3i) - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
isPointInside(Point3i) - Method in class org.anchoranalysis.mpp.mark.points.PointList
isPointInside(Point3i) - Method in class org.anchoranalysis.mpp.mark.points.Polygon
isPointInside(Point3i) - Method in class org.anchoranalysis.mpp.mark.points.PolygonCurve
isPointInside(Point3i) - Method in class org.anchoranalysis.mpp.mark.points.RotatableBoundingBox
isPrefix() - Method in class org.anchoranalysis.bean.define.adder.FromXMLList: If true, a prefix is prepended to the name of each added bean.
isPreserveAspectRatio() - Method in class org.anchoranalysis.image.bean.spatial.arrange.align.Grow: Whether to preserve the aspect-ratio of the smaller image when growing.
isPreserveAspectRatio() - Method in class org.anchoranalysis.plugin.image.bean.scale.FitTo: If true, the aspect-ratio is preserved between width and height.
isPreserveAspectRatio() - Method in class org.anchoranalysis.plugin.image.bean.scale.ToDimensions: If true, the ratio between x and y is kept constant when scaling.
isPreserveExtensionIfDuplicate() - Method in class org.anchoranalysis.plugin.io.bean.file.namer.RemoveExtension: Keeps the extension if the file-name (without the extension) becomes duplicated with another.
isPreserveSubdirectories() - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster.ClusterByTimestamp: If true, the entire relative-path is used when copying files into the cluster directory.
isPrioritizeInputContext() - Method in class org.anchoranalysis.io.input.bean.path.matcher.MatchExtensions: When true, any extensions available in the input-context are prioritized ahead of extensions.
isRadiusInMeters() - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.WithRadiusBase: If true, treats the radius as being in meters.
isReadFromResources() - Method in class org.anchoranalysis.plugin.onnx.bean.object.segment.stack.SegmentObjectsFromONNXModel: When true, rather than reading modelPath from the file-system, it is read from Java resources on the class-path.
isRecordedAsEnabled(String) - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputs: Is a particular output-name recorded as enabled?
isRecurseSubfolders() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader
isRecursive() - Method in class org.anchoranalysis.io.input.bean.files.SearchDirectory: If true the search is applied recursively over sub-directories.
isRejectIterationIfAllLow() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Erode
isRejectIterationIfDisconnected() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Erode
isRelativeForIdentifier() - Method in class org.anchoranalysis.io.input.InputContextParameters: If true, the entire filename or relative path (excluding extension) is used to determine a unique identifier.
isRelativeToDirectory() - Method in class org.anchoranalysis.io.input.file.FileNamerContext: If true, the namer should prefer to derive file-names relative to the directory, rather than only the varying elements in the file-names.
isRemoveExtension() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.path.FilePathPattern: if true, the extension is removed from paths before finding the pattern.
isRemoveExtensionInDescription() - Method in class org.anchoranalysis.plugin.io.bean.file.namer.LastDirectories: Whether to remove the file-extension from the filename.
isRemoveNaNColumns() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeaturesStyle: When true, columns containing all Double.NaN values are removed before outputting.
isRemoveNaNColumns() - Method in class org.anchoranalysis.plugin.image.task.feature.FeatureExporterContext: When true, columns containing all Double.NaN values are removed before outputting.
isRemoveTouchingBorderXY() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner
isReplaceMatchesWithSolids() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations: If true, matched objects are replaced with solid colors.
isReplaceWithMidpoint() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeGreedyToIncreaseObjectFeature
isReportFitterErrors() - Method in class org.anchoranalysis.plugin.points.bean.FitPoints: Whether to report fitter errors.
isRequireAllFilesMatch() - Method in class org.anchoranalysis.plugin.io.bean.file.group.GroupFiles
isRequireBBoxNeighbors() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithFeature: Requires for any potential merge that the bounding-boxes of the two objects must intersect or touch.
isRequireTouching() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithFeature: Requires the object-masks to touch.
isResultUnusual(double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.replace.ReplaceInfinity
isResultUnusual(double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.replace.ReplaceNaN
isResultUnusual(double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.replace.ReplaceUnusualValue: Determines if the feature result is considered unusual and should be replaced.
isRewardHigherSide() - Method in class org.anchoranalysis.plugin.operator.feature.bean.statistics.GaussianCumulative: If true, treats the higher side as if it's the full CDF.
isRewardLowerSide() - Method in class org.anchoranalysis.plugin.operator.feature.bean.statistics.GaussianCumulative: If true, treats the lower side as if it's 1 minus the full CDF.
isRgb() - Method in class org.anchoranalysis.image.core.stack.ImageMetadata: Whether the image is RGB or not.
isRgb() - Method in class org.anchoranalysis.io.bioformats.copyconvert.ImageFileEncoding: Whether the source bytes encoded as RGB (i.e. with the three colors coded into a 4 bytes coding per voxel).
isRgb() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.FromChannelOrMask: If true, the output contains three channels (the input and two duplicates) instead of one.
isRgb() - Method in class org.anchoranalysis.plugin.image.task.channel.aggregator.NamedChannels: Whether the channels originate from a Stack that is RGB, or not.
isRGB() - Method in class org.anchoranalysis.image.core.stack.DisplayStack: Does the display-stack contain an RGB image?
isRGB() - Method in class org.anchoranalysis.image.core.stack.Stack: If true, and the stack has exactly three channels, this stack can be interpreted as a RGB image.
isRGB() - Method in class org.anchoranalysis.image.io.stack.output.box.ScaleableBackground: Does the display-stack contain an RGB image?
isRGB(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.Default
isRGB(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceBitsPerPixel
isRGB(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceNumberChannels
isRGB(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceTimeSeriesToStack
isRGB(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptions: Is it an image with three channels (red, green and blue)?
isRGB(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptionsDelegate
isRGB(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.SwitchChannelTime
isRGB(Logger) - Method in class org.anchoranalysis.image.io.channel.map.NamedChannelsConcatenate
isRGB(Logger) - Method in interface org.anchoranalysis.image.io.channel.map.NamedChannelsMap: Whether the channels describe an RGB image.
isRGB(Logger) - Method in class org.anchoranalysis.image.io.channel.map.OpenedNamedChannels
isRGB(Logger) - Method in interface org.anchoranalysis.image.io.stack.input.OpenedImageFile: Whether the image-file has RGB encoded voxels.
isRGB(Logger) - Method in class org.anchoranalysis.plugin.io.multifile.OpenedMultiFile
isSecond() - Method in class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierAuto: Only relevant if time==true.
isSelective() - Method in class org.anchoranalysis.io.generator.sequence.pattern.OutputPattern: Whether the output should be checked to see if it is allowed or not.
isSeparateEachLabel() - Method in class org.anchoranalysis.image.inference.bean.segment.instance.SuppressNonMaximum: If true, each label is reduced separately. if false, all labels are reduced together.
isShuffle() - Method in class org.anchoranalysis.io.input.InputContextParameters: If true, the order of the inputs are shuffled (randomized).
isSigmaInMeters() - Method in class org.anchoranalysis.plugin.image.bean.blur.BlurStrategy: If true, treats sigma as if it's in meters (physical units).
isSilentlyDeleteExisting() - Method in class org.anchoranalysis.io.output.bean.OutputManager: Whether to silently first delete any existing output at the intended path, or rather throw an error.
isSingleChannel() - Method in class org.anchoranalysis.image.io.stack.output.StackWriteAttributes: The number of channels is guaranteed to be 1 in the output.
isSkipAtBorder() - Method in class org.anchoranalysis.plugin.imagej.bean.mask.provider.FillHoles: If true, holes that touch the border of the mask are not filled.
isSkipComparisonForRGB() - Method in class org.anchoranalysis.test.image.rasterwriter.comparison.ComparisonPlan
isSkipFileName() - Method in class org.anchoranalysis.plugin.io.bean.file.namer.LastDirectories: Iff true the filename is not considered, only the subdirectories.
isSkipMissingChannels() - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
isSlicesSeparately() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.FitBoxToOnVoxels
isSlicewise() - Method in class org.anchoranalysis.plugin.image.task.bean.combine.AggregateChannelTask: When true, a 3D image is added slice-by-slice to the aggregation, treating each slice as a separate image.
isSortIfNotRequested() - Method in class org.anchoranalysis.plugin.io.bean.input.ShuffleIfRequested: When true, the inputs are sorted alphabetically, if a shuffle is not requested.
isStackBackground() - Method in class org.anchoranalysis.plugin.mpp.bean.define.VisualizeOnBackground
isStrongEdgeEnhancer() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.AnisotropicDiffusion: If true uses, the strong-edge-enhancer diffusion function, otherwise the wide-region-enhancer.
isSubtractFromMaskOnly() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.SubtractMean: Whether to subtract the mean only from voxels within the mask.
isSuppress3D() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.MorphologicalOperatorBase: Whether to suppress 3D operations and only perform 2D operations.
isSuppress3D() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.surface.SurfaceNumberVoxelsBase: If true, suppresses 3D calculations and treats the object as 2D.
isSuppressDirectories() - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.FromDescriptiveName: If true, any directory separators in the identifier in a descriptive-name are replaced by underscores.
isSuppressErrors() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeaturesStyle: When false, an image is reported as errored, if any exception is thrown during calculation.
isSuppressErrors() - Method in class org.anchoranalysis.plugin.image.task.feature.FeatureCalculationContext: When false, an image is reported as errored, if any exception is thrown during calculation.
isSuppressErrors() - Method in class org.anchoranalysis.plugin.image.task.feature.FeatureExporterContext: If false, an image is reported as errored, if any exception is thrown during calculation.
isSuppressExceptions() - Method in class org.anchoranalysis.experiment.bean.processor.JobProcessor: When true, any exception thrown processing and input is caught and logged.
isSuppressExceptions() - Method in class org.anchoranalysis.experiment.task.ParametersUnbound
isSuppressOutlineZ() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase: If true, the outline is suppressed in the z-dimension i.e. a boundary only in z-dimension is not outlined (only relevant if outline==true).
isSuppressRootOut() - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Rooted: if true, the root is not added to the outFilePath, and the path is instead localized against the location of the BeanXML. if false, nothing is changed
isSuppressSeries() - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat: If true, the series index is not included in the outputted file-names.
isSuppressSubfolders() - Method in class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputter: If true, suppresses the creation of subfolders for outputs.
isSuppressZ() - Method in class org.anchoranalysis.mpp.feature.addcriteria.BoundingBoxIntersection: If true, the Z dimension is ignored when checking for intersection.
isSuppressZ() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D: If true, suppresses the z-dimension in distance calculations.
isSuppressZ() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransformForEachObject3D
isSuppressZ() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithOptionalDistanceConstraint: If true, suppresses the Z-dimension when calculating distances between objects.
isSuppressZ() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.CostOverlapWithinMidpointDistance
isSuppressZ() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.ImageMomentsBase: If true co-variance is suppressed in z-dimension.
isSuppressZ() - Method in class org.anchoranalysis.plugin.points.bean.feature.EllipsoidBase: If true, suppresses covariance in the z-direction.
isSuppressZCovariance() - Method in class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresEllipsoidFitter
isTemporary(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedIntBuffer: Checks if the value at the given offset is temporary.
isTemporary(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels: Checks if the given code represents a temporary value.
isThreeChannels() - Method in class org.anchoranalysis.image.io.stack.output.StackWriteAttributes: The number of channels is guaranteed to be 3 in the output.
isThrowExceptionForInsufficientPoints() - Method in class org.anchoranalysis.mpp.bean.points.CreateMarkFromPoints: Whether to throw an exception when there are insufficient points.
isThumbnailsEnabled() - Method in class org.anchoranalysis.plugin.image.task.feature.FeatureCalculationContext: Whether thumbnails are enabled for output.
isTime() - Method in class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierAuto: If true, the current time (HH.mm.ss) is included in the output.
isTransposed() - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
isUniformlySized() - Method in class org.anchoranalysis.image.core.stack.StackNotUniformSized: Do all channels have identical dimensions?
isUniformTyped() - Method in class org.anchoranalysis.image.core.stack.StackNotUniformSized: Do all Channels in the stack have identical voxel data-type?
isUnsigned() - Method in class org.anchoranalysis.image.voxel.datatype.FloatVoxelType
isUnsigned() - Method in class org.anchoranalysis.image.voxel.datatype.SignedVoxelType
isUnsigned() - Method in class org.anchoranalysis.image.voxel.datatype.UnsignedVoxelType
isUnsigned() - Method in class org.anchoranalysis.image.voxel.datatype.VoxelDataType: Whether the data-type is unsigned?
isUnstarted() - Method in class org.anchoranalysis.experiment.task.processor.JobStateMonitor: Is a job unstarted?
isUnvisited(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedIntBuffer: Checks if the value at the given offset is unvisited.
isUnvisited(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels: Checks if the given code represents an unvisited value.
isUseLastSeriesIndexOnly() - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannels
isUseLastSeriesIndexOnly() - Method in class org.anchoranalysis.plugin.io.bean.input.stack.Stacks
isUseZ() - Method in class org.anchoranalysis.image.voxel.kernel.KernelApplicationParameters: Whether to additionally apply the kernel along the Z dimension, as well as X and Y?
isUseZ() - Method in class org.anchoranalysis.image.voxel.kernel.KernelPointCursor: Whether to additionally apply the kernel along the Z dimension, as well as X and Y?
isUseZ() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.RemoveTouchingBorder
isValidName(String, boolean) - Static method in class org.anchoranalysis.image.core.stack.RGBChannelNames: Whether the channel-name is one of red, green, or blue, or alpha.
isValidNameSet(Set<String>) - Static method in class org.anchoranalysis.image.core.stack.RGBChannelNames: Do the channel-names correspond exactly to those expected either RGB or RGBA.
isValidNameSet(Set<String>, boolean) - Static method in class org.anchoranalysis.image.core.stack.RGBChannelNames: Do the channel-names correspond exactly to those expected for one of RGB or RGBA.
isVaryColors() - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel: When true, the colors change for different objects in the image (using a default color set).
isVaryImageLocation() - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage: When true, the location of an image in the grid, as well as the number of images in each row are both allowed to vary to fill space.
isVaryImageSize() - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage: When true, the images may vary in width/height in their respective rows to fill space, while preserving the aspect-ratio of each image.
isVaryNumberImagesPerRow() - Method in class org.anchoranalysis.image.bean.spatial.arrange.fill.Fill: When true the number of Extents per row is allowed vary, to sensibly fill space.
isVisuallyShortenDecimals() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeaturesStyle: When true, feature-values are shown as visually compressed as possible, including suppressing decimal places.
isVisuallyShortenDecimals() - Method in class org.anchoranalysis.plugin.image.task.feature.FeatureExporterContext: When true double values are printed to be as short as possible without losing precision.
isVoxelOn(Point3i) - Method in class org.anchoranalysis.image.core.mask.Mask: Does a particular voxel have the on state?
iterateEntries(CheckedBiConsumer<K, V, E>) - Method in class org.anchoranalysis.core.collection.MapCreate: Iterate over each entry in the map, and apply an operation.
IterateKernelHelper - Class in org.anchoranalysis.image.voxel.iterator.neighbor.kernel: Routines to iterate a Kernel over some or all of the voxels in a BinaryVoxels.
iterateMap(Map<K, V>, CheckedBiConsumer<K, V, E>) - Static method in class org.anchoranalysis.core.functional.FunctionalIterate: Iterate through all entries in a Map.
iterateOverSlices(Consumer<VoxelBuffer<T>>) - Method in interface org.anchoranalysis.image.voxel.buffer.slice.SliceBufferIndex: Calls sliceConsumer once for each slice with the respective buffer.
iterateOverSlicesAndOffsets(ProcessVoxelBufferUnary<T>) - Method in interface org.anchoranalysis.image.voxel.buffer.slice.SliceBufferIndex: Calls process for each offset in each slice.
iterateOverXY(OffsettedScalarTwoDimensionalConsumer<E>) - Method in class org.anchoranalysis.spatial.box.Extent: Calls processor once for each x and y-values in the range.
iterateOverXY(PointTwoDimensionalConsumer) - Method in class org.anchoranalysis.spatial.box.Extent: Calls processor once for each x and y-values in the range.
iterateOverXYOffset(CheckedIntConsumer<E>) - Method in class org.anchoranalysis.spatial.box.Extent: Calls processor once for each x and y-values but only passing an offset.
iterateOverXYOffset(OffsettedPointTwoDimensionalConsumer) - Method in class org.anchoranalysis.spatial.box.Extent: Calls processor once for each x and y-values in the range.
iterateOverXYWithShift(Point2i, PointTwoDimensionalConsumer) - Method in class org.anchoranalysis.spatial.box.Extent: Calls processor once for each x and y-values in the range, with a shift added.
iterateOverYXOffset(OffsettedPointTwoDimensionalConsumer) - Method in class org.anchoranalysis.spatial.box.Extent: Calls processor once for each x and y-values in the range.
iterateOverZ(CheckedIntConsumer<E>) - Method in class org.anchoranalysis.spatial.box.Extent: Calls processor once for each z-value in the range.
iterateOverZUntil(IntPredicate) - Method in class org.anchoranalysis.spatial.box.Extent: Calls processor once for each z-value in the range unless indexPredicate returns false.
iterateValues(Histogram.BinConsumer) - Method in class org.anchoranalysis.math.histogram.Histogram: Calls consumer for every value, increasing from min to max.
iterateValuesUntil(int, Histogram.BinConsumer) - Method in class org.anchoranalysis.math.histogram.Histogram: Calls consumer for every value until a limit, increasing from min to limit.
IterateVoxelsAll - Class in org.anchoranalysis.image.voxel.iterator: Utilities for iterating over all voxels in one or more Voxels.
IterateVoxelsBoundingBox - Class in org.anchoranalysis.image.voxel.iterator: Utilities for iterating over the subset of image voxels within a bounding-box.
IterateVoxelsEqualTo - Class in org.anchoranalysis.image.voxel.iterator: Like IterateVoxelsAll but specifically for equal-to operations on Voxels of type UnsignedByteBuffer.
IterateVoxelsIntersectingBounded - Class in org.anchoranalysis.image.voxel.iterator.intersecting: Like IterateVoxelsBoundingBox but specifically for processing areas of intersection between BoundedVoxels of type UnsignedByteBuffer.
IterateVoxelsMask - Class in org.anchoranalysis.image.core.mask: Utilities for iterating over the subset of voxels corresponding to an on state in a Mask.
IterateVoxelsNeighbors - Class in org.anchoranalysis.image.voxel.iterator.neighbor: Utilities for iterating over the neighboring voxels to a given point.
IterateVoxelsObjectMask - Class in org.anchoranalysis.image.voxel.iterator: Utilities for iterating over the subset of voxels corresponding to an on state in an ObjectMask.
IterateVoxelsObjectMaskOptional - Class in org.anchoranalysis.image.voxel.iterator: Utilities for iterating over the subset of voxels corresponding to an on state in an optional ObjectMask.
IterateVoxelsRemaining - Class in org.anchoranalysis.image.voxel.iterator: Utilities for iterating over remaining voxels in one or more VoxelBuffers.
iterator() - Method in class org.anchoranalysis.bean.permute.property.SequenceInteger: An iterator for each element in the sequence.
iterator() - Method in class org.anchoranalysis.bean.primitive.DoubleList
iterator() - Method in class org.anchoranalysis.bean.primitive.DoubleSet
iterator() - Method in class org.anchoranalysis.bean.primitive.IntegerList
iterator() - Method in class org.anchoranalysis.bean.primitive.IntegerSet
iterator() - Method in class org.anchoranalysis.bean.primitive.StringList
iterator() - Method in class org.anchoranalysis.bean.primitive.StringSet
iterator() - Method in class org.anchoranalysis.core.color.ColorList
iterator() - Method in class org.anchoranalysis.core.identifier.provider.NameValueMap
iterator() - Method in class org.anchoranalysis.experiment.task.processor.ConcurrentJobMonitor
iterator() - Method in class org.anchoranalysis.feature.bean.list.FeatureList
iterator() - Method in class org.anchoranalysis.feature.io.name.CombinedName
iterator() - Method in class org.anchoranalysis.feature.io.name.SimpleName
iterator() - Method in class org.anchoranalysis.feature.name.FeatureNameList
iterator() - Method in class org.anchoranalysis.feature.results.ResultsVectorList
iterator() - Method in class org.anchoranalysis.feature.session.cache.finder.CacheTransferSourceCollection
iterator() - Method in class org.anchoranalysis.feature.shared.SharedFeatures
iterator() - Method in class org.anchoranalysis.feature.store.NamedFeatureStore
iterator() - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.StackArrangement
iterator() - Method in class org.anchoranalysis.image.core.object.properties.ObjectCollectionWithProperties
iterator() - Method in class org.anchoranalysis.image.core.stack.RGBStack
iterator() - Method in class org.anchoranalysis.image.core.stack.Stack
iterator() - Method in class org.anchoranalysis.image.core.stack.StackNotUniformSized
iterator() - Method in class org.anchoranalysis.image.io.stack.time.TimeSeries
iterator() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
iterator() - Method in class org.anchoranalysis.io.input.InputsWithDirectory: Returns an iterator over the elements in this list in proper sequence.
iterator() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedIndividual
iterator() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergySchemeSet
iterator() - Method in class org.anchoranalysis.mpp.feature.mark.MemoList
iterator() - Method in class org.anchoranalysis.mpp.mark.ColoredMarks
iterator() - Method in class org.anchoranalysis.mpp.mark.MarkCollection
iterator() - Method in class org.anchoranalysis.overlay.collection.ColoredOverlayCollection
iterator() - Method in class org.anchoranalysis.overlay.collection.OverlayCollection
iterator() - Method in class org.anchoranalysis.plugin.annotation.counter.ImageCounterList
iterator() - Method in class org.anchoranalysis.plugin.image.intensity.level.LevelResultCollection
iterator() - Method in class org.anchoranalysis.plugin.image.task.channel.aggregator.NamedChannels
iterator() - Method in class org.anchoranalysis.plugin.io.multifile.ParsedFilePathBag
iterator() - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetChannel

J

JobDescription - Class in org.anchoranalysis.experiment.task.processor: A description of the job's name and associated number.
JobDescription(String, int) - Constructor for class org.anchoranalysis.experiment.task.processor.JobDescription
JobExecutionException - Exception Class in org.anchoranalysis.experiment: An exception that occurs when a job is executed.
JobExecutionException(String) - Constructor for exception class org.anchoranalysis.experiment.JobExecutionException: Creates with a message only, but no cause.
JobExecutionException(String, Throwable) - Constructor for exception class org.anchoranalysis.experiment.JobExecutionException: A string message displayed to the user as well as a stack-trace of the cause.
JobExecutionException(Throwable) - Constructor for exception class org.anchoranalysis.experiment.JobExecutionException: Creates with a cause only, but no message.
JobProcessor<T,S> - Class in org.anchoranalysis.experiment.bean.processor: Base class for a method to apply a task on inputs.
JobProcessor() - Constructor for class org.anchoranalysis.experiment.bean.processor.JobProcessor
JobStartStopLogger - Class in org.anchoranalysis.experiment.task.processor: Logs events when jobs start and stop, with or without errors.
JobStartStopLogger(String, ConcurrentJobMonitor, boolean, int, Optional<MessageLogger>) - Constructor for class org.anchoranalysis.experiment.task.processor.JobStartStopLogger: Creates a job-logger.
JobStateMonitor - Class in org.anchoranalysis.experiment.task.processor: Monitor execution-state of a job, and how long it is taking/took to execute.
JobStateMonitor() - Constructor for class org.anchoranalysis.experiment.task.processor.JobStateMonitor
joinNonEmpty(String, String...) - Static method in class org.anchoranalysis.core.value.StringUtilities: Like String.join(java.lang.CharSequence, java.lang.CharSequence...) but ignores any empty strings, and returns Optional.empty() if all components are empty.
JoinRegExGroups - Class in org.anchoranalysis.plugin.io.bean.path.derive: Generates an outstring of the form
JoinRegExGroups() - Constructor for class org.anchoranalysis.plugin.io.bean.path.derive.JoinRegExGroups
JPEG - Class in org.anchoranalysis.plugin.io.bean.metadata.header: The headers found in a JPEG file.
JPEG - Enum constant in enum class org.anchoranalysis.core.format.ImageFileFormat: JPEG
JPEG() - Constructor for class org.anchoranalysis.plugin.io.bean.metadata.header.JPEG

K

KEEP_UNCHANGED - Enum constant in enum class org.anchoranalysis.image.core.dimensions.OrientationChange: No change in orientation.
Kernel - Class in org.anchoranalysis.image.voxel.kernel: A small matrix that is convolved with or otherwise combined across each voxel in an image.
Kernel(int) - Constructor for class org.anchoranalysis.image.voxel.kernel.Kernel: Creates a kernel with a given size in the X and Y dimensions.
KernelApplicationParameters - Class in org.anchoranalysis.image.voxel.kernel: Parameters used for applying a Kernel to a BinaryVoxels.
KernelApplicationParameters(OutsideKernelPolicy, boolean) - Constructor for class org.anchoranalysis.image.voxel.kernel.KernelApplicationParameters: Creates a new KernelApplicationParameters instance.
KernelPointCursor - Class in org.anchoranalysis.image.voxel.kernel: A mutable context around determining whether a particular point should be on or off with a BinaryKernel.
KernelPointCursor(int, Point3i, Extent, BinaryValuesByte, KernelApplicationParameters) - Constructor for class org.anchoranalysis.image.voxel.kernel.KernelPointCursor: Creates to be focused around a particular point in the image.
keys() - Method in interface org.anchoranalysis.core.identifier.provider.NamedProvider: Returns a set of keys associated with the provider.
keys() - Method in class org.anchoranalysis.core.identifier.provider.NamedProviderBridge
keys() - Method in class org.anchoranalysis.core.identifier.provider.NamedProviderCombine
keys() - Method in class org.anchoranalysis.core.identifier.provider.NameValueMap
keys() - Method in class org.anchoranalysis.core.identifier.provider.store.EagerEvaluationStore
keys() - Method in class org.anchoranalysis.core.identifier.provider.store.LazyEvaluationStore
keys() - Method in class org.anchoranalysis.core.value.Dictionary: All keys existing in the dictionary.
keys() - Method in class org.anchoranalysis.feature.shared.SharedFeatures
keys() - Method in class org.anchoranalysis.image.core.stack.named.NamedStacks
keys() - Method in class org.anchoranalysis.image.io.stack.time.ExtractFrameStore
keySet() - Method in class org.anchoranalysis.core.collection.MapCreate: The keys in the map.
keySet() - Method in class org.anchoranalysis.core.collection.MapCreateCountdown: The keys in the map.
keySet() - Method in class org.anchoranalysis.plugin.annotation.bean.label.GroupedAnnotationLabels: Gets the set of group keys.
kurtosis(Histogram) - Static method in class org.anchoranalysis.math.histogram.HistogramStatistics: Calculates the kurtosis of a distribution of values, represented by their histogram.
Kurtosis - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic: Calculates the kurtosis of all the values in the histogram.
Kurtosis() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Kurtosis

L

label(OperationContext) - Method in class org.anchoranalysis.annotation.io.AnnotationWithStrategy: A human-friendly textual description of the annotation, or Optional.empty() if no label is available.
labelElements(Channel, Iterable<T>, Optional<Map<Integer, T>>) - Method in class org.anchoranalysis.image.core.object.label.LabelObjects: Replaces the contents of the channel so that all element's voxels are labelled with successive unique integer identifiers 1,2,3 etc. and voxels in no element are 0.
labelFor(NoSharedState, ProvidesStackInput, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.BinaryClassifierImageLabeller: Determines the label for a given input image.
labelFor(NoSharedState, ProvidesStackInput, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.DescriptiveNameContainsImageLabeller
labelFor(ProvidesStackInput, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.labeller.SharedStateFilteredImageOutput: Determines a particular group-identifier for an input.
labelFor(ImageCSVLabellerInitialization, ProvidesStackInput, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageCSVLabeller
labelFor(ImageLabellerStringMapInitialization<T>, ProvidesStackInput, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageLabellerStringMap
labelFor(T, ProvidesStackInput, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageLabeller: Determines a particular group-identifier (label) for an input.
labelHeaders() - Method in class org.anchoranalysis.feature.io.results.FeatureOutputMetadata: Headers for the CSV File.
LabelHeaders - Class in org.anchoranalysis.feature.io.csv.metadata: Headers in a CSV file for the non-results (i.e. labels) part of a feature-row
LabelHeaders(String[]) - Constructor for class org.anchoranalysis.feature.io.csv.metadata.LabelHeaders: Creates with only non-group headers
LabelHeaders(String[], String[]) - Constructor for class org.anchoranalysis.feature.io.csv.metadata.LabelHeaders: Creates a new LabelHeaders instance.
LabelHeadersForCSV - Class in org.anchoranalysis.plugin.image.task.feature: Generates a list of header-names for columns unrelated to features (identifiers and groups)
LabelledResultsCollector - Interface in org.anchoranalysis.feature.io.results: Stores LabelledResultsVector as they are calculated, and writes to the file-system.
LabelledResultsCSVWriter - Class in org.anchoranalysis.feature.io.csv.results: Allows results to be written to a FeatureCSVWriter, possibly adding further processing.
LabelledResultsCSVWriter(FeatureCSVMetadataForOutput, FeatureCSVWriterFactory, Optional<Consumer<LabelledResultsVector>>) - Constructor for class org.anchoranalysis.feature.io.csv.results.LabelledResultsCSVWriter: Creates a new LabelledResultsCSVWriter instance.
LabelledResultsCSVWriterFactory - Class in org.anchoranalysis.feature.io.csv.results: Creates a new instance of LabelledResultsCSVWriter.
LabelledResultsVector - Class in org.anchoranalysis.feature.io.results: Like a ResultsVector but additionally contains labels to describe the calculated results.
LabelledResultsVector(Optional<MultiName>, ResultsVector) - Constructor for class org.anchoranalysis.feature.io.results.LabelledResultsVector: Creates with no additional labels other than a group.
LabelledResultsVector(RowLabels, ResultsVector) - Constructor for class org.anchoranalysis.feature.io.results.LabelledResultsVector: Creates a new LabelledResultsVector instance.
LabelledResultsVector(ResultsVector) - Constructor for class org.anchoranalysis.feature.io.results.LabelledResultsVector: Creates with no additional labels, and no group.
LabelledResultsVectorWithThumbnail - Class in org.anchoranalysis.plugin.image.task.feature: Like a ResultsVectorWithThumbnail but additionally contains labels to describe the calculated results.
LabelledResultsVectorWithThumbnail(RowLabels, ResultsVectorWithThumbnail) - Constructor for class org.anchoranalysis.plugin.image.task.feature.LabelledResultsVectorWithThumbnail: Creates a new LabelledResultsVectorWithThumbnail instance.
LabelledWithConfidence<T> - Class in org.anchoranalysis.image.inference.segment: Like WithConfidence but additionally adds a label.
LabelledWithConfidence(String, WithConfidence<T>) - Constructor for class org.anchoranalysis.image.inference.segment.LabelledWithConfidence: Creates a new LabelledWithConfidence instance.
LabelledWithConfidence(T, double, String) - Constructor for class org.anchoranalysis.image.inference.segment.LabelledWithConfidence: Create for given element, confidence and label.
LabelObjects<T> - Class in org.anchoranalysis.image.core.object.label: Writes a unique ID (successive integer IDs) for each elements's voxels into a channel, and 0 for background.
LabelObjects(Function<T, ObjectMask>, BiFunction<T, ReadableTuple3i, T>) - Constructor for class org.anchoranalysis.image.core.object.label.LabelObjects: Creates a new LabelObjects instance.
LabelObjects(Optional<UnaryOperator<T>>, Optional<Consumer<OverlappingObject<T>>>, Function<T, ObjectMask>, BiFunction<T, ReadableTuple3i, T>) - Constructor for class org.anchoranalysis.image.core.object.label.LabelObjects: Creates a new LabelObjects instance.
labels() - Method in class org.anchoranalysis.plugin.image.task.labeller.FileLabelMap: Gets a set of all unique labels in the map.
LabelsForInput - Interface in org.anchoranalysis.plugin.image.task.feature.calculator: Calculates labels for a given input (and index).
Lanczos - Class in org.anchoranalysis.image.voxel.resizer: Resizes with an interpolator that uses Lanczos resampling as implemented in Imglib2.
Lanczos() - Constructor for class org.anchoranalysis.image.voxel.resizer.Lanczos: Default constructor.
LanguageUtilities - Class in org.anchoranalysis.core.value: Utility functions for pluralizing words in strings.
LARGE_2D - Static variable in class org.anchoranalysis.test.image.ChannelFixture: Large 2D extent for testing.
LARGE_3D - Static variable in class org.anchoranalysis.test.image.ChannelFixture: Large 3D extent for testing.
LastDirectories - Class in org.anchoranalysis.plugin.io.bean.file.namer: Derives a name by taking the filename together with optionally several subdirectories names.
LastDirectories() - Constructor for class org.anchoranalysis.plugin.io.bean.file.namer.LastDirectories
LastDirectories(int) - Constructor for class org.anchoranalysis.plugin.io.bean.file.namer.LastDirectories: Creates for a particular number of subdirectories.
LastDirectoryAsPrefix - Class in org.anchoranalysis.plugin.io.bean.file.path.prefixer: Looks for the last directory-name, and removes it in favour of using it as a prefix on a filename
LastDirectoryAsPrefix() - Constructor for class org.anchoranalysis.plugin.io.bean.file.path.prefixer.LastDirectoryAsPrefix
Launch - Class in org.anchoranalysis.launcher: A command-line interface used for launching experiments.
LauncherConfig - Class in org.anchoranalysis.launcher.config: Specifies a configuration of the launcher for a particular application.
LauncherConfig() - Constructor for class org.anchoranalysis.launcher.config.LauncherConfig
LazyEvaluationStore<T> - Class in org.anchoranalysis.core.identifier.provider.store: Lazily delays evaluating items until when they are first retrieved.
LazyEvaluationStore(String) - Constructor for class org.anchoranalysis.core.identifier.provider.store.LazyEvaluationStore: Creates a new LazyEvaluationStore instance.
LEFT - Static variable in class org.anchoranalysis.image.bean.nonbean.spatial.align.PositionChoicesConstants: Align to the left in the X-dimension/
leftPad(String, int) - Static method in class org.anchoranalysis.core.value.StringUtilities: Left-pad a string with whitespace, so it reaches a fixed length.
leftSize() - Method in class org.anchoranalysis.annotation.io.assignment.OverlappingObjects: The total number of objects in the left set.
length() - Method in class org.anchoranalysis.spatial.point.Tuple3d: The magnitude of the tuple.
LessThan - Class in org.anchoranalysis.math.relation: Returns true iff valueFirst is less than valueSecond.
LessThan() - Constructor for class org.anchoranalysis.math.relation.LessThan
LessThanBean - Class in org.anchoranalysis.bean.shared.relation: A relation double1 < double2.
LessThanBean() - Constructor for class org.anchoranalysis.bean.shared.relation.LessThanBean
LessThanEqualTo - Class in org.anchoranalysis.math.relation: Returns true iff valueFirst is less than or equal to valueSecond.
LessThanEqualTo() - Constructor for class org.anchoranalysis.math.relation.LessThanEqualTo
LessThanEqualToBean - Class in org.anchoranalysis.bean.shared.relation: A relation double1 <= double2.
LessThanEqualToBean() - Constructor for class org.anchoranalysis.bean.shared.relation.LessThanEqualToBean
lessThanMaxX() - Method in class org.anchoranalysis.image.voxel.kernel.KernelPointCursor: Whether the current point is less than the image's extent in the X-dimension?
lessThanMaxY() - Method in class org.anchoranalysis.image.voxel.kernel.KernelPointCursor: Whether the current point is less than the image's extent in the Y-dimension?
LevelFromHistogram - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.threshold: Calculates a level (a threshold-value) from a histogram.
LevelFromHistogram() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.LevelFromHistogram
LevelPerObjectBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider.object: Creates a channel with a level calculated for each object using various methods.
LevelPerObjectBase() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectBase
LevelPerObjectIndependently - Class in org.anchoranalysis.plugin.image.bean.channel.provider.object: Creates a channel with different threshold-levels for each object, calculating the level only from the histogram of the particular object.
LevelPerObjectIndependently() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectIndependently
LevelPerObjectNeighbors - Class in org.anchoranalysis.plugin.image.bean.channel.provider.object: Calculates a threshold-level for each object collectively based on other objects
LevelPerObjectNeighbors() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectNeighbors
LevelResult - Class in org.anchoranalysis.plugin.image.intensity.level: Represents the result of a level operation, containing the level value, object mask, and histogram.
LevelResult(int, ObjectMask, Histogram) - Constructor for class org.anchoranalysis.plugin.image.intensity.level.LevelResult: Creates a new LevelResult instance.
LevelResultCollection - Class in org.anchoranalysis.plugin.image.intensity.level: A collection of LevelResult objects that can be iterated over and searched.
LevelResultCollection() - Constructor for class org.anchoranalysis.plugin.image.intensity.level.LevelResultCollection
LevelResultCollectionFactory - Class in org.anchoranalysis.plugin.image.intensity.level: Factory for creating LevelResultCollection objects.
Limit - Class in org.anchoranalysis.plugin.io.bean.file.provider
Limit<T> - Class in org.anchoranalysis.plugin.io.bean.input: Limits the number of input-objects to a certain hard-maximum
Limit() - Constructor for class org.anchoranalysis.plugin.io.bean.file.provider.Limit
Limit() - Constructor for class org.anchoranalysis.plugin.io.bean.input.Limit
LimitIfRequested<T> - Class in org.anchoranalysis.plugin.io.bean.input: Like Limit if it is requested in the InputContextParameters, makes no change to the inputs.
LimitIfRequested() - Constructor for class org.anchoranalysis.plugin.io.bean.input.LimitIfRequested
LimitWithDirectory - Class in org.anchoranalysis.plugin.io.bean.file.provider
LimitWithDirectory() - Constructor for class org.anchoranalysis.plugin.io.bean.file.provider.LimitWithDirectory
Linear - Class in org.anchoranalysis.image.voxel.resizer: Resizes with an interpolator that uses linear interpolation as implemented in Imglib2.
Linear() - Constructor for class org.anchoranalysis.image.voxel.resizer.Linear: Default constructor.
LinearLeastSquaresEllipseFitter - Class in org.anchoranalysis.plugin.points.bean.fitter: Fits a set of points to an ellipse using a linear least squares method.
LinearLeastSquaresEllipseFitter() - Constructor for class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresEllipseFitter
LinearLeastSquaresEllipsoidFitter - Class in org.anchoranalysis.plugin.points.bean.fitter: Fits an ellipsoid to points using a linear least squares approach
LinearLeastSquaresEllipsoidFitter() - Constructor for class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresEllipsoidFitter
LinearLeastSquaresViaNormalEquationBase - Class in org.anchoranalysis.plugin.points.bean.fitter: Base class for linear least squares fitting using the normal equation method.
LinearLeastSquaresViaNormalEquationBase() - Constructor for class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresViaNormalEquationBase
LineSegment - Class in org.anchoranalysis.mpp.mark.points: Represents a line segment in 3D space as a Mark.
LineSegment() - Constructor for class org.anchoranalysis.mpp.mark.points.LineSegment
LineSegment(Point3i, Point3i) - Constructor for class org.anchoranalysis.mpp.mark.points.LineSegment: Constructs a LineSegment with given start and end points.
list() - Method in class org.anchoranalysis.spatial.box.BoundedList: The collection of element with bounding-boxes.
listAfter(List<T>) - Method in class org.anchoranalysis.image.inference.segment.ReductionOutcome: Generates a list of elements that exist after the reduction.
ListBeanFactory<T> - Class in org.anchoranalysis.bean.xml.factory: Factory for creating a List of beans.
ListBeanFactory() - Constructor for class org.anchoranalysis.bean.xml.factory.ListBeanFactory
ListBeanFactory(Function<List<T>, Object>) - Constructor for class org.anchoranalysis.bean.xml.factory.ListBeanFactory: Creates a new ListBeanFactory instance.
listFor(Class<?>) - Method in class org.anchoranalysis.bean.define.Define: Retrieves the list of elements associated with a grouping-root.
listFrom2i(Mask) - Static method in class org.anchoranalysis.image.core.points.PointsFromMask: All points that have on state in a Mask as a list with type Point2i.
listFrom2i(ObjectMask) - Static method in class org.anchoranalysis.image.core.points.PointsFromObject: A list of two-dimensional integer points from the entire object-mask.
listFrom3d(ObjectMask) - Static method in class org.anchoranalysis.image.core.points.PointsFromObject: A list of points from the entire object-mask as Point3d.
listFrom3i(Mask) - Static method in class org.anchoranalysis.image.core.points.PointsFromMask: All points that have on state in a Mask as a list with type Point3i.
listFrom3i(ObjectMask) - Static method in class org.anchoranalysis.image.core.points.PointsFromObject: A list of three-dimensional integer points from the entire object-mask.
listFromAllOutlines2i(ObjectCollection) - Static method in class org.anchoranalysis.image.core.points.PointsFromObject: A list of points as three-dimensional integers from the outline of all objects in a collection.
listFromOutline2i(ObjectMask) - Static method in class org.anchoranalysis.image.core.points.PointsFromObject: A list of points as three-dimensional integers from the outline of an object-mask
listFromOutline3i(ObjectMask) - Static method in class org.anchoranalysis.image.core.points.PointsFromObject: A list of points as Point3i from the outline of an object-mask.
listIterator() - Method in class org.anchoranalysis.io.input.InputsWithDirectory: Returns a list iterator over the elements in this list (in proper sequence).
listWithLabels() - Method in class org.anchoranalysis.image.inference.segment.SegmentedObjectsAtScale: Create a List of all contained objects, including confidence.
listWithoutLabels() - Method in class org.anchoranalysis.image.inference.segment.SegmentedObjectsAtScale: Create a List of all contained objects, including confidence.
ListWithThumbnails<T,S> - Class in org.anchoranalysis.plugin.image.feature.object: A list of items with an associated thumbnail-batch.
ListWithThumbnails(List<T>) - Constructor for class org.anchoranalysis.plugin.image.feature.object.ListWithThumbnails: Creates a new instance without a thumbnail batch.
ListWithThumbnails(List<T>, ThumbnailBatch<S>) - Constructor for class org.anchoranalysis.plugin.image.feature.object.ListWithThumbnails: Creates a new instance with a thumbnail batch.
loadAsObjects(Path, Dimensions, boolean, OperationContext) - Method in class org.anchoranalysis.annotation.io.bean.comparer.ComparableSource: Loads the source of elements from the file-system and converts to a ObjectCollection.
loadAsObjects(Path, Dimensions, boolean, OperationContext) - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.MaskAsObject
loadAsObjects(Path, Dimensions, boolean, OperationContext) - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.Objects
loadBean(Path) - Static method in class org.anchoranalysis.bean.xml.BeanXMLLoader: Creates a bean by loading an XML description from the filesystem
loadBean(Path, String) - Static method in class org.anchoranalysis.bean.xml.BeanXMLLoader: Creates a bean by loading an XML description from the filesystem.
loadBeanAssociatedXml(Path, String) - Static method in class org.anchoranalysis.bean.xml.BeanXMLLoader: Creates a bean by loading an XML description from the filesystem.
loadBeanLocalized(Path, String) - Static method in class org.anchoranalysis.bean.xml.BeanXMLLoader: Creates a bean by loading an XML description from the filesystem.
localise(Path) - Method in class org.anchoranalysis.bean.AnchorBean: Called once after the bean is created, localising the bean to a path on the filesystem.
LocalisedBeanException - Exception Class in org.anchoranalysis.bean.xml.exception: Combines a chain of many exceptions into a single exception, searching for an ultimate cause and incorporating the messages from the chain into a single unified message.
LocalisedBeanException(String, Throwable) - Constructor for exception class org.anchoranalysis.bean.xml.exception.LocalisedBeanException: Create with a message and a cause.
LocalSlices - Class in org.anchoranalysis.image.voxel.kernel: Caches a small number of slices around which we wish to work, so the memory is efficiently accessed.
LocalSlices(int, int, Voxels<UnsignedByteBuffer>) - Constructor for class org.anchoranalysis.image.voxel.kernel.LocalSlices: Create with focus around a particular slice.
log(String) - Method in interface org.anchoranalysis.core.log.MessageLogger: Logs a message.
log(String) - Method in class org.anchoranalysis.core.log.NullMessageLogger
log(String) - Method in class org.anchoranalysis.experiment.bean.log.StatefulNullMessageLogger
log(String) - Method in class org.anchoranalysis.experiment.log.ConsoleMessageLogger
log(String) - Method in class org.anchoranalysis.experiment.log.FailureOnlyMessageLogger
log(String) - Method in class org.anchoranalysis.experiment.log.MessageLoggerIntoString
log(String) - Method in class org.anchoranalysis.experiment.log.MultipleLoggers
log(String) - Method in class org.anchoranalysis.experiment.log.TextFileMessageLogger
logConversionMessages(MessageLogger) - Method in class org.anchoranalysis.plugin.mpp.shared.ConvertedInput: Logs any messages stored from from conversion.
logDescription() - Method in class org.anchoranalysis.plugin.image.object.merge.GraphLogger: Logs a description of the entire graph.
logEmptyLine() - Method in interface org.anchoranalysis.core.log.MessageLogger: Writes an empty line to the log file.
logEnd(JobDescription, JobStateMonitor) - Method in class org.anchoranalysis.experiment.task.processor.JobStartStopLogger: Performs logging for when a job ends.
logFormatted(String, Object...) - Method in interface org.anchoranalysis.core.log.MessageLogger: Logs a message, derived from a format-string.
logFormatted(String, Object...) - Method in class org.anchoranalysis.core.log.NullMessageLogger
logFormatted(String, Object...) - Method in class org.anchoranalysis.experiment.bean.log.StatefulNullMessageLogger
logFormatted(String, Object...) - Method in class org.anchoranalysis.experiment.log.ConsoleMessageLogger
logFormatted(String, Object...) - Method in class org.anchoranalysis.experiment.log.FailureOnlyMessageLogger
logFormatted(String, Object...) - Method in class org.anchoranalysis.experiment.log.MessageLoggerIntoString
logFormatted(String, Object...) - Method in class org.anchoranalysis.experiment.log.MultipleLoggers
logFormatted(String, Object...) - Method in class org.anchoranalysis.experiment.log.TextFileMessageLogger
logger() - Method in class org.anchoranalysis.io.output.writer.ElementOutputter: The associated logger.
Logger - Class in org.anchoranalysis.core.log: A logging-mechanism for both messages and errors.
Logger(MessageLogger) - Constructor for class org.anchoranalysis.core.log.Logger: Constructs with an error-reporter that writes into the message logger.
Logger(MessageLogger, ErrorReporter) - Constructor for class org.anchoranalysis.core.log.Logger: Creates a new Logger instance.
LoggerFixture - Class in org.anchoranalysis.test: Fixture to create a Logger that don't output anything.
LoggingDestination - Class in org.anchoranalysis.experiment.bean.log: The destination(s) to which log-messages are sent.
LoggingDestination() - Constructor for class org.anchoranalysis.experiment.bean.log.LoggingDestination
logGraphDescription() - Method in class org.anchoranalysis.plugin.image.object.merge.MergeGraph: Logs a description of the current graph state.
logMemoryUsage(String, MessageLogger) - Static method in class org.anchoranalysis.core.system.MemoryUtilities: Logs a message to logger describing current memory usage of the JVM.
logStart(JobDescription) - Method in class org.anchoranalysis.experiment.task.processor.JobStartStopLogger: Performs logging for when a job starts.
LONG_OPTION_GROUP - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions: Activates grouping from a subset of the identifier's elements.
LONG_OPTION_INPUT_RANDOM_SAMPLE - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions: Randomly samples a number of inputs.
LONG_OPTION_OUTPUT - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions: Changes output manager.
LONG_OPTION_OUTPUT_CONSOLE_ONLY - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions: Output console only.
lowerCountExistsThan(int) - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateAtCorner
lowerCountExistsThan(int) - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateImplementation
lowerCountExistsThan(int) - Method in interface org.anchoranalysis.image.voxel.extracter.predicate.VoxelsPredicate: Whether the count is less than a particular threshold.
LRUCache<K,V> - Class in org.anchoranalysis.core.cache: A cache that discards items that haven't being used recently or frequently.
LRUCache(int, CheckedFunction<K, V, E>) - Constructor for class org.anchoranalysis.core.cache.LRUCache: Constructor.

M

main(String[]) - Static method in class org.anchoranalysis.launcher.Launch: Entry point for command-line application.
makeCopy(Path, Path) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.method.CopyFilesMethod: Makes a copy of the file at source at destination.
makeCopyWithDirectory(Path, Path) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.method.Bytewise
makeCopyWithDirectory(Path, Path) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.method.CompressAnyTIFF
makeCopyWithDirectory(Path, Path) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.method.CopyFilesMethod: Like CopyFilesMethod.makeCopy(Path,Path) but after any necessary directories are created so destination can be written.
makeOutputPath(String) - Method in class org.anchoranalysis.io.output.outputter.OutputterChecked: Creates a full absolute path that completes the part of the path present in the outputter with an additional suffix.
makeOutputPath(Optional<String>, String, String) - Method in class org.anchoranalysis.io.output.outputter.OutputterChecked: Like OutputterChecked.makeOutputPath(String) but additionally adds an extension.
makeOutputPath(Optional<String>, String, String) - Method in class org.anchoranalysis.io.output.writer.ElementOutputter: Creates a full absolute path that completes the part of the path present in the outputter with an additional suffix.
makePathAbsolute(Optional<String>, Optional<String>, String) - Method in class org.anchoranalysis.io.output.path.prefixer.DirectoryWithPrefix
makePathAbsolute(Optional<String>, Optional<String>, String) - Method in interface org.anchoranalysis.io.output.path.prefixer.PathCreator: Generates a full path, given the final part (suffix) of a path.
makePathRelative(Path) - Method in class org.anchoranalysis.io.output.path.prefixer.DirectoryWithPrefix
makePathRelative(Path) - Method in interface org.anchoranalysis.io.output.path.prefixer.PathCreator: Extracts a relative-file path, given the final part (suffix) of a path.
makeRGBStack(Stack, boolean) - Static method in class org.anchoranalysis.plugin.opencv.convert.ConvertToMat: Derives a Mat representing an RGB stack.
makeSureConfigured() - Method in class org.anchoranalysis.io.bioformats.ConfigureBioformatsLogging: Makes sure logging is configured
map(Function<T, S>) - Method in class org.anchoranalysis.image.inference.segment.DualScale: Create a derived DualScale by applying an identical mapping to each element.
map(Function<T, S>) - Method in class org.anchoranalysis.image.inference.segment.LabelledWithConfidence: Maps the existing object to another object, while retaining an identical confidence score.
map(Function<T, S>) - Method in class org.anchoranalysis.image.inference.segment.WithConfidence: Maps the existing object to another object, while retaining an identical confidence score.
map(Function<T, S>) - Method in class org.anchoranalysis.io.input.InputsWithDirectory: Creates a new InputsWithDirectory which is the result of mapping the existing inputs.
map(UnaryOperator<Integer>, Function<T, S>) - Method in class org.anchoranalysis.image.inference.segment.ReductionOutcome: Creates a new ReductionOutcome where both the retained-indices and the newly-added elements may be mapped.
map(UnaryOperator<ObjectMask>) - Method in class org.anchoranalysis.image.core.object.properties.ObjectWithProperties: Maps the underlying object-mask to another object-mask, reusing the same properties object.
map(Optional<S>, CheckedFunction<S, T, E>) - Static method in class org.anchoranalysis.core.functional.OptionalUtilities: Like Optional.map(java.util.function.Function<? super T, ? extends U>) but tolerates an exception in the mapping function, which is immediately thrown.
map(Stream<S>, Class<? extends Exception>, CheckedFunction<S, T, E>) - Static method in class org.anchoranalysis.core.functional.CheckedStream: Performs a Stream.map(java.util.function.Function<? super T, ? extends R>) but accepts a function that can throw a checked-exception.
map(CheckedFunction<Feature<T>, Feature<S>, E>) - Method in class org.anchoranalysis.feature.bean.list.FeatureList: Creates a new feature-list where each feature is the result of applying a map-function to an existing feature.
map(CheckedFunction<ObjectMask, ObjectMask, E>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream: Creates a new ObjectCollection after mapping each item to another.
map(CheckedFunction<T, S, E>, Class<? extends E>) - Method in class org.anchoranalysis.io.input.InputsWithDirectory: Creates a new InputsWithDirectory which is the result of mapping the existing inputs.
mapBoth(Optional, Optional<V>, CheckedBiFunction<U, V, T, E>) - Static method in class org.anchoranalysis.core.functional.OptionalUtilities: Mapping only occurs if both Optionals are non-empty (equivalent to a logical and on the optionals)
mapBoundingBoxChangeExtent(BoundingBox) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Applies a function to map the bounding-box to a new-value (whose extent is expected to change in value).
mapBoundingBoxChangeExtent(BoundingBox) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream: Creates a new ObjectCollection after mapping the bounding-box on each object (while maybe changing the extent).
mapBoundingBoxPreserveExtent(UnaryOperator<BoundingBox>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Applies a function to map the bounding-box to a new-value (whose extent should be unchanged in value).
mapBoundingBoxPreserveExtent(UnaryOperator<BoundingBox>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream: Creates a new ObjectCollection after mapping the bounding-box on each object (whose extent should remain unchanged).
mapBoundingBoxPreserveExtent(BoundingBox) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: Applies a function to map the bounding-box to a new-value.
mapCalculator(UnaryOperator<FeatureCalculatorMulti<T>>) - Method in class org.anchoranalysis.image.feature.calculator.NamedFeatureCalculatorMulti: Creates a new instance by applying a mapping function to the calculator.
mapChannel(CheckedUnaryOperator<Channel, OperationFailedException>) - Method in class org.anchoranalysis.image.core.stack.RGBStack: Produces a new stack with a particular mapping applied to each channel.
mapChannel(CheckedUnaryOperator<Channel, OperationFailedException>) - Method in class org.anchoranalysis.image.core.stack.Stack: Produces a new stack with a particular mapping applied to each channel.
mapChannelIfSupported(int, BiFunction<Channel, ChannelConverterAttached<Channel, UnsignedByteBuffer>, T>, Function<Channel, T>) - Method in class org.anchoranalysis.image.core.stack.ChannelMapper: Maps a Channel with mapFunction if a corresponding converter exists, otherwise with fallback.
mapChannelWithIndex(CheckedBiFunction<Channel, Integer, Channel, OperationFailedException>) - Method in class org.anchoranalysis.image.core.stack.Stack: Produces a new stack with a particular mapping applied to each channel (with an index of the channel also available).
MapCreate<K,V> - Class in org.anchoranalysis.core.collection: A tree map that creates a new item, if it doesn't already exist upon a get operation.
MapCreate(Supplier<V>) - Constructor for class org.anchoranalysis.core.collection.MapCreate: Creates without a comparator, using a HashMap internally.
MapCreate(Supplier<V>, Comparator<K>) - Constructor for class org.anchoranalysis.core.collection.MapCreate: Creates with an explicit comparator, and using a TreeMap internally.
MapCreateCountdown<K,V> - Class in org.anchoranalysis.core.collection: Like a MapCreate but with an associated counter for each element.
MapCreateCountdown(Supplier<V>, CheckedBiConsumer<K, V, OperationFailedException>) - Constructor for class org.anchoranalysis.core.collection.MapCreateCountdown: Creates without a comparator, using a HashMap internally.
mapFrom(Iterable<S>, CheckedFunction<S, Feature<T>, E>) - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory: Creates a new feature-list by mapping an Iterable to Feature
mapFrom(Iterable<T>, Class<? extends E>, CheckedFunction<T, ObjectMask, E>) - Static method in class org.anchoranalysis.image.voxel.object.ObjectCollectionFactory: Creates a new collection by mapping an Iterable to ObjectMask.
mapFrom(Iterable<T>, Function<T, ObjectMask>) - Static method in class org.anchoranalysis.image.voxel.object.ObjectCollectionFactory: Creates a new collection by mapping an Iterable to ObjectMask.
mapFromFiltered(Iterable<S>, Predicate<S>, CheckedFunction<S, Feature<T>, E>) - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory: Creates a new feature-list by filtering an iterable and then mapping it to a feature
mapFromOptional(Iterable<T>, Class<? extends Exception>, CheckedFunction<T, Optional<ObjectMask>, E>) - Static method in class org.anchoranalysis.image.voxel.object.ObjectCollectionFactory: Creates a new collection by mapping an Iterable to Optional.
mapFromOptional(Iterable<T>, Function<T, Optional<ObjectMask>>) - Static method in class org.anchoranalysis.image.voxel.object.ObjectCollectionFactory: Creates a new collection by mapping an Iterable to Optional.
mapFromOptional(Iterator<T>, Class<? extends Exception>, CheckedFunction<T, Optional<ObjectMask>, E>) - Static method in class org.anchoranalysis.image.voxel.object.ObjectCollectionFactory: Creates a new collection by mapping an Iterator to Optional.
mapFromOptional(Iterator<T>, Function<T, Optional<ObjectMask>>) - Static method in class org.anchoranalysis.image.voxel.object.ObjectCollectionFactory: Creates a new collection by mapping an Iterator to Optional.
mapFromRange(int, int, Class<? extends Exception>, CheckedIntFunction<ObjectMask, E>) - Static method in class org.anchoranalysis.image.voxel.object.ObjectCollectionFactory: Creates a new collection by mapping integers (from a range) each to a ObjectMask.
mapFromRange(int, int, IntFunction<Feature<T>>) - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory: Creates a new feature-list by mapping integers (from a range) each to a feature
mapFromRange(int, int, IntFunction<ObjectMask>) - Static method in class org.anchoranalysis.image.voxel.object.ObjectCollectionFactory: Creates a new collection by mapping integers (from a range) each to a ObjectMask.
mapFromRangeOptional(int, int, Class<? extends Exception>, CheckedIntFunction<Optional<Feature<T>>, E>) - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory: Creates a new feature-list by mapping integers (from a range) each to an optional feature
mapIdentifier(BiFunction<String, File, String>) - Method in class org.anchoranalysis.io.input.file.NamedFile: Immutably renames the file, by assigning it a new identifier.
mapIntStream(IntStream, Class<? extends Exception>, CheckedIntFunction<T, E>) - Static method in class org.anchoranalysis.core.functional.CheckedStream: Creates a new feature-list by mapping integers (from a range) each to an optional feature accepting a checked-exception
mapRangeToList(int, int, IntFunction<T>) - Static method in class org.anchoranalysis.core.functional.FunctionalList: Creates a list of elements, where each element corresponds to an index in a range.
mapToInt(Stream<S>, Class<? extends Exception>, CheckedToIntFunction<S, E>) - Static method in class org.anchoranalysis.core.functional.CheckedStream: Performs a Stream.mapToInt(java.util.function.ToIntFunction<? super T>) but accepts a function that can throw a checked-exception.
mapToList(Collection<S>, Class<? extends Exception>, CheckedFunction<S, T, E>) - Static method in class org.anchoranalysis.core.functional.FunctionalList: Like FunctionalList.mapToList(Object[], Function) but tolerates exceptions in the mapping function.
mapToList(Collection<S>, Collection, BiFunction<S, U, T>) - Static method in class org.anchoranalysis.core.functional.FunctionalList: Maps a collection to a list with each element derived from a corresponding element in the original collection, as well as a corresponding argument from a second list.
mapToList(Collection<S>, Function<S, T>) - Static method in class org.anchoranalysis.core.functional.FunctionalList: Maps a collection to a list with each element derived from a corresponding element in the original collection.
mapToList(Stream<S>, Class<? extends Exception>, CheckedFunction<S, T, E>) - Static method in class org.anchoranalysis.core.functional.FunctionalList: Like FunctionalList.mapToList(Stream, Function) but tolerates exceptions in the mapping function.
mapToList(Stream<S>, Function<S, T>) - Static method in class org.anchoranalysis.core.functional.FunctionalList: Maps a stream to a list with each element derived from a corresponding element in the original collection.
mapToList(CheckedFunction<ObjectMask, T, E>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream: Creates a new List after mapping each item to another type.
mapToList(S[], Class<? extends Exception>, CheckedFunction<S, T, E>) - Static method in class org.anchoranalysis.core.functional.FunctionalList: Like FunctionalList.mapToList(Object[], Function) but tolerates exceptions in the mapping function.
mapToList(S[], Function<S, T>) - Static method in class org.anchoranalysis.core.functional.FunctionalList: Maps an array to a list with each element derived from a corresponding element in the original array.
mapToListOptional(Collection<S>, Class<? extends Exception>, CheckedFunction<S, Optional<T>, E>) - Static method in class org.anchoranalysis.core.functional.FunctionalList: Maps a collection to a list with each element in the original collection maybe producing an element in the output.
mapToListOptional(Collection<S>, Class<? extends Exception>, CheckedFunction<S, Optional<T>, E>) - Static method in class org.anchoranalysis.core.functional.FunctionalListParallel: Maps a collection to a list with each element in the original collection maybe producing an element in the output.
mapToListOptional(Collection<S>, Function<S, Optional<T>>) - Static method in class org.anchoranalysis.core.functional.FunctionalList: Maps a collection to a list with each element in the original collection maybe producing an element in the output.
mapToListOptional(Stream<S>, Class<? extends Exception>, CheckedFunction<S, Optional<T>, E>) - Static method in class org.anchoranalysis.core.functional.FunctionalList: Maps a stream to a list with each element in the original collection maybe producing an element in the output.
mapToListOptional(CheckedFunction<ObjectMask, Optional<T>, E>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream: Creates a new List after mapping each item to another (optional) type
mapToListOptionalWithIndex(List<S>, Class<? extends Exception>, CheckedFunctionWithInt<S, Optional<T>, E>) - Static method in class org.anchoranalysis.core.functional.FunctionalList: Maps a list to a new list with each element in the original collection maybe producing an element in the output.
mapToListWithIndex(List<S>, Class<? extends Exception>, CheckedFunctionWithInt<S, T, E>) - Static method in class org.anchoranalysis.core.functional.FunctionalList: Maps a collection to a list with each element derived from a corresponding element in the original collection - and also letting the map function use an index.
mapToListWithIndex(List<S>, FunctionWithInt<S, T>) - Static method in class org.anchoranalysis.core.functional.FunctionalList: Maps a collection to a list with each element derived from a corresponding element in the original collection - and also letting the map function use an index.
mapToObj(IntStream, Class<? extends Exception>, CheckedIntFunction<T, E>) - Static method in class org.anchoranalysis.core.functional.CheckedStream: Performs a IntStream.mapToObj(java.util.function.IntFunction<? extends U>) but accepts a function that can throw a checked-exception.
mapToSortedSet(CheckedFunction<ObjectMask, T, E>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream: Creates a new SortedSet after mapping each item to another type.
Mark - Class in org.anchoranalysis.mpp.mark: Abstract base class representing a mark in 3D space.
Mark() - Constructor for class org.anchoranalysis.mpp.mark.Mark
Mark(Mark) - Constructor for class org.anchoranalysis.mpp.mark.Mark: Copy constructor.
markAsCompleted(boolean) - Method in class org.anchoranalysis.experiment.task.processor.JobStateMonitor: Indicates that a job has stopped executing, and has completed.
markAsExecuting() - Method in class org.anchoranalysis.experiment.task.processor.JobStateMonitor: Indicates that a job is currently executing.
markAsTemporary(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedIntBuffer: Marks the value at the given offset as temporary.
markBounds() - Method in class org.anchoranalysis.mpp.init.MarksInitialization: Store for mark bounds.
MarkBounds - Class in org.anchoranalysis.mpp.bean.bound: Abstract base class for defining bounds on marks in a marked point process.
MarkBounds() - Constructor for class org.anchoranalysis.mpp.bean.bound.MarkBounds
MarkBoundsProvider - Class in org.anchoranalysis.mpp.bean.provider: An abstract provider for MarkBounds.
MarkBoundsProvider() - Constructor for class org.anchoranalysis.mpp.bean.provider.MarkBoundsProvider
MarkCollection - Class in org.anchoranalysis.mpp.mark: An ordered collection of Marks.
MarkCollection() - Constructor for class org.anchoranalysis.mpp.mark.MarkCollection: Creates with no elements in the collection.
MarkCollection(List) - Constructor for class org.anchoranalysis.mpp.mark.MarkCollection: Creates a new MarkCollection instance.
MarkCollection(Stream) - Constructor for class org.anchoranalysis.mpp.mark.MarkCollection: Creates from a stream of Marks.
MarkCollection(Mark) - Constructor for class org.anchoranalysis.mpp.mark.MarkCollection: Creates from a single Mark.
MarkCollectionProposer - Class in org.anchoranalysis.mpp.bean.proposer: An abstract base class for proposing an entire collection (configuration) of marks.
MarkCollectionProposer() - Constructor for class org.anchoranalysis.mpp.bean.proposer.MarkCollectionProposer
markCollectionProposers() - Method in class org.anchoranalysis.mpp.init.MarksInitialization: Store for mark collection proposers.
MarkCollectionProvider - Class in org.anchoranalysis.mpp.bean.provider: Provides a collection of marks
MarkCollectionProvider() - Constructor for class org.anchoranalysis.mpp.bean.provider.MarkCollectionProvider
MarkConicFactory - Class in org.anchoranalysis.mpp.mark.conic: Factory class for creating conic marks (ellipses and ellipsoids) from points.
MarkEllipseFactory - Class in org.anchoranalysis.mpp.bean.mark.factory: A factory for creating Ellipse marks.
MarkEllipseFactory() - Constructor for class org.anchoranalysis.mpp.bean.mark.factory.MarkEllipseFactory
MarkEllipsoidFactory - Class in org.anchoranalysis.mpp.bean.mark.factory: A factory for creating Ellipsoid marks.
MarkEllipsoidFactory() - Constructor for class org.anchoranalysis.mpp.bean.mark.factory.MarkEllipsoidFactory
MarkEvaluator - Class in org.anchoranalysis.mpp.feature.bean.mark: A bean for evaluating marks using features and energy schemes.
MarkEvaluator() - Constructor for class org.anchoranalysis.mpp.feature.bean.mark.MarkEvaluator
MarkFactory - Class in org.anchoranalysis.mpp.bean.mark.factory: An abstract base class for factories that create Mark objects.
MarkFactory() - Constructor for class org.anchoranalysis.mpp.bean.mark.factory.MarkFactory
MarkFromCollectionProposer - Class in org.anchoranalysis.mpp.bean.proposer: An abstract base class for proposing a selection of a single mark from a collection of marks.
MarkFromCollectionProposer() - Constructor for class org.anchoranalysis.mpp.bean.proposer.MarkFromCollectionProposer
MarkMergeProposer - Class in org.anchoranalysis.mpp.bean.proposer: An abstract base class for proposing merges between marks.
MarkMergeProposer() - Constructor for class org.anchoranalysis.mpp.bean.proposer.MarkMergeProposer
markMergeProposers() - Method in class org.anchoranalysis.mpp.init.MarksInitialization: Store for mark merge proposers.
MarkPair<T> - Class in org.anchoranalysis.mpp.pair: Represents a pair of marks, with a source and destination.
MarkPair(T, T) - Constructor for class org.anchoranalysis.mpp.pair.MarkPair: Constructs a new MarkPair.
MarkPairCollection - Class in org.anchoranalysis.mpp.feature.mark: A collection of MarkPairs with Marks as the underlying type.
MarkPairCollection() - Constructor for class org.anchoranalysis.mpp.feature.mark.MarkPairCollection: Creates a new MarkPairCollection.
markPairs() - Method in class org.anchoranalysis.mpp.init.MarksInitialization: Store for random collections of mark pairs.
MarkPointListFactory - Class in org.anchoranalysis.mpp.bean.mark.factory: A factory for creating PointList marks.
MarkPointListFactory() - Constructor for class org.anchoranalysis.mpp.bean.mark.factory.MarkPointListFactory
MarkProposer - Class in org.anchoranalysis.mpp.bean.proposer: An abstract base class for proposing changes to a mark.
MarkProposer() - Constructor for class org.anchoranalysis.mpp.bean.proposer.MarkProposer
markProposers() - Method in class org.anchoranalysis.mpp.init.MarksInitialization: Store for mark proposers.
MarkProposerStrategy - Class in org.anchoranalysis.plugin.annotation.bean.strategy: Annotates each image with a mark using a mark proposer and points fitter.
MarkProposerStrategy() - Constructor for class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy
MarkRegion - Class in org.anchoranalysis.mpp.bean.mark: An abstract base class for defining regions associated with marks.
MarkRegion() - Constructor for class org.anchoranalysis.mpp.bean.mark.MarkRegion
marks() - Method in interface org.anchoranalysis.annotation.mark.AnnotationWithMarks: The marks associated with the annotation
marks() - Method in class org.anchoranalysis.annotation.mark.DualMarksAnnotation
marks() - Method in class org.anchoranalysis.mpp.init.MarksInitialization: Store for mark collections.
marks() - Method in class org.anchoranalysis.mpp.io.input.MultiInput: Gets the map of MarkCollections.
marksAt(Point3i, RegionMap, int) - Method in class org.anchoranalysis.mpp.mark.MarkCollection: Finds marks at a specific point that belong to a specific region.
MarksBaseProvider<T,S> - Class in org.anchoranalysis.mpp.bean.provider: Base class for MarksBean that implements Provider to provide an object of type S.
MarksBaseProvider() - Constructor for class org.anchoranalysis.mpp.bean.provider.MarksBaseProvider
MarksBean<T> - Class in org.anchoranalysis.mpp.bean: An abstract base class for beans related to marks in MPP (Marked Point Process).
MarksBean() - Constructor for class org.anchoranalysis.mpp.bean.MarksBean: Creates a new instance of MarksBean.
marksDeriver() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy: Gets the marks deriver path if set.
marksFromOverlays(ColoredOverlayCollection) - Static method in class org.anchoranalysis.mpp.overlay.OverlayCollectionMarkFactory: Creates ColoredMarks from a ColoredOverlayCollection.
marksFromOverlays(OverlayCollection) - Static method in class org.anchoranalysis.mpp.overlay.OverlayCollectionMarkFactory: Creates a MarkCollection from an OverlayCollection.
MarksInitialization - Class in org.anchoranalysis.mpp.init: Initialization class for marks-related components in the MPP framework.
MarksInitialization(ImageInitialization) - Constructor for class org.anchoranalysis.mpp.init.MarksInitialization: Constructs a MarksInitialization with the given ImageInitialization.
MarksInitializationFactory - Class in org.anchoranalysis.mpp.io.input: Factory for creating MarksInitialization instances.
MarkSplitProposer - Class in org.anchoranalysis.mpp.bean.proposer: An abstract base class for proposing splits of a mark into two new marks.
MarkSplitProposer() - Constructor for class org.anchoranalysis.mpp.bean.proposer.MarkSplitProposer
markSplitProposers() - Method in class org.anchoranalysis.mpp.init.MarksInitialization: Store for mark split proposers.
MarksWithEnergyBreakdown - Class in org.anchoranalysis.mpp.feature.energy.marks: Marks with both the total energy and a breakdown by clique.
MarksWithEnergyBreakdown(MarksWithTotalEnergy) - Constructor for class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown: Creates a new instance with the given marks and total energy.
MarksWithEnergyBreakdown(MarksWithTotalEnergy, EnergySavedIndividual, EnergySavedPairs, EnergySavedAll) - Constructor for class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown: Creates a new MarksWithEnergyBreakdown instance.
MarksWithTotalEnergy - Class in org.anchoranalysis.mpp.feature.energy.marks: A collection of marks with an associated (total) energy.
MarksWithTotalEnergy(MarkCollection, EnergySchemeWithSharedFeatures) - Constructor for class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy: Creates a new instance with the given marks and energy scheme.
MarkToObjectConverter - Class in org.anchoranalysis.mpp.mark: Converts a confidence-associated Mark to an equivalent ObjectMask.
MarkToObjectConverter(Optional<ScaleFactor>, Dimensions) - Constructor for class org.anchoranalysis.mpp.mark.MarkToObjectConverter: Create for particular Dimensions with a scaling-factor.
MarkToObjectConverter(Optional<ScaleFactor>, Dimensions, RegionMembershipWithFlags, BinaryValuesByte) - Constructor for class org.anchoranalysis.mpp.mark.MarkToObjectConverter: Creates a new MarkToObjectConverter instance.
MarkToObjectConverter(Dimensions) - Constructor for class org.anchoranalysis.mpp.mark.MarkToObjectConverter: Create for particular Dimensions without a scaling-factor.
MarkWithIdentifierFactory - Class in org.anchoranalysis.mpp.bean.mark.factory: A factory for creating marks with unique identifiers.
MarkWithIdentifierFactory() - Constructor for class org.anchoranalysis.mpp.bean.mark.factory.MarkWithIdentifierFactory
MarkWithIdentifierFactory(MarkFactory) - Constructor for class org.anchoranalysis.mpp.bean.mark.factory.MarkWithIdentifierFactory: Constructs a MarkWithIdentifierFactory with a specified template mark factory.
MarkWithPosition - Class in org.anchoranalysis.mpp.mark: An abstract base class for marks that have a position in 3D space.
MarkWithPosition() - Constructor for class org.anchoranalysis.mpp.mark.MarkWithPosition: Constructs a new MarkWithPosition with a default position at the origin.
MarkWithPosition(MarkWithPosition) - Constructor for class org.anchoranalysis.mpp.mark.MarkWithPosition: Copy constructor for MarkWithPosition.
MarkWithPositionAndSingleRadius - Class in org.anchoranalysis.mpp.mark.conic: Base-class for a conic that has a single radius (circle, sphere etc.)
MarkWithPositionAndSingleRadius() - Constructor for class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
MarkWithPositionAndSingleRadius(Bound) - Constructor for class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius: Constructor with a bound on the radius.
MarkWithPositionAndSingleRadius(MarkWithPositionAndSingleRadius) - Constructor for class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius: Copy constructor.
mask(String) - Static method in class org.anchoranalysis.plugin.image.provider.ReferenceFactory: Creates a reference to a mask.
Mask - Class in org.anchoranalysis.image.core.mask: A channel whose voxel-values are restricted to two states (on and off).
Mask(Channel) - Constructor for class org.anchoranalysis.image.core.mask.Mask: Creates a mask from an existing channel using default values for off (0) and on (255).
Mask(Channel, BinaryValuesInt) - Constructor for class org.anchoranalysis.image.core.mask.Mask: Creates a mask from an existing channel.
Mask(Dimensions, BinaryValuesInt) - Constructor for class org.anchoranalysis.image.core.mask.Mask: Creates a new empty mask of particular dimensions and with particular BinaryValuesInt.
Mask(BinaryVoxels<UnsignedByteBuffer>) - Constructor for class org.anchoranalysis.image.core.mask.Mask: Creates a mask from an existing binary-voxels using default image resolution.
Mask(BinaryVoxels<UnsignedByteBuffer>, Optional<Resolution>) - Constructor for class org.anchoranalysis.image.core.mask.Mask: Creates a mask from an existing binary-voxels and a specific image resolution.
MaskAnd - Class in org.anchoranalysis.image.core.mask.combine: Performs a logical and operation on corresponding voxels in two Masks.
MaskAsObject - Class in org.anchoranalysis.plugin.annotation.bean.comparer: Loads Mask to compared, converting it into an ObjectMask.
MaskAsObject() - Constructor for class org.anchoranalysis.plugin.annotation.bean.comparer.MaskAsObject
MaskAsSingleObject<T> - Class in org.anchoranalysis.plugin.image.feature.bean.shared.object: Calculates a feature, treating a mask as a single-object on the energy-stack.
MaskAsSingleObject() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.shared.object.MaskAsSingleObject
maskExtent(boolean) - Static method in class org.anchoranalysis.test.image.MaskFixture: The **size** across multiple dimensions of the mask that will be created.
MaskFactory - Class in org.anchoranalysis.image.core.mask: Helper routines to create new instances of Mask.
MaskFixture - Class in org.anchoranalysis.test.image: Creates two or three-dimensional Masks for tests.
MaskFromObjects - Class in org.anchoranalysis.image.core.mask: Creates a Mask from one or more ObjectMasks.
MaskIntersectionAssigner - Class in org.anchoranalysis.plugin.annotation.bean.comparison.assigner: No outputs are produced.
MaskIntersectionAssigner() - Constructor for class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.MaskIntersectionAssigner
MaskInverter - Class in org.anchoranalysis.image.core.mask: Inverts masks and objects.
MaskOr - Class in org.anchoranalysis.image.core.mask.combine: Performs a logical or operation on corresponding voxels in two Masks.
MaskProvider - Class in org.anchoranalysis.image.bean.provider: Base class for beans that implement Provider to provide a Mask and associated Stack.
MaskProvider() - Constructor for class org.anchoranalysis.image.bean.provider.MaskProvider
MaskProviderUnary - Class in org.anchoranalysis.image.bean.provider: Implementation of MaskProvider that calls a single delegate MaskProvider.
MaskProviderUnary() - Constructor for class org.anchoranalysis.image.bean.provider.MaskProviderUnary
MaskReader - Class in org.anchoranalysis.image.io.stack.input: Utility functions for reading a Mask from the file-system.
masks() - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitialization: A collection of Masks, indexed by name.
MaskXor - Class in org.anchoranalysis.image.core.mask.combine: Performs a logical xor (exclusive or) operation on corresponding voxels in two Masks.
match(int, int) - Method in class org.anchoranalysis.math.optimization.HungarianAlgorithm: Helper method to record a matching between worker w and job j.
match(String) - Method in class org.anchoranalysis.bean.shared.regex.RegEx: Returns an array of string components it matches successfully, or Optional.empty() if it cannot match.
match(String) - Method in class org.anchoranalysis.bean.shared.regex.RegExList
match(String) - Method in class org.anchoranalysis.bean.shared.regex.RegExSimple
match(String, ZoneOffset) - Method in class org.anchoranalysis.plugin.io.bean.file.pattern.TimestampPattern: Matches certain times.
match(ObjectMask, Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.collective.DiscardOutliers
match(ObjectMask, Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.GreaterIntersectionWith
match(ObjectMask, Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntensityGreaterEqualThan
match(ObjectMask, Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntersectsWith
match(ObjectMask, Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.NotTouchingSceneBorder
match(ObjectMask, Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterPredicate: A predicate condition for an object to be kept in the collection.
match(ObjectMask, Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterRelation
match(ObjectMask, Optional<Dimensions>, DoubleBiPredicate) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.collective.RelationWithMatches
match(ObjectMask, Optional<Dimensions>, DoubleBiPredicate) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedFeature
match(ObjectMask, Optional<Dimensions>, DoubleBiPredicate) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedVolume
match(ObjectMask, Optional<Dimensions>, DoubleBiPredicate) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterRelation: Performs the matching operation using the resolved relation.
Match - Class in org.anchoranalysis.plugin.image.bean.object.provider.filter: Provides an ObjectCollection by matching objects using a specified ObjectMatcher.
Match() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.filter.Match
matchAllDimensions(IntPredicate) - Method in interface org.anchoranalysis.spatial.point.ReadableTuple3i: Whether the values in all dimensions satisfy a predicate.
matchAllDimensions(ReadableTuple3i, IntBinaryPredicate) - Method in interface org.anchoranalysis.spatial.point.ReadableTuple3i: Whether the values in each dimension satisfy a predicate, where the value in the current object is the left argument, and the corresponding value in point forms the right argument.
MatchedObject - Class in org.anchoranalysis.image.core.object: An object with associated matches.
MatchedObject(ObjectMask, ObjectCollection) - Constructor for class org.anchoranalysis.image.core.object.MatchedObject: Creates a new MatchedObject instance.
MatcherIntersectionHelper - Class in org.anchoranalysis.plugin.image.bean.object.match: Helper class for matching objects based on intersection.
matches(String) - Method in interface org.anchoranalysis.core.format.FileFormat: Does a file-path (or file-name) end with an extension expected by this format?
matches(String) - Method in enum class org.anchoranalysis.core.format.ImageFileFormat
matches(String) - Method in enum class org.anchoranalysis.core.format.NonImageFileFormat
matches(String, String) - Static method in class org.anchoranalysis.core.format.FormatExtensions: Does a filePath match an extension?
matches(Path) - Method in interface org.anchoranalysis.core.format.FileFormat: Does a filePath (or fileName) have an extension expected by this format?
matchesIdentifier(String) - Method in interface org.anchoranalysis.core.format.FileFormat: Does an identifier equal the extension expected by this format?
matchesIdentifier(String) - Method in enum class org.anchoranalysis.core.format.ImageFileFormat
matchesIdentifier(String) - Method in enum class org.anchoranalysis.core.format.NonImageFileFormat
MatchExtensions - Class in org.anchoranalysis.io.input.bean.path.matcher: Maybe imposes a file-extension condition, optionally on top of an existing matcher.
MatchExtensions() - Constructor for class org.anchoranalysis.io.input.bean.path.matcher.MatchExtensions
MatchExtensions(String...) - Constructor for class org.anchoranalysis.io.input.bean.path.matcher.MatchExtensions: Create for specific extensions.
matchFile(Path) - Method in class org.anchoranalysis.io.input.path.matcher.DualPathPredicates: Whether the path to a particular file matches the predicate file?
MatchGlob - Class in org.anchoranalysis.io.input.bean.path.matcher: Matches paths using a Java-style glob.
MatchGlob() - Constructor for class org.anchoranalysis.io.input.bean.path.matcher.MatchGlob
MatchGlob(String) - Constructor for class org.anchoranalysis.io.input.bean.path.matcher.MatchGlob: Creates a new MatchGlob instance.
matchingFiles(Path, boolean) - Method in class org.anchoranalysis.io.input.bean.path.matcher.FilePathMatcher: Like FilePathMatcher.matchingFiles(Path, boolean, boolean, boolean, Optional, Optional) but uses sensible defaults.
matchingFiles(Path, boolean, boolean, boolean, Optional<Integer>, Optional<InputManagerParameters>) - Method in class org.anchoranalysis.io.input.bean.path.matcher.FilePathMatcher: Finds a collection of files that match particular conditions on their paths.
matchingFilesForDirectory(Path, InputManagerParameters) - Method in class org.anchoranalysis.io.input.bean.files.FilesProviderWithDirectory: The matching files for this provider that exist in a particular directory.
matchingFilesForDirectory(Path, InputManagerParameters) - Method in class org.anchoranalysis.io.input.bean.files.FilesProviderWithDirectoryUnary
matchingFilesForDirectory(Path, InputManagerParameters) - Method in class org.anchoranalysis.io.input.bean.files.SearchDirectory
matchingFilesForDirectory(Path, InputManagerParameters) - Method in class org.anchoranalysis.io.input.bean.files.SingleFile
matchingFilesForDirectory(Path, InputManagerParameters) - Method in class org.anchoranalysis.plugin.io.bean.file.provider.FileSetFromStringSet
matchingFilesForDirectory(Path, InputManagerParameters) - Method in class org.anchoranalysis.plugin.io.bean.input.files.provider.DirectoryDepth
matchingLeafDirectories(List<Path>) - Method in class org.anchoranalysis.io.input.path.matcher.DualPathPredicates: Creates a new list of paths to leaf-directories that match the predicate directory.
matchIntersectingObjects(ObjectCollection, ObjectCollection) - Static method in class org.anchoranalysis.plugin.image.bean.object.match.MatcherIntersectionHelper: Matches objects from the source collection with intersecting objects from the search collection.
MatchRegularExpression - Class in org.anchoranalysis.io.input.bean.path.matcher: Predicates that matches a file-path against a regular expression.
MatchRegularExpression() - Constructor for class org.anchoranalysis.io.input.bean.path.matcher.MatchRegularExpression
max() - Method in class org.anchoranalysis.math.arithmetic.RunningSumExtrema: The maximum across all values passed to RunningSumExtrema.add(double) or Double.MIN_VALUE if the method was never called.
max(double) - Method in class org.anchoranalysis.spatial.point.Point3d: Element-wise maximum between this point and a scalar.
max(int) - Method in class org.anchoranalysis.spatial.point.Tuple3i: Element-wise maximum between this point and a scalar.
max(StackRGBState) - Method in enum class org.anchoranalysis.image.io.stack.output.StackRGBState: Finds the maximum of this value and another, according to an ordering.
max(ReadableTuple3i) - Method in class org.anchoranalysis.spatial.point.Tuple3i: Element-wise maximum between this point and another.
max(Tuple3d) - Method in class org.anchoranalysis.spatial.point.Point3d: Element-wise maximum between this point and another.
MAX - Enum constant in enum class org.anchoranalysis.image.bean.nonbean.spatial.align.AlignmentOnDimension: Aligns to the maximum position along the axis.
MAX_IN_TO_STRING - Static variable in class org.anchoranalysis.image.voxel.Voxels: The maximum number of rows/columns/slices to show in Voxels.toString().
MAX_VALUE - Static variable in class org.anchoranalysis.image.voxel.datatype.FloatVoxelType: Minimum supported value for the type.
MAX_VALUE - Static variable in class org.anchoranalysis.image.voxel.datatype.SignedShortVoxelType: Maximum supported value for the type.
MAX_VALUE - Static variable in class org.anchoranalysis.image.voxel.datatype.UnsignedByteVoxelType: Minimum supported value for the type, as a long.
MAX_VALUE - Static variable in class org.anchoranalysis.image.voxel.datatype.UnsignedIntVoxelType: Maximum supported value for the type.
MAX_VALUE - Static variable in class org.anchoranalysis.image.voxel.datatype.UnsignedShortVoxelType: Minimum supported value for the type, as a long.
MAX_VALUE - Static variable in class org.anchoranalysis.plugin.image.segment.watershed.encoding.ChainCodesDirection: The maximum value for a chain code, corresponding to code 0.
MAX_VALUE_INT - Static variable in class org.anchoranalysis.image.voxel.datatype.UnsignedByteVoxelType: Maximum supported value for the type, as an int.
MAX_VALUE_INT - Static variable in class org.anchoranalysis.image.voxel.datatype.UnsignedShortVoxelType: Maximum supported value for the type, as an int.
maxAsInt(ToIntFunction<ObjectMask>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream: Finds the maximum value of a function applied to each object in the collection.
MaxFeatureIntersectingObjects - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting: 1.
MaxFeatureIntersectingObjects() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.MaxFeatureIntersectingObjects
Maximum - Class in org.anchoranalysis.feature.bean.results: The maximum of the results from a particular feature.
Maximum - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold: The maximum value of one or more {#link org.anchoranalysis.image.bean.threshold.CalculateLevel}
Maximum - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic: Calculates the maximum value in a histogram.
Maximum<T> - Class in org.anchoranalysis.plugin.operator.feature.bean.list: A feature that calculates the maximum value from a list of features.
Maximum() - Constructor for class org.anchoranalysis.feature.bean.results.Maximum
Maximum() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.Maximum
Maximum() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Maximum
Maximum() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.list.Maximum
MaximumIntensityProjection - Class in org.anchoranalysis.plugin.image.bean.channel.provider.slice: Creates a maximum intensity projection of a 3D Channel.
MaximumIntensityProjection() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.slice.MaximumIntensityProjection
MaximumNumberContourVoxelsOnSlice - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.slice: Maximum number of voxels on any slice's contour (edge voxels) across all slices.
MaximumNumberContourVoxelsOnSlice() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.slice.MaximumNumberContourVoxelsOnSlice
MaximumNumberVoxelsOnSlice - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.slice: Maximum number of voxels in the object-mask across all slices.
MaximumNumberVoxelsOnSlice() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.slice.MaximumNumberVoxelsOnSlice
MaxIntensity - Class in org.anchoranalysis.image.core.channel.convert.attached.channel: Converts a Channel to UnsignedByteBuffer by scaling against the maximum intensity value that appears in it.
MaxIntensity() - Constructor for class org.anchoranalysis.image.core.channel.convert.attached.channel.MaxIntensity: Default constructor.
MaxIntensityFromHistogram - Class in org.anchoranalysis.image.core.channel.convert.attached.histogram: Converts a Channel to UnsignedByteBuffer by scaling against the maximum intensity value from a corresponding histogram.
MaxIntensityFromHistogram() - Constructor for class org.anchoranalysis.image.core.channel.convert.attached.histogram.MaxIntensityFromHistogram: Default constructor.
MaxIntensityProjection - Class in org.anchoranalysis.image.voxel.projection.extrema: Creates buffers for performing a Maximum Intensity Projection.
MaxIntensityProjection() - Constructor for class org.anchoranalysis.image.voxel.projection.extrema.MaxIntensityProjection: Constructor.
MaxProjection<T> - Class in org.anchoranalysis.plugin.image.bean.channel.aggregator: Maximum-intensity-projection across Channels.
MaxProjection() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.aggregator.MaxProjection
MaxTwoChannels - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic: Creates a new channel by taking the maximum value of corresponding voxels from two input channels.
MaxTwoChannels() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.MaxTwoChannels: Constructs a new MaxTwoChannels instance.
maxValue() - Method in class org.anchoranalysis.image.voxel.datatype.VoxelDataType: The maximum value this type can represent, or VoxelDataType.VALUE_NOT_COMPATIBLE if it cannot be represented in a long.
MaxWithConstant - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic: Replaces voxel values with a constant value if the constant is greater than the original voxel value.
MaxWithConstant() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.MaxWithConstant
maybeAlways2D(boolean) - Static method in class org.anchoranalysis.image.io.stack.output.StackWriteAttributesFactory: A StackWriteAttributes which, depending on a flag, may be guaranteed to be 2D.
maybeConsumeResults(LabelledResultsVector) - Method in class org.anchoranalysis.feature.io.csv.results.LabelledResultsCSVWriter: Consumes the LabelledResultsVector if consumeAfterAdding is present.
maybeCreateUserFriendlyException(Throwable) - Static method in class org.anchoranalysis.bean.xml.exception.FriendlyExceptionCreator: Possibly replaces an exception with a more user-friendly description
maybeDistanceCondition() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithOptionalDistanceConstraint: Creates a BeforeCondition that checks the distance between objects before merging.
maybeDropResolution(Dimensions) - Method in class org.anchoranalysis.image.bean.channel.ChannelAggregator: Removes the Resolution component in Dimensions.
maybeRGB(boolean, boolean, boolean) - Static method in class org.anchoranalysis.image.io.stack.output.StackWriteAttributesFactory: A StackWriteAttributes which depending on a flags, may be RGB/RGBA or not, may be guaranteed to be 2D or not.
maybeRGBWithoutAlpha(boolean) - Static method in class org.anchoranalysis.image.io.stack.output.StackWriteAttributesFactory: A StackWriteAttributes which depending on a flags, may be RGB or not.
maybeSubdirectory(Optional<String>, boolean) - Method in interface org.anchoranalysis.io.output.outputter.InputOutputContext: Optionally creates a new context like with InputOutputContext.subdirectory(java.lang.String, boolean) but only if a directory-name is defined
maybeSuppressDirectories(String, boolean) - Method in class org.anchoranalysis.io.output.path.prefixer.OutputPrefixerSettings: Derives an identifier that maybe has its directories suppressed.
mean() - Method in interface org.anchoranalysis.image.voxel.statistics.VoxelStatistics: The mean of all voxel values.
mean() - Method in class org.anchoranalysis.math.arithmetic.RunningSum: Calculates the mean.
mean() - Method in class org.anchoranalysis.math.arithmetic.RunningSumExtrema: Calculates the mean.
mean() - Method in class org.anchoranalysis.math.histogram.Histogram: Calculates the mean of the histogram values, considering their frequency.
mean() - Method in class org.anchoranalysis.math.statistics.VarianceCalculatorDouble: Calculate the mean, based on the current state of running-sums.
mean() - Method in class org.anchoranalysis.math.statistics.VarianceCalculatorLong: Calculate the mean, based on the current state of running-sums.
mean() - Method in class org.anchoranalysis.spatial.point.RunningSumPoint: The mean value of all points added to the running-sum, separately for all three-dimensions.
mean(double) - Method in class org.anchoranalysis.math.arithmetic.RunningSum: Calculates the mean.
mean(double) - Method in class org.anchoranalysis.math.histogram.Histogram: Calculates the mean of the values in the distribution, if each value is raised to a power.
mean(double, double) - Method in class org.anchoranalysis.math.histogram.Histogram: Like Histogram.mean(double) but a value may be subtracted before raising to a power.
Mean - Class in org.anchoranalysis.feature.bean.results: The mean of the results from a particular feature.
Mean - Class in org.anchoranalysis.image.feature.bean.histogram: Calculates the mean value of a histogram.
Mean<T> - Class in org.anchoranalysis.plugin.operator.feature.bean.list: Arithmetic mean of a list of features
Mean() - Constructor for class org.anchoranalysis.feature.bean.results.Mean
Mean() - Constructor for class org.anchoranalysis.image.feature.bean.histogram.Mean
Mean() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.list.Mean
MeanAcrossObjects<T> - Class in org.anchoranalysis.plugin.image.feature.bean.shared.object: Calculates the mean of a feature applied to each connected component
MeanAcrossObjects() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.shared.object.MeanAcrossObjects
meanAndReset() - Method in class org.anchoranalysis.math.arithmetic.RunningSum: Calculate the mean and then reset to zero.
meanAndReset() - Method in class org.anchoranalysis.math.arithmetic.RunningSumCollection: Calculate the mean of each item and reset to zero.
meanExecutionTimeFailed() - Method in class org.anchoranalysis.experiment.task.TaskStatistics: Mean execution-time of failed jobs in milliseconds.
meanExecutionTimeSeconds() - Method in class org.anchoranalysis.core.time.RecordedExecutionTimes.RecordedOperation: The mean execution time in seconds for the operation.
meanExecutionTimeSuccess() - Method in class org.anchoranalysis.experiment.task.TaskStatistics: Mean execution-time of successfully-completed jobs in milliseconds.
MeanFilter2D - Class in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.moments: Applies a 2D mean filter to a channel using ImageJ's RankFilters.
MeanFilter2D() - Constructor for class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.moments.MeanFilter2D: Creates a new MeanFilter2D instance.
MeanGeometric<T> - Class in org.anchoranalysis.plugin.operator.feature.bean.list: A feature that calculates the geometric mean of a list of features.
MeanGeometric() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.list.MeanGeometric
MeanIntensityProjection - Class in org.anchoranalysis.image.voxel.projection: Creates buffers for performing a mean-intensity-projection.
MeanIntensityProjection - Class in org.anchoranalysis.plugin.image.bean.channel.provider.slice: Creates a mean intensity projection of a 3D Channel.
MeanIntensityProjection() - Constructor for class org.anchoranalysis.image.voxel.projection.MeanIntensityProjection
MeanIntensityProjection() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.slice.MeanIntensityProjection
MeanProjection<T> - Class in org.anchoranalysis.plugin.image.bean.channel.aggregator: Mean-intensity-projection across Channels.
MeanProjection() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.aggregator.MeanProjection
MeanRaisedToPower - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic: Calculates the mean value in a Histogram, and raises it to a power.
MeanRaisedToPower() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.MeanRaisedToPower
MeanScale - Class in org.anchoranalysis.math.statistics: Stores the mean and scale for a distribution.
MeanScale() - Constructor for class org.anchoranalysis.math.statistics.MeanScale
MeanScale(double, double) - Constructor for class org.anchoranalysis.math.statistics.MeanScale: Creates a new MeanScale instance.
MeanThreeChannels - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic: Creates a new channel that is the mean of three input channels.
MeanThreeChannels() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.MeanThreeChannels
meanXY() - Method in class org.anchoranalysis.spatial.point.RunningSumPoint: The mean value of all points added to the running-sum, only for the X- and Y-dimensions.
measureTime(boolean, String...) - Method in class org.anchoranalysis.core.time.ExecutionTimeRecorder: Indicates operationIdentifier is being recorded, and returns the current clock timestamp.
measureTime(boolean, String...) - Method in class org.anchoranalysis.core.time.ExecutionTimeRecorderIgnore
Median - Class in org.anchoranalysis.plugin.image.bean.channel.provider.intensity: Applies a median-filter with square kernel
Median - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic: Calculates the median value in a Histogram.
Median() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.Median
Median() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Median
MedianFilter2D - Class in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank: Applies a 2D median filter to a channel using ImageJ's RankFilters.
MedianFilter2D() - Constructor for class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank.MedianFilter2D: Creates a new MedianFilter2D instance.
MedianFilter3D - Class in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank: Applies a 3D median filter to a channel using a hybrid 3D median filter ImageJ plugin.
MedianFilter3D() - Constructor for class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank.MedianFilter3D
MEDIUM_2D - Static variable in class org.anchoranalysis.test.image.ChannelFixture: Medium 2D extent for testing.
MEDIUM_3D - Static variable in class org.anchoranalysis.test.image.ChannelFixture: Medium 3D extent for testing.
membershipForIndex(int) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMap: Gets the region membership for a specific index.
membershipWithFlagsForIndex(int) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMap: Gets the region membership with flags for a specific index.
MemoForIndex - Interface in org.anchoranalysis.mpp.mark.voxelized.memo: An interface for accessing voxelized mark memos by index.
MemoList - Class in org.anchoranalysis.mpp.feature.mark: A list of VoxelizedMarkMemo objects that implements MemoForIndex and Iterable.
MemoList() - Constructor for class org.anchoranalysis.mpp.feature.mark.MemoList
MemoryUtilities - Class in org.anchoranalysis.core.system: Logs a message about approximate memory (RAM) usage of the JVM.
merge(Stream<BoundingBox>) - Static method in class org.anchoranalysis.spatial.box.BoundingBoxMerger: Merges all the bounding boxes in a stream.
merge(TypedEdge<ObjectVertex, PrioritisedVertex>) - Method in class org.anchoranalysis.plugin.image.object.merge.MergeGraph: Merges two vertices in the graph.
merge(ObjectCollection) - Static method in class org.anchoranalysis.image.core.merge.ObjectMaskMerger: Merges all the objects together that are found in a collection.
merge(ObjectMask, ObjectMask) - Static method in class org.anchoranalysis.image.core.merge.ObjectMaskMerger: Merges two objects together.
MergeBase - Class in org.anchoranalysis.plugin.image.bean.object.provider.merge: A base class for algorithms that merge object-masks.
MergeBase() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeBase
MergeBase.MergeObjects - Interface in org.anchoranalysis.plugin.image.bean.object.provider.merge: Functional interface for merging objects.
mergeBoundingBoxes(Stream<ObjectMask>) - Static method in class org.anchoranalysis.image.core.merge.ObjectMaskMerger: Merges all the bounding boxes of a stream of objects.
mergeBoundingBoxes(ObjectCollection) - Static method in class org.anchoranalysis.image.core.merge.ObjectMaskMerger: Merges all the bounding boxes of a collection of objects.
Merged - Class in org.anchoranalysis.image.feature.bean.object.pair: Evaluates a feature on the merged object created from a pair of objects.
Merged() - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.Merged
Merged(Feature<FeatureInputSingleObject>) - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.Merged: Creates a new instance that will evaluate the given feature on the merged object of a pair.
MERGED - Enum constant in enum class org.anchoranalysis.image.feature.calculation.CalculateInputFromPair.Extract: Extract the merged object from the pair.
MergedPairsFeatures - Class in org.anchoranalysis.image.feature.calculator.merged: The list of features that can be used in a PairsTableCalculator
MergedPairsFeatures(FeatureList<FeatureInputPairObjects>) - Constructor for class org.anchoranalysis.image.feature.calculator.merged.MergedPairsFeatures: Creates to only calculate pair features.
MergedPairsFeatures(FeatureList<FeatureInputStack>, FeatureList<FeatureInputSingleObject>, FeatureList<FeatureInputPairObjects>) - Constructor for class org.anchoranalysis.image.feature.calculator.merged.MergedPairsFeatures: Creates with features for single, pair and image as a whole.
MergedPairsInclude - Class in org.anchoranalysis.image.feature.calculator.merged: Specifies which parts of a merged pair to include in calculations.
MergedPairsInclude() - Constructor for class org.anchoranalysis.image.feature.calculator.merged.MergedPairsInclude: Constructs a MergedPairsInclude with all options set to true.
MergedPairsInclude(boolean, boolean, boolean) - Constructor for class org.anchoranalysis.image.feature.calculator.merged.MergedPairsInclude: Constructs a MergedPairsInclude with specified inclusion options.
MergeGraph - Class in org.anchoranalysis.plugin.image.object.merge: A graph that stores each object as a vertex, where edges represent a neighborhood relation.
MergeGraph(PayloadCalculator, UpdatableBeforeCondition, Optional<UnitConverter>, AssignPriority, Logger, boolean) - Constructor for class org.anchoranalysis.plugin.image.object.merge.MergeGraph: Constructor.
MergeGreedyToIncreaseObjectFeature - Class in org.anchoranalysis.plugin.image.bean.object.provider.merge: Naive greedy merge strategy when any two neighboring objects are merged if it increases a feature.
MergeGreedyToIncreaseObjectFeature() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeGreedyToIncreaseObjectFeature
mergeMultiplex(ObjectCollection, MergeBase.MergeObjects) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeBase: Merges objects either in a container or altogether.
mergeObjects(ObjectCollection) - Method in interface org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeBase.MergeObjects: Merges a collection of objects.
MergePairs - Class in org.anchoranalysis.plugin.image.bean.object.provider.merge: Merges objects if a pair feature value satisfies a condition.
MergePairs() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergePairs
MergeToIncreaseObjectFeature - Class in org.anchoranalysis.plugin.image.bean.object.provider.merge: Merges neighboring objects if it results in an increase in the average feature-value calculated on each single object.
MergeToIncreaseObjectFeature() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeToIncreaseObjectFeature
MergeTwoCollectionsItemwise - Class in org.anchoranalysis.plugin.image.bean.object.provider.merge: Merges itemwise objects from two collections.
MergeTwoCollectionsItemwise() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeTwoCollectionsItemwise
mergeVertices(ObjectForReduction, ObjectForReduction, ObjectForReduction) - Method in class org.anchoranalysis.image.inference.bean.reduce.ReduceObjectsGraph: Merges two existing vertices together.
mergeVertices(V, V, V) - Method in class org.anchoranalysis.core.graph.GraphWithoutPayload: Merges two existing vertices together.
mergeViaZeroCheck(Channel, Channel, VoxelDataType, double) - Static method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.IfVoxelZero: Creates a new channel which is a merged version of two input channels according to rules.
MergeWithFeature - Class in org.anchoranalysis.plugin.image.bean.object.provider.merge: Base class for object-merging strategies that involve calculating a feature.
MergeWithFeature() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithFeature
MergeWithOptionalDistanceConstraint - Class in org.anchoranalysis.plugin.image.bean.object.provider.merge: Expands MergeBase by optionally imposing a maximum-distance requirement between objects that are possibly merged.
MergeWithOptionalDistanceConstraint() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithOptionalDistanceConstraint
messageLogger() - Method in class org.anchoranalysis.core.log.Logger: Where messages are logged to.
MessageLogger - Interface in org.anchoranalysis.core.log: Logs messages (strings) somewhere.
MessageLoggerIntoString - Class in org.anchoranalysis.experiment.log: Logs error messages into a String via StringBuilder.
MessageLoggerIntoString(StringBuilder) - Constructor for class org.anchoranalysis.experiment.log.MessageLoggerIntoString
metadata() - Method in class org.anchoranalysis.feature.io.csv.metadata.FeatureCSVMetadataForOutput: Derives metadata for writing to a CSV file
metadata() - Method in class org.anchoranalysis.image.io.stack.input.ImageMetadataInput: The associated image metadata.
metadata(int, Logger) - Method in class org.anchoranalysis.image.io.channel.input.NamedChannelsInput: The image-metadata associated with a particular series.
metadata(int, Logger) - Method in interface org.anchoranalysis.image.io.stack.input.OpenedImageFile: Extracts metadata about the image.
MICRO - Enum constant in enum class org.anchoranalysis.image.core.dimensions.SpatialUnits.UnitSuffix: 1e-6.
midpoint() - Method in class org.anchoranalysis.spatial.box.BoundingBox: A mid-point in the bounding box, corresponding to the exact half-way point between (corner+extent)/2.
midpoint(ObjectWithProperties, boolean) - Static method in class org.anchoranalysis.image.io.object.ExtractMidpoint: Calculates the midpoint of object.
MILLI - Enum constant in enum class org.anchoranalysis.image.core.dimensions.SpatialUnits.UnitSuffix: 1e-3.
min() - Method in class org.anchoranalysis.math.arithmetic.RunningSumExtrema: The minimum across all values passed to RunningSumExtrema.add(double) or Double.MAX_VALUE if the method was never called.
min(StackRGBState) - Method in enum class org.anchoranalysis.image.io.stack.output.StackRGBState: Finds the minimum of this value and another, according to an ordering.
min(ReadableTuple3i) - Method in class org.anchoranalysis.spatial.point.Point3d: Element-wise minimum between this point and another.
min(ReadableTuple3i) - Method in class org.anchoranalysis.spatial.point.Tuple3i: Element-wise minimum between this point and another.
min(Tuple3d) - Method in class org.anchoranalysis.spatial.point.Point3d: Element-wise minimum between this point and another.
MIN - Enum constant in enum class org.anchoranalysis.image.bean.nonbean.spatial.align.AlignmentOnDimension: Aligns to the minimum position along the axis.
MIN_VALUE - Static variable in class org.anchoranalysis.image.voxel.datatype.FloatVoxelType: Maximum supported value for the type.
MIN_VALUE - Static variable in class org.anchoranalysis.image.voxel.datatype.SignedShortVoxelType: Minimum supported value for the type.
minAsInt(ToIntFunction<ObjectMask>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream: Finds the minimum value of a function applied to each object in the collection.
MinFeatureIntersectingObjectsAboveThreshold - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting: 1.
MinFeatureIntersectingObjectsAboveThreshold() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.MinFeatureIntersectingObjectsAboveThreshold
MinimaImposition - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima: Abstract base class for imposing minima on a channel for watershed segmentation.
MinimaImposition() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.MinimaImposition
MinimaImpositionGrayscaleReconstruction - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima: Imposes minima on a channel using grayscale reconstruction by erosion.
MinimaImpositionGrayscaleReconstruction() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.MinimaImpositionGrayscaleReconstruction
minimum(Extent) - Method in class org.anchoranalysis.spatial.box.Extent: An extent that contains the minimum of two extents for each dimension respectively.
Minimum - Class in org.anchoranalysis.feature.bean.results: The minimum of the results from a particular feature.
Minimum - Class in org.anchoranalysis.image.feature.bean.object.pair: Calculates the minimum value of a feature applied to both objects in a pair.
Minimum - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold: The minimum value of one or more {#link org.anchoranalysis.image.bean.threshold.CalculateLevel}
Minimum - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic: Calculates the minimum value in a Histogram.
Minimum<T> - Class in org.anchoranalysis.plugin.operator.feature.bean.list: A feature that calculates the minimum value from a list of features.
Minimum() - Constructor for class org.anchoranalysis.feature.bean.results.Minimum
Minimum() - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.Minimum
Minimum() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.Minimum
Minimum() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Minimum
Minimum() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.list.Minimum
Minimum(Feature<FeatureInputSingleObject>) - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.Minimum: Creates a new instance that will calculate the minimum feature value from a pair of objects.
minimumDimension() - Method in class org.anchoranalysis.spatial.scale.ScaleFactor: Which is the minimum scaling-factor among all dimensions?
MinimumFilter - Class in org.anchoranalysis.plugin.fiji.bean.channel.provider: Applies a minimum filter to a channel using ImageJ's MinMaxMedian plugin.
MinimumFilter() - Constructor for class org.anchoranalysis.plugin.fiji.bean.channel.provider.MinimumFilter
MinimumXYResolution - Class in org.anchoranalysis.plugin.image.bean.scale: Calculates a scale factor to ensure a minimum XY resolution is achieved.
MinimumXYResolution() - Constructor for class org.anchoranalysis.plugin.image.bean.scale.MinimumXYResolution
MinIntensityProjection - Class in org.anchoranalysis.image.voxel.projection.extrema: Creates buffers for performing a minimum intensity projection, similarly to MaxIntensityProjection but calculating the minimum.
MinIntensityProjection() - Constructor for class org.anchoranalysis.image.voxel.projection.extrema.MinIntensityProjection: Constructor.
MinMaxRange - Class in org.anchoranalysis.image.voxel.iterator: The minimum and maximum associated with a range of values.
MinMaxRange(long, long) - Constructor for class org.anchoranalysis.image.voxel.iterator.MinMaxRange: Creates a new MinMaxRange instance.
minNumPoints() - Method in class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresViaNormalEquationBase: Returns the minimum number of points required for fitting.
MinProjection<T> - Class in org.anchoranalysis.plugin.image.bean.channel.aggregator: Minimum-intensity-projection across Channels.
MinProjection() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.aggregator.MinProjection
MinTwoChannels - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic: Creates a new channel by taking the minimum value of corresponding voxels from two input channels.
MinTwoChannels() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.MinTwoChannels: Constructs a new MinTwoChannels instance.
minValue() - Method in class org.anchoranalysis.image.voxel.datatype.VoxelDataType: The minimum value this type can represent, or VoxelDataType.VALUE_NOT_COMPATIBLE if it cannot be represented in a long.
MinWithConstant - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic: Replaces voxel values with a constant value if the constant is less than the original voxel value.
MinWithConstant() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.MinWithConstant
MIRROR_WITHOUT_ROTATION - Enum constant in enum class org.anchoranalysis.image.core.dimensions.OrientationChange: No change in orientation, but mirroring across the X dimension.
MockFeatureWithCalculation - Class in org.anchoranalysis.test.feature.plugins.mockfeature: A feature that returns the number-of-voxels in an object by using am internal mock-calculation.
MockFeatureWithCalculation() - Constructor for class org.anchoranalysis.test.feature.plugins.mockfeature.MockFeatureWithCalculation
MockFeatureWithCalculationFixture - Class in org.anchoranalysis.test.feature.plugins.mockfeature: Creates a mock-feature which used a mock CalculationPart under the hood
Mode - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic: Calculates the skewness of all the values in the histogram.
Mode() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Mode
modelDirectory() - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitialization: Directory where machine-learning models can be found.
modelDirectory() - Method in class org.anchoranalysis.test.image.load.CarImageLoader: Returns the root directory path for the model files.
MonitoredSequentialExecutor<T> - Class in org.anchoranalysis.experiment.task.processor: Runs executes sequence of jobs/tasks/whatever monitoring various pieces of information - how many have run?
MonitoredSequentialExecutor(Predicate<T>, Function<T, String>, Optional<MessageLogger>, boolean) - Constructor for class org.anchoranalysis.experiment.task.processor.MonitoredSequentialExecutor: Creates a new MonitoredSequentialExecutor instance.
Montage - Class in org.anchoranalysis.plugin.image.task.bean.combine: Creates a montage of images, by tiling them side-by-side.
Montage() - Constructor for class org.anchoranalysis.plugin.image.task.bean.combine.Montage
MontageSharedState - Class in org.anchoranalysis.plugin.image.task.slice: A Stack into which individual images are written, together with the necessary information on where to write each image.
MontageSharedState(Map<Path, BoundingBoxEnclosed>, Extent, VoxelsResizer, ExecutionTimeRecorder) - Constructor for class org.anchoranalysis.plugin.image.task.slice.MontageSharedState: Create with a mapping from Paths to boxes.
MontageSlices - Class in org.anchoranalysis.plugin.imagej.bean.stack.provider: Creates a montage of slices from a stack.
MontageSlices() - Constructor for class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices
moreThanOneObject() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.AnnotationComparisonAssigner: Checks if more than one object can exist in the assignment.
moreThanOneObject() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner
moreThanOneObject() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.MaskIntersectionAssigner
MorphologicalDilation - Class in org.anchoranalysis.image.voxel.object.morphological: Performs morphological dilation on an ObjectMask or BinaryVoxels.
MorphologicalErosion - Class in org.anchoranalysis.image.voxel.object.morphological: Performs morphological erosion operation on an ObjectMask or BinaryVoxels.
MorphologicalIterations - Class in org.anchoranalysis.plugin.image.feature.bean.morphological: Specifies a certain number of iterations of the morphological operations of dilation and erosion.
MorphologicalIterations() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations
MorphologicalOperation - Class in org.anchoranalysis.plugin.imagej.bean.mask.provider: Applies an ImageJ (2D) morphological operation to each slice
MorphologicalOperation() - Constructor for class org.anchoranalysis.plugin.imagej.bean.mask.provider.MorphologicalOperation
MorphologicalOperatorBase - Class in org.anchoranalysis.plugin.image.bean.mask.provider.morphological: Base class for performing morphological operations on BinaryVoxels.
MorphologicalOperatorBase() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.MorphologicalOperatorBase
Mser - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel: Applies the MSER algorithm from imglib2
Mser() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.channel.Mser
MultiBufferSized - Class in org.anchoranalysis.plugin.io.multifile.buffer
MultiBufferSized(Stack, SizeExtents) - Constructor for class org.anchoranalysis.plugin.io.multifile.buffer.MultiBufferSized
MultiFileReader - Class in org.anchoranalysis.plugin.io.bean.stack.reader
MultiFileReader() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader
MultiInput - Class in org.anchoranalysis.mpp.io.input: An input to an experiment that combines a particular Stack with other types of entities.
MultiInput(String, ProvidesStackInput) - Constructor for class org.anchoranalysis.mpp.io.input.MultiInput: Creates a new MultiInput with a specified name for the main input object.
MultiInput(ProvidesStackInput) - Constructor for class org.anchoranalysis.mpp.io.input.MultiInput: Creates a new MultiInput with a default name for the main input object.
MultiInputManager - Class in org.anchoranalysis.mpp.io.bean.input: Manages input for MultiInput objects, combining various input sources.
MultiInputManager() - Constructor for class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
MultiInputManager(String, InputManager<? extends ProvidesStackInput>) - Constructor for class org.anchoranalysis.mpp.io.bean.input.MultiInputManager: Creates a new MultiInputManager with specified input name and input manager.
MultiInputSubMap<T> - Interface in org.anchoranalysis.mpp.io.input: A sub-item of a MultiInput that manages a map of objects.
MultiLevelAnd - Class in org.anchoranalysis.io.output.enabled.multi: Outputs are enabled if they are contained in both of two MultiLevelOutputEnableds.
MultiLevelAnd(MultiLevelOutputEnabled, MultiLevelOutputEnabled) - Constructor for class org.anchoranalysis.io.output.enabled.multi.MultiLevelAnd: Creates using two MultiLevelOutputEnableds.
MultiLevelBinary - Class in org.anchoranalysis.io.output.enabled.multi: Base class for operations that combines two MultiLevelOutputEnableds.
MultiLevelBinary(MultiLevelOutputEnabled, MultiLevelOutputEnabled) - Constructor for class org.anchoranalysis.io.output.enabled.multi.MultiLevelBinary: Creates a new MultiLevelBinary instance.
MultiLevelNot - Class in org.anchoranalysis.io.output.enabled.multi: The complement of an existing MultiLevelOutputEnabled where disabled outputs are enabled, and vice-versa.
MultiLevelNot(MultiLevelOutputEnabled) - Constructor for class org.anchoranalysis.io.output.enabled.multi.MultiLevelNot: Creates a new MultiLevelNot instance.
MultiLevelOr - Class in org.anchoranalysis.io.output.enabled.multi: Outputs are enabled if they are contained in either of two MultiLevelOutputEnableds.
MultiLevelOr(MultiLevelOutputEnabled, MultiLevelOutputEnabled) - Constructor for class org.anchoranalysis.io.output.enabled.multi.MultiLevelOr: Creates using two MultiLevelOutputEnableds.
MultiLevelOutputEnabled - Interface in org.anchoranalysis.io.output.enabled.multi: Whether an output is enabled or not in a context of hierarchy of different rules for outputting.
MultiLevelRecordedOutputs - Class in org.anchoranalysis.io.output.recorded: Like RecordedOutputs but accepts two levels, first and second, like in a MultiLevelRecordedOutputs.
MultiLevelRecordedOutputs() - Constructor for class org.anchoranalysis.io.output.recorded.MultiLevelRecordedOutputs
MultiName - Interface in org.anchoranalysis.feature.io.name: A name that that uniquely identifies an entity, and is composed of two parts.
MultiNameFactory - Class in org.anchoranalysis.feature.io.name: Creates MultiName.
MultipleComparer - Class in org.anchoranalysis.annotation.io.bean.comparer: Allows comparison of an annotation with multiple other entities.
MultipleComparer() - Constructor for class org.anchoranalysis.annotation.io.bean.comparer.MultipleComparer
MultipleFileTypeGenerator<T> - Interface in org.anchoranalysis.io.generator: A Generator that creates multiple different file-types.
MultipleLoggers - Class in org.anchoranalysis.experiment.log: Logs messages to multiple other loggers.
MultipleLoggers(Stream<StatefulMessageLogger>) - Constructor for class org.anchoranalysis.experiment.log.MultipleLoggers: Creates with a stream of loggers.
multipleProcessors(int, int) - Static method in class org.anchoranalysis.inference.concurrency.ConcurrencyPlan: Creates a plan for a multiple CPU-processors.
multiplex(boolean) - Method in class org.anchoranalysis.io.output.recorded.RecordingWriters: Multiplexes between the selective and permissive writers based on a flag.
multiplex(boolean, boolean) - Static method in enum class org.anchoranalysis.image.io.stack.output.StackRGBState: Returns one of the three RGB_ states based upon two boolean flags.
multiplex(int, int, int) - Method in enum class org.anchoranalysis.image.voxel.kernel.OutsideKernelPolicy: Multiplexes between three-values depending on which policy is currently selected.
multiplexAlpha(boolean) - Static method in enum class org.anchoranalysis.image.io.stack.output.StackRGBState: Returns one of the two RGB_ states based upon a boolean flag.
multiplexPlural(long, String, String) - Static method in class org.anchoranalysis.core.value.LanguageUtilities: Returns a single or plural word depending on the number.
Multiply<T> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic: A feature that multiplies the results of multiple features together.
Multiply() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.Multiply
multiplyBy(double) - Method in interface org.anchoranalysis.image.voxel.arithmetic.VoxelsArithmetic: Multiplies the value of all voxels by a factor.
multiplyBy(ObjectMask, double) - Method in interface org.anchoranalysis.image.voxel.arithmetic.VoxelsArithmetic: Multiplies each voxel by constant factor but only for voxels inside an ObjectMask.
multiplyByConstant(double) - Method in class org.anchoranalysis.spatial.orientation.RotationMatrix: Multiplies each element in the rotation-matrix by a value.
MultiplyByConstant<T> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic: A feature that multiplies the result of another feature by a constant value.
MultiplyByConstant() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.MultiplyByConstant
MultiplyByConstant(Feature<T>, double) - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.MultiplyByConstant: Creates a new MultiplyByConstant with a specified feature and constant value.
MultiplyConstant - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic: Multiplies each voxel value in a channel by a constant value.
MultiplyConstant() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.MultiplyConstant
MultiplyTwoChannels - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic: Creates a new channel by multiplying corresponding voxels from two input channels.
MultiplyTwoChannels() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.MultiplyTwoChannels: Constructs a new MultiplyTwoChannels instance.
MultiScaleObject - Class in org.anchoranalysis.image.inference.segment: An ObjectMask that exists at multiple scales.
MultiScaleObject(Supplier<ObjectMask>, Supplier<ObjectMask>) - Constructor for class org.anchoranalysis.image.inference.segment.MultiScaleObject: Creates with a separate supplier of an ObjectMask for each respective scale.
multModulo(int, int, int) - Static method in class org.anchoranalysis.test.image.ChannelFixture: Calculates intensity as the product of coordinates modulo 256.

N

name() - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster.ClusterIdentifier: Derives a name for the cluster, based upon its contents.
NamedBean<T> - Class in org.anchoranalysis.bean: A bean with an associated textual name.
NamedBean() - Constructor for class org.anchoranalysis.bean.NamedBean
NamedBean(String, T) - Constructor for class org.anchoranalysis.bean.NamedBean: Creates a new NamedBean instance.
NamedChannel - Class in org.anchoranalysis.plugin.image.task.grouped: Associates a name with a Channel.
NamedChannel(String, Channel) - Constructor for class org.anchoranalysis.plugin.image.task.grouped.NamedChannel: Creates a new NamedChannel instance.
NamedChannels - Class in org.anchoranalysis.plugin.image.task.channel.aggregator: A collection of Channels each with an associated unique-name.
NamedChannels - Class in org.anchoranalysis.plugin.io.bean.input.channel: An image viewed as a set of channels, each with a unique name.
NamedChannels() - Constructor for class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannels
NamedChannels(boolean) - Constructor for class org.anchoranalysis.plugin.image.task.channel.aggregator.NamedChannels: Creates a new NamedChannels instance.
NamedChannels(Stream<NamedChannels>) - Constructor for class org.anchoranalysis.plugin.image.task.channel.aggregator.NamedChannels: Creates by combining multiple existing NamedChannels.
NamedChannelsAppend - Class in org.anchoranalysis.plugin.io.bean.input.channel
NamedChannelsAppend() - Constructor for class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
NamedChannelsBase - Class in org.anchoranalysis.plugin.io.bean.input.channel: Parent for all the NamedChannels classes
NamedChannelsBase() - Constructor for class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsBase
NamedChannelsConcatenate - Class in org.anchoranalysis.image.io.channel.map: Exposes one or more instances of a NamedChannelsMap as a single aggregated NamedChannelsMap.
NamedChannelsConcatenate(NamedChannelsMap...) - Constructor for class org.anchoranalysis.image.io.channel.map.NamedChannelsConcatenate: Create with arguments to concatenate.
NamedChannelsInput - Class in org.anchoranalysis.image.io.channel.input: Provides a set of channels as an input, with each channel having a name.
NamedChannelsInput() - Constructor for class org.anchoranalysis.image.io.channel.input.NamedChannelsInput
NamedChannelsInputPart - Class in org.anchoranalysis.image.io.channel.input: One part of a NamedChannelsInput that can be combined with others.
NamedChannelsInputPart() - Constructor for class org.anchoranalysis.image.io.channel.input.NamedChannelsInputPart
NamedChannelsMap - Interface in org.anchoranalysis.image.io.channel.map: A collection of Channels, each identified by a unique name and a time-index.
NamedFeatureCalculateException - Exception Class in org.anchoranalysis.feature.calculate: An exception that occurs when a feature fails to successfully calculate.
NamedFeatureCalculateException(Exception) - Constructor for exception class org.anchoranalysis.feature.calculate.NamedFeatureCalculateException: Creates with a calculation error that doesn't pertain to any particular feature.
NamedFeatureCalculateException(String) - Constructor for exception class org.anchoranalysis.feature.calculate.NamedFeatureCalculateException: Creates with a general failure message that doesn't pertain to any particular feature.
NamedFeatureCalculateException(String, String) - Constructor for exception class org.anchoranalysis.feature.calculate.NamedFeatureCalculateException: Creates with a failure message associated with a particular feature.
NamedFeatureCalculatorMulti<T> - Class in org.anchoranalysis.image.feature.calculator: A FeatureCalculatorMulti with associated feature-names.
NamedFeatureCalculatorMulti(FeatureCalculatorMulti<T>, FeatureNameList) - Constructor for class org.anchoranalysis.image.feature.calculator.NamedFeatureCalculatorMulti: Creates a new NamedFeatureCalculatorMulti instance.
NamedFeatureStore<T> - Class in org.anchoranalysis.feature.store: Stores Features, each with an associated name, with list-like access and map-like access.
NamedFeatureStore() - Constructor for class org.anchoranalysis.feature.store.NamedFeatureStore
NamedFeatureStoreFactory - Class in org.anchoranalysis.feature.store: Creates a NamedFeatureStore.
NamedFile - Class in org.anchoranalysis.io.input.file: A file with an associated unique name.
NamedFile(String, File) - Constructor for class org.anchoranalysis.io.input.file.NamedFile: Create with an identifier and a file.
NamedFiles - Class in org.anchoranalysis.plugin.io.bean.input.files: Implementation of NamedFilesBase that is an InputManager that accepts FileInput as input and derives a name.
NamedFiles() - Constructor for class org.anchoranalysis.plugin.io.bean.input.files.NamedFiles
NamedFiles(FilesProvider) - Constructor for class org.anchoranalysis.plugin.io.bean.input.files.NamedFiles
NamedFiles(FilesProvider, FileNamer) - Constructor for class org.anchoranalysis.plugin.io.bean.input.files.NamedFiles
NamedFilesBase<T> - Class in org.anchoranalysis.plugin.io.bean.input.files: Base class for an InputManager that produces inputs that are created from a NamedFile.
NamedFilesBase() - Constructor for class org.anchoranalysis.plugin.io.bean.input.files.NamedFilesBase
NamedFilesBase(FileNamer) - Constructor for class org.anchoranalysis.plugin.io.bean.input.files.NamedFilesBase
NamedFilesWithDirectory - Class in org.anchoranalysis.plugin.io.bean.input.files: Like NamedFiles but rather accepts a FileWithDirectoryInput rather than a FileInput.
NamedFilesWithDirectory() - Constructor for class org.anchoranalysis.plugin.io.bean.input.files.NamedFilesWithDirectory
NamedPath - Class in org.anchoranalysis.io.output.path.prefixer: A path and associated name.
NamedPath(String, Path) - Constructor for class org.anchoranalysis.io.output.path.prefixer.NamedPath: Creates a new NamedPath instance.
NamedProvider<T> - Interface in org.anchoranalysis.core.identifier.provider: A collection of elements, each with an associated name.
NamedProviderBridge<S,T> - Class in org.anchoranalysis.core.identifier.provider: Exposes elements in a NamedProvider as a different type.
NamedProviderBridge(NamedProvider<S>, CheckedFunction<S, T, ? extends Exception>) - Constructor for class org.anchoranalysis.core.identifier.provider.NamedProviderBridge: Creates with a particular provider and bridge.
NamedProviderBridge(NamedProvider<S>, CheckedFunction<S, T, ? extends Exception>, boolean) - Constructor for class org.anchoranalysis.core.identifier.provider.NamedProviderBridge: Creates a new NamedProviderBridge instance.
NamedProviderCombine<T> - Class in org.anchoranalysis.core.identifier.provider: Combines one more NamedProviders into a unitary NamedProvider.
NamedProviderCombine(Stream<NamedProvider<T>>) - Constructor for class org.anchoranalysis.core.identifier.provider.NamedProviderCombine: Create from a stream of NamedProviders.
NamedProviderGetException - Exception Class in org.anchoranalysis.core.identifier.provider: When a get operation fails with a NamedProvider.
NamedProviderGetException(String, Throwable) - Constructor for exception class org.anchoranalysis.core.identifier.provider.NamedProviderGetException: Create with a particular cause.
NamedProviderOutputter<T> - Class in org.anchoranalysis.io.generator.collection: Outputs entities from a NamedProvider into a directory using the names of each entity for a corresponding generated file.
NamedProviderOutputter(NamedProvider<T>, Generator<T>, OutputterChecked) - Constructor for class org.anchoranalysis.io.generator.collection.NamedProviderOutputter: Creates a new NamedProviderOutputter instance.
NamedProviderStore<T> - Interface in org.anchoranalysis.core.identifier.provider.store: A NamedProvider, in which items can also be added.
NamedStacks - Class in org.anchoranalysis.image.core.stack.named: A set of image-stacks each with a name.
NamedStacks() - Constructor for class org.anchoranalysis.image.core.stack.named.NamedStacks
NamedStacksOutputter - Class in org.anchoranalysis.image.io.stack.output: Outputs a named-set of stacks, performing appropriate checks on what is enabled or not.
NamedStacksSupplier - Interface in org.anchoranalysis.image.core.stack.named: Supplies a NamedProvider of Stacks.
NamedStacksUniformSize - Class in org.anchoranalysis.image.core.stack.named: Like NamedStacks but enforces a condition that all stacks must have the same dimensions.
NamedStacksUniformSize() - Constructor for class org.anchoranalysis.image.core.stack.named.NamedStacksUniformSize
NameElementRange - Class in org.anchoranalysis.io.input.bean.path: Constructs a Path from a sub-range of the name-elements of the Path.
NameElementRange() - Constructor for class org.anchoranalysis.io.input.bean.path.NameElementRange
nameFor(LocalDateTime, LocalDateTime, DateStyle, TimeStyle) - Method in class org.anchoranalysis.plugin.io.naming.interval.TimeIntervalNamer: Derives a name from the time-range in the cluster and some parameters.
names() - Method in class org.anchoranalysis.image.io.channel.input.ChannelMap: The names of the Channels in the map.
names() - Method in class org.anchoranalysis.plugin.image.task.channel.aggregator.NamedChannels: The names of the Channels.
NameValue<T> - Interface in org.anchoranalysis.core.identifier.name: A pair combining a name and a value.
NameValueMap<T> - Class in org.anchoranalysis.core.identifier.provider: Builds a mapping from names to values, given NameValue instances.
NameValueMap() - Constructor for class org.anchoranalysis.core.identifier.provider.NameValueMap
NameValueMap(Iterable<? extends NameValue<T>>) - Constructor for class org.anchoranalysis.core.identifier.provider.NameValueMap: Creates and populates with elements from an Iterable.
NANO - Enum constant in enum class org.anchoranalysis.image.core.dimensions.SpatialUnits.UnitSuffix: 1e-9
NearestNeighbor - Class in org.anchoranalysis.image.voxel.resizer: Resizes with an interpolator that uses nearest neighbor interpolation as implemented in Imglib2.
NearestNeighbor() - Constructor for class org.anchoranalysis.image.voxel.resizer.NearestNeighbor: Default constructor.
negative() - Method in class org.anchoranalysis.spatial.orientation.Orientation: Derives a new Orientation in the opposite (negative) direction to the current instance.
negative() - Method in class org.anchoranalysis.spatial.orientation.Orientation2D
negative() - Method in class org.anchoranalysis.spatial.orientation.Orientation3DEulerAngles
negative() - Method in class org.anchoranalysis.spatial.orientation.OrientationAxisAngle
negative() - Method in class org.anchoranalysis.spatial.orientation.OrientationRotationMatrix
NeighborGraph - Class in org.anchoranalysis.image.voxel.neighborhood: Creates a graph where each vertex represents an ObjectMask and edges between indicate that two objects neighbor each other.
Neighborhood - Interface in org.anchoranalysis.image.voxel.neighborhood: A region in proximity to a voxel, encompassing this voxel as well as others.
NeighborhoodCondition - Class in org.anchoranalysis.plugin.image.object.merge.condition: A condition to determine if two objects are potential neighbors and candidates for merging.
NeighborhoodCondition(boolean, boolean) - Constructor for class org.anchoranalysis.plugin.image.object.merge.condition.NeighborhoodCondition: Creates a new NeighborhoodCondition.
NeighborhoodFactory - Class in org.anchoranalysis.image.voxel.neighborhood: Creates either a big voxel-neighborhood or a small voxel-neighborhood.
NeighborPredicate - Interface in org.anchoranalysis.image.voxel.iterator.neighbor.kernel: A predicate on whether a neighbor satisfies a condition in relation to a particular point that it neighbors.
newlinesBeforeError() - Method in class org.anchoranalysis.launcher.config.LauncherConfig: Determines if extra newlines should be inserted before error messages.
NEWLY_ADDED - Static variable in class org.anchoranalysis.image.inference.bean.reduce.ObjectForReduction: A special index value to indicate that an object has been newly-added.
newTemplateMark() - Method in class org.anchoranalysis.mpp.bean.mark.factory.MarkWithIdentifierFactory: Creates a new mark based on the template and assigns it a unique identifier.
nextIndex(int) - Method in interface org.anchoranalysis.core.index.range.IndexRangeSeek: Finds the next index in the range after index.
nextValue() - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.PriorityQueueIndexRangeDownhill: Returns the index value of the next item to be retrieved.
NO_RESTRICTIONS - Static variable in class org.anchoranalysis.image.io.stack.output.OutputSequenceStackFactory: A factory with no restrictions on what kind of stacks can be outputted.
noCPUProcessor() - Static method in class org.anchoranalysis.inference.concurrency.ConcurrencyPlan: Creates a plan for no CPU processors with the default number of GPUs.
noInterpolation() - Method in class org.anchoranalysis.image.voxel.resizer.VoxelsResizerFactory: A VoxelsResizer that is effectively disabled, and performs no interpolation, copying a single (minimal corner) value for each voxel.
None - Class in org.anchoranalysis.image.bean.interpolator: An implementation of Interpolator that performs no interpolation.
None - Class in org.anchoranalysis.io.output.bean.enabled: No outputs are enabled.
None() - Constructor for class org.anchoranalysis.image.bean.interpolator.None
None() - Constructor for class org.anchoranalysis.io.output.bean.enabled.None
NONE - Enum constant in enum class org.anchoranalysis.image.core.dimensions.SpatialUnits.UnitSuffix: No suffix.
NoneExcept - Class in org.anchoranalysis.io.output.bean.rules: All outputs are disabled except particular ones.
NoneExcept() - Constructor for class org.anchoranalysis.io.output.bean.rules.NoneExcept
NoneExcept(String) - Constructor for class org.anchoranalysis.io.output.bean.rules.NoneExcept: Create with a single first-level output-name.
NoneExcept(StringSet) - Constructor for class org.anchoranalysis.io.output.bean.rules.NoneExcept: Create with first-level output names
NonEmpty - Annotation Interface in org.anchoranalysis.bean.annotation: Indicates that a collection must have at least one item.
nonExistingItem(String) - Static method in exception class org.anchoranalysis.core.identifier.provider.NamedProviderGetException: Creates using a standard-error message for a non-existing item
nonExistingItem(String, String) - Static method in exception class org.anchoranalysis.core.identifier.provider.NamedProviderGetException: Like NamedProviderGetException.nonExistingItem(String) but with a message that also includes a user-friendly-name for the NamedProvider.
nonFeatureHeaders() - Method in class org.anchoranalysis.feature.io.csv.metadata.FeatureCSVMetadataForOutput: Headers for the CSV File
NonImageFileFormat - Enum Class in org.anchoranalysis.core.format: Non image file-formats that are read or writeten to the filesystem, each with an associated extension.
NonNegative - Annotation Interface in org.anchoranalysis.bean.annotation: The bean-field should have a value >= 0.
nonNegativeX() - Method in class org.anchoranalysis.image.voxel.kernel.KernelPointCursor: Whether the current point is non-negative in the X-dimension?
nonNegativeY() - Method in class org.anchoranalysis.image.voxel.kernel.KernelPointCursor: Whether the current point is non-negative in the Y-dimension?
noOverlapWith(Mark, int) - Method in interface org.anchoranalysis.mpp.mark.QuickOverlapCalculation: A quick (computationally-efficient) test to see if we can reject the possibility of overlap
normalisedRadii(Ellipsoid, Optional<Resolution>) - Static method in class org.anchoranalysis.mpp.mark.conic.EllipsoidUtilities: Calculates the normalized radii of an Ellipsoid mark, taking into account rotation and optional resolution.
normalize() - Method in class org.anchoranalysis.spatial.point.Tuple3d: Normalizes the tuple by dividing each component's value by the overall length.
NormalizeByConstant - Class in org.anchoranalysis.plugin.image.feature.bean.score: Normalizes the voxel intensity by dividing it by a constant value.
NormalizeByConstant() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.NormalizeByConstant
NormalizeByMax - Class in org.anchoranalysis.plugin.image.feature.bean.score: This assumes the histograms correspond to the energy channels exactly (in terms of indexing)
NormalizeByMax() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.NormalizeByMax
NormalizeDifferenceToMedian - Class in org.anchoranalysis.plugin.image.bean.channel.provider.intensity: Corrects a channel in the following way
NormalizeDifferenceToMedian() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.NormalizeDifferenceToMedian
NormalizedPath - Class in org.anchoranalysis.plugin.io.bean.file.namer: Uses the normalized path (always with forward slashes) of each file as it's descriptive-name
NormalizedPath() - Constructor for class org.anchoranalysis.plugin.io.bean.file.namer.NormalizedPath
NormalizedRange<T> - Class in org.anchoranalysis.plugin.operator.feature.bean.range: The range of two feature values (i.e. max - min), divided by their mean.
NormalizedRange() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.range.NormalizedRange
NormalizeObjectIntensity - Class in org.anchoranalysis.plugin.image.bean.channel.provider.intensity: Rewrites the intensity for each object-mask (assume no overlap) so that its mean is 128
NormalizeObjectIntensity() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.NormalizeObjectIntensity
normalizeToLowerCase(String) - Static method in class org.anchoranalysis.core.format.FormatExtensions: Normalize an extension to lower-case.
noScaling(DisplayStack) - Static method in class org.anchoranalysis.image.io.stack.output.box.ScaleableBackground: Creates a background from a stack without any scaling.
NoSharedState - Class in org.anchoranalysis.experiment.task: Fake shared-state to use to indicate none exists (for type safety)
NOT_RGB - Enum constant in enum class org.anchoranalysis.image.io.stack.output.StackRGBState: Not a RGB image.
NotEqualTo - Class in org.anchoranalysis.math.relation: Returns true if two values are not equal, and false otherwise.
NotEqualTo() - Constructor for class org.anchoranalysis.math.relation.NotEqualTo
NotFound<T> - Class in org.anchoranalysis.annotation.io.image.findable: A negative-result when an object is not found at a particular location.
NotFound(Path, String) - Constructor for class org.anchoranalysis.annotation.io.image.findable.NotFound: Creates a new NotFound instance.
notifyBuffer(LocalSlices, int) - Method in class org.anchoranalysis.image.voxel.kernel.AndKernel
notifyBuffer(LocalSlices, int) - Method in class org.anchoranalysis.image.voxel.kernel.ConditionalKernel
notifyBuffer(LocalSlices, int) - Method in class org.anchoranalysis.image.voxel.kernel.count.CountKernel
notifyBuffer(LocalSlices, int) - Method in class org.anchoranalysis.image.voxel.kernel.Kernel: Called to inform the Kernel of buffers that are currently being processed.
notifyBuffer(LocalSlices, int) - Method in class org.anchoranalysis.image.voxel.kernel.morphological.BinaryKernelMorphological
notifyBuffer(LocalSlices, int) - Method in class org.anchoranalysis.image.voxel.kernel.outline.OutlineKernelNeighborMatchValue
notifyChangeSlice(int) - Method in interface org.anchoranalysis.image.voxel.iterator.predicate.PredicateBufferBinary: Notifies the processor that there has been a change in slice (z global coordinate).
notifyChangeSlice(int) - Method in interface org.anchoranalysis.image.voxel.iterator.predicate.PredicateKernelPointCursor: Notifies the processor that there has been a change in z-coordinate.
notifyChangeSlice(int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.buffer.ProcessBufferBinary: Notifies the processor that there has been a change in slice.
notifyChangeSlice(int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.buffer.ProcessBufferBinaryMixed: Notifies the processor that there has been a change in slice.
notifyChangeSlice(int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.buffer.ProcessBufferBinaryWithoutOffset: Notifies the processor that there has been a change in slice.
notifyChangeSlice(int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.buffer.ProcessBufferTernary: Notifies the processor that there has been a change in slice.
notifyChangeSlice(int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.buffer.ProcessBufferUnary: Notifies the processor that there has been a change in slice.
notifyChangeSlice(int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.ProcessKernelPointCursor: Notifies the processor that there has been a change in z-coordinate.
notifyChangeSlice(int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.ProcessPoint: Notifies the processor that there has been a change in Z-coordinate.
notifyChangeSlice(int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.ProcessPointAndIndex: Notifies the processor that there has been a change in Z-coordinate.
notifyChangeY(int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.ProcessPoint: Notifies the processor that there has been a change in Y-coordinate.
notifyChangeY(int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.ProcessPointAndIndex: Notifies the processor that there has been a change in Y-coordinate.
notifyChangeZ(int) - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighbor: Notifies the processor that there has been a change in z-coordinate.
notifyChangeZ(int, int) - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsolute: Notifies the processor that there has been a change in z-coordinate.
notifyChangeZ(int, int) - Method in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsoluteWithSlidingBuffer
notifyChangeZ(int, int, UnsignedByteBuffer) - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.ProcessChangedPointAbsoluteMasked: Notifies the processor that there has been a change in z-coordinate.
NotInContainer - Class in org.anchoranalysis.plugin.image.bean.object.provider.filter: Filters objects to keep only those which are NOT in the container.
NotInContainer() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.filter.NotInContainer
NotTouchingSceneBorder - Class in org.anchoranalysis.plugin.image.bean.object.filter.independent: Keeps only objects that are not adjacent to the scene-border (i.e. have a bounding-box on the very edge of the image)
NotTouchingSceneBorder() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.independent.NotTouchingSceneBorder
NullInitialization - Class in org.anchoranalysis.bean.initializable.parameters: When initialization should occur of a bean, but no parameters (containing data) are required.
NullMessageLogger - Class in org.anchoranalysis.core.log: Does nothing with with any messages logged.
NullMessageLogger() - Constructor for class org.anchoranalysis.core.log.NullMessageLogger
NullParametersBean<T> - Class in org.anchoranalysis.bean: A base class for beans that require initialization but the initializations needs no parameters.
NullParametersBean() - Constructor for class org.anchoranalysis.bean.NullParametersBean: Default constructor.
NUMBER_DECIMAL_PLACES - Static variable in class org.anchoranalysis.feature.io.csv.FeatureCSVWriter: The number of decimal places to use for double values, unless visuallyShortened==true.
NUMBER_OBJECTS_ATTRIBUTE_NAME - Static variable in class org.anchoranalysis.image.io.object.output.hdf5.HDF5ObjectsGenerator: Name of the attribute in the root of the HDF5 that stores the number of objects.
numberBorderPixels(ObjectMask, KernelApplicationParameters) - Static method in class org.anchoranalysis.plugin.image.feature.bean.object.single.border.NumberVoxelsAtBorder: Calculates the number of border voxels for a given object.
numberBytes() - Method in class org.anchoranalysis.image.voxel.datatype.VoxelDataType: The number of bytes needed to represent this data-type.
numberChannels() - Method in class org.anchoranalysis.image.io.channel.map.NamedChannelsConcatenate
numberChannels() - Method in interface org.anchoranalysis.image.io.channel.map.NamedChannelsMap: The number of channels that exist for the series.
numberChannels() - Method in class org.anchoranalysis.image.io.channel.map.OpenedNamedChannels
numberChannels(Logger) - Method in class org.anchoranalysis.image.io.channel.input.NamedChannelsInput: Number of channels.
numberChannels(Logger) - Method in interface org.anchoranalysis.image.io.stack.input.OpenedImageFile: The number of channels in the image-file e.g. 1 for grayscale, 3 for RGB.
numberChannels(Logger) - Method in class org.anchoranalysis.plugin.io.multifile.OpenedMultiFile
NumberChannels - Class in org.anchoranalysis.plugin.image.feature.bean.metadata: The number of channels in an image.
NumberChannels - Class in org.anchoranalysis.plugin.image.feature.bean.stack.intensity: The number of channels in an image-stack.
NumberChannels - Class in org.anchoranalysis.plugin.io.bean.summarizer.image
NumberChannels() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.metadata.NumberChannels
NumberChannels() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.stack.intensity.NumberChannels
NumberChannels() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.image.NumberChannels
numberCompletedFailed() - Method in class org.anchoranalysis.experiment.task.TaskStatistics: The number of jobs that completed with failure.
numberCompletedFailureJobs() - Method in class org.anchoranalysis.experiment.task.processor.ConcurrentJobMonitor: The number of jobs that have completed in a state of failure.
numberCompletedJobs() - Method in class org.anchoranalysis.experiment.task.processor.ConcurrentJobMonitor: The number of jobs that have completed, regardless of failure state.
numberCompletedSuccess() - Method in class org.anchoranalysis.experiment.task.TaskStatistics: The number of jobs that completed successfully.
numberCompletedSuccessfullyJobs() - Method in class org.anchoranalysis.experiment.task.processor.ConcurrentJobMonitor: The number of jobs that have completed in a state of success.
numberCompletedTotal() - Method in class org.anchoranalysis.experiment.task.TaskStatistics: The number of jobs that completed in total.
numberCPUs() - Method in class org.anchoranalysis.inference.concurrency.ConcurrencyPlan: The number of CPUs to be used in the plan.
numberDimensions() - Method in class org.anchoranalysis.mpp.mark.conic.Circle
numberDimensions() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
numberDimensions() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
numberDimensions() - Method in class org.anchoranalysis.mpp.mark.conic.Sphere
numberDimensions() - Method in class org.anchoranalysis.mpp.mark.Mark: Returns the number of dimensions of this mark.
numberDimensions() - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
numberDimensions() - Method in class org.anchoranalysis.mpp.mark.points.PointList
numberDimensions() - Method in class org.anchoranalysis.mpp.mark.points.Polygon
numberDimensions() - Method in class org.anchoranalysis.mpp.mark.points.PolygonCurve
numberDimensions() - Method in class org.anchoranalysis.mpp.mark.points.RotatableBoundingBox
numberDimensions() - Method in class org.anchoranalysis.spatial.orientation.Orientation: The dimensionality of space the orientation is valid for.
numberDimensions() - Method in class org.anchoranalysis.spatial.orientation.Orientation2D
numberDimensions() - Method in class org.anchoranalysis.spatial.orientation.Orientation3DEulerAngles
numberDimensions() - Method in class org.anchoranalysis.spatial.orientation.OrientationAxisAngle
numberDimensions() - Method in class org.anchoranalysis.spatial.orientation.OrientationRotationMatrix
numberDisabled() - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputs: Number of output-names that were not enabled.
numberDistinctChannelsSource() - Method in class org.anchoranalysis.io.bioformats.copyconvert.ImageFileEncoding: When RGB-encoded and non-interleaved, the source array is considered 1 channel (not three).
NumberDistinctValues - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic: Number of unique values in histogram.
NumberDistinctValues() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.NumberDistinctValues
numberEdges() - Method in class org.anchoranalysis.core.graph.GraphWithoutPayload: The number of edges in the graph.
numberEdges() - Method in class org.anchoranalysis.core.graph.GraphWithPayload: The number of edges in the graph.
numberEnabled() - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputs: Number of output-names that were enabled.
numberExecutingJobs() - Method in class org.anchoranalysis.experiment.task.processor.ConcurrentJobMonitor: The number of jobs that are currently executing.
numberFrames() - Method in class org.anchoranalysis.image.io.channel.input.NamedChannelsInput
numberFrames() - Method in interface org.anchoranalysis.image.io.stack.input.ProvidesStackInput: The number of time-frames in the underlying input image.
numberFrames() - Method in class org.anchoranalysis.mpp.io.input.MultiInput
numberFrames() - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertNamedChannelsInputToStack
numberFrames(Logger) - Method in interface org.anchoranalysis.image.io.stack.input.OpenedImageFile: The number of frames in the image-file i.e. distinct images for a particular time-point.
numberFrames(Logger) - Method in class org.anchoranalysis.plugin.io.multifile.OpenedMultiFile
NumberFrames - Class in org.anchoranalysis.plugin.image.feature.bean.metadata: The number of frames in an image.
NumberFrames() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.metadata.NumberFrames
numberGPUs() - Method in class org.anchoranalysis.inference.concurrency.ConcurrencyPlan: The number of GPUs to be used in the plan.
numberGroups() - Method in class org.anchoranalysis.plugin.annotation.bean.label.GroupedAnnotationLabels: Gets the number of unique groups.
numberImageFeatures() - Method in class org.anchoranalysis.image.feature.calculator.merged.MergedPairsFeatures: Gets the number of image features.
NumberIntersectingObjects - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting: A feature that calculates the number of objects intersecting with the input object.
NumberIntersectingObjects() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.NumberIntersectingObjects
NumberIntersectingObjectsAboveThreshold - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting: 1.
NumberIntersectingObjectsAboveThreshold() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.NumberIntersectingObjectsAboveThreshold
numberItemsCurrentlyStored() - Method in class org.anchoranalysis.feature.calculate.part.CalculationPartMap: Number of items currently stored in cache.
numberMatches() - Method in class org.anchoranalysis.image.core.object.MatchedObject: The number of objects in matches.
NumberNeighboringVoxels - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.energy: Calculates the number of voxels on the object that have a neighbor.
NumberNeighboringVoxels() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.NumberNeighboringVoxels
numberNotCompleted() - Method in class org.anchoranalysis.experiment.task.TaskStatistics: Number of jobs that have not been completed.
NumberObjects - Class in org.anchoranalysis.plugin.image.feature.bean.object.collection: Calculates the number of objects in a FeatureInputObjectCollection.
NumberObjects() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.collection.NumberObjects
numberPaired() - Method in interface org.anchoranalysis.annotation.io.assignment.Assignment: The number of items that are paired.
numberPaired() - Method in class org.anchoranalysis.annotation.io.assignment.ObjectVoxelIntersection
numberPaired() - Method in class org.anchoranalysis.annotation.io.assignment.OverlappingObjects
numberPairFeatures() - Method in class org.anchoranalysis.image.feature.calculator.merged.MergedPairsFeatures: Gets the number of pair features.
numberRegions() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
numberRegions() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
numberRegions() - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
numberRegions() - Method in class org.anchoranalysis.mpp.mark.Mark: Returns the number of regions in this mark.
numberRegions() - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
numberRegions() - Method in class org.anchoranalysis.mpp.mark.points.PointList
numberRegions() - Method in class org.anchoranalysis.mpp.mark.points.Polygon
numberRegions() - Method in class org.anchoranalysis.mpp.mark.points.PolygonCurve
numberRegions() - Method in class org.anchoranalysis.mpp.mark.points.RotatableBoundingBox
NumberRemovedVoxelsAfterClosing - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.morphological: How many pixels are removed after a morphological closing operation on the object-mask.
NumberRemovedVoxelsAfterClosing() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.NumberRemovedVoxelsAfterClosing
NumberResolutionLevels - Class in org.anchoranalysis.plugin.image.feature.bean.metadata: The number of resolution-levels in an image in a file.
NumberResolutionLevels() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.metadata.NumberResolutionLevels
numberSeries() - Method in class org.anchoranalysis.image.io.channel.input.NamedChannelsInput: Number of series that exist.
numberSeries() - Method in interface org.anchoranalysis.image.io.stack.input.OpenedImageFile: The number of series (distinct sets of images) in the image-file.
numberSeries() - Method in class org.anchoranalysis.plugin.io.multifile.OpenedMultiFile
NumberSeries - Class in org.anchoranalysis.plugin.image.feature.bean.metadata: The number of series in an image-file.
NumberSeries() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.metadata.NumberSeries
numberSingleFeatures() - Method in class org.anchoranalysis.image.feature.calculator.merged.MergedPairsFeatures: Gets the number of single object features.
numberSlices() - Method in interface org.anchoranalysis.mpp.index.VoxelPartition: Gets the number of slices in the partition.
numberSlices() - Method in class org.anchoranalysis.mpp.index.VoxelPartitionHistogram
NumberToStringConverter - Class in org.anchoranalysis.plugin.io.shared: Converts a number to a strings of constant width by padding with leading zeros.
NumberToStringConverter(int) - Constructor for class org.anchoranalysis.plugin.io.shared.NumberToStringConverter: Creates with a constant width just enough to be able to represent maxNumberToRepresent.
numberTotalScheduledJobs() - Method in class org.anchoranalysis.experiment.task.TaskStatistics: Total number of scheduled jobs.
NumberTouchingVoxelFaces - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.touching: A scheme for counting the touching voxels by intersection of object-masks
NumberTouchingVoxelFaces() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.NumberTouchingVoxelFaces
NumberTouchingVoxels - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.touching: A scheme for counting touching voxels.
NumberTouchingVoxels() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.NumberTouchingVoxels
numberUnassigned(boolean) - Method in interface org.anchoranalysis.annotation.io.assignment.Assignment: The number of items in a particular set that are not paired.
numberUnassigned(boolean) - Method in class org.anchoranalysis.annotation.io.assignment.ObjectVoxelIntersection
numberUnassigned(boolean) - Method in class org.anchoranalysis.annotation.io.assignment.OverlappingObjects
numberUnassignedLeft() - Method in class org.anchoranalysis.annotation.io.assignment.OverlappingObjects: The number of unassigned objects in the left set.
numberUnassignedRight() - Method in class org.anchoranalysis.annotation.io.assignment.OverlappingObjects: The number of unassigned objects in the right set.
numberUncompletedJobs() - Method in class org.anchoranalysis.experiment.task.processor.ConcurrentJobMonitor: The number of jobs that remain uncompleted.
numberUniqueColors() - Method in interface org.anchoranalysis.core.color.ColorIndex: The number of unique colors being described by the index.
numberUniqueColors() - Method in class org.anchoranalysis.core.color.ColorIndexModulo
numberUniqueColors() - Method in class org.anchoranalysis.core.color.ColorList
numberUniqueColors() - Method in class org.anchoranalysis.core.color.SingleColor
numberVertices() - Method in class org.anchoranalysis.core.graph.GraphWithoutPayload: The number of vertices in the graph.
numberVertices() - Method in class org.anchoranalysis.core.graph.GraphWithPayload: The number of vertices in the graph.
numberVoxels() - Method in class org.anchoranalysis.plugin.image.object.merge.ObjectVertex: Gets the number of voxels in the object.
NumberVoxels - Class in org.anchoranalysis.image.feature.bean.object.single: Calculates the number of voxels in a single object.
NumberVoxels() - Constructor for class org.anchoranalysis.image.feature.bean.object.single.NumberVoxels
NumberVoxelsAtBorder - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.border: Calculates the number of voxels at the border of an object.
NumberVoxelsAtBorder() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.border.NumberVoxelsAtBorder
numberVoxelsOn() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: The number of on voxels on the object-mask.
numFrames() - Method in class org.anchoranalysis.mpp.io.input.StackWithMap: Gets the number of frames.
numRegions() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMap: Gets the number of regions in the map.
numSlices() - Method in class org.anchoranalysis.mpp.index.IndexByRegion: Gets the number of slices in each region.
numSlices() - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetChannel

O

ObjectAggregationBase<T> - Class in org.anchoranalysis.plugin.image.feature.bean.shared.object: Calculates a feature for a set of objects using this stack as an energy-stack, and aggregates.
ObjectAggregationBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.shared.object.ObjectAggregationBase
ObjectAsMaskGenerator - Class in org.anchoranalysis.image.io.object.output.mask: Writes an object-mask as a mask (i.e. as a raster image)
ObjectAsMaskGenerator() - Constructor for class org.anchoranalysis.image.io.object.output.mask.ObjectAsMaskGenerator: Creates using a default image-resolution.
ObjectAsMaskGenerator(Optional<Resolution>) - Constructor for class org.anchoranalysis.image.io.object.output.mask.ObjectAsMaskGenerator
ObjectCollection - Class in org.anchoranalysis.image.voxel.object: A collection of ObjectMasks.
ObjectCollection(ArrayList<ObjectMask>) - Constructor for class org.anchoranalysis.image.voxel.object.ObjectCollection: Creates with the underlying list.
ObjectCollection(Stream<ObjectMask>) - Constructor for class org.anchoranalysis.image.voxel.object.ObjectCollection: Creates with elements from a stream.
ObjectCollectionFactory - Class in org.anchoranalysis.image.voxel.object: Creates ObjectCollection using various utility and helper methods.
ObjectCollectionProvider - Class in org.anchoranalysis.image.bean.provider: Base class for beans that implement Provider to provide an ObjectCollection.
ObjectCollectionProvider() - Constructor for class org.anchoranalysis.image.bean.provider.ObjectCollectionProvider
ObjectCollectionProviderFilterBase - Class in org.anchoranalysis.plugin.image.bean.object.provider.filter: Base class for object collection providers that apply a filter to the objects.
ObjectCollectionProviderFilterBase() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.filter.ObjectCollectionProviderFilterBase
ObjectCollectionProviderMorphological - Class in org.anchoranalysis.plugin.image.bean.object.provider.morphological: Base class for providers that apply morphological operations to an ObjectCollection.
ObjectCollectionProviderMorphological() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.morphological.ObjectCollectionProviderMorphological
ObjectCollectionProviderUnary - Class in org.anchoranalysis.image.bean.provider: Implementation of ObjectCollectionProvider that calls a single delegate Provider<ObjectCollection>.
ObjectCollectionProviderUnary() - Constructor for class org.anchoranalysis.image.bean.provider.ObjectCollectionProviderUnary
ObjectCollectionProviderWithFeature - Class in org.anchoranalysis.plugin.image.bean.object.provider.feature: An abstract base class for object collection providers that use a feature evaluator.
ObjectCollectionProviderWithFeature() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.feature.ObjectCollectionProviderWithFeature
ObjectCollectionReader - Class in org.anchoranalysis.image.io.object.input: Reads an ObjectCollection from the filesystem
ObjectCollectionWithProperties - Class in org.anchoranalysis.image.core.object.properties: Like an ObjectCollection but each object has associated properties.
ObjectCollectionWithProperties(int) - Constructor for class org.anchoranalysis.image.core.object.properties.ObjectCollectionWithProperties: Create with zero objects.
ObjectCollectionWithProperties(Stream<ObjectWithProperties>) - Constructor for class org.anchoranalysis.image.core.object.properties.ObjectCollectionWithProperties: Create with a stream of objects with properties.
ObjectCollectionWithProperties(ObjectCollection) - Constructor for class org.anchoranalysis.image.core.object.properties.ObjectCollectionWithProperties: Create with a stream of objects, assign empty properties to each.
ObjectCollectionWithProperties(ObjectMask) - Constructor for class org.anchoranalysis.image.core.object.properties.ObjectCollectionWithProperties: Create with a single object.
ObjectCollectionWriter - Class in org.anchoranalysis.image.io.object.output.hdf5: Centralized point to access a Generator which writes an ObjectCollection to the file-system.
objectCopyTo(ObjectMask, Voxels<T>, BoundingBox) - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter: Copies an area corresponding to an object-mask to another Voxels.
ObjectDrawAttributes - Class in org.anchoranalysis.overlay.writer: A means of extracting attributes associated with a particular object (e.g. color, ID) when drawing
ObjectDrawAttributes(ColorIndex) - Constructor for class org.anchoranalysis.overlay.writer.ObjectDrawAttributes: Creates with a specific color-index and uses the iteration-index as both the ID and color-ID
ObjectDrawAttributes(ColorIndex, IdentifierGetter<ObjectWithProperties>, IdentifierGetter<ObjectWithProperties>) - Constructor for class org.anchoranalysis.overlay.writer.ObjectDrawAttributes: Creates a new ObjectDrawAttributes instance.
ObjectFilter - Class in org.anchoranalysis.image.bean.object: Base class for filtering an ObjectCollection to remove objects according to a criteria.
ObjectFilter() - Constructor for class org.anchoranalysis.image.bean.object.ObjectFilter
ObjectFilterCombine - Class in org.anchoranalysis.plugin.image.bean.object.filter.combine: A filter that combines other filters (in a list)
ObjectFilterCombine() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.combine.ObjectFilterCombine
ObjectFilterPredicate - Class in org.anchoranalysis.plugin.image.bean.object.filter: Uses a predicate to make a decision whether to keep objects or not.
ObjectFilterPredicate() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterPredicate
ObjectFilterRelation - Class in org.anchoranalysis.plugin.image.bean.object.filter: An independent object-filter that uses a relation in its predicate.
ObjectFilterRelation() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterRelation
objectFor(ObjectMask) - Method in class org.anchoranalysis.image.core.object.scale.AccessObjectMaskSimple
objectFor(T) - Method in interface org.anchoranalysis.image.core.object.scale.AccessObjectMask: An object-mask for a given element.
ObjectForReduction - Class in org.anchoranalysis.image.inference.bean.reduce: An object that can be reduced.
ObjectForReduction(LabelledWithConfidence<ObjectMask>) - Constructor for class org.anchoranalysis.image.inference.bean.reduce.ObjectForReduction: Creates with a ObjectMask that is considered newly-added.
ObjectForReduction(LabelledWithConfidence<ObjectMask>, int) - Constructor for class org.anchoranalysis.image.inference.bean.reduce.ObjectForReduction: Creates a new ObjectForReduction instance.
ObjectForReductionFactory - Class in org.anchoranalysis.image.inference.bean.reduce: Utility functions for creating one or more ObjectForReductions.
ObjectFromPointsFactory - Class in org.anchoranalysis.image.core.object: Create an ObjectMask from a collection of points.
ObjectInputStreamDeserializer<T> - Class in org.anchoranalysis.core.serialize: Deserializes using Java's Native serialization framework.
ObjectInputStreamDeserializer() - Constructor for class org.anchoranalysis.core.serialize.ObjectInputStreamDeserializer
ObjectIntersectionRemover - Class in org.anchoranalysis.plugin.image.object: Utility class for removing intersecting voxels between objects in a collection.
ObjectMask - Class in org.anchoranalysis.image.voxel.object: A localized-mask in an image, expressed as a BoundingBox, with a corresponding mask sized to match the bounding-box.
ObjectMask(BinaryVoxels<UnsignedByteBuffer>) - Constructor for class org.anchoranalysis.image.voxel.object.ObjectMask: Creates from a BinaryVoxels to be located at the origin.
ObjectMask(BoundedVoxels<UnsignedByteBuffer>) - Constructor for class org.anchoranalysis.image.voxel.object.ObjectMask: Creates from a BoundedVoxels with UnsignedByteBuffer.
ObjectMask(BoundedVoxels<UnsignedByteBuffer>, BinaryValuesInt) - Constructor for class org.anchoranalysis.image.voxel.object.ObjectMask: Creates from BoundedVoxels and corresponding BinaryValuesInt.
ObjectMask(Voxels<UnsignedByteBuffer>) - Constructor for class org.anchoranalysis.image.voxel.object.ObjectMask: Creates from a Voxels mask that is cornered at the origin.
ObjectMask(BoundingBox) - Constructor for class org.anchoranalysis.image.voxel.object.ObjectMask: Creates as a bounding-box with all corresponding mask voxels set to off.
ObjectMask(BoundingBox, BinaryVoxels<UnsignedByteBuffer>) - Constructor for class org.anchoranalysis.image.voxel.object.ObjectMask: Creates from a BinaryVoxels and a corresponding bounding-box.
ObjectMask(BoundingBox, Voxels<UnsignedByteBuffer>) - Constructor for class org.anchoranalysis.image.voxel.object.ObjectMask: Creates from Voxels and a BoundingBox with default BinaryValuesInt.
ObjectMask(BoundingBox, Voxels<UnsignedByteBuffer>, BinaryValuesByte) - Constructor for class org.anchoranalysis.image.voxel.object.ObjectMask: Like ObjectMask(BoundingBox, Voxels, BinaryValuesInt) but specifies the binary-values as bytes.
ObjectMask(BoundingBox, Voxels<UnsignedByteBuffer>, BinaryValuesInt) - Constructor for class org.anchoranalysis.image.voxel.object.ObjectMask: Creates from Voxels and a corresponding BoundingBox and BinaryValuesInt.
ObjectMaskMerger - Class in org.anchoranalysis.image.core.merge: Merges one or more ObjectMasks into a single object.
ObjectMaskStream - Class in org.anchoranalysis.image.voxel.object: A custom "stream" like class for various functional-programming operations on ObjectCollection
ObjectMaskStream(ObjectCollection) - Constructor for class org.anchoranalysis.image.voxel.object.ObjectMaskStream
ObjectMatcher - Class in org.anchoranalysis.image.bean.object: Matches an object with other objects.
ObjectMatcher() - Constructor for class org.anchoranalysis.image.bean.object.ObjectMatcher
ObjectOutputStreamGenerator<T> - Class in org.anchoranalysis.io.generator.serialized: Generator that writes an element to the file-system using the Java ObjectOutputStream format.
ObjectOutputStreamGenerator() - Constructor for class org.anchoranalysis.io.generator.serialized.ObjectOutputStreamGenerator
ObjectRadiusStandardDeviation - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shape: Calculates the standard deviation of distances from surface voxels to the centroid of an ObjectMask.
ObjectRadiusStandardDeviation() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.shape.ObjectRadiusStandardDeviation
objects() - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitialization: A collection of ObjectCollections, indexed by name.
objects() - Method in class org.anchoranalysis.image.inference.segment.SegmentedObjectsAtScale: Create a ObjectCollection of all contained objects, excluding confidence.
objects() - Method in class org.anchoranalysis.mpp.io.input.MultiInput: Gets the map of ObjectCollections.
objects(String) - Static method in class org.anchoranalysis.plugin.image.provider.ReferenceFactory: Creates a reference to objects.
Objects - Class in org.anchoranalysis.plugin.annotation.bean.comparer: An ObjectCollection to be compared against something else.
Objects() - Constructor for class org.anchoranalysis.plugin.annotation.bean.comparer.Objects
OBJECTS_ROOT_WITH_SEPERATORS - Static variable in class org.anchoranalysis.image.io.object.HDF5PathHelper: Hardcoded string that identifies in the HDF5 file for where the object-collection is stored.
ObjectsAsGrayscaleGenerator - Class in org.anchoranalysis.image.io.object.output.grayscale: Base class for generators that accept a set of objects as input.
ObjectsAsGrayscaleGenerator(Dimensions) - Constructor for class org.anchoranalysis.image.io.object.output.grayscale.ObjectsAsGrayscaleGenerator: Creates a new ObjectsAsGrayscaleGenerator instance.
ObjectsAsRGBGenerator - Class in org.anchoranalysis.image.io.object.output.rgb: A base class for generators that draw an ObjectCollection upon a RGBStack.
ObjectsAsRGBGenerator(DrawObject, ObjectDrawAttributes, Either<Dimensions, DisplayStack>) - Constructor for class org.anchoranalysis.image.io.object.output.rgb.ObjectsAsRGBGenerator: Creates a new ObjectsAsRGBGenerator instance.
ObjectsAsUniqueValueGenerator - Class in org.anchoranalysis.image.io.object.output.grayscale: Writes objects as an image with an incrementing unique integer id value for each object.
ObjectsAsUniqueValueGenerator(Dimensions) - Constructor for class org.anchoranalysis.image.io.object.output.grayscale.ObjectsAsUniqueValueGenerator: Create with a particular dimensions.
ObjectScalingMethod - Interface in org.anchoranalysis.image.core.object.scale.method: A way to scale a group of ObjectMasks, scaling each object independently or collectively.
ObjectScalingMethodFactory - Class in org.anchoranalysis.image.core.object.scale.method: Determines which instance of ObjectScalingMethod to apply.
objectsForThumbnail(FeatureInputPairObjects) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
objectsForThumbnail(FeatureInputSingleObject) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.EachObjectIndependently
objectsForThumbnail(T) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.CombineObjectsForFeatures: Selects objects from an input that will be used for thumbnail generation.
ObjectsFromConnectedComponentsFactory - Class in org.anchoranalysis.image.voxel.binary.connected: Creates a ObjectCollection from the connected-components of a mask or binary-voxels.
ObjectsFromConnectedComponentsFactory() - Constructor for class org.anchoranalysis.image.voxel.binary.connected.ObjectsFromConnectedComponentsFactory: Creates to use a small-neighborhood.
ObjectsFromConnectedComponentsFactory(boolean) - Constructor for class org.anchoranalysis.image.voxel.binary.connected.ObjectsFromConnectedComponentsFactory: Creates to use a specified type of neighborhood.
ObjectsFromConnectedComponentsFactory(boolean, int) - Constructor for class org.anchoranalysis.image.voxel.binary.connected.ObjectsFromConnectedComponentsFactory: Creates to use a specified type of neighborhood, and minimum number of voxels.
ObjectsFromConnectedComponentsFactory(int) - Constructor for class org.anchoranalysis.image.voxel.binary.connected.ObjectsFromConnectedComponentsFactory: Creates to use a minimum number of voxels for each connected component.
ObjectsMergedAsMaskGenerator - Class in org.anchoranalysis.image.io.object.output.grayscale: Writes objects merged together as a mask.
ObjectsMergedAsMaskGenerator(Dimensions) - Constructor for class org.anchoranalysis.image.io.object.output.grayscale.ObjectsMergedAsMaskGenerator: Create with particular size for the mask image.
ObjectsToCompare - Class in org.anchoranalysis.plugin.annotation.comparison: Holds two ObjectCollections for comparison purposes.
ObjectsToCompare(ObjectCollection, ObjectCollection) - Constructor for class org.anchoranalysis.plugin.annotation.comparison.ObjectsToCompare: Creates a new ObjectsToCompare instance.
objectsToDraw(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBaseWithGenerator: The objects to draw (without any colors) on the background.
objectsToDraw(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredObjects
objectsToDraw(Dimensions) - Method in class org.anchoranalysis.plugin.mpp.bean.stack.provider.ColoredMarks
objectsWithProperties() - Method in class org.anchoranalysis.image.inference.segment.SegmentedObjectsAtScale: Like SegmentedObjectsAtScale.objects() but instead creates a ObjectCollectionWithProperties containing empty properties.
ObjectVertex - Class in org.anchoranalysis.plugin.image.object.merge: A vertex in a merge graph representing an object (and an associated payload).
ObjectVertex(ObjectMask, double) - Constructor for class org.anchoranalysis.plugin.image.object.merge.ObjectVertex: Creates a new ObjectVertex instance.
ObjectVoxelIntersection - Class in org.anchoranalysis.annotation.io.assignment: Creates an assignment between intersecting voxels in two objects.
ObjectVoxelIntersection(ObjectMask, ObjectMask) - Constructor for class org.anchoranalysis.annotation.io.assignment.ObjectVoxelIntersection: Determines a voxel-assignment between two objects.
ObjectWithBoundingBoxGenerator - Class in org.anchoranalysis.image.io.object.output.mask: Like ObjectAsMaskGenerator but additionally outputs a serialized bounding box.
ObjectWithBoundingBoxGenerator(Optional<Resolution>) - Constructor for class org.anchoranalysis.image.io.object.output.mask.ObjectWithBoundingBoxGenerator: Create with a resolution, if it is known.
objectWithColor(RGBColor) - Method in class org.anchoranalysis.image.core.stack.RGBStack: Extracts an ObjectMask from a Channel of all voxels that have a particular color.
ObjectWithEllipse - Class in org.anchoranalysis.plugin.points.calculate.ellipse: A pair containing an ObjectMask and its corresponding best-fit Ellipse.
ObjectWithEllipse(ObjectMask, Ellipse) - Constructor for class org.anchoranalysis.plugin.points.calculate.ellipse.ObjectWithEllipse: Creates a new ObjectWithEllipse instance.
ObjectWithMaximumFeature - Class in org.anchoranalysis.plugin.image.bean.object.provider.feature: Finds the object with the maximum feature-value from a collection.
ObjectWithMaximumFeature() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.feature.ObjectWithMaximumFeature
ObjectWithMaximumFeatureFromEachMatchedCollection - Class in org.anchoranalysis.plugin.image.bean.object.provider.feature: Finds the object with the maximum feature among a group of matches for each object.
ObjectWithMaximumFeatureFromEachMatchedCollection() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.feature.ObjectWithMaximumFeatureFromEachMatchedCollection
ObjectWithProperties - Class in org.anchoranalysis.image.core.object.properties: An ObjectMask with associated key-value properties.
ObjectWithProperties(ObjectMask) - Constructor for class org.anchoranalysis.image.core.object.properties.ObjectWithProperties: Creates with an existing ObjectMask and empty properties.
ObjectWithProperties(ObjectMask, Map<String, Object>) - Constructor for class org.anchoranalysis.image.core.object.properties.ObjectWithProperties: Creates a new ObjectWithProperties instance.
ObjectWithProperties(BoundingBox) - Constructor for class org.anchoranalysis.image.core.object.properties.ObjectWithProperties: Creates as a bounding-box with all corresponding mask voxels set to off.
of(boolean) - Static method in class org.anchoranalysis.image.core.object.scale.method.ObjectScalingMethodFactory: Determines which method to use, given circumstances.
of(boolean) - Static method in class org.anchoranalysis.image.voxel.neighborhood.NeighborhoodFactory: Gets an appropriate neighborhood
of(boolean, boolean) - Static method in enum class org.anchoranalysis.image.voxel.kernel.OutsideKernelPolicy: Multiplexes between all three possible enums.
of(Collection<ObjectMask>...) - Static method in class org.anchoranalysis.image.voxel.object.ObjectCollectionFactory: Creates a new collection with elements copied from existing collections.
of(Optional<ObjectCollection>...) - Static method in class org.anchoranalysis.image.voxel.object.ObjectCollectionFactory: Creates a new collection with elements copied from existing collections, if they exist.
of(Stream<T>) - Static method in class org.anchoranalysis.core.functional.FunctionalList: Creates a list from a stream.
of(FeatureCalculationInput<FeatureInputSingleObject>, boolean) - Static method in class org.anchoranalysis.plugin.points.calculate.ellipsoid.CalculateEllipsoidLeastSquares: Calculates an Ellipsoid for the given input.
of(CalculationPartResolver<FeatureInputSingleObject>, int, boolean) - Static method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateDilation: Creates a new ResolvedPart for calculating dilation.
of(CalculationPartResolver<FeatureInputSingleObject>, int, boolean) - Static method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateErosion: Creates a new CalculationPart for calculating erosion.
of(CalculationPartResolver<FeatureInputSingleObject>, MorphologicalIterations, int, boolean) - Static method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateShellObjectMask: Creates a new CalculateShellObjectMask instance.
of(BinaryVoxels<UnsignedByteBuffer>...) - Static method in class org.anchoranalysis.image.voxel.object.ObjectCollectionFactory: Creates a new collection with elements from the parameter-list of BinaryVoxels converting the voxels in their entirety to an object-mask at the origin.
of(ObjectCollection...) - Static method in class org.anchoranalysis.image.voxel.object.ObjectCollectionFactory: Creates a new collection with elements copied from existing collections.
of(ObjectMask...) - Static method in class org.anchoranalysis.image.voxel.object.ObjectCollectionFactory: Creates a new collection with elements from the parameter-list.
offset(int, int) - Method in class org.anchoranalysis.image.core.dimensions.Dimensions: Calculates a XY-offset of a point in a buffer whose dimensions are this extent.
offset(int, int) - Method in class org.anchoranalysis.spatial.box.Extent: Calculates a XY-offset of a point in a buffer whose dimensions are this extent.
offset(int, int, int) - Method in class org.anchoranalysis.spatial.box.Extent: Calculates a XYZ-offset of a point in a buffer whose dimensions are this extent.
offset(Point2i) - Method in class org.anchoranalysis.spatial.box.Extent: Calculates a XY-offset of a point in a buffer whose dimensions are this extent.
offset(Point3i) - Method in class org.anchoranalysis.image.core.dimensions.Dimensions: Calculates a XYZ-offset of a point in a buffer whose dimensions are this extent.
offset(ReadableTuple3i) - Method in class org.anchoranalysis.spatial.box.Extent: Calculates a XYZ-offset of a point in a buffer whose dimensions are this extent.
offsetGlobal(int, int) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Calculates an offset for locating a voxel inside the buffer, with global encoding of coordinates.
offsetRelative(int, int) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Calculates an offset for locating a voxel inside the buffer, with local encoding of coordinates.
offsetSlice(Point3i) - Method in class org.anchoranalysis.image.core.dimensions.Dimensions: Calculates a XY-offset of a point in a buffer whose dimensions are this extent.
offsetSlice(ReadableTuple3i) - Method in class org.anchoranalysis.spatial.box.Extent: Calculates a XY-offset of a point in a buffer whose dimensions are this extent.
OffsettedPointTwoDimensionalConsumer - Interface in org.anchoranalysis.spatial.point.consumer: Like a PointTwoDimensionalConsumer but also has a buffer offset.
OffsettedScalarTwoDimensionalConsumer<E> - Interface in org.anchoranalysis.spatial.point.consumer: Like a ScalarTwoDimensionalConsumer but accepts two coordinates of a point and an offset value.
ofResolved(CalculationPartResolver<FeatureInputSingleObject>, int, boolean) - Static method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateErosion: Creates a new ResolvedPart for calculating erosion.
OME_TIFF - Enum constant in enum class org.anchoranalysis.core.format.ImageFileFormat: OME TIFF
OME_XML - Enum constant in enum class org.anchoranalysis.core.format.ImageFileFormat: OME XML
OMETiff - Class in org.anchoranalysis.io.bioformats.bean.writer: Writes a stack to the filesystem as an OME-TIFF using the Bioformats library.
OMETiff() - Constructor for class org.anchoranalysis.io.bioformats.bean.writer.OMETiff: Default constructor.
OMEXML - Class in org.anchoranalysis.io.bioformats.bean.writer: Writes a stack to the filesystem as an OME-XML using the Bioformats library.
OMEXML() - Constructor for class org.anchoranalysis.io.bioformats.bean.writer.OMEXML: Default constructor.
OMIT - Enum constant in enum class org.anchoranalysis.plugin.io.naming.interval.DateStyle: The date is omitted from the name.
OMIT - Enum constant in enum class org.anchoranalysis.plugin.io.naming.interval.TimeStyle: The time is omitted from the name.
One - Class in org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels: Selects one specific channel from a set of stacks
One() - Constructor for class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.One
oneOnly(String, String, boolean, boolean) - Static method in class org.anchoranalysis.bean.initializable.CheckMisconfigured: Checks that one of two properties is defined, but not both simultaneously.
OneOrThreeChannelsWriter - Class in org.anchoranalysis.image.io.bean.stack.writer: A base-class for a StackWriter that writes an image that has either one or three channels.
OneOrThreeChannelsWriter() - Constructor for class org.anchoranalysis.image.io.bean.stack.writer.OneOrThreeChannelsWriter
OneStageGenerator<T> - Class in org.anchoranalysis.io.generator: A SingleFileTypeGenerator that does not transform an element before generating.
OneStageGenerator() - Constructor for class org.anchoranalysis.io.generator.OneStageGenerator
onInitialization() - Method in class org.anchoranalysis.bean.NullParametersBean: As there's no parameters we expose a different method.
onInitialization() - Method in class org.anchoranalysis.mpp.bean.mark.factory.MarkWithIdentifierFactory
onInitialization(NullInitialization) - Method in class org.anchoranalysis.bean.NullParametersBean
onInitialization(DictionaryInitialization) - Method in class org.anchoranalysis.bean.shared.dictionary.DictionaryProviderReference
onInitialization(FeatureInitialization) - Method in class org.anchoranalysis.feature.bean.Feature: Called after initialization.
onInitialization(FeatureRelatedInitialization) - Method in class org.anchoranalysis.feature.bean.list.ReferencingFeatureListProvider
onInitialization(FeatureRelatedInitialization) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeature
onInitialization(ImageInitialization) - Method in class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationReference
onInitialization(ImageInitialization) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromInput
onInitialization(ImageInitialization) - Method in class org.anchoranalysis.plugin.image.bean.dimensions.provider.FromChannel
onInitialization(ImageInitialization) - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.Reference
onInitialization(ImageInitialization) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromStackChannel
onInitialization(ImageInitialization) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.ReferenceOrElse
onInitialization(ImageInitialization) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.FromInput
onInitialization(PointsInitialization) - Method in class org.anchoranalysis.plugin.points.bean.fitter.Reference
onInitialization(P) - Method in class org.anchoranalysis.bean.initializable.InitializableBean: Called after initialization.
OnlyIf - Class in org.anchoranalysis.experiment.bean.log: Logs messages to a particular location ONLY if debug-mode is enabled.
OnlyIf() - Constructor for class org.anchoranalysis.experiment.bean.log.OnlyIf
OnnxModel - Class in org.anchoranalysis.plugin.onnx.model: A model that can be used for inference using the ONNX Runtime's Java API.
OnnxModel(OrtSession) - Constructor for class org.anchoranalysis.plugin.onnx.model.OnnxModel
open(int, Logger) - Method in interface org.anchoranalysis.image.io.stack.input.OpenedImageFile: Open when we don't have a specific-type.
open(int, Logger) - Method in class org.anchoranalysis.plugin.io.multifile.OpenedMultiFile
open(Path) - Static method in class org.anchoranalysis.io.input.csv.CSVReaderByLine: Opens a CSV file for reading.
open(Path, String, boolean) - Static method in class org.anchoranalysis.io.input.csv.CSVReaderByLine: Opens a CSV file for reading.
open(Path, String, boolean, boolean) - Static method in class org.anchoranalysis.io.input.csv.CSVReaderByLine: Opens a CSV file for reading.
open(Logger) - Method in interface org.anchoranalysis.image.io.stack.input.OpenedImageFile: Open the first series when we don't have a specific-type.
openChannelFromFilePath(Path) - Method in class org.anchoranalysis.test.image.io.TestLoaderImage: Opens a channel from a file path.
openChannelFromTestPath(String) - Method in class org.anchoranalysis.test.image.io.TestLoaderImage: Opens a channel from a test path.
openCheckType(int, VoxelDataType, Logger) - Method in interface org.anchoranalysis.image.io.stack.input.OpenedImageFile: Opens a time-series, and checks that it is a particular type.
OpenCV - Class in org.anchoranalysis.plugin.opencv.bean.interpolate: Interpolation using OpenCV for resizing an image.
OpenCV() - Constructor for class org.anchoranalysis.plugin.opencv.bean.interpolate.OpenCV
OpenCVModel - Class in org.anchoranalysis.plugin.opencv.segment: A model that can be used for inference using OpenCV's DNN module.
OpenCVModel(Net) - Constructor for class org.anchoranalysis.plugin.opencv.segment.OpenCVModel: Creates a new OpenCVModel instance.
OpenCVReader - Class in org.anchoranalysis.plugin.opencv.bean.stack: Reads a stack from the file-system using OpenCV.
OpenCVReader() - Constructor for class org.anchoranalysis.plugin.opencv.bean.stack.OpenCVReader
OpenCVWriter - Class in org.anchoranalysis.plugin.opencv.bean.stack: Writes a stack to the file-system using OpenCV and a specified extension.
OpenCVWriter() - Constructor for class org.anchoranalysis.plugin.opencv.bean.stack.OpenCVWriter
OpenedCSVFile() - Constructor for class org.anchoranalysis.io.input.csv.CSVReader.OpenedCSVFile
OpenedImageFile - Interface in org.anchoranalysis.image.io.stack.input: An image file that has been opened for reading containing one or more series of image-Stacks.
OpenedMultiFile - Class in org.anchoranalysis.plugin.io.multifile: A OpenedImageFile where the image is formed from more than one file on the file-system.
OpenedMultiFile(StackReader, ParsedFilePathBag, ExecutionTimeRecorder) - Constructor for class org.anchoranalysis.plugin.io.multifile.OpenedMultiFile
OpenedNamedChannels - Class in org.anchoranalysis.image.io.channel.map: A set of named Channels available from an OpenedImageFile.
OpenedNamedChannels(OpenedImageFile, ChannelMap, int) - Constructor for class org.anchoranalysis.image.io.channel.map.OpenedNamedChannels: Creates a new OpenedNamedChannels instance.
openFile(Path, ExecutionTimeRecorder) - Method in class org.anchoranalysis.image.io.bean.stack.reader.StackReader: Opens a file containing one or more images.
openFile(Path, ExecutionTimeRecorder) - Method in class org.anchoranalysis.io.bioformats.bean.BioformatsReader
openFile(Path, ExecutionTimeRecorder) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.BranchExtension
openFile(Path, ExecutionTimeRecorder) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.FlattenAsChannel
openFile(Path, ExecutionTimeRecorder) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ImposeResolution
openFile(Path, ExecutionTimeRecorder) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader
openFile(Path, ExecutionTimeRecorder) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ReadVoxelExtentXml
openFile(Path, ExecutionTimeRecorder) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.RejectIfConditionXYResolution
openFile(Path, ExecutionTimeRecorder) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.RotateImageToMatchEXIFOrientation
openFile(Path, ExecutionTimeRecorder) - Method in class org.anchoranalysis.plugin.opencv.bean.stack.OpenCVReader
openFile(Path, StackReader, OperationContext) - Method in class org.anchoranalysis.image.io.bean.stack.metadata.reader.FromStackReader
openFile(Path, StackReader, OperationContext) - Method in class org.anchoranalysis.image.io.bean.stack.metadata.reader.ImageMetadataReader: Opens a file containing one or more images but does not read an image.
openFile(Path, StackReader, OperationContext) - Method in class org.anchoranalysis.plugin.io.bean.metadata.reader.AlwaysReject
openFile(Path, StackReader, OperationContext) - Method in class org.anchoranalysis.plugin.io.bean.metadata.reader.InferFromHeader
openFile(Path, CalculateOrientationChange, ExecutionTimeRecorder) - Method in class org.anchoranalysis.image.io.bean.stack.reader.StackReaderOrientationCorrection: Opens a file containing one or more images but does not read an image.
openFile(Path, CalculateOrientationChange, ExecutionTimeRecorder) - Method in class org.anchoranalysis.io.bioformats.bean.BioformatsReader
openFile(Path, CalculateOrientationChange, ExecutionTimeRecorder) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.RotateImageToMatchEXIFOrientation
openLargestObjectFrom(String) - Method in class org.anchoranalysis.test.image.object.TestLoaderObjects: Opens the largest object from an image stack identified by a suffix.
openMask(StackReader, Path, BinaryValuesInt, OperationContext) - Static method in class org.anchoranalysis.image.io.stack.input.MaskReader: Utility functions for opening a single-channeled stack as a Mask.
openObjectsFromFilePath(Path) - Method in class org.anchoranalysis.test.image.io.TestLoaderImage: Opens an obj-mask-collection from a path to a file
openObjectsFromTestPath(String) - Method in class org.anchoranalysis.test.image.io.TestLoaderImage: Opens an object collection from a test path.
openStackFromFilePath(Path) - Method in class org.anchoranalysis.test.image.io.TestLoaderImage: Opens a stack from a file path.
openStackFromTestPath(String) - Method in class org.anchoranalysis.test.image.io.TestLoaderImage: Opens a stack from a test path.
openXmlAbsoluteFilePath(String) - Static method in class org.anchoranalysis.test.TestLoader: Opens a XML document - with an absolute path on the filesystem.
openXmlAbsoluteFilePath(Path) - Static method in class org.anchoranalysis.test.TestLoader: Opens a XML document - with an absolute path on the filesystem.
openXmlFromTestPath(String) - Method in class org.anchoranalysis.test.TestLoader: Opens a XML document - with a path relative to the test root.
operationContext() - Method in interface org.anchoranalysis.io.output.outputter.InputOutputContext: Creates a OperationContext based upon the state in this class.
OperationContext - Class in org.anchoranalysis.core.time: Context objects for general operations that allow for logging and recording execution time.
OperationContext(Logger) - Constructor for class org.anchoranalysis.core.time.OperationContext: Creates with a Logger ignoring execution-times.
OperationContext(ExecutionTimeRecorder, Logger) - Constructor for class org.anchoranalysis.core.time.OperationContext: Creates a new OperationContext instance.
OperationFailedException - Exception Class in org.anchoranalysis.core.exception: Generic checked exception that can be thrown when a particular operation fails.
OperationFailedException(String) - Constructor for exception class org.anchoranalysis.core.exception.OperationFailedException: Creates with only a message.
OperationFailedException(String, Throwable) - Constructor for exception class org.anchoranalysis.core.exception.OperationFailedException: Creates with both a message and cause.
OperationFailedException(Throwable) - Constructor for exception class org.anchoranalysis.core.exception.OperationFailedException: Creates with only a cause.
OperationFailedRuntimeException - Exception Class in org.anchoranalysis.core.exception: Generic runtime exception that can be thrown when a particular operation fails.
OperationFailedRuntimeException(Exception) - Constructor for exception class org.anchoranalysis.core.exception.OperationFailedRuntimeException: Creates with only a cause.
OperationFailedRuntimeException(String) - Constructor for exception class org.anchoranalysis.core.exception.OperationFailedRuntimeException: Creates with only a message.
OperationMap<T> - Class in org.anchoranalysis.mpp.io.input: Stores objects as operations in a map, implementing the MultiInputSubMap interface.
OperationMap() - Constructor for class org.anchoranalysis.mpp.io.input.OperationMap
OptionalBean - Annotation Interface in org.anchoranalysis.bean.annotation: Indicates that a field of a class can be set to null (omitted), otherwise by default a bean must always have a non-null value.
OptionalComparator - Class in org.anchoranalysis.core.functional: Creates a Comparator that can work with Optionals.
OptionalFactory - Class in org.anchoranalysis.core.functional: Utility functions to create Optional from flags.
OptionalNameValue<V> - Class in org.anchoranalysis.io.generator.combined: A simple container expressing a value and an associationed optional name.
OptionalNameValue(Optional<String>, V) - Constructor for class org.anchoranalysis.io.generator.combined.OptionalNameValue: Creates a new OptionalNameValue instance.
OptionalPointProposer - Interface in org.anchoranalysis.mpp.proposer: An interface for proposing a position in 3D space.
OptionalProviderFactory - Class in org.anchoranalysis.bean: Utility functions to create Optional from nullable Providers.
OptionalUtilities - Class in org.anchoranalysis.core.functional: Additional utility functions for Optional and exceptions.
or(StackWriteAttributes) - Method in class org.anchoranalysis.image.io.stack.output.StackWriteAttributes: Combines with another StackWriteAttributes by performing a logical or on each field.
Or - Class in org.anchoranalysis.plugin.image.bean.mask.provider.combine: Outputs the logical operation or voxelwise on both masks, modifying {mask} with the result.
Or - Class in org.anchoranalysis.plugin.image.bean.object.filter.combine: Applies multiples filter with logical OR i.e. an object must pass any one of the filter steps to remain.
Or() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.combine.Or
Or() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.combine.Or
OrderedFeatureList<T> - Interface in org.anchoranalysis.mpp.feature.addcriteria: An interface for providing an ordered list of features.
orderedListOfFeatures() - Method in class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaEnergyPair
orderedListOfFeatures() - Method in class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaNever
orderedListOfFeatures() - Method in class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaOr
orderedListOfFeatures() - Method in class org.anchoranalysis.mpp.feature.addcriteria.ArbitraryPointCommon
orderedListOfFeatures() - Method in class org.anchoranalysis.mpp.feature.addcriteria.BoundingBoxIntersection
orderedListOfFeatures() - Method in interface org.anchoranalysis.mpp.feature.addcriteria.OrderedFeatureList: Retrieves an ordered list of features used to determine the AddCriteria.
orElseGet(Optional<T>, CheckedSupplier<T, E>) - Static method in class org.anchoranalysis.core.functional.OptionalUtilities: Like Optional.orElseGet(java.util.function.Supplier<? extends T>) but tolerates an exception in the supplier function, which is immediately thrown.
orElseGetFlat(Optional<T>, CheckedSupplier<Optional<T>, E>...) - Static method in class org.anchoranalysis.core.functional.OptionalUtilities: Like OptionalUtilities.orElseGet(java.util.Optional<T>, org.anchoranalysis.core.functional.checked.CheckedSupplier<T, E>) but returns a Optional and can chain many alternatives.
orFlat(Iterable<Optional<T>>) - Static method in class org.anchoranalysis.core.functional.OptionalUtilities: The first optional if it's present, or the second, or the third etc. using an Iterable.
orFlat(Optional<T>...) - Static method in class org.anchoranalysis.core.functional.OptionalUtilities: Like OptionalUtilities.orFlat(Iterable) but allows Optionals to be specified as variable-arguments.
orFlat(Stream<Optional<T>>) - Static method in class org.anchoranalysis.core.functional.OptionalUtilities: The first optional if it's present, or the second, or the third etc. using an Stream.
orFlatSupplier(Iterable<CheckedSupplier<Optional<T>, E>>) - Static method in class org.anchoranalysis.core.functional.OptionalUtilities: The first optional if it's present, or the second, or the third etc. using an iterable and a CheckedSupplier.
orFlatSupplier(CheckedSupplier<Optional<T>, E>...) - Static method in class org.anchoranalysis.core.functional.OptionalUtilities: Like OptionalUtilities.orFlatSupplier(Iterable) but allows Optionals to be specified as variable-arguments.
org.anchoranalysis.annotation - package org.anchoranalysis.annotation: Ground truth for an image in diverse forms.
org.anchoranalysis.annotation.image - package org.anchoranalysis.annotation.image: Annotations that apply to an image as a whole.
org.anchoranalysis.annotation.io - package org.anchoranalysis.annotation.io: Reading and writing annotations to the filesystem.
org.anchoranalysis.annotation.io.assignment - package org.anchoranalysis.annotation.io.assignment: A pairing of objects from two collections (bipartite matching).
org.anchoranalysis.annotation.io.assignment.generator - package org.anchoranalysis.annotation.io.assignment.generator: Generates output images to illustrate a Assignment between annotations.
org.anchoranalysis.annotation.io.bean - package org.anchoranalysis.annotation.io.bean: Beans related to reading / writing / specifying annotations.
org.anchoranalysis.annotation.io.bean.comparer - package org.anchoranalysis.annotation.io.bean.comparer: What to compare an annotation (ground truth) against?
org.anchoranalysis.annotation.io.comparer - package org.anchoranalysis.annotation.io.comparer: Non-bean classes involving comparing results and annotations.
org.anchoranalysis.annotation.io.image - package org.anchoranalysis.annotation.io.image: Reading and writing whole-image label annotations.
org.anchoranalysis.annotation.io.image.findable - package org.anchoranalysis.annotation.io.image.findable: The outcome of searching for annotations or images on the file-system.
org.anchoranalysis.annotation.io.mark - package org.anchoranalysis.annotation.io.mark: Reading and writing Mark-related annotations from/to the file-system.
org.anchoranalysis.annotation.mark - package org.anchoranalysis.annotation.mark: Annotations that use one or more marks to describe entities in an image.
org.anchoranalysis.bean - package org.anchoranalysis.bean: Defining, loading, initializing Anchor Beans.
org.anchoranalysis.bean.annotation - package org.anchoranalysis.bean.annotation: Annotations that decorate fields in an Anchor Bean.
org.anchoranalysis.bean.define - package org.anchoranalysis.bean.define: Define and related-classes.
org.anchoranalysis.bean.define.adder - package org.anchoranalysis.bean.define.adder: DefineAdder and related-classes.
org.anchoranalysis.bean.exception - package org.anchoranalysis.bean.exception: Exceptions that can occur executing generic operations on Anchor Beans.
org.anchoranalysis.bean.initializable - package org.anchoranalysis.bean.initializable: Initializing beans with particular parameters, including recursively.
org.anchoranalysis.bean.initializable.parameters - package org.anchoranalysis.bean.initializable.parameters: Some parameterization used when initializing beans.
org.anchoranalysis.bean.initializable.property - package org.anchoranalysis.bean.initializable.property: Initializating a bean with parameters.
org.anchoranalysis.bean.permute - package org.anchoranalysis.bean.permute: Applying permutations to a bean's fields.
org.anchoranalysis.bean.permute.assign - package org.anchoranalysis.bean.permute.assign: Imposes a permutation value on one or more properties of a bean.
org.anchoranalysis.bean.permute.property - package org.anchoranalysis.bean.permute.property: Applying permutations to the properties of a bean.
org.anchoranalysis.bean.primitive - package org.anchoranalysis.bean.primitive: Beans that implement collections of primitive element types, as well as String.
org.anchoranalysis.bean.shared - package org.anchoranalysis.bean.shared: Utility beans which have a generally broader use than a specific module.
org.anchoranalysis.bean.shared.color - package org.anchoranalysis.bean.shared.color: Beans that specify colors.
org.anchoranalysis.bean.shared.color.scheme - package org.anchoranalysis.bean.shared.color.scheme: Beans that create lists or indices of colors according to particular schemes.
org.anchoranalysis.bean.shared.dictionary - package org.anchoranalysis.bean.shared.dictionary: Setting, referencing and initializing key-value parameters.
org.anchoranalysis.bean.shared.path - package org.anchoranalysis.bean.shared.path: Defines a root path directory on the filesystem whre files are read / written.
org.anchoranalysis.bean.shared.random - package org.anchoranalysis.bean.shared.random: Specifies a particular type of random-number generator.
org.anchoranalysis.bean.shared.regex - package org.anchoranalysis.bean.shared.regex: Specifies regular-expressions.
org.anchoranalysis.bean.shared.relation - package org.anchoranalysis.bean.shared.relation: Specifies a binary relation of some kind between scalars.
org.anchoranalysis.bean.shared.relation.threshold - package org.anchoranalysis.bean.shared.relation.threshold: Specifies a unary relation to a threshold value.
org.anchoranalysis.bean.xml - package org.anchoranalysis.bean.xml: Reading Beans from XML files.
org.anchoranalysis.bean.xml.creator - package org.anchoranalysis.bean.xml.creator: Creates beans from XML.
org.anchoranalysis.bean.xml.exception - package org.anchoranalysis.bean.xml.exception: Exceptions that can thrown when loading beans from XML.
org.anchoranalysis.bean.xml.factory - package org.anchoranalysis.bean.xml.factory: Custom factories for loading beans in custom ways from XML.
org.anchoranalysis.bean.xml.factory.primitive - package org.anchoranalysis.bean.xml.factory.primitive: Factories to create beans in org.anchoranalysis.bean.primitive.
org.anchoranalysis.core.cache - package org.anchoranalysis.core.cache: Caching (memozing) calls to a method so an operation does not need to be repeated.
org.anchoranalysis.core.collection - package org.anchoranalysis.core.collection: Collection-related classes with general applicability that don't belong elsewhere.
org.anchoranalysis.core.color - package org.anchoranalysis.core.color: Specifying particular colors and groups of colors.
org.anchoranalysis.core.exception - package org.anchoranalysis.core.exception: Very general exceptions and base classes for exceptions with wide applicability.
org.anchoranalysis.core.exception.combinable - package org.anchoranalysis.core.exception.combinable: Nested exceptions of similar type that can be combined together in a summary.
org.anchoranalysis.core.exception.friendly - package org.anchoranalysis.core.exception.friendly: Particular types of exceptions that are guaranteed to have a text/form that gives user-friendly error descriptions.
org.anchoranalysis.core.format - package org.anchoranalysis.core.format: File formats and associated extensions.
org.anchoranalysis.core.functional - package org.anchoranalysis.core.functional: Utilities and interfaces for applying functional-programming.
org.anchoranalysis.core.functional.checked - package org.anchoranalysis.core.functional.checked: Versions of many functional-interfaces in java.util.function that throw checked-exceptions.
org.anchoranalysis.core.functional.unchecked - package org.anchoranalysis.core.functional.unchecked: Adds additional functional-interfaces, that are unavailable in java.util.function, and do not throw checked exceptions.
org.anchoranalysis.core.graph - package org.anchoranalysis.core.graph: Data-structures for directed and undirected graphs, with or without an edge payload.
org.anchoranalysis.core.identifier.getter - package org.anchoranalysis.core.identifier.getter: Data structures for adding a unique name (a String or integer identifier) to other entities.
org.anchoranalysis.core.identifier.name - package org.anchoranalysis.core.identifier.name: Data structures for name (String) and value associations.
org.anchoranalysis.core.identifier.provider - package org.anchoranalysis.core.identifier.provider: A collection of named-elements, a NamedProvider and related operations.
org.anchoranalysis.core.identifier.provider.store - package org.anchoranalysis.core.identifier.provider.store: Data structures like NamedProvider with supporting for adding new elements.
org.anchoranalysis.core.index - package org.anchoranalysis.core.index: Classes to support getting / setting / specifying unique-integers (indices) for elements.
org.anchoranalysis.core.index.range - package org.anchoranalysis.core.index.range: A range of indices from minimum to maximum.
org.anchoranalysis.core.log - package org.anchoranalysis.core.log: Interfaces to log messages, both information and error messages.
org.anchoranalysis.core.log.error - package org.anchoranalysis.core.log.error: Mechanism for reporting errors (exceptions/throwables) to the user.
org.anchoranalysis.core.random - package org.anchoranalysis.core.random: Generating random numbers.
org.anchoranalysis.core.serialize - package org.anchoranalysis.core.serialize: Utilities for serializing and deserializing objects.
org.anchoranalysis.core.system - package org.anchoranalysis.core.system: Utilities for interacting with the operating system or computer system generally
org.anchoranalysis.core.system.path - package org.anchoranalysis.core.system.path: Utilities for converting/manipulating file-paths.
org.anchoranalysis.core.time - package org.anchoranalysis.core.time: Recording the execution-time of operations for profiling.
org.anchoranalysis.core.value - package org.anchoranalysis.core.value: Encapsulating values or sets of named-values.
org.anchoranalysis.experiment - package org.anchoranalysis.experiment: Classes related to executing an experiment by calling jobs on inputs.
org.anchoranalysis.experiment.arguments - package org.anchoranalysis.experiment.arguments: Arguments that can further specify an experiment in addition to its bean specification.
org.anchoranalysis.experiment.bean - package org.anchoranalysis.experiment.bean: Beans related to executing an experiment by calling jobs on inputs.
org.anchoranalysis.experiment.bean.identifier - package org.anchoranalysis.experiment.bean.identifier: Assigning unique names to experiments.
org.anchoranalysis.experiment.bean.io - package org.anchoranalysis.experiment.bean.io: Generic experiments that handle input and output in structured ways.
org.anchoranalysis.experiment.bean.log - package org.anchoranalysis.experiment.bean.log: Different approaches to where messages on the progress/status of an experiment are logged to.
org.anchoranalysis.experiment.bean.processor - package org.anchoranalysis.experiment.bean.processor: How a task is executed on multiple inputs.
org.anchoranalysis.experiment.bean.require - package org.anchoranalysis.experiment.bean.require: A test whether certain conditions on arguments to experiments are fulfilled.
org.anchoranalysis.experiment.bean.task - package org.anchoranalysis.experiment.bean.task: Defines a task, which is a set of operations run on an input, that may or may not generate an output.
org.anchoranalysis.experiment.io - package org.anchoranalysis.experiment.io: Interfaces for replacing attributes of an experiment: input, output, task etc.
org.anchoranalysis.experiment.log - package org.anchoranalysis.experiment.log: Helpful classes for logging.
org.anchoranalysis.experiment.task - package org.anchoranalysis.experiment.task: Non-bean classes related to a Task.
org.anchoranalysis.experiment.task.processor - package org.anchoranalysis.experiment.task.processor: Non-bean classes related to JobProcessor.
org.anchoranalysis.experiment.time - package org.anchoranalysis.experiment.time: How long particular operations take to execute.
org.anchoranalysis.feature.bean - package org.anchoranalysis.feature.bean: Beans pertaining to feature-calculation.
org.anchoranalysis.feature.bean.list - package org.anchoranalysis.feature.bean.list: A feature-list (custom list type for features) and associated providers.
org.anchoranalysis.feature.bean.operator - package org.anchoranalysis.feature.bean.operator: Features that are sufficiently generic to work on any input-type.
org.anchoranalysis.feature.bean.provider - package org.anchoranalysis.feature.bean.provider: Provider of a single feature.
org.anchoranalysis.feature.bean.results - package org.anchoranalysis.feature.bean.results: Defines base class FeatureResults together with some implementations.
org.anchoranalysis.feature.calculate - package org.anchoranalysis.feature.calculate: Sub-feature units of calculation that can be cached.
org.anchoranalysis.feature.calculate.bound - package org.anchoranalysis.feature.calculate.bound: Interfaces like FeatureCalculator but bound to particular features.
org.anchoranalysis.feature.calculate.cache - package org.anchoranalysis.feature.calculate.cache: Classes to cache feature-results or parts of feature-results that occur repeatedly among features or across calculations of the same feature.
org.anchoranalysis.feature.calculate.cache.part - package org.anchoranalysis.feature.calculate.cache.part: Equivalent classes to org.anchoranalysis.feature.calculate.part after having been resolved against a cache.
org.anchoranalysis.feature.calculate.part - package org.anchoranalysis.feature.calculate.part: A sub-part of the calculation of a feature, that can be cached, and reused by other features.
org.anchoranalysis.feature.energy - package org.anchoranalysis.feature.energy: A particular stack used in feature-calculations called a EnergyStack together with related classes.
org.anchoranalysis.feature.initialization - package org.anchoranalysis.feature.initialization: Initialization parameters used for beans in org.anchoranalysis.feature.bean.
org.anchoranalysis.feature.input - package org.anchoranalysis.feature.input: Base classes providing inputs to feature calculations.
org.anchoranalysis.feature.io.csv - package org.anchoranalysis.feature.io.csv: Metadata for writing feature calculation-results in CSV format.
org.anchoranalysis.feature.io.csv.metadata - package org.anchoranalysis.feature.io.csv.metadata: Writing the results of feature calculations to the file-system.
org.anchoranalysis.feature.io.csv.results - package org.anchoranalysis.feature.io.csv.results: Writing the results from feature-calculation to a CSV file.
org.anchoranalysis.feature.io.csv.table - package org.anchoranalysis.feature.io.csv.table: A Generator for writing a table of feature values as a CSV.
org.anchoranalysis.feature.io.name - package org.anchoranalysis.feature.io.name: Naming items in a weay that breaks down into multiple elements.
org.anchoranalysis.feature.io.results - package org.anchoranalysis.feature.io.results: Writes feature-calculation results in different formats, also grouped results.
org.anchoranalysis.feature.io.results.group - package org.anchoranalysis.feature.io.results.group: Various different outputs that can be written for the a grouped version of the results in LabelledResultsCollector.
org.anchoranalysis.feature.name - package org.anchoranalysis.feature.name: Data objects for the names of features.
org.anchoranalysis.feature.results - package org.anchoranalysis.feature.results: Results from one or more feature calculations.
org.anchoranalysis.feature.session - package org.anchoranalysis.feature.session: A defined context in which one or more features are provided inputs and produce results.
org.anchoranalysis.feature.session.cache - package org.anchoranalysis.feature.session.cache: Creates a FeatureCalculationCache to use during feature-calculations.
org.anchoranalysis.feature.session.cache.finder - package org.anchoranalysis.feature.session.cache.finder: Strategies to determine which child-cache (among hierarchy) to employ for a particular feature calculation.
org.anchoranalysis.feature.session.calculator - package org.anchoranalysis.feature.session.calculator: Base classes for methods to calculate results from features.
org.anchoranalysis.feature.session.replace - package org.anchoranalysis.feature.session.replace: Strategies on whether to reuse or invalidate a feature-input's cache.
org.anchoranalysis.feature.shared - package org.anchoranalysis.feature.shared: Features shared for referencing among calculations.
org.anchoranalysis.feature.store - package org.anchoranalysis.feature.store: A collection of named-Features.
org.anchoranalysis.image.bean - package org.anchoranalysis.image.bean: Core (bean) classes for image processing.
org.anchoranalysis.image.bean.channel - package org.anchoranalysis.image.bean.channel: Base classes for performing operations on Channels.
org.anchoranalysis.image.bean.displayer - package org.anchoranalysis.image.bean.displayer
org.anchoranalysis.image.bean.interpolator - package org.anchoranalysis.image.bean.interpolator: Beans for specifying image interpolators.
org.anchoranalysis.image.bean.nonbean - package org.anchoranalysis.image.bean.nonbean: Classes that are used elsewhere in this package but which aren't themselves AnchorBeans.
org.anchoranalysis.image.bean.nonbean.init - package org.anchoranalysis.image.bean.nonbean.init: Classes that aren't AnchorBeans that pertain to the initialization of image-related beans.
org.anchoranalysis.image.bean.nonbean.segment - package org.anchoranalysis.image.bean.nonbean.segment: Non-bean classes relating to image-segmentation.
org.anchoranalysis.image.bean.nonbean.spatial.align - package org.anchoranalysis.image.bean.nonbean.spatial.align: Non-bean classes to help specify the position of one entity relative to the others.
org.anchoranalysis.image.bean.nonbean.spatial.arrange - package org.anchoranalysis.image.bean.nonbean.spatial.arrange: Non-beans to specify how to form a single-image by spatially combining other images.
org.anchoranalysis.image.bean.object - package org.anchoranalysis.image.bean.object: Beans pertaining to ObjectMask and their collections.
org.anchoranalysis.image.bean.provider - package org.anchoranalysis.image.bean.provider: Base classes for providers of different core data entities related to images.
org.anchoranalysis.image.bean.provider.stack - package org.anchoranalysis.image.bean.provider.stack: A provider of Stacks.
org.anchoranalysis.image.bean.segment - package org.anchoranalysis.image.bean.segment: Base classes to perform image segmentation, transforming an image into another meaningful entity or entities.
org.anchoranalysis.image.bean.segment.binary - package org.anchoranalysis.image.bean.segment.binary: Base classes to perform binary-segmentation.
org.anchoranalysis.image.bean.segment.object - package org.anchoranalysis.image.bean.segment.object: Base classes to segment a channel into objects.
org.anchoranalysis.image.bean.spatial - package org.anchoranalysis.image.bean.spatial: Beans to define entities or operate that consider Euclidian space.
org.anchoranalysis.image.bean.spatial.arrange - package org.anchoranalysis.image.bean.spatial.arrange: Beans to specify how to form a single-image by spatially combining other images.
org.anchoranalysis.image.bean.spatial.arrange.align - package org.anchoranalysis.image.bean.spatial.arrange.align: Aligning a BoundingBox to fit inside another BoundingBox.
org.anchoranalysis.image.bean.spatial.arrange.fill - package org.anchoranalysis.image.bean.spatial.arrange.fill: Montages images together to completely fill the available space, while preserving aspect ratio.
org.anchoranalysis.image.bean.spatial.arrange.overlay - package org.anchoranalysis.image.bean.spatial.arrange.overlay: Combining other images through overlaying.
org.anchoranalysis.image.bean.spatial.arrange.tile - package org.anchoranalysis.image.bean.spatial.arrange.tile: Combining other images through tiling.
org.anchoranalysis.image.bean.spatial.direction - package org.anchoranalysis.image.bean.spatial.direction: Beans to specify a direction.
org.anchoranalysis.image.bean.threshold - package org.anchoranalysis.image.bean.threshold: Base classes for thresholding and calculating levels for thresholding.
org.anchoranalysis.image.bean.threshold.relation - package org.anchoranalysis.image.bean.threshold.relation: Reusable relations to a threshold.
org.anchoranalysis.image.bean.unitvalue.distance - package org.anchoranalysis.image.bean.unitvalue.distance: Converting quantities of distance between units.
org.anchoranalysis.image.bean.unitvalue.extent - package org.anchoranalysis.image.bean.unitvalue.extent: Converting quantities of extent (area or volume) between units.
org.anchoranalysis.image.bean.unitvalue.extent.area - package org.anchoranalysis.image.bean.unitvalue.extent.area: Converting quantities of area between units.
org.anchoranalysis.image.bean.unitvalue.extent.volume - package org.anchoranalysis.image.bean.unitvalue.extent.volume: Converting quantities of volume between units.
org.anchoranalysis.image.core.bufferedimage - package org.anchoranalysis.image.core.bufferedimage: Conversions and operations involving Java AWT's BufferedImage.
org.anchoranalysis.image.core.channel - package org.anchoranalysis.image.core.channel: The Channel core data-class and related operations and converters.
org.anchoranalysis.image.core.channel.convert - package org.anchoranalysis.image.core.channel.convert: Converts a channel to other data-types.
org.anchoranalysis.image.core.channel.convert.attached - package org.anchoranalysis.image.core.channel.convert.attached: Converts a channel to another data-type based upon another object to which it is attached.
org.anchoranalysis.image.core.channel.convert.attached.channel - package org.anchoranalysis.image.core.channel.convert.attached.channel: Converts a channel to another data-type based upon a Channel to which it is attached.
org.anchoranalysis.image.core.channel.convert.attached.histogram - package org.anchoranalysis.image.core.channel.convert.attached.histogram: Converts a channel to another data-type based upon a Histogram to which it is attached.
org.anchoranalysis.image.core.channel.factory - package org.anchoranalysis.image.core.channel.factory: Factory classes for creating Channel for various voxel data-types.
org.anchoranalysis.image.core.contour - package org.anchoranalysis.image.core.contour: Finds outline voxels, the pixels on the contour/edge of the object.
org.anchoranalysis.image.core.dimensions - package org.anchoranalysis.image.core.dimensions: Classes to describe the size of images or components of images both in voxels and physically.
org.anchoranalysis.image.core.dimensions.size.suggestion - package org.anchoranalysis.image.core.dimensions.size.suggestion: Suggestions on a size for an image.
org.anchoranalysis.image.core.mask - package org.anchoranalysis.image.core.mask: An image with only two permissible states.
org.anchoranalysis.image.core.mask.combine - package org.anchoranalysis.image.core.mask.combine: Binary operations involving voxelwise combination of Mask.
org.anchoranalysis.image.core.merge - package org.anchoranalysis.image.core.merge: Merges two or more entities.
org.anchoranalysis.image.core.object - package org.anchoranalysis.image.core.object: The key data entity org.anchoranalysis.image.voxel.object and related-classes and operations.
org.anchoranalysis.image.core.object.label - package org.anchoranalysis.image.core.object.label: Labelling elements (object-masks or similar) with unique successive integers in a channel.
org.anchoranalysis.image.core.object.properties - package org.anchoranalysis.image.core.object.properties: An ObjectCollection with associated key-value pairs.
org.anchoranalysis.image.core.object.scale - package org.anchoranalysis.image.core.object.scale: Scaling object-collections, or lists of elements with object-representations.
org.anchoranalysis.image.core.object.scale.method - package org.anchoranalysis.image.core.object.scale.method: Scaling elements with an associated ObjectMask either collectively or independently.
org.anchoranalysis.image.core.points - package org.anchoranalysis.image.core.points: Operations that extract points from image data entities or vice versa.
org.anchoranalysis.image.core.stack - package org.anchoranalysis.image.core.stack: Defines the key data object, Stack, and related classes.
org.anchoranalysis.image.core.stack.named - package org.anchoranalysis.image.core.stack.named: A collection of Stacks, each with a unique identifier as a name.
org.anchoranalysis.image.feature.bean - package org.anchoranalysis.image.feature.bean: Beans pertaining to feature definition and calculation.
org.anchoranalysis.image.feature.bean.evaluator - package org.anchoranalysis.image.feature.bean.evaluator: Beans that define context (which feature, which energy-stack) for evaluating feature-inputs.
org.anchoranalysis.image.feature.bean.histogram - package org.anchoranalysis.image.feature.bean.histogram: Features that operate on a Histogram.
org.anchoranalysis.image.feature.bean.object.collection - package org.anchoranalysis.image.feature.bean.object.collection: Features that operate on a ObjectCollection.
org.anchoranalysis.image.feature.bean.object.pair - package org.anchoranalysis.image.feature.bean.object.pair: Features that operate on a pair of ObjectMasks.
org.anchoranalysis.image.feature.bean.object.single - package org.anchoranalysis.image.feature.bean.object.single: Features that operate on a single ObjectMask.
org.anchoranalysis.image.feature.bean.physical - package org.anchoranalysis.image.feature.bean.physical: Features that convert to/from physical spatial units (e.g. meters) as opposed to pixels/voxels.
org.anchoranalysis.image.feature.calculation - package org.anchoranalysis.image.feature.calculation: Reusable implementations of CalculationPart related to images.
org.anchoranalysis.image.feature.calculator - package org.anchoranalysis.image.feature.calculator: Implementations of FeatureCalculatorMulti related to images, especially to create tables of feature-calculations.
org.anchoranalysis.image.feature.calculator.merged - package org.anchoranalysis.image.feature.calculator.merged: A particular implementation of FeatureCalculatorMulti for feature-calculations based upon pairs of image-objects.
org.anchoranalysis.image.feature.input - package org.anchoranalysis.image.feature.input: Image-related implementations of FeatureInput.
org.anchoranalysis.image.inference - package org.anchoranalysis.image.inference: Inference of machine learning models on images.
org.anchoranalysis.image.inference.bean.reduce - package org.anchoranalysis.image.inference.bean.reduce: Beans to reduce the number of results that are returned from inference, by removing overlaping entities etc.
org.anchoranalysis.image.inference.bean.segment.instance - package org.anchoranalysis.image.inference.bean.segment.instance: Instance-segmentation of a Stack.
org.anchoranalysis.image.inference.bean.segment.reduce - package org.anchoranalysis.image.inference.bean.segment.reduce: Non-bean classes to reduce the number of results that are returned from inference, by removing overlapping entities etc.
org.anchoranalysis.image.inference.segment - package org.anchoranalysis.image.inference.segment: Non-beans pertaining to segmentation of images via model inference.
org.anchoranalysis.image.io - package org.anchoranalysis.image.io: Reading and writing of image-related data objects to and from the filesystem.
org.anchoranalysis.image.io.bean.channel - package org.anchoranalysis.image.io.bean.channel: Beans pertaining to reading Channels as input.
org.anchoranalysis.image.io.bean.object.draw - package org.anchoranalysis.image.io.bean.object.draw: How to represent an object-mask in a raster that is being drawn.
org.anchoranalysis.image.io.bean.object.feature - package org.anchoranalysis.image.io.bean.object.feature: Beans to specify the outputting of features into CSV from a ObjectCollection.
org.anchoranalysis.image.io.bean.stack.combine - package org.anchoranalysis.image.io.bean.stack.combine: Beans to combine multiple stacks into a single stack before outputting.
org.anchoranalysis.image.io.bean.stack.metadata.reader - package org.anchoranalysis.image.io.bean.stack.metadata.reader: Bean classes for reading ImageMetadata from the file-system.
org.anchoranalysis.image.io.bean.stack.reader - package org.anchoranalysis.image.io.bean.stack.reader: Bean classes for reading raster-files from the filesystem.
org.anchoranalysis.image.io.bean.stack.writer - package org.anchoranalysis.image.io.bean.stack.writer: Bean classes for writing raster-files to the filesystem.
org.anchoranalysis.image.io.channel.input - package org.anchoranalysis.image.io.channel.input: Non-bean classes for reading a Channel from the filesystem.
org.anchoranalysis.image.io.channel.map - package org.anchoranalysis.image.io.channel.map: Non-bean classes for a mapping of names to Channels.
org.anchoranalysis.image.io.channel.output - package org.anchoranalysis.image.io.channel.output: Non-bean classes for writing a Channel to the filesystem.
org.anchoranalysis.image.io.histogram.input - package org.anchoranalysis.image.io.histogram.input: Non-bean classes for reading a Histogram from the filesystem.
org.anchoranalysis.image.io.histogram.output - package org.anchoranalysis.image.io.histogram.output: Non-bean classes for writing a Histogram to the filesystem.
org.anchoranalysis.image.io.object - package org.anchoranalysis.image.io.object: Non-bean classes for reading / writing an ObjectCollection from and to the filesystem.
org.anchoranalysis.image.io.object.input - package org.anchoranalysis.image.io.object.input: Non-bean classes for reading an ObjectCollection from the filesystem.
org.anchoranalysis.image.io.object.output.grayscale - package org.anchoranalysis.image.io.object.output.grayscale: Writing an ObjectCollection to the filesystem as a single-channeled stack.
org.anchoranalysis.image.io.object.output.hdf5 - package org.anchoranalysis.image.io.object.output.hdf5: Writing an ObjectCollection to the filesystem in HDF5 format.
org.anchoranalysis.image.io.object.output.mask - package org.anchoranalysis.image.io.object.output.mask: Writing an ObjectCollection to the filesystem as multiple binary singled-channeled images.
org.anchoranalysis.image.io.object.output.rgb - package org.anchoranalysis.image.io.object.output.rgb: Writing an ObjectCollection to the filesystem as RGB raster-images.
org.anchoranalysis.image.io.stack - package org.anchoranalysis.image.io.stack: Non-bean classes for reading / writing a Stack from and to the filesystem.
org.anchoranalysis.image.io.stack.input - package org.anchoranalysis.image.io.stack.input: Non-bean classes for reading a Stack from the filesystem.
org.anchoranalysis.image.io.stack.output - package org.anchoranalysis.image.io.stack.output: Non-bean classes for writing a Stack to the filesystem.
org.anchoranalysis.image.io.stack.output.box - package org.anchoranalysis.image.io.stack.output.box: Base classes for generators that ultimately write only a bounding-box portion of a Stack to the filesystem.
org.anchoranalysis.image.io.stack.output.generator - package org.anchoranalysis.image.io.stack.output.generator: Base classes for generators that ultimately write a Stack to the filesystem.
org.anchoranalysis.image.io.stack.time - package org.anchoranalysis.image.io.stack.time: A time-sequence of Stacks.
org.anchoranalysis.image.voxel - package org.anchoranalysis.image.voxel: Data-structures to store and manipulate image raster-data or voxels.
org.anchoranalysis.image.voxel.arithmetic - package org.anchoranalysis.image.voxel.arithmetic: Arithmetic operations for Voxels.
org.anchoranalysis.image.voxel.assigner - package org.anchoranalysis.image.voxel.assigner: Assigns values to some or all voxels.
org.anchoranalysis.image.voxel.binary - package org.anchoranalysis.image.voxel.binary: The BinaryVoxels class and related operations.
org.anchoranalysis.image.voxel.binary.connected - package org.anchoranalysis.image.voxel.binary.connected: Creating an ObjectCollection that is a connected component labelling of a BinaryVoxels.
org.anchoranalysis.image.voxel.binary.values - package org.anchoranalysis.image.voxel.binary.values: Defining on and off intensity-values to interpret an image in a binary way.
org.anchoranalysis.image.voxel.buffer - package org.anchoranalysis.image.voxel.buffer: A buffer of voxel-values, usually corresponding to a single z-slice in Voxels.
org.anchoranalysis.image.voxel.buffer.primitive - package org.anchoranalysis.image.voxel.buffer.primitive: Conversion of both primitive data types and image structures between Anchor's data-structures and other representations.
org.anchoranalysis.image.voxel.buffer.slice - package org.anchoranalysis.image.voxel.buffer.slice: A container with voxel-buffers for each z-slice.
org.anchoranalysis.image.voxel.convert - package org.anchoranalysis.image.voxel.convert: Converting Voxels to different data-types.
org.anchoranalysis.image.voxel.convert.bufferedimage - package org.anchoranalysis.image.voxel.convert.bufferedimage: Converts anchor data-structures to the BufferedImage used by Java's AWT.
org.anchoranalysis.image.voxel.convert.imglib2 - package org.anchoranalysis.image.voxel.convert.imglib2: Converts anchor data-structures to those used by ImgLib2.
org.anchoranalysis.image.voxel.datatype - package org.anchoranalysis.image.voxel.datatype: The different data-types that can be used to represent voxels.
org.anchoranalysis.image.voxel.extracter - package org.anchoranalysis.image.voxel.extracter: Methods to read/copy/duplicate portions of voxels.
org.anchoranalysis.image.voxel.extracter.predicate - package org.anchoranalysis.image.voxel.extracter.predicate: Methods to find or count voxels that satisfy a predicate.
org.anchoranalysis.image.voxel.factory - package org.anchoranalysis.image.voxel.factory: Creates new instances of Voxels and VoxelsUntyped with specific data-types.
org.anchoranalysis.image.voxel.iterator - package org.anchoranalysis.image.voxel.iterator: Utilities to iterate over voxel-locations in images and sub-regions of images.
org.anchoranalysis.image.voxel.iterator.intersecting - package org.anchoranalysis.image.voxel.iterator.intersecting: Like org.anchoranalysis.image.voxel.iterator but refers to iterators that operation over the intersecting regions of two entities.
org.anchoranalysis.image.voxel.iterator.neighbor - package org.anchoranalysis.image.voxel.iterator.neighbor: Iterating over a point's neighboring voxels.
org.anchoranalysis.image.voxel.iterator.neighbor.kernel - package org.anchoranalysis.image.voxel.iterator.neighbor.kernel: Routines for moving a KernelPointCursor around the neighboring voxels of the point.
org.anchoranalysis.image.voxel.iterator.predicate - package org.anchoranalysis.image.voxel.iterator.predicate: Functional-interfaces for processing different combinations of points and buffers that return a boolean.
org.anchoranalysis.image.voxel.iterator.process - package org.anchoranalysis.image.voxel.iterator.process: Functional-interfaces for processing different combinations of points and buffers that do not return a value.
org.anchoranalysis.image.voxel.iterator.process.buffer - package org.anchoranalysis.image.voxel.iterator.process.buffer: Functional-interfaces for processing different combinations of points and raw buffers, but not VoxelBuffer.
org.anchoranalysis.image.voxel.iterator.process.voxelbuffer - package org.anchoranalysis.image.voxel.iterator.process.voxelbuffer: Functional-interfaces for processing different combinations of points and VoxelBuffer but not raw buffers.
org.anchoranalysis.image.voxel.kernel - package org.anchoranalysis.image.voxel.kernel: Applying a kernel via convolution to voxels.
org.anchoranalysis.image.voxel.kernel.count - package org.anchoranalysis.image.voxel.kernel.count: Kernels to count the number of voxels that are equal to a particular value.
org.anchoranalysis.image.voxel.kernel.morphological - package org.anchoranalysis.image.voxel.kernel.morphological: Kernels that apply morphological operations.
org.anchoranalysis.image.voxel.kernel.outline - package org.anchoranalysis.image.voxel.kernel.outline: Kernel to find outline voxels on an object.
org.anchoranalysis.image.voxel.neighborhood - package org.anchoranalysis.image.voxel.neighborhood: A region in proximity to a voxel, encompassing this voxel as well as others.
org.anchoranalysis.image.voxel.object - package org.anchoranalysis.image.voxel.object: The fundamental data class that is an ObjectMask and related structures.
org.anchoranalysis.image.voxel.object.morphological - package org.anchoranalysis.image.voxel.object.morphological: Morphological operations applied to ObjectMasks.
org.anchoranalysis.image.voxel.object.morphological.predicate - package org.anchoranalysis.image.voxel.object.morphological.predicate: Predicates to match certain voxels as used in org.anchoranalysis.image.voxel.object.morphological.
org.anchoranalysis.image.voxel.projection - package org.anchoranalysis.image.voxel.projection: Classes for calculating differnet kind of projections of voxel values across multiple buffers.
org.anchoranalysis.image.voxel.projection.extrema - package org.anchoranalysis.image.voxel.projection.extrema: Classes for performing both a Maximum Intensity Projection and a minimum projection.
org.anchoranalysis.image.voxel.resizer - package org.anchoranalysis.image.voxel.resizer: Different interpolator methods to use when scaling voxels.
org.anchoranalysis.image.voxel.statistics - package org.anchoranalysis.image.voxel.statistics: Statistics about aggregated voxel intensities.
org.anchoranalysis.image.voxel.thresholder - package org.anchoranalysis.image.voxel.thresholder: Thresholding operations on voxels.
org.anchoranalysis.inference - package org.anchoranalysis.inference: High-level classes for performing machine learning model inference.
org.anchoranalysis.inference.concurrency - package org.anchoranalysis.inference.concurrency: Specifying how many CPUs and GPUs can be allocated for some purpose.
org.anchoranalysis.io.bioformats - package org.anchoranalysis.io.bioformats: Non-bean classes for filesystem I/O using Bioformats.
org.anchoranalysis.io.bioformats.bean - package org.anchoranalysis.io.bioformats.bean: Beans for filesystem I/O using Bioformats.
org.anchoranalysis.io.bioformats.bean.options - package org.anchoranalysis.io.bioformats.bean.options: User-specified options that can modify metadata or other attributes of a loaded Bioformats image.
org.anchoranalysis.io.bioformats.bean.writer - package org.anchoranalysis.io.bioformats.bean.writer: Writing stacks to the file system using the Bioformats library.
org.anchoranalysis.io.bioformats.copyconvert - package org.anchoranalysis.io.bioformats.copyconvert: Converts the byte stream opened by Bioformats into channels of particular data-type.
org.anchoranalysis.io.bioformats.copyconvert.tobyte - package org.anchoranalysis.io.bioformats.copyconvert.tobyte: Converts the byte stream opened by Bioformats into channels of ByteBuffer.
org.anchoranalysis.io.bioformats.copyconvert.tofloat - package org.anchoranalysis.io.bioformats.copyconvert.tofloat: Converts the byte stream opened by Bioformats into channels of FloatBuffer.
org.anchoranalysis.io.bioformats.copyconvert.toint - package org.anchoranalysis.io.bioformats.copyconvert.toint: Converts the byte stream opened by Bioformats into channels of IntBuffer.
org.anchoranalysis.io.bioformats.copyconvert.toshort - package org.anchoranalysis.io.bioformats.copyconvert.toshort: Converts the byte stream opened by Bioformats into channels of ShortBuffer.
org.anchoranalysis.io.bioformats.metadata - package org.anchoranalysis.io.bioformats.metadata: Reading metadata information from files using EXIF and/or other metadata headers.
org.anchoranalysis.io.generator - package org.anchoranalysis.io.generator: Base-classes and utilities for generators, which write different types of objects to the file system.
org.anchoranalysis.io.generator.collection - package org.anchoranalysis.io.generator.collection: Outputting more than one element collectively using a generator.
org.anchoranalysis.io.generator.combined - package org.anchoranalysis.io.generator.combined: Combining multiple generators into one.
org.anchoranalysis.io.generator.sequence - package org.anchoranalysis.io.generator.sequence: Writing a sequence of elements using a generator.
org.anchoranalysis.io.generator.sequence.pattern - package org.anchoranalysis.io.generator.sequence.pattern: A particular naming pattern files follow when outputted.
org.anchoranalysis.io.generator.serialized - package org.anchoranalysis.io.generator.serialized: Generators for writing serialized objects.
org.anchoranalysis.io.generator.tabular - package org.anchoranalysis.io.generator.tabular: Generators for writing tabular data, including CSV.
org.anchoranalysis.io.generator.text - package org.anchoranalysis.io.generator.text: Generators for writing textual data, including strings.
org.anchoranalysis.io.generator.xml - package org.anchoranalysis.io.generator.xml: Generators for writing XML data.
org.anchoranalysis.io.imagej.bean.interpolator - package org.anchoranalysis.io.imagej.bean.interpolator: Performing interpolation with ImageJ.
org.anchoranalysis.io.imagej.bean.stack.writer - package org.anchoranalysis.io.imagej.bean.stack.writer: Raster-writers that use ImageJ to write images to the filesystem.
org.anchoranalysis.io.imagej.convert - package org.anchoranalysis.io.imagej.convert: Converts to and from ImageJ data-structures for images.
org.anchoranalysis.io.imagej.resizer - package org.anchoranalysis.io.imagej.resizer: Image interpolation when scaling using ImageJ.
org.anchoranalysis.io.input - package org.anchoranalysis.io.input: Classes relating to creating inputs for an experiment / task.
org.anchoranalysis.io.input.bean - package org.anchoranalysis.io.input.bean: Beans related to collecting inputs from the file-system for an experiment.
org.anchoranalysis.io.input.bean.dictionary - package org.anchoranalysis.io.input.bean.dictionary: Methods to provide a Dictionary.
org.anchoranalysis.io.input.bean.files - package org.anchoranalysis.io.input.bean.files: Methods to provide a collection of Files.
org.anchoranalysis.io.input.bean.grouper - package org.anchoranalysis.io.input.bean.grouper: Determines how inputs are aggregated into groups, if at all.
org.anchoranalysis.io.input.bean.namer - package org.anchoranalysis.io.input.bean.namer: Beans to derive names (compact unique identifiers) from files.
org.anchoranalysis.io.input.bean.path - package org.anchoranalysis.io.input.bean.path: Beans pertaining to manipulating and matching against file-paths.
org.anchoranalysis.io.input.bean.path.matcher - package org.anchoranalysis.io.input.bean.path.matcher: Beans to find a subset of files that match a particular conditions on their paths.
org.anchoranalysis.io.input.bean.path.provider - package org.anchoranalysis.io.input.bean.path.provider: Methods to provide a single file-path.
org.anchoranalysis.io.input.csv - package org.anchoranalysis.io.input.csv: Classes for reading comma-separated-values (CSV) files.
org.anchoranalysis.io.input.file - package org.anchoranalysis.io.input.file: Non-bean classes that relate to using files during inputting.
org.anchoranalysis.io.input.grouper - package org.anchoranalysis.io.input.grouper: Non-bean classes pertaining grouping inputs.
org.anchoranalysis.io.input.path - package org.anchoranalysis.io.input.path: Non-bean classes pertaining to getting/extracting/manipulating paths as used in inputting.
org.anchoranalysis.io.input.path.matcher - package org.anchoranalysis.io.input.path.matcher: Non-bean classes to help with org.anchoranalysis.io.input.bean.path.matcher.
org.anchoranalysis.io.output.bean - package org.anchoranalysis.io.output.bean: Beans for the framework around writing files to the file-system.
org.anchoranalysis.io.output.bean.enabled - package org.anchoranalysis.io.output.bean.enabled: Beans indicating whether a particular output is enabled or not.
org.anchoranalysis.io.output.bean.path.prefixer - package org.anchoranalysis.io.output.bean.path.prefixer: Beans for generating paths for outputting files by adding a prefix, suffix etc.
org.anchoranalysis.io.output.bean.rules - package org.anchoranalysis.io.output.bean.rules: Rules for determining if a particular output is enabled or not in a context of a hierarchy.
org.anchoranalysis.io.output.enabled - package org.anchoranalysis.io.output.enabled: Non-beans pertaining to whether a particular output is enabled or not.
org.anchoranalysis.io.output.enabled.multi - package org.anchoranalysis.io.output.enabled.multi: Non-beans that pertain to whether multiple-levels have outputs that are enabled or not.
org.anchoranalysis.io.output.enabled.single - package org.anchoranalysis.io.output.enabled.single: Non-beans that pertain to whether a single level has outputs that are enabled or not.
org.anchoranalysis.io.output.error - package org.anchoranalysis.io.output.error: Exceptions that may be thrown when writing files to the file-system.
org.anchoranalysis.io.output.namestyle - package org.anchoranalysis.io.output.namestyle: Methods of naming a file with an index in the file-name.
org.anchoranalysis.io.output.outputter - package org.anchoranalysis.io.output.outputter: Classes for outputting to particular directories.
org.anchoranalysis.io.output.outputter.directory - package org.anchoranalysis.io.output.outputter.directory: BoundDirectory and related classes.
org.anchoranalysis.io.output.path.prefixer - package org.anchoranalysis.io.output.path.prefixer: Non-beans for generating paths for outputting files by adding a prefix, suffix etc.
org.anchoranalysis.io.output.recorded - package org.anchoranalysis.io.output.recorded: Classes for recording the output-names used as they are written / queried.
org.anchoranalysis.io.output.writer - package org.anchoranalysis.io.output.writer: Allows a generators to write element(s) to the filesystem.
org.anchoranalysis.io.output.xml - package org.anchoranalysis.io.output.xml: Outputting XML to the file-system.
org.anchoranalysis.launcher - package org.anchoranalysis.launcher: Parent package and entry-point classes for the Anchor command-line launcher application.
org.anchoranalysis.launcher.config - package org.anchoranalysis.launcher.config: Specifies a configuration of the launcher for a particular application.
org.anchoranalysis.launcher.executor - package org.anchoranalysis.launcher.executor: Runs a particular experiment after identifying necessary paths and input files.
org.anchoranalysis.launcher.executor.selectparam - package org.anchoranalysis.launcher.executor.selectparam: Different methods of selecting a object T that is used as a parameter for an experiment.
org.anchoranalysis.launcher.executor.selectparam.experiment - package org.anchoranalysis.launcher.executor.selectparam.experiment: SelectParams for loading a Experiment.
org.anchoranalysis.launcher.executor.selectparam.path - package org.anchoranalysis.launcher.executor.selectparam.path: SelectParams for loading a Optional<Path> for inputs, outputs or tasks.
org.anchoranalysis.launcher.executor.selectparam.path.convert - package org.anchoranalysis.launcher.executor.selectparam.path.convert: Converting paths to/from different formats as needed by org.anchoranalysis.launcher.executor.selectparam.path.
org.anchoranalysis.launcher.options - package org.anchoranalysis.launcher.options: A centralized location for all command-line options used by the launcher.
org.anchoranalysis.launcher.options.process - package org.anchoranalysis.launcher.options.process: Adding/removing/changing the arguments (input and output) from the experiment via command-line-options.
org.anchoranalysis.launcher.resources - package org.anchoranalysis.launcher.resources: Reading and integrating resources for the launcher.
org.anchoranalysis.launcher.run - package org.anchoranalysis.launcher.run: Parses command-line arguments and runs an experiment.
org.anchoranalysis.launcher.run.tasks - package org.anchoranalysis.launcher.run.tasks: Loading and displaying pre-defined tasks.
org.anchoranalysis.math.arithmetic - package org.anchoranalysis.math.arithmetic: Performing primitive type conversion, counting and summing.
org.anchoranalysis.math.equation - package org.anchoranalysis.math.equation: Solving or manipulating equations.
org.anchoranalysis.math.histogram - package org.anchoranalysis.math.histogram: The Histogram data class and related operations.
org.anchoranalysis.math.optimization - package org.anchoranalysis.math.optimization: Mathemathical optimization algorithms.
org.anchoranalysis.math.relation - package org.anchoranalysis.math.relation: Different kinds of binary-relations.
org.anchoranalysis.math.statistics - package org.anchoranalysis.math.statistics: Data structures and algorithms to calculate statistics.
org.anchoranalysis.math.statistics.moment - package org.anchoranalysis.math.statistics.moment: Calculates first and second image moments from a covariance matrix of points.
org.anchoranalysis.mpp.bean - package org.anchoranalysis.mpp.bean: Beans pertaining to marked-point-processes.
org.anchoranalysis.mpp.bean.bound - package org.anchoranalysis.mpp.bean.bound: Lower and upper limits set around variables.
org.anchoranalysis.mpp.bean.bound.rotation - package org.anchoranalysis.mpp.bean.bound.rotation: Bounds on how to rotate an entity in Euclidean space.
org.anchoranalysis.mpp.bean.mark - package org.anchoranalysis.mpp.bean.mark: Beans generally related to Marks.
org.anchoranalysis.mpp.bean.mark.factory - package org.anchoranalysis.mpp.bean.mark.factory: Beans related to creating Marks.
org.anchoranalysis.mpp.bean.points - package org.anchoranalysis.mpp.bean.points: Operations based on sets of points.
org.anchoranalysis.mpp.bean.points.fitter - package org.anchoranalysis.mpp.bean.points.fitter: Fitting structures to sets of points.
org.anchoranalysis.mpp.bean.proposer - package org.anchoranalysis.mpp.bean.proposer: Proposing Marks or other data-structures with particular attributes.
org.anchoranalysis.mpp.bean.provider - package org.anchoranalysis.mpp.bean.provider: Implementations of Provider involving Marks.
org.anchoranalysis.mpp.bean.regionmap - package org.anchoranalysis.mpp.bean.regionmap: Voxel subregions of Marks.
org.anchoranalysis.mpp.feature.addcriteria - package org.anchoranalysis.mpp.feature.addcriteria: Criteria for adding edges during optimization of marked-point-processes.
org.anchoranalysis.mpp.feature.bean.energy.element - package org.anchoranalysis.mpp.feature.bean.energy.element: Implementations and helper classes for calculating energy during an energy-minimization optimization scheme.
org.anchoranalysis.mpp.feature.bean.energy.scheme - package org.anchoranalysis.mpp.feature.bean.energy.scheme: Creating EnergySchemes.
org.anchoranalysis.mpp.feature.bean.mark - package org.anchoranalysis.mpp.feature.bean.mark: Features calculated on a Mark.
org.anchoranalysis.mpp.feature.bean.mark.collection - package org.anchoranalysis.mpp.feature.bean.mark.collection: Features calculated on a org.anchoranalysis.mpp.feature.bean.mark.collection.
org.anchoranalysis.mpp.feature.energy - package org.anchoranalysis.mpp.feature.energy: Non-bean classes pertaining to calculating energy during an energy-minimization optimization scheme.
org.anchoranalysis.mpp.feature.energy.marks - package org.anchoranalysis.mpp.feature.energy.marks: Non-bean classes pertaining to calculating energy of {org.anchoranalysis.mpp.mark.Mark}s.
org.anchoranalysis.mpp.feature.energy.saved - package org.anchoranalysis.mpp.feature.energy.saved: Saved snapshots of energy-calculations.
org.anchoranalysis.mpp.feature.energy.scheme - package org.anchoranalysis.mpp.feature.energy.scheme: Factorized form of storing the energy during an energy-minimization optimization scheme.
org.anchoranalysis.mpp.feature.input - package org.anchoranalysis.mpp.feature.input: Inputs to mark-point-processes related Features.
org.anchoranalysis.mpp.feature.mark - package org.anchoranalysis.mpp.feature.mark: Non-bean classes for calculating feature-values related to Marks.
org.anchoranalysis.mpp.index - package org.anchoranalysis.mpp.index: Indexing voxel-values in different ways.
org.anchoranalysis.mpp.index.factory - package org.anchoranalysis.mpp.index.factory: Factories for classes in org.anchoranalysis.mpp.index.
org.anchoranalysis.mpp.init - package org.anchoranalysis.mpp.init: Parameters used to initialize certain types of beans.
org.anchoranalysis.mpp.io.bean.input - package org.anchoranalysis.mpp.io.bean.input: Beans for reading data structures related to marked point processes from the file system.
org.anchoranalysis.mpp.io.input - package org.anchoranalysis.mpp.io.input: Non-beans for reading data structures related to marked point processes from the file system.
org.anchoranalysis.mpp.io.output - package org.anchoranalysis.mpp.io.output: Non-beans for writing data structures related to marked point processes from the file system.
org.anchoranalysis.mpp.mark - package org.anchoranalysis.mpp.mark: Non-bean classes related to Marks.
org.anchoranalysis.mpp.mark.conic - package org.anchoranalysis.mpp.mark.conic: Marks implementing conic sections.
org.anchoranalysis.mpp.mark.points - package org.anchoranalysis.mpp.mark.points: Marks implementing structures based on points.
org.anchoranalysis.mpp.mark.voxelized - package org.anchoranalysis.mpp.mark.voxelized: A mark after a voxel-representation has been inferred.
org.anchoranalysis.mpp.mark.voxelized.memo - package org.anchoranalysis.mpp.mark.voxelized.memo: Memoization of VoxelizedMarks.
org.anchoranalysis.mpp.overlap - package org.anchoranalysis.mpp.overlap: Calculating overlaps between two Marks.
org.anchoranalysis.mpp.overlay - package org.anchoranalysis.mpp.overlay: Any Overlay related to a Mark.
org.anchoranalysis.mpp.pair - package org.anchoranalysis.mpp.pair: Pairs of Marks.
org.anchoranalysis.mpp.proposer - package org.anchoranalysis.mpp.proposer: Non-bean classes for proposing Marks or other data-structures with particular attributes.
org.anchoranalysis.mpp.proposer.error - package org.anchoranalysis.mpp.proposer.error: Recording errors related to proposing Marks or other data-structures with particular attributes.
org.anchoranalysis.overlay - package org.anchoranalysis.overlay: Overlays and related classes involving drawing entities on top of an image.
org.anchoranalysis.overlay.bean - package org.anchoranalysis.overlay.bean: Beans relating to drawing an Overlay on an image.
org.anchoranalysis.overlay.collection - package org.anchoranalysis.overlay.collection: Collections of Overlays.
org.anchoranalysis.overlay.object - package org.anchoranalysis.overlay.object: An implementation of an Overlay that draws an ObjectMask on an image.
org.anchoranalysis.overlay.writer - package org.anchoranalysis.overlay.writer: Drawing an overlay on an image.
org.anchoranalysis.plugin.annotation.bean.aggregate - package org.anchoranalysis.plugin.annotation.bean.aggregate: Beans to combine two or more annotations.
org.anchoranalysis.plugin.annotation.bean.comparer - package org.anchoranalysis.plugin.annotation.bean.comparer: Comparing the similarity of annotations from two images to each other.
org.anchoranalysis.plugin.annotation.bean.comparison - package org.anchoranalysis.plugin.annotation.bean.comparison: Task to compare a set of annotations to a segmentation or another set of annotations.
org.anchoranalysis.plugin.annotation.bean.comparison.assigner - package org.anchoranalysis.plugin.annotation.bean.comparison.assigner: Pairs annotations from two different sets, creating an assignment of some type.
org.anchoranalysis.plugin.annotation.bean.file - package org.anchoranalysis.plugin.annotation.bean.file: FilesProviders for providing annotations.
org.anchoranalysis.plugin.annotation.bean.label - package org.anchoranalysis.plugin.annotation.bean.label: A label as used for annotating.
org.anchoranalysis.plugin.annotation.bean.strategy - package org.anchoranalysis.plugin.annotation.bean.strategy: Strategies for how to annotate an image, such label per image etc.
org.anchoranalysis.plugin.annotation.comparison - package org.anchoranalysis.plugin.annotation.comparison: Non-bean classes for comparing two sets of annotations.
org.anchoranalysis.plugin.annotation.counter - package org.anchoranalysis.plugin.annotation.counter: Utility classes for counting images incrementally.
org.anchoranalysis.plugin.fiji.bean.channel.grayscalereconstruction - package org.anchoranalysis.plugin.fiji.bean.channel.grayscalereconstruction: Morphological grayscale-reconstruction algorithm.
org.anchoranalysis.plugin.fiji.bean.channel.provider - package org.anchoranalysis.plugin.fiji.bean.channel.provider: Implementations of ChannelProvider that use FIJI.
org.anchoranalysis.plugin.fiji.bean.channel.provider.distance - package org.anchoranalysis.plugin.fiji.bean.channel.provider.distance: Euclidean Distance Transform implementations via FIJI.
org.anchoranalysis.plugin.fiji.bean.mask.provider - package org.anchoranalysis.plugin.fiji.bean.mask.provider: Implementations of MaskProvider that use FIJI.
org.anchoranalysis.plugin.fiji.bean.threshold - package org.anchoranalysis.plugin.fiji.bean.threshold: Implementations of Thresholder that use FIJI.
org.anchoranalysis.plugin.image.bean.blur - package org.anchoranalysis.plugin.image.bean.blur: Filters that perform blurring.
org.anchoranalysis.plugin.image.bean.channel.aggregator - package org.anchoranalysis.plugin.image.bean.channel.aggregator: Implementations of ConvertChannelTo and ConvertChannelToWithHistogram.
org.anchoranalysis.plugin.image.bean.channel.convert - package org.anchoranalysis.plugin.image.bean.channel.convert: Implementations of ConvertChannelTo and ConvertChannelToWithHistogram.
org.anchoranalysis.plugin.image.bean.channel.provider - package org.anchoranalysis.plugin.image.bean.channel.provider: Implementations of ChannelProvider that are generic base-classes or otherwise abstract or general.
org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic - package org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic: Implementations of ChannelProvider that perform arithmetic on voxels in one or more Channels.
org.anchoranalysis.plugin.image.bean.channel.provider.assign - package org.anchoranalysis.plugin.image.bean.channel.provider.assign: Implementations of ChannelProvider that sets the values of the voxels in a Channel.
org.anchoranalysis.plugin.image.bean.channel.provider.convert - package org.anchoranalysis.plugin.image.bean.channel.provider.convert: Implementations of ChannelProvider that converts a Channel from one voxel-type to another.
org.anchoranalysis.plugin.image.bean.channel.provider.gradient - package org.anchoranalysis.plugin.image.bean.channel.provider.gradient: Implementations of ChannelProvider that calculate the gradient of a Channel's voxels in one or more dimensions.
org.anchoranalysis.plugin.image.bean.channel.provider.intensity - package org.anchoranalysis.plugin.image.bean.channel.provider.intensity: Implementations of ChannelProvider that manipulate the intensity-values of the voxels of a Channel's voxels.
org.anchoranalysis.plugin.image.bean.channel.provider.mask - package org.anchoranalysis.plugin.image.bean.channel.provider.mask: Implementations of ChannelProvider that involve conversion from or application of Masks.
org.anchoranalysis.plugin.image.bean.channel.provider.object - package org.anchoranalysis.plugin.image.bean.channel.provider.object: Implementations of ChannelProvider that involve conversion from or application of ObjectMasks.
org.anchoranalysis.plugin.image.bean.channel.provider.score - package org.anchoranalysis.plugin.image.bean.channel.provider.score: Implementations of ChannelProvider that assign a score to particular subregions of a channel.
org.anchoranalysis.plugin.image.bean.channel.provider.slice - package org.anchoranalysis.plugin.image.bean.channel.provider.slice: Implementations of ChannelProvider that process 3D channels slice-by-slice.
org.anchoranalysis.plugin.image.bean.color.provider - package org.anchoranalysis.plugin.image.bean.color.provider: Implementations of ColorProvider.
org.anchoranalysis.plugin.image.bean.dictionary - package org.anchoranalysis.plugin.image.bean.dictionary: Beans pertaining to Dictionary.
org.anchoranalysis.plugin.image.bean.dimensions.provider - package org.anchoranalysis.plugin.image.bean.dimensions.provider: Implementations of DimensionsProvider.
org.anchoranalysis.plugin.image.bean.histogram.provider - package org.anchoranalysis.plugin.image.bean.histogram.provider: Implementations of HistogramProvider.
org.anchoranalysis.plugin.image.bean.histogram.threshold - package org.anchoranalysis.plugin.image.bean.histogram.threshold: Thresholding of intensity values represented in at Histogram.
org.anchoranalysis.plugin.image.bean.mask.provider - package org.anchoranalysis.plugin.image.bean.mask.provider: Implementations of MaskProvider.
org.anchoranalysis.plugin.image.bean.mask.provider.combine - package org.anchoranalysis.plugin.image.bean.mask.provider.combine: Implementations of MaskProvider that combine existing providers.
org.anchoranalysis.plugin.image.bean.mask.provider.convert - package org.anchoranalysis.plugin.image.bean.mask.provider.convert: Implementations of MaskProvider that convert providers of other types to ObjectMasks.
org.anchoranalysis.plugin.image.bean.mask.provider.morphological - package org.anchoranalysis.plugin.image.bean.mask.provider.morphological: Implementations of MaskProvider that implement morphological operations.
org.anchoranalysis.plugin.image.bean.mask.provider.predicate - package org.anchoranalysis.plugin.image.bean.mask.provider.predicate: Provides if-else conditions to a MaskProvider.
org.anchoranalysis.plugin.image.bean.mask.provider.segment - package org.anchoranalysis.plugin.image.bean.mask.provider.segment: Implementations of MaskProvider where an ObjectCollection is created by segmenting a Channel.
org.anchoranalysis.plugin.image.bean.mask.provider.slice - package org.anchoranalysis.plugin.image.bean.mask.provider.slice: Implementations of MaskProvider that process 3D masks slice-by-slice.
org.anchoranalysis.plugin.image.bean.object.filter - package org.anchoranalysis.plugin.image.bean.object.filter: Implementations of ObjectFilter.
org.anchoranalysis.plugin.image.bean.object.filter.collective - package org.anchoranalysis.plugin.image.bean.object.filter.collective: Implementations of ObjectFilter that assess each element in a collection collectively.
org.anchoranalysis.plugin.image.bean.object.filter.combine - package org.anchoranalysis.plugin.image.bean.object.filter.combine: Implementations of ObjectFilter that combine two or more other ObjectFilters.
org.anchoranalysis.plugin.image.bean.object.filter.independent - package org.anchoranalysis.plugin.image.bean.object.filter.independent: Implementations of ObjectFilter that independently assess each element in a collection.
org.anchoranalysis.plugin.image.bean.object.match - package org.anchoranalysis.plugin.image.bean.object.match: Implementations of ObjectMatcher.
org.anchoranalysis.plugin.image.bean.object.provider - package org.anchoranalysis.plugin.image.bean.object.provider: Implementations of ObjectCollectionProvider.
org.anchoranalysis.plugin.image.bean.object.provider.connected - package org.anchoranalysis.plugin.image.bean.object.provider.connected: Implementations of ObjectCollectionProvider involving connected-components.
org.anchoranalysis.plugin.image.bean.object.provider.feature - package org.anchoranalysis.plugin.image.bean.object.provider.feature: Implementations of ObjectCollectionProvider involving feature calculation.
org.anchoranalysis.plugin.image.bean.object.provider.filter - package org.anchoranalysis.plugin.image.bean.object.provider.filter: Implementations of ObjectCollectionProvider that filter objects.
org.anchoranalysis.plugin.image.bean.object.provider.mask - package org.anchoranalysis.plugin.image.bean.object.provider.mask: Implementations of ObjectCollectionProvider involving a Mask.
org.anchoranalysis.plugin.image.bean.object.provider.merge - package org.anchoranalysis.plugin.image.bean.object.provider.merge: Implementations of ObjectCollectionProvider involving merging objects together.
org.anchoranalysis.plugin.image.bean.object.provider.morphological - package org.anchoranalysis.plugin.image.bean.object.provider.morphological: Implementations of ObjectCollectionProvider involving morphological operations.
org.anchoranalysis.plugin.image.bean.object.provider.segment - package org.anchoranalysis.plugin.image.bean.object.provider.segment: Implementations of ObjectCollectionProvider involving segmentation.
org.anchoranalysis.plugin.image.bean.object.provider.slice - package org.anchoranalysis.plugin.image.bean.object.provider.slice: Implementations of ObjectCollectionProvider involving z-slice processing.
org.anchoranalysis.plugin.image.bean.object.provider.split - package org.anchoranalysis.plugin.image.bean.object.provider.split: Implementations of ObjectCollectionProvider involving splitting objects into smaller objects.
org.anchoranalysis.plugin.image.bean.object.segment.channel - package org.anchoranalysis.plugin.image.bean.object.segment.channel: Implementations of SegmentChannelIntoObjects.
org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima - package org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima: Minima imposition for a Watershed transformation.
org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction - package org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction: Grayscale reconstruction to support the Watershed transformation.
org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong - package org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong: Implementation of a Watershed transformation based on Yeong et al. 2009.
org.anchoranalysis.plugin.image.bean.object.segment.reduce - package org.anchoranalysis.plugin.image.bean.object.segment.reduce: Strategies for reducing the number of elements with a list by merging/removing lower-confidence elements that overlap.
org.anchoranalysis.plugin.image.bean.scale - package org.anchoranalysis.plugin.image.bean.scale: Implementations of ScaleCalculator for calculating a scaling-factor from dimensions.
org.anchoranalysis.plugin.image.bean.segment.binary - package org.anchoranalysis.plugin.image.bean.segment.binary: Implementations of BinarySegmentation.
org.anchoranalysis.plugin.image.bean.stack.provider - package org.anchoranalysis.plugin.image.bean.stack.provider: Implementations of StackProvider.
org.anchoranalysis.plugin.image.bean.stack.provider.color - package org.anchoranalysis.plugin.image.bean.stack.provider.color: Implementations of StackProvider that color portions of an image.
org.anchoranalysis.plugin.image.bean.thumbnail.object - package org.anchoranalysis.plugin.image.bean.thumbnail.object: Implementations of ThumbnailFromObjects.
org.anchoranalysis.plugin.image.bean.thumbnail.stack - package org.anchoranalysis.plugin.image.bean.thumbnail.stack: Implementations of ThumbnailFromStack.
org.anchoranalysis.plugin.image.channel - package org.anchoranalysis.plugin.image.channel: Non-beans for operations or calculations relating to Channels.
org.anchoranalysis.plugin.image.feature.bean.dimensions - package org.anchoranalysis.plugin.image.feature.bean.dimensions: Features that are calculated from Dimensions.
org.anchoranalysis.plugin.image.feature.bean.histogram.statistic - package org.anchoranalysis.plugin.image.feature.bean.histogram.statistic: Implementations of FeatureHistogram that calculate statistics.
org.anchoranalysis.plugin.image.feature.bean.histogram.threshold - package org.anchoranalysis.plugin.image.feature.bean.histogram.threshold: Implementations of FeatureHistogram that perform thresholding.
org.anchoranalysis.plugin.image.feature.bean.list - package org.anchoranalysis.plugin.image.feature.bean.list: Implementations of FeatureListProvider.
org.anchoranalysis.plugin.image.feature.bean.list.pair - package org.anchoranalysis.plugin.image.feature.bean.list.pair: Implementations of FeatureListProvider with input-type FeatureInputPairObjects.
org.anchoranalysis.plugin.image.feature.bean.list.permute - package org.anchoranalysis.plugin.image.feature.bean.list.permute: Implementations of FeatureListProvider that derive new features with permuted property-values.
org.anchoranalysis.plugin.image.feature.bean.metadata - package org.anchoranalysis.plugin.image.feature.bean.metadata: Implementations of FeatureImageMetadata.
org.anchoranalysis.plugin.image.feature.bean.morphological - package org.anchoranalysis.plugin.image.feature.bean.morphological: Beans that affects how morphological operations occur.
org.anchoranalysis.plugin.image.feature.bean.object.collection - package org.anchoranalysis.plugin.image.feature.bean.object.collection: Implementations of FeatureObjectCollection.
org.anchoranalysis.plugin.image.feature.bean.object.combine - package org.anchoranalysis.plugin.image.feature.bean.object.combine: Features from combinations of ObjectMasks.
org.anchoranalysis.plugin.image.feature.bean.object.pair - package org.anchoranalysis.plugin.image.feature.bean.object.pair: Features from pairs of ObjectMasks.
org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap - package org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap: Features that calculate the degree of overlap between two ObjectMasks.
org.anchoranalysis.plugin.image.feature.bean.object.pair.touching - package org.anchoranalysis.plugin.image.feature.bean.object.pair.touching: Features that calculate how many other objects an ObjectMask directly neighbors.
org.anchoranalysis.plugin.image.feature.bean.object.single - package org.anchoranalysis.plugin.image.feature.bean.object.single: Implementations of FeatureSingleObject.
org.anchoranalysis.plugin.image.feature.bean.object.single.border - package org.anchoranalysis.plugin.image.feature.bean.object.single.border: Implementations of FeatureSingleObject that determine if an object lies at the border of an image.
org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox - package org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox: Implementations of FeatureSingleObject that consider an object's bounding-box.
org.anchoranalysis.plugin.image.feature.bean.object.single.energy - package org.anchoranalysis.plugin.image.feature.bean.object.single.energy: Implementations of FeatureSingleObject that reference a particular Channel in the associated EnergyStack.
org.anchoranalysis.plugin.image.feature.bean.object.single.intensity - package org.anchoranalysis.plugin.image.feature.bean.object.single.intensity: Implementations of FeatureSingleObject that measure an object's intensity on a corresponding Channel.
org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient - package org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient: Implementations of FeatureSingleObject that measure an object's gradient from corresponding Channels storing the gradient.
org.anchoranalysis.plugin.image.feature.bean.object.single.moments - package org.anchoranalysis.plugin.image.feature.bean.object.single.moments: Implementations of FeatureSingleObject based on calculating image moments, with or without image intensity.
org.anchoranalysis.plugin.image.feature.bean.object.single.morphological - package org.anchoranalysis.plugin.image.feature.bean.object.single.morphological: Implementations of FeatureSingleObject that implement morphological operations.
org.anchoranalysis.plugin.image.feature.bean.object.single.shape - package org.anchoranalysis.plugin.image.feature.bean.object.single.shape: Implementations of FeatureSingleObject that measure the shape of the ObjectMask.
org.anchoranalysis.plugin.image.feature.bean.object.single.shared - package org.anchoranalysis.plugin.image.feature.bean.object.single.shared: Implementations of FeatureSingleObject that use SharedObjects for calculations.
org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting - package org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting: Implementations of FeatureSingleObject that use SharedObjects for calculations, and measure the degree of intersection between objects.
org.anchoranalysis.plugin.image.feature.bean.object.single.slice - package org.anchoranalysis.plugin.image.feature.bean.object.single.slice: Implementations of FeatureSingleObject that processes an object slice-by-slice in the z-dimension.
org.anchoranalysis.plugin.image.feature.bean.object.single.surface - package org.anchoranalysis.plugin.image.feature.bean.object.single.surface: Implementations of FeatureSingleObject that measures aspects of the surface of an ObjectMask.
org.anchoranalysis.plugin.image.feature.bean.physical - package org.anchoranalysis.plugin.image.feature.bean.physical: Beans involving physical units for measurement.
org.anchoranalysis.plugin.image.feature.bean.score - package org.anchoranalysis.plugin.image.feature.bean.score: Implementations of VoxelScore.
org.anchoranalysis.plugin.image.feature.bean.shared - package org.anchoranalysis.plugin.image.feature.bean.shared: Beans involving SharedObjects.
org.anchoranalysis.plugin.image.feature.bean.shared.object - package org.anchoranalysis.plugin.image.feature.bean.shared.object: Beans involving SharedObjects and ObjectCollection.
org.anchoranalysis.plugin.image.feature.bean.stack.intensity - package org.anchoranalysis.plugin.image.feature.bean.stack.intensity: Implementations of FeatureStack or other features that involve processing a Stack.
org.anchoranalysis.plugin.image.feature.bean.stack.object - package org.anchoranalysis.plugin.image.feature.bean.stack.object: Implementations of FeatureStack that process an ObjectCollection.
org.anchoranalysis.plugin.image.feature.object - package org.anchoranalysis.plugin.image.feature.object: Non-bean classes that help calculate features from ObjectMasks.
org.anchoranalysis.plugin.image.feature.object.calculation.delegate - package org.anchoranalysis.plugin.image.feature.object.calculation.delegate: Implementations of CalculationPart as used by features elsewhere in this package.
org.anchoranalysis.plugin.image.feature.object.calculation.single - package org.anchoranalysis.plugin.image.feature.object.calculation.single: Implementations of CalculationPart that that process a single ObjectMask.
org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological - package org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological: Implementations of CalculationPart that that process a single ObjectMask - with morphological operations.
org.anchoranalysis.plugin.image.feature.stack.calculation - package org.anchoranalysis.plugin.image.feature.stack.calculation: Implementations of CalculationPart that process Stacks as used by features elsewhere in this package.
org.anchoranalysis.plugin.image.intensity - package org.anchoranalysis.plugin.image.intensity: Non-bean for operations or calculations relating to intensity.
org.anchoranalysis.plugin.image.intensity.level - package org.anchoranalysis.plugin.image.intensity.level: Non-beans for calculating a thresholding level from itensity values.
org.anchoranalysis.plugin.image.object - package org.anchoranalysis.plugin.image.object: Non-beans pertaining to ObjectMasks.
org.anchoranalysis.plugin.image.object.merge - package org.anchoranalysis.plugin.image.object.merge: Merging ObjectMasks.
org.anchoranalysis.plugin.image.object.merge.condition - package org.anchoranalysis.plugin.image.object.merge.condition: Conditions for merging ObjectMasks.
org.anchoranalysis.plugin.image.object.merge.priority - package org.anchoranalysis.plugin.image.object.merge.priority: Assigning priority when merging ObjectMasks.
org.anchoranalysis.plugin.image.provider - package org.anchoranalysis.plugin.image.provider: Non-bean classes pertaining to Providers.
org.anchoranalysis.plugin.image.segment.thresholder.slice - package org.anchoranalysis.plugin.image.segment.thresholder.slice: Non-beans pertaining to segmenting a z-stack slice-by-slice.
org.anchoranalysis.plugin.image.segment.watershed.encoding - package org.anchoranalysis.plugin.image.segment.watershed.encoding: Encoding voxels in a watershed-transformation implementation.
org.anchoranalysis.plugin.image.task.bean - package org.anchoranalysis.plugin.image.task.bean: A parent package for many different kinds of tasks.
org.anchoranalysis.plugin.image.task.bean.combine - package org.anchoranalysis.plugin.image.task.bean.combine: Combining multiple images together into a single image.
org.anchoranalysis.plugin.image.task.bean.feature - package org.anchoranalysis.plugin.image.task.bean.feature: Tasks pertaining to Features.
org.anchoranalysis.plugin.image.task.bean.feature.source - package org.anchoranalysis.plugin.image.task.bean.feature.source: Source of rows in feature-tables with FeatureSource and derived classes.
org.anchoranalysis.plugin.image.task.bean.format - package org.anchoranalysis.plugin.image.task.bean.format: Tasks for converting image-formats.
org.anchoranalysis.plugin.image.task.bean.format.convertstyle - package org.anchoranalysis.plugin.image.task.bean.format.convertstyle: Different approaches for converting sets of channels (RGB, independently etc.) to another image format.
org.anchoranalysis.plugin.image.task.bean.grouped - package org.anchoranalysis.plugin.image.task.bean.grouped: Tasks that involved stacks (usually each channel from an image) that are somehow grouped-together.
org.anchoranalysis.plugin.image.task.bean.grouped.histogram - package org.anchoranalysis.plugin.image.task.bean.grouped.histogram: Task(s) to export histograms of intensity values.
org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels - package org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels: Selecting a subset of a set of channels.
org.anchoranalysis.plugin.image.task.bean.labeller - package org.anchoranalysis.plugin.image.task.bean.labeller: Associating labels with images.
org.anchoranalysis.plugin.image.task.bean.scale - package org.anchoranalysis.plugin.image.task.bean.scale: Tasks to scale an image.
org.anchoranalysis.plugin.image.task.bean.segment - package org.anchoranalysis.plugin.image.task.bean.segment: Tasks to segment an image.
org.anchoranalysis.plugin.image.task.bean.slice - package org.anchoranalysis.plugin.image.task.bean.slice: Tasks that process on one or more slices from a z-stack.
org.anchoranalysis.plugin.image.task.channel.aggregator - package org.anchoranalysis.plugin.image.task.channel.aggregator: Combines multiple Channels voxel-wise to form a single aggregated Channel.
org.anchoranalysis.plugin.image.task.feature - package org.anchoranalysis.plugin.image.task.feature: Non-bean classes pertaining to Features as used in tasks.
org.anchoranalysis.plugin.image.task.feature.calculator - package org.anchoranalysis.plugin.image.task.feature.calculator: Non-beans for calculating Features.
org.anchoranalysis.plugin.image.task.grouped - package org.anchoranalysis.plugin.image.task.grouped: Non-bean classes about grouping channels or other inputs.
org.anchoranalysis.plugin.image.task.labeller - package org.anchoranalysis.plugin.image.task.labeller: Non-bean classes about labelling images.
org.anchoranalysis.plugin.image.task.segment - package org.anchoranalysis.plugin.image.task.segment: Non-bean classes for image-segmentation.
org.anchoranalysis.plugin.image.task.size - package org.anchoranalysis.plugin.image.task.size: Non-bean classes pertaining to determining the size of an image.
org.anchoranalysis.plugin.image.task.slice - package org.anchoranalysis.plugin.image.task.slice: Non-bean classes pertaining to combining stacks into a single stack.
org.anchoranalysis.plugin.image.task.stack - package org.anchoranalysis.plugin.image.task.stack: Non-bean classes pertaining to stacks and channels as used in tasks.
org.anchoranalysis.plugin.image.thumbnail - package org.anchoranalysis.plugin.image.thumbnail: Non-bean classes for thumbnail creation.
org.anchoranalysis.plugin.imagej.bean.channel.provider - package org.anchoranalysis.plugin.imagej.bean.channel.provider: Implementations of ChannelProvider that call ImageJ.
org.anchoranalysis.plugin.imagej.bean.channel.provider.filter - package org.anchoranalysis.plugin.imagej.bean.channel.provider.filter: Filters using ImageJ.
org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.moments - package org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.moments: Non-linear filters using ImageJ that use the statistical moments of the intensity values in the kernel.
org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank - package org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank: Non-linear filters using ImageJ that use the statistical rank of the intensity values in the kernel.
org.anchoranalysis.plugin.imagej.bean.define - package org.anchoranalysis.plugin.imagej.bean.define: Implementations of DefineAdderBean that call ImageJ.
org.anchoranalysis.plugin.imagej.bean.mask.provider - package org.anchoranalysis.plugin.imagej.bean.mask.provider: Implementations of MaskProvider that call ImageJ.
org.anchoranalysis.plugin.imagej.bean.object.provider - package org.anchoranalysis.plugin.imagej.bean.object.provider: Implementations of ObjectCollectionProvider that call ImageJ.
org.anchoranalysis.plugin.imagej.bean.object.segment - package org.anchoranalysis.plugin.imagej.bean.object.segment: Implementations of ObjectCollectionProvider that call ImageJ to perform segmentation.
org.anchoranalysis.plugin.imagej.bean.stack.provider - package org.anchoranalysis.plugin.imagej.bean.stack.provider: Implementations of StackProvider that call ImageJ.
org.anchoranalysis.plugin.imagej.bean.threshold - package org.anchoranalysis.plugin.imagej.bean.threshold: Implementations of Thresholder that call ImageJ.
org.anchoranalysis.plugin.imagej.channel.provider - package org.anchoranalysis.plugin.imagej.channel.provider: Implementations of ChannelProvider that call ImageJ.
org.anchoranalysis.plugin.imagej.mask - package org.anchoranalysis.plugin.imagej.mask: Non-bean classes involving ObjectMask that call ImageJ.
org.anchoranalysis.plugin.io.bean.channel.map - package org.anchoranalysis.plugin.io.bean.channel.map: Implementations of ChannelMapCreator.
org.anchoranalysis.plugin.io.bean.file.copy.method - package org.anchoranalysis.plugin.io.bean.file.copy.method: Methods for copying files on the file-system.
org.anchoranalysis.plugin.io.bean.file.copy.naming - package org.anchoranalysis.plugin.io.bean.file.copy.naming: Rules for preserving or changing the naming of files when copying on the file-system.
org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster - package org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster: Implementations of CopyFilesNaming that perform clustering of files.
org.anchoranalysis.plugin.io.bean.file.group - package org.anchoranalysis.plugin.io.bean.file.group: Grouping files together so that they collectively represent a single entity.
org.anchoranalysis.plugin.io.bean.file.group.check - package org.anchoranalysis.plugin.io.bean.file.group.check: Tests that are applied when grouping files in org.anchoranalysis.plugin.io.bean.file.group
org.anchoranalysis.plugin.io.bean.file.group.parser - package org.anchoranalysis.plugin.io.bean.file.group.parser: Parsing file-paths to determine file-grouping in org.anchoranalysis.plugin.io.bean.file.group
org.anchoranalysis.plugin.io.bean.file.namer - package org.anchoranalysis.plugin.io.bean.file.namer: Implementations of FileNamer.
org.anchoranalysis.plugin.io.bean.file.namer.patternspan - package org.anchoranalysis.plugin.io.bean.file.namer.patternspan: Implementations of FileNamer that look for a pattern across many files.
org.anchoranalysis.plugin.io.bean.file.path - package org.anchoranalysis.plugin.io.bean.file.path: Beans to specify a file-path.
org.anchoranalysis.plugin.io.bean.file.path.prefixer - package org.anchoranalysis.plugin.io.bean.file.path.prefixer: Implementations of PathPrefixer.
org.anchoranalysis.plugin.io.bean.file.pattern - package org.anchoranalysis.plugin.io.bean.file.pattern: Extracting a pattern from a file-path.
org.anchoranalysis.plugin.io.bean.file.provider - package org.anchoranalysis.plugin.io.bean.file.provider: Implementations of FilesProvider.
org.anchoranalysis.plugin.io.bean.grouper - package org.anchoranalysis.plugin.io.bean.grouper: Implementations of Grouper.
org.anchoranalysis.plugin.io.bean.input - package org.anchoranalysis.plugin.io.bean.input: Implementations of InputManager.
org.anchoranalysis.plugin.io.bean.input.channel - package org.anchoranalysis.plugin.io.bean.input.channel: InputManagers that accept a set of named-channels.
org.anchoranalysis.plugin.io.bean.input.files - package org.anchoranalysis.plugin.io.bean.input.files: InputManagers that accept a set of named-files.
org.anchoranalysis.plugin.io.bean.input.files.provider - package org.anchoranalysis.plugin.io.bean.input.files.provider: Implementations of FilesProvider.
org.anchoranalysis.plugin.io.bean.input.filter - package org.anchoranalysis.plugin.io.bean.input.filter: Implementations of InputManager that filter inputs.
org.anchoranalysis.plugin.io.bean.input.stack - package org.anchoranalysis.plugin.io.bean.input.stack: Implementations of InputManager that process Stacks.
org.anchoranalysis.plugin.io.bean.metadata.header - package org.anchoranalysis.plugin.io.bean.metadata.header: Different types of image-file-formats whose headers can provide ImageMetadata.
org.anchoranalysis.plugin.io.bean.metadata.reader - package org.anchoranalysis.plugin.io.bean.metadata.reader: Implementations of ImageMetadataReader.
org.anchoranalysis.plugin.io.bean.path.derive - package org.anchoranalysis.plugin.io.bean.path.derive: Implementations of DerivePath.
org.anchoranalysis.plugin.io.bean.stack.reader - package org.anchoranalysis.plugin.io.bean.stack.reader: Implementations of StackReader.
org.anchoranalysis.plugin.io.bean.stack.writer - package org.anchoranalysis.plugin.io.bean.stack.writer: Implementations of StackWriter.
org.anchoranalysis.plugin.io.bean.summarizer - package org.anchoranalysis.plugin.io.bean.summarizer: Summarizing a set of elements into a descriptive-string.
org.anchoranalysis.plugin.io.bean.summarizer.image - package org.anchoranalysis.plugin.io.bean.summarizer.image: Implementations of Summarizer that summarize images.
org.anchoranalysis.plugin.io.bean.summarizer.input - package org.anchoranalysis.plugin.io.bean.summarizer.input: Implementations of Summarizer that summarize generically InputFromManagers.
org.anchoranalysis.plugin.io.bean.summarizer.path - package org.anchoranalysis.plugin.io.bean.summarizer.path: Implementations of Summarizer that summarize generically Paths.
org.anchoranalysis.plugin.io.bean.task - package org.anchoranalysis.plugin.io.bean.task: Implementations of Task related to file-system I/O.
org.anchoranalysis.plugin.io.file.copy - package org.anchoranalysis.plugin.io.file.copy: Non-bean classes to help tasks in org.anchoranalysis.plugin.io.bean.file.copy.
org.anchoranalysis.plugin.io.input.filter - package org.anchoranalysis.plugin.io.input.filter: Non-bean classes to help tasks in org.anchoranalysis.plugin.io.bean.input.filter.
org.anchoranalysis.plugin.io.input.path - package org.anchoranalysis.plugin.io.input.path: Non-bean classes to help in processing paths.
org.anchoranalysis.plugin.io.multifile - package org.anchoranalysis.plugin.io.multifile: Non-bean classes to help use multiple files to represent a single Stack.
org.anchoranalysis.plugin.io.multifile.buffer - package org.anchoranalysis.plugin.io.multifile.buffer: Buffers used in org.anchoranalysis.plugin.io.multifile.
org.anchoranalysis.plugin.io.naming.interval - package org.anchoranalysis.plugin.io.naming.interval: How to write parts of a time-interval in a file-name.
org.anchoranalysis.plugin.io.shared - package org.anchoranalysis.plugin.io.shared: Objects used in shared-state in Tasks in this plugin.
org.anchoranalysis.plugin.io.xml - package org.anchoranalysis.plugin.io.xml: Reading and writing metadata XML.
org.anchoranalysis.plugin.mpp.bean.convert - package org.anchoranalysis.plugin.mpp.bean.convert: Converting from NamedChannelsInput to the input-type expected by a Task.
org.anchoranalysis.plugin.mpp.bean.define - package org.anchoranalysis.plugin.mpp.bean.define: Beans related to Define involving Mark or related classes.
org.anchoranalysis.plugin.mpp.bean.object.provider - package org.anchoranalysis.plugin.mpp.bean.object.provider: Implementations of ObjectCollectionProvider.
org.anchoranalysis.plugin.mpp.bean.provider.collection - package org.anchoranalysis.plugin.mpp.bean.provider.collection: Implementation of MarkCollectionProvider.
org.anchoranalysis.plugin.mpp.bean.stack.provider - package org.anchoranalysis.plugin.mpp.bean.stack.provider: Implementations of StackProvider involving Mark or related classes.
org.anchoranalysis.plugin.mpp.shared - package org.anchoranalysis.plugin.mpp.shared: Shared-state use across tasks in this JAR.
org.anchoranalysis.plugin.onnx.bean.object.segment.decode.instance.maskrcnn - package org.anchoranalysis.plugin.onnx.bean.object.segment.decode.instance.maskrcnn: Decodes the outputted tensors from a Mask R-CNN implementation.
org.anchoranalysis.plugin.onnx.bean.object.segment.decode.instance.text - package org.anchoranalysis.plugin.onnx.bean.object.segment.decode.instance.text: Decodes the outputted tensors from text-segmentation models.
org.anchoranalysis.plugin.onnx.bean.object.segment.stack - package org.anchoranalysis.plugin.onnx.bean.object.segment.stack: Segmenting a Stack using the ONNX Runtime to produce an ObjectCollection.
org.anchoranalysis.plugin.onnx.model - package org.anchoranalysis.plugin.onnx.model: Non-bean classes for running an inference model with the ONNX Runtime.
org.anchoranalysis.plugin.opencv - package org.anchoranalysis.plugin.opencv: Plugins that call OpenCV.
org.anchoranalysis.plugin.opencv.bean.color - package org.anchoranalysis.plugin.opencv.bean.color: Operations involving color-spaces and OpenCV.
org.anchoranalysis.plugin.opencv.bean.feature - package org.anchoranalysis.plugin.opencv.bean.feature: Extracting features using OpenCV.
org.anchoranalysis.plugin.opencv.bean.interpolate - package org.anchoranalysis.plugin.opencv.bean.interpolate: Interpolation beans that use OpenCV.
org.anchoranalysis.plugin.opencv.bean.object.segment.stack - package org.anchoranalysis.plugin.opencv.bean.object.segment.stack: Segmentation of a Stack using OpenCV.
org.anchoranalysis.plugin.opencv.bean.stack - package org.anchoranalysis.plugin.opencv.bean.stack: Implementations of StackWriter and StackReader that involve OpenCV.
org.anchoranalysis.plugin.opencv.convert - package org.anchoranalysis.plugin.opencv.convert: Conversion to/from OpenCV data-structures.
org.anchoranalysis.plugin.opencv.resizer - package org.anchoranalysis.plugin.opencv.resizer: Interpolation non-beans that use OpenCV.
org.anchoranalysis.plugin.opencv.segment - package org.anchoranalysis.plugin.opencv.segment: Non-bean classes pertaining to segmentation.
org.anchoranalysis.plugin.operator.feature.bean - package org.anchoranalysis.plugin.operator.feature.bean: Features that combine or convert other features in a generic way.
org.anchoranalysis.plugin.operator.feature.bean.arithmetic - package org.anchoranalysis.plugin.operator.feature.bean.arithmetic: Arithmetic involving features.
org.anchoranalysis.plugin.operator.feature.bean.conditional - package org.anchoranalysis.plugin.operator.feature.bean.conditional: Conditional operations involving features.
org.anchoranalysis.plugin.operator.feature.bean.list - package org.anchoranalysis.plugin.operator.feature.bean.list: Operations that extract a single value from a list of features.
org.anchoranalysis.plugin.operator.feature.bean.range - package org.anchoranalysis.plugin.operator.feature.bean.range: Features that compare against a range of values.
org.anchoranalysis.plugin.operator.feature.bean.replace - package org.anchoranalysis.plugin.operator.feature.bean.replace: Replaces particular values if they are returned from a feature.
org.anchoranalysis.plugin.operator.feature.bean.statistics - package org.anchoranalysis.plugin.operator.feature.bean.statistics: Converts feature values based upon a statistical measure of distribution.
org.anchoranalysis.plugin.operator.feature.physical - package org.anchoranalysis.plugin.operator.feature.physical: Converting to/from physical units.
org.anchoranalysis.plugin.operator.feature.statistics - package org.anchoranalysis.plugin.operator.feature.statistics: Non-bean statistical operations.
org.anchoranalysis.plugin.points.bean - package org.anchoranalysis.plugin.points.bean: Beans that fit or otherwise manipulate sets of points.
org.anchoranalysis.plugin.points.bean.convexhull - package org.anchoranalysis.plugin.points.bean.convexhull: Convex hull operations.
org.anchoranalysis.plugin.points.bean.feature - package org.anchoranalysis.plugin.points.bean.feature: Features related to points and fitting points to conics.
org.anchoranalysis.plugin.points.bean.fitter - package org.anchoranalysis.plugin.points.bean.fitter: Fitting geometric structures to points.
org.anchoranalysis.plugin.points.calculate.ellipse - package org.anchoranalysis.plugin.points.calculate.ellipse: CalculationPart related to fitting ellipses to points by least-squares.
org.anchoranalysis.plugin.points.calculate.ellipsoid - package org.anchoranalysis.plugin.points.calculate.ellipsoid: CalculationPart related to fitting ellipsoids to points by least-squares.
org.anchoranalysis.plugin.points.convexhull - package org.anchoranalysis.plugin.points.convexhull: Non-bean convex hull operations.
org.anchoranalysis.spatial.axis - package org.anchoranalysis.spatial.axis: Identifying the three standard axes in 3D cartesian coordinates.
org.anchoranalysis.spatial.box - package org.anchoranalysis.spatial.box: Axis-aligned bounding-boxes and related operations.
org.anchoranalysis.spatial.orientation - package org.anchoranalysis.spatial.orientation: Various methods to specify the orientation (general direction) of an entity.
org.anchoranalysis.spatial.point - package org.anchoranalysis.spatial.point: A cartesian-coordinate, across varying primitive types, in 2D and 3D space.
org.anchoranalysis.spatial.point.consumer - package org.anchoranalysis.spatial.point.consumer: Functional interfaces that accept cartesian coordinate points specified in different ways.
org.anchoranalysis.spatial.rtree - package org.anchoranalysis.spatial.rtree: R-Tree data structure and related operations.
org.anchoranalysis.spatial.scale - package org.anchoranalysis.spatial.scale: How to much to scale an entity in Cartesian space by.
org.anchoranalysis.test - package org.anchoranalysis.test: Testing utilities and fixtures with no greater downstream dependency than anchor-core.
org.anchoranalysis.test.experiment - package org.anchoranalysis.test.experiment: Testing utilities and fixtures with no greater downstream dependency than anchor-experiment or anchor-mpp or anchor-mpp-io.
org.anchoranalysis.test.experiment.launcher - package org.anchoranalysis.test.experiment.launcher: Launches an anchor binary from a shell and runs an experiment.
org.anchoranalysis.test.experiment.task - package org.anchoranalysis.test.experiment.task: Helper classes to execute Tasks in tests.
org.anchoranalysis.test.feature - package org.anchoranalysis.test.feature: Testing utilities and fixtures with no greater downstream dependency than anchor-feature.
org.anchoranalysis.test.feature.plugins - package org.anchoranalysis.test.feature.plugins: Testing utilities and fixtures with no greater downstream dependency than anchor-image-feature or anchor-mpp.
org.anchoranalysis.test.feature.plugins.mockfeature - package org.anchoranalysis.test.feature.plugins.mockfeature: A mocked feature internally using a feature-calculation.
org.anchoranalysis.test.feature.plugins.objects - package org.anchoranalysis.test.feature.plugins.objects: Fixtures for creating object-masks and related feature-inputs.
org.anchoranalysis.test.image - package org.anchoranalysis.test.image: Testing utilities and fixtures with no greater downstream dependency than anchor-image-io or anchor-io-bioformats or anchor-imagej.
org.anchoranalysis.test.image.csv - package org.anchoranalysis.test.image.csv: Comparing two CSV files for equality (by a certain definition).
org.anchoranalysis.test.image.io - package org.anchoranalysis.test.image.io: Utilities for testing-related reading and writing to the filesystem.
org.anchoranalysis.test.image.load - package org.anchoranalysis.test.image.load: Load test image data.
org.anchoranalysis.test.image.object - package org.anchoranalysis.test.image.object: Fixtures for creating object-masks.
org.anchoranalysis.test.image.rasterwriter.comparison - package org.anchoranalysis.test.image.rasterwriter.comparison: Different ways for comparing images.
org.anchoranalysis.test.image.segment - package org.anchoranalysis.test.image.segment: Fixtures or other helper classes for testing image segmentation algorithms.
org.anchoranalysis.test.image.stackwriter - package org.anchoranalysis.test.image.stackwriter: Fixtures for testing StackWriter and related classes.
org.anchoranalysis.test.io.output - package org.anchoranalysis.test.io.output: Fixtures for an OutputManager and related-classes.
Orientation - Class in org.anchoranalysis.spatial.orientation: The orientation (direction) in 2D or 3D Euclidean space.
Orientation() - Constructor for class org.anchoranalysis.spatial.orientation.Orientation
Orientation2D - Class in org.anchoranalysis.spatial.orientation: A simple angular orientation the 2D plane, relative to the x-axis.
Orientation2D() - Constructor for class org.anchoranalysis.spatial.orientation.Orientation2D
Orientation2D(double) - Constructor for class org.anchoranalysis.spatial.orientation.Orientation2D: Creates a new Orientation2D instance.
Orientation3DEulerAngles - Class in org.anchoranalysis.spatial.orientation: An orientation using three angle parameters for the rotation.
Orientation3DEulerAngles(double, double, double) - Constructor for class org.anchoranalysis.spatial.orientation.Orientation3DEulerAngles: Creates a new Orientation3DEulerAngles instance.
OrientationAxisAngle - Class in org.anchoranalysis.spatial.orientation: An orientation in axis-angle representation.
OrientationAxisAngle(Vector3d, double) - Constructor for class org.anchoranalysis.spatial.orientation.OrientationAxisAngle: Creates a new OrientationAxisAngle instance.
OrientationChange - Enum Class in org.anchoranalysis.image.core.dimensions: Changes orientation of an image in the XY plane.
OrientationProposer - Class in org.anchoranalysis.mpp.bean.proposer: An abstract base class for proposing orientations for marks.
OrientationProposer() - Constructor for class org.anchoranalysis.mpp.bean.proposer.OrientationProposer
OrientationReader - Class in org.anchoranalysis.io.bioformats.metadata: Reads the image-orientation from EXIF metadata, if specified in an image-file.
OrientationRotationMatrix - Class in org.anchoranalysis.spatial.orientation: Orients an object by rotating anti-clockwise with an explicit RotationMatrix.
OrientationRotationMatrix() - Constructor for class org.anchoranalysis.spatial.orientation.OrientationRotationMatrix
OrientationRotationMatrix(RotationMatrix) - Constructor for class org.anchoranalysis.spatial.orientation.OrientationRotationMatrix: Creates a new OrientationRotationMatrix instance.
ORIGIN - Static variable in class org.anchoranalysis.spatial.point.Point3i: A constant Point3i where all dimensions are zero.
otherVertex(V) - Method in class org.anchoranalysis.core.graph.TypedEdge: The other vertex on the edge
Otsu - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold: Performs auto-thresholding using Otsu's method.
Otsu() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.Otsu
OtsuWeighted - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold: Similar to Otsu, but weighs the variances differently of background and foreground.
OtsuWeighted() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.OtsuWeighted
OtsuWeighted(double, double) - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.OtsuWeighted
outFilePrefix(NamedPath, Optional<String>, PathPrefixerContext) - Method in class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixer: Provides a prefix which can be prepended to all output files.
outFilePrefix(NamedPath, Optional<String>, PathPrefixerContext) - Method in class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixerAvoidResolve
outFilePrefix(NamedPath, Optional<String>, PathPrefixerContext) - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.HomeSubdirectory
outFilePrefix(NamedPath, Optional<String>, PathPrefixerContext) - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.Rooted
outFilePrefixAvoidResolve(NamedPath, Optional<String>, PathPrefixerContext) - Method in class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixerAvoidResolve: Provides a prefix which can be prepended to all output files.
outFilePrefixFromPath(NamedPath, Path, PathPrefixerContext) - Method in class org.anchoranalysis.io.output.bean.path.prefixer.IncrementingNumber
outFilePrefixFromPath(NamedPath, Path, PathPrefixerContext) - Method in class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixerAvoidResolve: Determines the out-file prefix from a path.
outFilePrefixFromPath(NamedPath, Path, PathPrefixerContext) - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.DirectoryStructure
outFilePrefixFromPath(NamedPath, Path, PathPrefixerContext) - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.FromDescriptiveName
outFilePrefixFromPath(NamedPath, Path, PathPrefixerContext) - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.IfIncrementingNumberRequested
outFilePrefixFromPath(NamedPath, Path, PathPrefixerContext) - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.LastDirectoryAsPrefix
outFilePrefixFromPath(NamedPath, Path, PathPrefixerContext) - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.PathRegEx
outgoingEdgesFor(V) - Method in class org.anchoranalysis.core.graph.GraphWithPayload: All outgoing edges for a given vertex.
Outline - Class in org.anchoranalysis.image.io.bean.object.draw: Draws the outline of each object-mask.
Outline() - Constructor for class org.anchoranalysis.image.io.bean.object.draw.Outline: Creates with an outline-width of 1 voxel.
Outline(int) - Constructor for class org.anchoranalysis.image.io.bean.object.draw.Outline: Create with a particular outline-width.
Outline(int, boolean) - Constructor for class org.anchoranalysis.image.io.bean.object.draw.Outline: Creates a new Outline instance.
OutlineKernel - Class in org.anchoranalysis.image.voxel.kernel.outline: Sets voxels on the outline of an object to be on and otherwise off.
OutlineKernel() - Constructor for class org.anchoranalysis.image.voxel.kernel.outline.OutlineKernel
OutlineKernelBase - Class in org.anchoranalysis.image.voxel.kernel.outline: A base class for kernels that find the outline of an ObjectMask.
OutlineKernelBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single: Base class for features that apply a kernel to the outline of an object.
OutlineKernelBase() - Constructor for class org.anchoranalysis.image.voxel.kernel.outline.OutlineKernelBase: Default constructor.
OutlineKernelBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.OutlineKernelBase
OutlineKernelNeighborMatchValue - Class in org.anchoranalysis.image.voxel.kernel.outline: Outputs the outline of an object-mask, but only for voxels on the exterior which neighbor a binary-mask.
OutlineKernelNeighborMatchValue(BinaryVoxels<UnsignedByteBuffer>) - Constructor for class org.anchoranalysis.image.voxel.kernel.outline.OutlineKernelNeighborMatchValue: Creates for an object.
OutlinePreserveRelativeSize - Class in org.anchoranalysis.plugin.image.bean.thumbnail.object: Create a thumbnail by drawing an outline of an object at a particular-scale, and placing it centered in a window of a certain size.
OutlinePreserveRelativeSize() - Constructor for class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize
outlineSingleColor(int, DisplayStack, RGBColor) - Static method in class org.anchoranalysis.image.io.object.output.rgb.DrawObjectsGenerator: Creates a generator that draws an outline around objects on a background using a single color for all objects.
outlineVariedColors(int, int, Either<Dimensions, DisplayStack>) - Static method in class org.anchoranalysis.image.io.object.output.rgb.DrawObjectsGenerator: Creates a generator that draws an outline around objects on a background using varied colors for the objects.
outlineVariedColors(int, int, DisplayStack) - Static method in class org.anchoranalysis.image.io.object.output.rgb.DrawObjectsGenerator: Creates a generator that draws an outline around objects on a background using varied colors for the objects.
outlineWithColorIndex(int, ColorIndex) - Static method in class org.anchoranalysis.image.io.object.output.rgb.DrawObjectsGenerator: Creates a generator that draws an outline around objects using a particular ColorIndex.
output() - Method in class org.anchoranalysis.experiment.arguments.ExecutionArguments: Arguments to help specify the outputs from the experiment.
output(String, boolean) - Method in class org.anchoranalysis.io.generator.collection.NamedProviderOutputter: Outputs the entities using a particular output-name.
output(NamedProvider<Stack>, String, boolean, OutputterChecked) - Static method in class org.anchoranalysis.image.io.stack.output.NamedStacksOutputter: Writes all or a subset from a set of named-stacks to a directory as a raster.
output(InputOutputContext) - Method in class org.anchoranalysis.image.io.bean.object.feature.OutputFeatureTable: Outputs the feature-table.
OUTPUT_BY_GROUP - Static variable in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations: Output name for the CSV file containing summary statistics for all groups of images.
OUTPUT_DEFAULT_NON_AGGREGATED - Static variable in class org.anchoranalysis.feature.io.results.FeatureOutputNames: If not otherwise specified, the output name for a non-aggregated CSV of the results.
OUTPUT_ENERGY_STACK_DIRECTORY - Static variable in class org.anchoranalysis.mpp.io.output.EnergyStackWriter: The output name for the directory containing energy stack channels.
OUTPUT_EXECUTION_TIME - Static variable in class org.anchoranalysis.experiment.bean.io.OutputExperiment: The name for the output that records the total execution-time of the experiment.
OUTPUT_FEATURE_TABLE - Static variable in class org.anchoranalysis.image.io.bean.object.feature.OutputFeatureTable: The output-name for a CSV table of feature-values.
OUTPUT_NAMES - Static variable in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures: Default names for various outputs from the task.
OUTPUT_SUFFIX_AGGREGATED - Static variable in class org.anchoranalysis.feature.io.results.FeatureOutputNames: Suffix appended to FeatureOutputNames.csvFeaturesNonAggregated to form an output-name for aggregated features.
OUTPUT_SUFFIX_AGGREGATED_GROUP - Static variable in class org.anchoranalysis.feature.io.results.FeatureOutputNames: Suffix appended to FeatureOutputNames.csvFeaturesNonAggregated to form an output-name for aggregated grouped features.
OUTPUT_SUFFIX_GROUP - Static variable in class org.anchoranalysis.feature.io.results.FeatureOutputNames: Suffix appended to FeatureOutputNames.csvFeaturesNonAggregated to form an output-name for grouped features.
OUTPUT_THUMBNAILS - Static variable in class org.anchoranalysis.plugin.image.task.feature.FeatureExporter: The output-name for writing thumbnails.
outputAnyRemainingGroups() - Method in class org.anchoranalysis.plugin.image.task.grouped.GroupMapByName: Outputs any groups that have not already been outputted.
OutputArguments - Class in org.anchoranalysis.experiment.arguments: Arguments that can further specify an experiment's output in addition to its bean specification.
OutputArguments() - Constructor for class org.anchoranalysis.experiment.arguments.OutputArguments
OutputDirectoryAlreadyExistsException - Exception Class in org.anchoranalysis.io.output.error: When an output-directory already exists.
OutputDirectoryAlreadyExistsException(String) - Constructor for exception class org.anchoranalysis.io.output.error.OutputDirectoryAlreadyExistsException: Create with a message only.
OutputEnabled - Class in org.anchoranalysis.io.output.bean.enabled: Whether a particular output, identified by a textual name, is enabled or not.
OutputEnabled() - Constructor for class org.anchoranalysis.io.output.bean.enabled.OutputEnabled
OutputEnabledDelta - Class in org.anchoranalysis.io.output.recorded: Additional output-names to enable or disable from an existing set of output-enabled rules.
OutputEnabledDelta() - Constructor for class org.anchoranalysis.io.output.recorded.OutputEnabledDelta
OutputEnabledMutable - Class in org.anchoranalysis.io.output.enabled: A specific set of first-level outputs are enabled, to which more can be added.
OutputEnabledMutable(String...) - Constructor for class org.anchoranalysis.io.output.enabled.OutputEnabledMutable: Creates with one or more enabled outputs.
OutputEnabledMutable(SingleLevelOutputEnabled, String...) - Constructor for class org.anchoranalysis.io.output.enabled.OutputEnabledMutable: Creates with one or more enabled outputs.
OutputEnabledRules - Class in org.anchoranalysis.io.output.bean.rules: Bean that specifies an implementation of MultiLevelOutputEnabled.
OutputEnabledRules() - Constructor for class org.anchoranalysis.io.output.bean.rules.OutputEnabledRules
OutputEnableRulesSpecify - Class in org.anchoranalysis.io.output.bean.rules: Base class for an OutputEnabledRules that specifies particular output-names for first and second levels.
OutputEnableRulesSpecify() - Constructor for class org.anchoranalysis.io.output.bean.rules.OutputEnableRulesSpecify
OutputEnableRulesSpecify(StringSet) - Constructor for class org.anchoranalysis.io.output.bean.rules.OutputEnableRulesSpecify: Create with a specific set of first-level output names.
OutputExperiment - Class in org.anchoranalysis.experiment.bean.io: An Experiment that produces output files, as defined by a OutputManager.
OutputExperiment() - Constructor for class org.anchoranalysis.experiment.bean.io.OutputExperiment
OutputFactory - Class in org.anchoranalysis.launcher.executor.selectparam.path: SelectParam<Path> factory for outputs.
OutputFeatureTable - Class in org.anchoranalysis.image.io.bean.object.feature: Specifies a table of feature-calculations on objects.
OutputFeatureTable() - Constructor for class org.anchoranalysis.image.io.bean.object.feature.OutputFeatureTable
outputFormatString() - Method in class org.anchoranalysis.io.output.namestyle.IndexableOutputNameStyle: A format-string as recognized by String.format(java.lang.String, java.lang.Object...) that expects a single string element.
outputFormatString() - Method in class org.anchoranalysis.io.output.namestyle.IntegerSuffixOutputNameStyle
outputFormatString() - Method in class org.anchoranalysis.io.output.namestyle.StringSuffixOutputNameStyle
outputGroupIntoSubdirectory(Collection<Map.Entry<String, T>>, Function<Boolean, InputOutputContext>, Optional<String>) - Method in class org.anchoranalysis.plugin.image.task.grouped.GroupMapByName: Output a particular group into a subdirectory.
OutputManager - Class in org.anchoranalysis.io.output.bean: Responsible for making decisions on where output goes and what form it takes.
OutputManager() - Constructor for class org.anchoranalysis.io.output.bean.OutputManager
OutputManagerFixture - Class in org.anchoranalysis.test.io.output: A fixture that implements a basic implementation of a OutputManager.
outputMetadata - Variable in class org.anchoranalysis.feature.io.csv.results.LabelledResultsCSVWriter: Metadata defining which CSV file to write to, and which headers.
outputName() - Method in class org.anchoranalysis.feature.io.csv.metadata.FeatureCSVMetadataForOutput: Names for the produced output.
outputNameForGroups() - Method in class org.anchoranalysis.plugin.image.task.bean.combine.AggregateChannelTask
outputNameForGroups() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase: The first-level output-name used for determining if groups are written.
outputNameForGroups() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.histogram.ExportImageHistograms
outputNames() - Method in class org.anchoranalysis.feature.io.results.FeatureOutputMetadata: Names for any outputs produced by LabelledResultsCollector.
OutputNameStyle - Class in org.anchoranalysis.io.output.namestyle: Base class for an approach to generate a filename for an output.
OutputNameStyle() - Constructor for class org.anchoranalysis.io.output.namestyle.OutputNameStyle
OutputNameStyle(String) - Constructor for class org.anchoranalysis.io.output.namestyle.OutputNameStyle: Creates a new OutputNameStyle instance.
OutputPattern - Class in org.anchoranalysis.io.generator.sequence.pattern: A particular naming pattern files follow when outputted.
OutputPattern(Optional<String>, IndexableOutputNameStyle, boolean) - Constructor for class org.anchoranalysis.io.generator.sequence.pattern.OutputPattern: Creates a new OutputPattern instance.
OutputPatternIntegerSuffix - Class in org.anchoranalysis.io.generator.sequence.pattern: A OutputPattern that outputs a file-name with a trailing integer index.
OutputPatternIntegerSuffix(String, boolean) - Constructor for class org.anchoranalysis.io.generator.sequence.pattern.OutputPatternIntegerSuffix: Creates in a subdirectory, using the outputName as both the subdirectory name and the prefix.
OutputPatternIntegerSuffix(String, boolean, String, int, boolean) - Constructor for class org.anchoranalysis.io.generator.sequence.pattern.OutputPatternIntegerSuffix: Creates with a full set of flexibility about how the filename appears and whether a subdirectory is used.
OutputPatternIntegerSuffix(String, int, boolean) - Constructor for class org.anchoranalysis.io.generator.sequence.pattern.OutputPatternIntegerSuffix: Like OutputPatternIntegerSuffix(String, boolean) but also whether to check outputs against rules.
OutputPatternIntegerSuffix(String, String) - Constructor for class org.anchoranalysis.io.generator.sequence.pattern.OutputPatternIntegerSuffix: Creates in a subdirectory, using the output-name as the subdirectory name, and a specific prefix.
OutputPatternIntegerSuffix(String, String, int, boolean) - Constructor for class org.anchoranalysis.io.generator.sequence.pattern.OutputPatternIntegerSuffix: Like OutputPatternIntegerSuffix(String, String) but with additional options about the number of digits, and whether to check outputs against rules.
OutputPatternStringSuffix - Class in org.anchoranalysis.io.generator.sequence.pattern: A OutputPattern that outputs a file-name with a trailing string index.
OutputPatternStringSuffix(String, boolean) - Constructor for class org.anchoranalysis.io.generator.sequence.pattern.OutputPatternStringSuffix: Creates without a prefix.
OutputPatternStringSuffix(String, boolean, String) - Constructor for class org.anchoranalysis.io.generator.sequence.pattern.OutputPatternStringSuffix: Creates with a prefix.
OutputPrefixerSettings - Class in org.anchoranalysis.io.output.path.prefixer: Arguments influencing into which directory outputs are written, and how identifiers are expressed.
OutputPrefixerSettings() - Constructor for class org.anchoranalysis.io.output.path.prefixer.OutputPrefixerSettings
OutputPrefixWithExtension - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming: Copies files using whatever prefix is assigned to an input by the OutputManager as the file-name, adding the same extension as the source file.
OutputPrefixWithExtension() - Constructor for class org.anchoranalysis.plugin.io.bean.file.copy.naming.OutputPrefixWithExtension
outputSelectParam(CommandLine) - Static method in class org.anchoranalysis.launcher.executor.selectparam.SelectParamFactory: Creates a SelectParam for output selection.
outputsEnabled() - Method in class org.anchoranalysis.io.output.outputter.Outputter: Which outputs are enabled or not enabled.
OutputSequenceFactory<T> - Class in org.anchoranalysis.io.generator.sequence: Creates and starts an output-seqience with a particular generator and context.
OutputSequenceFactory(Generator<T>, OutputterChecked) - Constructor for class org.anchoranalysis.io.generator.sequence.OutputSequenceFactory: Creates a new OutputSequenceFactory instance.
OutputSequenceIncrementing<T> - Class in org.anchoranalysis.io.generator.sequence: A sequence of outputs that use the same generator, where each output increments an index by one in the filename.
OutputSequenceIncrementing(BoundOutputter<T>) - Constructor for class org.anchoranalysis.io.generator.sequence.OutputSequenceIncrementing: Create with an outputter.
OutputSequenceIndexed<T,S> - Class in org.anchoranalysis.io.generator.sequence: A sequence of outputs that use the same generator with non-incrementing indexes for each output.
OutputSequenceStackFactory - Class in org.anchoranalysis.image.io.stack.output: Creates output-sequences of different kinds for writing stacks to a directory.
outputSharedObjects(SharedObjects, Optional<EnergyStack>, Outputter) - Method in class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputter: Outputs shared objects and optionally an energy stack.
outputter(Optional<Path>) - Static method in class org.anchoranalysis.test.image.io.OutputterFixture: Creates an Outputter instance with optionally a path to a temporary directory for outtputting files.
outputter(OutputManager, OutputEnabledRules) - Static method in class org.anchoranalysis.test.image.io.OutputterFixture: Creates an Outputter instance with a specified OutputManager and OutputEnabledRules.
Outputter - Class in org.anchoranalysis.io.output.outputter: Like OutputterChecked but exceptions are reported in a ErrorReporter.
Outputter(OutputterChecked, ErrorReporter) - Constructor for class org.anchoranalysis.io.output.outputter.Outputter
outputterChecked(Optional<Path>) - Static method in class org.anchoranalysis.test.image.io.OutputterFixture: Creates an OutputterChecked instance with optionally a path to a temporary directory for outputting files.
OutputterChecked - Class in org.anchoranalysis.io.output.outputter: A particular directory on the filesystem in which outputting can occur.
OutputterCheckedFixture - Class in org.anchoranalysis.test.io.output: A fixture that implements a basic implementation of a OutputterChecked.
OutputterFixture - Class in org.anchoranalysis.test.image.io: Utility class for creating Outputter instances for testing purposes.
OutputterTarget - Class in org.anchoranalysis.io.output.outputter.directory: The directory and prefix an outputter writes to.
OutputterTarget(DirectoryWithPrefix, DirectoryCreationParameters) - Constructor for class org.anchoranalysis.io.output.outputter.directory.OutputterTarget: Creates for a particular directory, with optionally an associated prefix.
OutputWriteContext - Class in org.anchoranalysis.io.output.outputter: Settings and user-arguments for writing files.
OutputWriteContext() - Constructor for class org.anchoranalysis.io.output.outputter.OutputWriteContext: Create with default state, including no default beans assigned.
OutputWriteContext(OutputWriteSettings) - Constructor for class org.anchoranalysis.io.output.outputter.OutputWriteContext: Create from OutputWriteSettings and otherwise with defaults.
OutputWriteContext(OutputWriteSettings, Optional<ImageFileFormat>, ExecutionTimeRecorder) - Constructor for class org.anchoranalysis.io.output.outputter.OutputWriteContext: Creates a new OutputWriteContext instance.
OutputWriteFailedException - Exception Class in org.anchoranalysis.io.output.error: When an output could not be successfully written to the file-system.
OutputWriteFailedException(String) - Constructor for exception class org.anchoranalysis.io.output.error.OutputWriteFailedException: Creates with a message only.
OutputWriteFailedException(String, AnchorCombinableException) - Constructor for exception class org.anchoranalysis.io.output.error.OutputWriteFailedException: Creates with a message and a cause that can be combined with others in summary form.
OutputWriteFailedException(String, HasFriendlyErrorMessage) - Constructor for exception class org.anchoranalysis.io.output.error.OutputWriteFailedException: Creates with a message and a cause that provides a friendly error message.
OutputWriteFailedException(Throwable) - Constructor for exception class org.anchoranalysis.io.output.error.OutputWriteFailedException: Creates with a cause only.
OutputWriteSettings - Class in org.anchoranalysis.io.output.bean: Settings for how to write output, including default writers.
OutputWriteSettings() - Constructor for class org.anchoranalysis.io.output.bean.OutputWriteSettings
OutsideKernelPolicy - Enum Class in org.anchoranalysis.image.voxel.kernel: How to handle voxels whose neighbors are outside the scene.
OutsideRange - Class in org.anchoranalysis.plugin.image.feature.bean.score: Calculates a voxel score based on whether the voxel intensity is outside a specified range.
OutsideRange() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.OutsideRange
overAll(Kernel, BinaryVoxels<UnsignedByteBuffer>, KernelApplicationParameters, ProcessKernelPointCursor) - Static method in class org.anchoranalysis.image.voxel.iterator.neighbor.kernel.IterateKernelHelper: Iterates over all voxels.
overBox(Kernel, BinaryVoxels<UnsignedByteBuffer>, BoundingBox, KernelApplicationParameters, ProcessKernelPointCursor) - Static method in class org.anchoranalysis.image.voxel.iterator.neighbor.kernel.IterateKernelHelper: Iterates over only voxels contained within a bounding-box.
overBoxUntil(Kernel, BinaryVoxels<UnsignedByteBuffer>, BoundingBox, KernelApplicationParameters, PredicateKernelPointCursor) - Static method in class org.anchoranalysis.image.voxel.iterator.neighbor.kernel.IterateKernelHelper: Iterates over only voxels contained within a bounding-box until a predicate is matched on a voxel.
OverlappingObject<T> - Class in org.anchoranalysis.image.core.object.label: An object-mask that is founded to overlap with another during labelling.
OverlappingObject(T, ObjectMask) - Constructor for class org.anchoranalysis.image.core.object.label.OverlappingObject: Creates a new OverlappingObject instance.
OverlappingObjects - Class in org.anchoranalysis.annotation.io.assignment: Pairs an ObjectMask in one set with an ObjectMask in another, if deemed to overlap sufficiently.
OverlappingObjects() - Constructor for class org.anchoranalysis.annotation.io.assignment.OverlappingObjects
OverlapRelative - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap: Expresses the number of intersecting pixels between two objects as a ratio to a denominator.
OverlapRelative() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.OverlapRelative
OverlapRelativeToFirst - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap: Calculates the overlap ratio between two objects relative to the size of the first object.
OverlapRelativeToFirst() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.OverlapRelativeToFirst
OverlapRelativeToMaxVolume - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap: Overlap ratio to the maximum number of pixels
OverlapRelativeToMaxVolume() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.OverlapRelativeToMaxVolume
OverlapRelativeToMerged - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap: Calculates the overlap ratio between two objects relative to the size of the merged object.
OverlapRelativeToMerged() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.OverlapRelativeToMerged
OverlapRelativeToSecond - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap: Calculates the overlap ratio between two objects relative to the size of the second object.
OverlapRelativeToSecond() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.OverlapRelativeToSecond
OverlapUtilities - Class in org.anchoranalysis.mpp.overlap: Utility class for calculating overlap between voxelized marks.
overlapWith(VoxelizedMarkMemo, VoxelizedMarkMemo, int) - Static method in class org.anchoranalysis.mpp.overlap.OverlapUtilities: Calculates the overlap between two voxelized marks for a specific region.
overlapWithMaskGlobal(VoxelizedMarkMemo, VoxelizedMarkMemo, int, Voxels<UnsignedByteBuffer>, byte) - Static method in class org.anchoranalysis.mpp.overlap.OverlapUtilities: Counts the number of overlapping voxels between two VoxelizedMarkMemo objects, considering a global mask.
Overlay - Class in org.anchoranalysis.image.bean.spatial.arrange.overlay: Overlays one image on the other.
Overlay - Class in org.anchoranalysis.overlay: An entity that will eventually be drawn on top of an image.
Overlay() - Constructor for class org.anchoranalysis.image.bean.spatial.arrange.overlay.Overlay
Overlay() - Constructor for class org.anchoranalysis.overlay.Overlay
Overlay(String, String, String) - Constructor for class org.anchoranalysis.image.bean.spatial.arrange.overlay.Overlay: Creates with alignment text for each axis.
Overlay(Align) - Constructor for class org.anchoranalysis.image.bean.spatial.arrange.overlay.Overlay: Creates a new Overlay instance.
OverlayCollection - Class in org.anchoranalysis.overlay.collection: A collection of Overlay objects.
OverlayCollection() - Constructor for class org.anchoranalysis.overlay.collection.OverlayCollection: Creates an empty collection.
OverlayCollection(Stream<Overlay>) - Constructor for class org.anchoranalysis.overlay.collection.OverlayCollection: Creates the collection from a stream of Overlays.
OverlayCollectionMarkFactory - Class in org.anchoranalysis.mpp.overlay: Factory for creating OverlayCollections from marks and retrieving marks from OverlayCollections.
OverlayMark - Class in org.anchoranalysis.mpp.overlay: An implementation of Overlay that draws a Mark on an image.
OverlayMark(Mark, RegionMembershipWithFlags) - Constructor for class org.anchoranalysis.mpp.overlay.OverlayMark: Creates a new OverlayMark instance.
OverlayObjectMask - Class in org.anchoranalysis.overlay.object: An implementation of Overlay that draws an ObjectMask on an image.
OverlayObjectMask(ObjectMask, int) - Constructor for class org.anchoranalysis.overlay.object.OverlayObjectMask: Creates with a particular ObjectMask and identifier.

P

Padding - Class in org.anchoranalysis.image.bean.spatial: Padding (whitespace of certain extent) placed around an object in XY direction and in Z direction.
Padding() - Constructor for class org.anchoranalysis.image.bean.spatial.Padding
paired(boolean) - Method in interface org.anchoranalysis.annotation.io.assignment.Assignment: The items that are paired for a particular set.
paired(boolean) - Method in class org.anchoranalysis.annotation.io.assignment.ObjectVoxelIntersection
paired(boolean) - Method in class org.anchoranalysis.annotation.io.assignment.OverlappingObjects
PairedWithMask - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shared: Evaluates the object as a pair-feature together with the binary-mask from the shared objects.
PairedWithMask() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.PairedWithMask
PairNeighbors - Class in org.anchoranalysis.plugin.image.feature.bean.object.combine: Creates a set of features, that creates pairs of neighboring-objects and applies a mixture of single-object features and pair features.
PairNeighbors() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
PairsTableCalculator - Class in org.anchoranalysis.image.feature.calculator.merged: A feature-session to evaluate pairs of objects.
PairsTableCalculator(MergedPairsFeatures) - Constructor for class org.anchoranalysis.image.feature.calculator.merged.PairsTableCalculator: Constructs a PairsTableCalculator with default inclusion and error suppression.
PairsTableCalculator(MergedPairsFeatures, MergedPairsInclude, boolean) - Constructor for class org.anchoranalysis.image.feature.calculator.merged.PairsTableCalculator
PairVoxelizedMarkMemo - Class in org.anchoranalysis.mpp.pair: Represents a pair of VoxelizedMarkMemo objects, with a defined source and destination.
PairVoxelizedMarkMemo(VoxelizedMarkMemo, VoxelizedMarkMemo) - Constructor for class org.anchoranalysis.mpp.pair.PairVoxelizedMarkMemo: Constructs a new PairVoxelizedMarkMemo.
ParallelProcessor<T,S> - Class in org.anchoranalysis.experiment.bean.processor: Executes jobs in parallel across cores on the system.
ParallelProcessor() - Constructor for class org.anchoranalysis.experiment.bean.processor.ParallelProcessor
ParametersExperiment - Class in org.anchoranalysis.experiment.task: Parameters for executing a task, when the log etc. are still bound to the experiment.
ParametersExperiment(ExecutionArguments, String, OutputterChecked, PathPrefixer, ExperimentFeedbackContext) - Constructor for class org.anchoranalysis.experiment.task.ParametersExperiment: Creates with initialization arguments.
parametersOnly() - Static method in class org.anchoranalysis.feature.store.NamedFeatureStoreFactory: The custom-names of the features are derived only from their parameters, but not their name.
ParametersUnbound<T,S> - Class in org.anchoranalysis.experiment.task
ParametersUnbound(ParametersExperiment, T, S, boolean) - Constructor for class org.anchoranalysis.experiment.task.ParametersUnbound
ParamFromCollection<T> - Class in org.anchoranalysis.plugin.image.feature.bean.shared: Retrieves a parameter as stored in a Dictionary in SharedObjects.
ParamFromCollection() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.shared.ParamFromCollection
parse(File) - Static method in class org.anchoranalysis.core.serialize.XMLParser: Parses a XML file to produce a Document.
parse(String) - Static method in class org.anchoranalysis.core.index.range.IndexRangeNegativeFactory: Parses a string to convert it into an IndexRangeNegative.
parseAndRun(String[], LauncherConfig) - Method in class org.anchoranalysis.launcher.run.ParseArgumentsAndRunExperiment: Parses the arguments to a command-line experiment and runs an experiment.
ParseArgumentsAndRunExperiment - Class in org.anchoranalysis.launcher.run: Parses command-line arguments and runs an experiment.
ParseArgumentsAndRunExperiment(Logger) - Constructor for class org.anchoranalysis.launcher.run.ParseArgumentsAndRunExperiment: Creates a new ParseArgumentsAndRunExperiment instance.
ParsedFilePathBag - Class in org.anchoranalysis.plugin.io.multifile: A collection of FileDetails objects with methods to query their properties.
ParsedFilePathBag() - Constructor for class org.anchoranalysis.plugin.io.multifile.ParsedFilePathBag
parsePath(Path) - Method in class org.anchoranalysis.plugin.io.bean.file.group.parser.FilePathParser
parsePath(Path) - Method in class org.anchoranalysis.plugin.io.bean.file.group.parser.RegularExpression
path(boolean) - Method in class org.anchoranalysis.plugin.io.bean.file.path.FilePath
path(boolean) - Method in class org.anchoranalysis.plugin.io.bean.file.path.RootedFilePath
path(boolean) - Method in class org.anchoranalysis.plugin.io.bean.file.path.StaticFilePath
PATH_RESOURCES - Static variable in class org.anchoranalysis.test.TestLoader: Path to the resources directory, relative to the root of the project.
pathCreator() - Method in class org.anchoranalysis.io.output.outputter.directory.OutputterTarget: Creates the path into which output is written.
PathCreator - Interface in org.anchoranalysis.io.output.path.prefixer: Converts file-paths between relative and absolute.
PathDifference - Class in org.anchoranalysis.core.system.path: Calculates the "difference" between a path and a base.
PathDifferenceException - Exception Class in org.anchoranalysis.core.system.path: When an error occurs calculating the difference between two file-paths.
PathDifferenceException(String) - Constructor for exception class org.anchoranalysis.core.system.path.PathDifferenceException: Creates with only a message.
PathDifferenceException(String, Exception) - Constructor for exception class org.anchoranalysis.core.system.path.PathDifferenceException: Creates with message and cause.
pathFor(ProvidesStackInput) - Method in class org.anchoranalysis.annotation.io.bean.AnnotatorStrategy: The path to where an annotation file for a particular input would be located.
pathFor(ProvidesStackInput) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.SinglePathStrategy
pathForBinding() - Method in class org.anchoranalysis.io.input.file.SingleFileInputBase
pathForBinding() - Method in interface org.anchoranalysis.io.input.InputFromManager: A path to a file from which this input originated.
pathForBinding() - Method in class org.anchoranalysis.io.input.InputFromManagerDelegate
pathForBinding() - Method in class org.anchoranalysis.mpp.io.input.MultiInput
pathForBinding() - Method in class org.anchoranalysis.mpp.io.input.StackWithMap: Gets the path for binding.
pathForBindingRequired() - Method in interface org.anchoranalysis.io.input.InputFromManager: Like InputFromManager.pathForBinding() but throws an exception if a path isn't present.
pathFromArgument(String) - Static method in class org.anchoranalysis.launcher.executor.selectparam.path.convert.ArgumentConverter: Converts the string passed as a command-line argument to a path.
pathFromBean(AnchorBean<?>, String) - Static method in class org.anchoranalysis.bean.xml.factory.BeanPathCalculator: Calculates a path from the current bean.
PathFromGenerator - Class in org.anchoranalysis.plugin.annotation.bean.strategy: Utility class for deriving paths from a generator.
pathMavenWorkingDirectory(String) - Static method in class org.anchoranalysis.test.TestLoader: Determines the path to a directory inside the Maven Working Directory.
PathOperations - Class in org.anchoranalysis.plugin.io.file.copy: Helper routines for performing operations on Paths.
pathOrDirectory(String[], boolean) - Static method in class org.anchoranalysis.launcher.executor.selectparam.path.OutputFactory: Creates a SelectParam for output paths or directories.
pathOrDirectoryOrGlobOrExtension(String[]) - Static method in class org.anchoranalysis.launcher.executor.selectparam.path.InputFactory: Creates a SelectParam for path, directory, glob, or file extension inputs.
pathOrTaskName(String[], Path) - Static method in class org.anchoranalysis.launcher.executor.selectparam.path.TaskFactory: Creates a SelectParam for a path or task name.
pathOrTaskNameOrDefault(CommandLine, String, Path) - Static method in class org.anchoranalysis.launcher.executor.selectparam.SelectParamFactory: Creates a SelectParam for a path, task name, or default.
PathPrefixer - Class in org.anchoranalysis.io.output.bean.path.prefixer: Base classes for methods to determine an output directory and associated file prefix.
PathPrefixer() - Constructor for class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixer
PathPrefixerAvoidResolve - Class in org.anchoranalysis.io.output.bean.path.prefixer: A file-path-resolver that adds additional methods that perform the same function but output a relative-path rather than an absolute path after fully resolving paths
PathPrefixerAvoidResolve() - Constructor for class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixerAvoidResolve
PathPrefixerAvoidResolve(String) - Constructor for class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixerAvoidResolve: Creates with a prefix.
PathPrefixerContext - Class in org.anchoranalysis.io.output.path.prefixer: Context parameters provided to a link PathPrefixer.
PathPrefixerContext() - Constructor for class org.anchoranalysis.io.output.path.prefixer.PathPrefixerContext: Create with default parameters.
PathPrefixerContext(boolean, OutputPrefixerSettings) - Constructor for class org.anchoranalysis.io.output.path.prefixer.PathPrefixerContext: Create with specific parameters.
PathPrefixerException - Exception Class in org.anchoranalysis.io.output.path.prefixer: Thrown when unable to successfully determine a prefix for a path.
PathPrefixerException(String) - Constructor for exception class org.anchoranalysis.io.output.path.prefixer.PathPrefixerException: Creates from a message only.
PathPrefixerException(Throwable) - Constructor for exception class org.anchoranalysis.io.output.path.prefixer.PathPrefixerException: Creates from a cause only.
PathRegEx - Class in org.anchoranalysis.plugin.io.bean.file.path.prefixer: Matches a regex against incoming file-paths to form a prefix for output
PathRegEx() - Constructor for class org.anchoranalysis.plugin.io.bean.file.path.prefixer.PathRegEx
pathRelativeProperties() - Method in class org.anchoranalysis.launcher.config.LauncherConfig: Provides the path to a property file that defines a relative-path to the default experiment in bean XML.
PathSupplier - Interface in org.anchoranalysis.io.input.path: Utility interface to supply a Path or throw a DerivePathException.
pattern() - Method in enum class org.anchoranalysis.plugin.io.naming.interval.DateStyle: Derives a pattern for the formatter for the particular date-style.
PatternSpan - Class in org.anchoranalysis.plugin.io.bean.file.namer.patternspan: Finds a pattern in the file-path, and uses a portion of the file-path in that pattern to form the name.
PatternSpan() - Constructor for class org.anchoranalysis.plugin.io.bean.file.namer.patternspan.PatternSpan
patternWithDate(DateStyle) - Method in enum class org.anchoranalysis.plugin.io.naming.interval.TimeStyle: Derives a formatter for the particular date AND time-style.
PayloadCalculator - Interface in org.anchoranalysis.plugin.image.object.merge: Calculates a payload value for an ObjectMask.
peek() - Method in class org.anchoranalysis.image.inference.bean.reduce.ReduceObjectsGraph: The element at the top of the queue, returned without modifying the queue.
percentLeftAssigned() - Method in class org.anchoranalysis.annotation.io.assignment.OverlappingObjects: The percentage of objects in the left set that have been paired.
percentRightAssigned() - Method in class org.anchoranalysis.annotation.io.assignment.OverlappingObjects: The percentage of objects in the right set that have been paired.
performBinaryOperation(int, int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.AddConstant
performBinaryOperation(int, int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.ArithmeticWithConstantBase: The binary arithmetic operation that combines the voxel-value and the constant-value.
performBinaryOperation(int, int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.MultiplyConstant
performBinaryOperation(int, int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.SubtractFromConstant
performInference(OnnxTensor, String, List<String>, CheckedFunction<List<OnnxTensor>, S, OperationFailedException>) - Method in class org.anchoranalysis.plugin.onnx.model.OnnxModel
performInference(Mat, String, List<String>, CheckedFunction<List<Mat>, S, OperationFailedException>) - Method in class org.anchoranalysis.plugin.opencv.segment.OpenCVModel
performInference(T, String, List<String>, CheckedFunction<List<T>, S, OperationFailedException>) - Method in interface org.anchoranalysis.image.inference.ImageInferenceModel: Performs inference on a single-input, to create an output.
performTest(VoxelDataType[], int, boolean, Optional<VoxelDataType>, Optional<ImageComparer>) - Method in class org.anchoranalysis.test.image.stackwriter.StackTester: Performs a test on stack writing for specified channel types, number of channels, RGB setting, and optional forced first channel type.
performTest(VoxelDataType[], int, boolean, Optional<ImageComparer>) - Method in class org.anchoranalysis.test.image.stackwriter.StackTester: Performs a test on stack writing for specified channel types, number of channels, and RGB setting.
performTest(ChannelSpecification, Optional<VoxelDataType>, Optional<ImageComparer>) - Method in class org.anchoranalysis.test.image.stackwriter.StackTester: Performs a test on stack writing for a specified channel specification and optional forced first channel type.
performTest(ChannelSpecification, Optional<ImageComparer>) - Method in class org.anchoranalysis.test.image.stackwriter.StackTester: Performs a test on stack writing for a specified channel specification.
permissive() - Method in class org.anchoranalysis.io.output.recorded.RecordingWriters: A writer that allows all output-names, and records the written output-names.
Permissive - Class in org.anchoranalysis.io.output.bean.rules: Allows all output-names to be outputted in both first and second level.
Permissive() - Constructor for class org.anchoranalysis.io.output.bean.rules.Permissive
PermissiveExcept - Class in org.anchoranalysis.io.output.bean.rules: All outputs are enabled except particular ones.
PermissiveExcept() - Constructor for class org.anchoranalysis.io.output.bean.rules.PermissiveExcept
PermissiveExcept(StringSet) - Constructor for class org.anchoranalysis.io.output.bean.rules.PermissiveExcept: Create with first-level output names
PermutationAssigner - Interface in org.anchoranalysis.bean.permute.assign: Imposes a permutation on some property of a bean.
PermutationAssignerFactory - Class in org.anchoranalysis.bean.permute.assign: Creates instances of PermutationAssigner.
Permute - Class in org.anchoranalysis.plugin.image.bean.object.provider: Permutes some changes over an ObjectCollectionProvider and collects all the results in an ObjectCollection
Permute() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.Permute
PermutedCopyCreator<T> - Class in org.anchoranalysis.bean.permute: Applies a PermuteProperty to a bean to create new duplicated beans each with different permuted values.
PermutedCopyCreator(Function<T, String>, BiConsumer<T, String>) - Constructor for class org.anchoranalysis.bean.permute.PermutedCopyCreator: Creates a new PermutedCopyCreator instance.
PermuteDivideByParam<T> - Class in org.anchoranalysis.plugin.image.feature.bean.list.permute: Similar to FeatureListProviderPermute but embeds the feature in a GaussianScore
PermuteDivideByParam() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteDivideByParam
PermuteFeature<S,T> - Class in org.anchoranalysis.plugin.image.feature.bean.list.permute: Permutes one or more properties of a Feature, so as to create a set of Features
PermuteFeature() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeature
PermuteFeatureBase<T> - Class in org.anchoranalysis.plugin.image.feature.bean.list.permute: Creates permutations of a feature by modifying a particular property of it in different ways.
PermuteFeatureBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureBase
PermuteFeatureSequenceInteger<T> - Class in org.anchoranalysis.plugin.image.feature.bean.list.permute: Permutes a property on a feature with a sequence of integers.
PermuteFeatureSequenceInteger() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureSequenceInteger
PermuteFirstSecondOrder<T> - Class in org.anchoranalysis.plugin.image.feature.bean.list.permute: Permutes a feature by applying first and second order statistical operations.
PermuteFirstSecondOrder(PermuteFirstSecondOrder.CreateFirstSecondOrder<T>, double, double) - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFirstSecondOrder: Creates a new PermuteFirstSecondOrder instance.
PermuteFirstSecondOrder.CreateFirstSecondOrder<T> - Interface in org.anchoranalysis.plugin.image.feature.bean.list.permute: Functional interface for creating first and second order statistical operations.
PermuteGaussianScore<T> - Class in org.anchoranalysis.plugin.image.feature.bean.list.permute: Permutes a feature by embedding it in a GaussianCumulative score.
PermuteGaussianScore() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteGaussianScore: Creates a new instance of PermuteGaussianScore.
PermuteProperty<T> - Class in org.anchoranalysis.bean.permute.property: Changes properties of an AnchorBean to one of a range of possible values.
PermuteProperty() - Constructor for class org.anchoranalysis.bean.permute.property.PermuteProperty
PermutePropertyDoubleSet - Class in org.anchoranalysis.bean.permute.property: Assigns each element from a set of doubles to a particular property of a bean.
PermutePropertyDoubleSet() - Constructor for class org.anchoranalysis.bean.permute.property.PermutePropertyDoubleSet
PermutePropertySequence<T> - Class in org.anchoranalysis.bean.permute.property: Base class for assigning a sequence of numbers to a particular property of a bean.
PermutePropertySequence() - Constructor for class org.anchoranalysis.bean.permute.property.PermutePropertySequence
PermutePropertySequenceDouble - Class in org.anchoranalysis.bean.permute.property: Assigns an arithmetic sequence of doubles, derived by diving an integer sequence by a divider.
PermutePropertySequenceDouble() - Constructor for class org.anchoranalysis.bean.permute.property.PermutePropertySequenceDouble
PermutePropertySequenceInteger - Class in org.anchoranalysis.bean.permute.property: An arithmetic sequence of integers, each directly assigned to a property during permutation.
PermutePropertySequenceInteger() - Constructor for class org.anchoranalysis.bean.permute.property.PermutePropertySequenceInteger
PermutePropertyStringSet - Class in org.anchoranalysis.bean.permute.property: Assigns each element from a set of strings to a particular property of a bean.
PermutePropertyStringSet() - Constructor for class org.anchoranalysis.bean.permute.property.PermutePropertyStringSet
PermuteZScore<T> - Class in org.anchoranalysis.plugin.image.feature.bean.list.permute: Permutes a feature by embedding it in a ZScore.
PermuteZScore() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteZScore: Creates a new instance of PermuteZScore.
pluralize(String) - Static method in class org.anchoranalysis.core.value.LanguageUtilities: Given something, returns somethings.
pluralizeMaybe(long, String) - Static method in class org.anchoranalysis.core.value.LanguageUtilities: Returns something or somethings depending on the number.
PNG - Class in org.anchoranalysis.io.imagej.bean.stack.writer: Writes a PNG image using ImageJ.
PNG - Class in org.anchoranalysis.plugin.io.bean.metadata.header: The headers found in a PNG file.
PNG - Enum constant in enum class org.anchoranalysis.core.format.ImageFileFormat: PNG
PNG() - Constructor for class org.anchoranalysis.io.imagej.bean.stack.writer.PNG
PNG() - Constructor for class org.anchoranalysis.plugin.io.bean.metadata.header.PNG
PNGTestBase - Class in org.anchoranalysis.test.image.stackwriter: For testing all StackWriters that create PNGs.
PNGTestBase() - Constructor for class org.anchoranalysis.test.image.stackwriter.PNGTestBase
point(ReadableTuple3i) - Method in class org.anchoranalysis.spatial.box.BoundingBoxContains: Is this point within the bounding-box?
Point2d - Class in org.anchoranalysis.spatial.point: A two-dimensional point of double values.
Point2d() - Constructor for class org.anchoranalysis.spatial.point.Point2d
Point2d(double, double) - Constructor for class org.anchoranalysis.spatial.point.Point2d: Creates a new Point2d instance.
Point2d(Point2d) - Constructor for class org.anchoranalysis.spatial.point.Point2d: Creates with the same values as an existing Point2d.
Point2f - Class in org.anchoranalysis.spatial.point: A two-dimensional point of float values.
Point2f() - Constructor for class org.anchoranalysis.spatial.point.Point2f
Point2f(float, float) - Constructor for class org.anchoranalysis.spatial.point.Point2f: Creates a new Point2f instance.
Point2i - Class in org.anchoranalysis.spatial.point: A two-dimensional point of int values.
Point2i() - Constructor for class org.anchoranalysis.spatial.point.Point2i
Point2i(int, int) - Constructor for class org.anchoranalysis.spatial.point.Point2i: Creates a new Point2i instance.
Point2i(Point2i) - Constructor for class org.anchoranalysis.spatial.point.Point2i: Creates with the same values as an existing Point2i.
Point3d - Class in org.anchoranalysis.spatial.point: A three-dimensional point of double values.
Point3d() - Constructor for class org.anchoranalysis.spatial.point.Point3d
Point3d(double, double, double) - Constructor for class org.anchoranalysis.spatial.point.Point3d: Create with values for each dimension.
Point3d(Point3f) - Constructor for class org.anchoranalysis.spatial.point.Point3d: Creates with the same values as an existing Point3d.
Point3d(Tuple3d) - Constructor for class org.anchoranalysis.spatial.point.Point3d: Creates with the same values as an existing Tuple3d.
Point3f - Class in org.anchoranalysis.spatial.point: A three-dimensional point of float values.
Point3f() - Constructor for class org.anchoranalysis.spatial.point.Point3f: Creates the points with a 0 in each dimension.
Point3f(float, float, float) - Constructor for class org.anchoranalysis.spatial.point.Point3f: Create with values for each dimension.
Point3f(Point3f) - Constructor for class org.anchoranalysis.spatial.point.Point3f: Creates with the same values as an existing Point3f.
Point3i - Class in org.anchoranalysis.spatial.point: A three-dimensional point of int values.
Point3i() - Constructor for class org.anchoranalysis.spatial.point.Point3i: Creates the points with a 0 in each dimension.
Point3i(int) - Constructor for class org.anchoranalysis.spatial.point.Point3i: Create with an identical value in each dimension.
Point3i(int, int, int) - Constructor for class org.anchoranalysis.spatial.point.Point3i: Create with values for each dimension.
Point3i(ReadableTuple3i) - Constructor for class org.anchoranalysis.spatial.point.Point3i: Creates with the same values as an existing ReadableTuple3i.
PointClamper - Class in org.anchoranalysis.mpp.mark: Utility class to ensure a point has values contained inside image-dimensions.
PointConverter - Class in org.anchoranalysis.spatial.point: Conversion utilities between points with different types and dimensionalities.
pointIgnoreZ(Point3i) - Method in class org.anchoranalysis.spatial.box.BoundingBoxContains: Like BoundingBoxContains.point(ReadableTuple3i) but ignores the z-dimension.
PointList - Class in org.anchoranalysis.mpp.mark.points: A a list of 3D points.
PointList() - Constructor for class org.anchoranalysis.mpp.mark.points.PointList: Constructs an empty PointList.
PointList(Stream<Point3d>) - Constructor for class org.anchoranalysis.mpp.mark.points.PointList: Constructs a PointList from a stream of Point3d objects.
pointListAtFirstPoint(List<Point3i>) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels: Sets all points in a list to point at the first point (the root point) in the list.
PointListBase - Class in org.anchoranalysis.mpp.mark.points: A base class for marks that consist of a list of 3D points.
PointListBase() - Constructor for class org.anchoranalysis.mpp.mark.points.PointListBase: Constructs an empty PointListBase.
PointListBase(Stream<Point3d>) - Constructor for class org.anchoranalysis.mpp.mark.points.PointListBase: Constructs a PointListBase from a stream of Point3d objects.
PointListFactory - Class in org.anchoranalysis.mpp.mark.points: A factory for creating PointList objects from various types of point collections.
PointRange - Class in org.anchoranalysis.spatial.box: Tracks the range experienced by points in the X, Y and Z dimensions.
PointRange() - Constructor for class org.anchoranalysis.spatial.box.PointRange
points() - Method in class org.anchoranalysis.mpp.init.MarksInitialization: The points initialization associated with this marks initialization.
PointsBean<T> - Class in org.anchoranalysis.mpp.bean.points: An abstract base class for beans that work with points and require initialization.
PointsBean() - Constructor for class org.anchoranalysis.mpp.bean.points.PointsBean: Constructs a new PointsBean.
pointsDiscrete() - Method in class org.anchoranalysis.spatial.point.Contour: All the points in the contour, converted into Point3i.
PointsFitter - Class in org.anchoranalysis.mpp.bean.points.fitter: Abstract base class for fitting a mark (e.g., an ellipsoid) to a set of points.
PointsFitter() - Constructor for class org.anchoranalysis.mpp.bean.points.fitter.PointsFitter
PointsFitterException - Exception Class in org.anchoranalysis.mpp.bean.points.fitter: Exception thrown when an error occurs during the point fitting process.
PointsFitterException(Exception) - Constructor for exception class org.anchoranalysis.mpp.bean.points.fitter.PointsFitterException: Constructs a new PointsFitterException with the specified cause.
PointsFitterException(String) - Constructor for exception class org.anchoranalysis.mpp.bean.points.fitter.PointsFitterException: Constructs a new PointsFitterException with the specified detail message.
PointsFitterToMark - Class in org.anchoranalysis.plugin.points.bean.fitter: A bean for fitting points to a mark using a specified points fitter.
PointsFitterToMark() - Constructor for class org.anchoranalysis.plugin.points.bean.fitter.PointsFitterToMark
PointsFromMask - Class in org.anchoranalysis.image.core.points: Extracts list of points from a Mask.
PointsFromObject - Class in org.anchoranalysis.image.core.points: Derives collections of points from an ObjectMask or its contour.
PointsFromObjects - Class in org.anchoranalysis.plugin.mpp.bean.provider.collection: Creates a MarkCollection of point marks from an ObjectCollection.
PointsFromObjects() - Constructor for class org.anchoranalysis.plugin.mpp.bean.provider.collection.PointsFromObjects
PointsInitialization - Class in org.anchoranalysis.mpp.init: Initialization class for points-related components in the MPP framework.
PointsNeighborChecker - Class in org.anchoranalysis.spatial.point: Checks if two or more points fulfill certain neighbor relations to each other.
pointsOnAllOutlines(ObjectCollection) - Static method in class org.anchoranalysis.plugin.points.convexhull.ConvexHullUtilities: Get points on all outlines of a collection of objects.
pointsOnOutline(ObjectMask) - Static method in class org.anchoranalysis.plugin.points.convexhull.ConvexHullUtilities: Get points on the outline of a single object.
PointsProposer - Class in org.anchoranalysis.mpp.bean.proposer: An abstract base class for proposing a list of points based on a given point and mark.
PointsProposer() - Constructor for class org.anchoranalysis.mpp.bean.proposer.PointsProposer
PointTwoDimensionalConsumer - Interface in org.anchoranalysis.spatial.point.consumer: Like a IntConsumer but accepts two coordinates of a point as scalar arguments.
poll() - Method in class org.anchoranalysis.image.inference.bean.reduce.ReduceObjectsGraph: The element at the top of the queue, returned removing it from the queue and graph.
Polygon - Class in org.anchoranalysis.mpp.mark.points: Represents a polygon in 2D space as a Mark.
Polygon() - Constructor for class org.anchoranalysis.mpp.mark.points.Polygon
PolygonCurve - Class in org.anchoranalysis.mpp.mark.points: Represents a polygon curve in 3D space as a Mark.
PolygonCurve() - Constructor for class org.anchoranalysis.mpp.mark.points.PolygonCurve
populate(List<NamedBean<FeatureListProvider<FeatureInput>>>, Logger) - Method in class org.anchoranalysis.feature.initialization.FeatureRelatedInitialization: Adds features into the shared-feature storage from a list of named-beans.
populate(BeanInitializer<?>, Define, Logger) - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitialization: Adds diverse entities from a Define into the corresponding name-collections.
populate(BeanInitializer<?>, Define, Logger) - Method in class org.anchoranalysis.mpp.init.MarksInitialization: Populates the stores with beans from the given Define.
populate(BeanInitializer<?>, Define, Logger) - Method in class org.anchoranalysis.mpp.init.PointsInitialization: Populates the stores with beans from the given Define.
populateFrom(Path) - Method in class org.anchoranalysis.plugin.io.bean.metadata.header.HeaderFormat: Creates a ImageMetadata, if possible, from the metadata at path.
populateFrom(Stack, Optional<Integer>, Optional<Integer>, Optional<Integer>) - Method in class org.anchoranalysis.plugin.io.multifile.buffer.MultiBufferSized
populateFromList(List<LabelledWithConfidence<ObjectMask>>) - Static method in class org.anchoranalysis.image.inference.bean.reduce.ObjectForReductionFactory: Creates a list of ObjectForReductions from a corresponding list of labelled ObjectMasks.
populateFromMetadata(Metadata, ImageFileAttributes) - Method in class org.anchoranalysis.plugin.io.bean.metadata.header.BMP
populateFromMetadata(Metadata, ImageFileAttributes) - Method in class org.anchoranalysis.plugin.io.bean.metadata.header.HeaderFormat: Creates a ImageMetadata, if possible, from metadata.
populateFromMetadata(Metadata, ImageFileAttributes) - Method in class org.anchoranalysis.plugin.io.bean.metadata.header.JPEG
populateFromMetadata(Metadata, ImageFileAttributes) - Method in class org.anchoranalysis.plugin.io.bean.metadata.header.PNG
populateMissingFromArbitrarySlice(Stack) - Method in class org.anchoranalysis.plugin.io.multifile.SizeExtents
PopulateStoreFromDefine<V> - Class in org.anchoranalysis.image.bean.nonbean.init: Helps populates a NamedProviderStore from the contents of a Define.
PopulateStoreFromDefine(Define, BeanInitializer<?>, Logger) - Constructor for class org.anchoranalysis.image.bean.nonbean.init.PopulateStoreFromDefine: Creates a new PopulateStoreFromDefine instance.
position() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer: The position of the buffer ala Buffer.position.
position(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer: Assigns a new position to the buffer.
position(int) - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer: Assigns a new position to the buffer.
position(int) - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferUnsigned
PositionChoices - Class in org.anchoranalysis.image.bean.nonbean.spatial.align: The choices of text that may describe the position of an entity along a particular axis.
PositionChoices(String, String, String) - Constructor for class org.anchoranalysis.image.bean.nonbean.spatial.align.PositionChoices: Creates a new PositionChoices instance.
PositionChoices(String, String, String, Optional<String>) - Constructor for class org.anchoranalysis.image.bean.nonbean.spatial.align.PositionChoices: Creates a new PositionChoices instance.
PositionChoicesConstants - Class in org.anchoranalysis.image.bean.nonbean.spatial.align: A constant set of text strings used to indicate particular choices.
PositionProposer - Class in org.anchoranalysis.mpp.bean.proposer: An abstract base class for proposing positions.
PositionProposer() - Constructor for class org.anchoranalysis.mpp.bean.proposer.PositionProposer
positionString() - Method in class org.anchoranalysis.mpp.mark.MarkWithPosition: Describes the position of the mark as a string.
Positive - Annotation Interface in org.anchoranalysis.bean.annotation: The bean-field should have a value > 0.
precondition() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.MorphologicalOperatorBase: Creates a precondition for the morphological operation based on intensity values.
precondition(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.collective.DiscardOutliers
precondition(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.GreaterIntersectionWith
precondition(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntensityGreaterEqualThan
precondition(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntersectsWith
precondition(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.NotTouchingSceneBorder
precondition(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterPredicate: A precondition, which if evaluates to false, cancels the filter i.e. nothing is removed.
precondition(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterRelation
PredefinedTasks - Class in org.anchoranalysis.launcher.run.tasks: Loading and printing predefined-tasks.
predicate(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfKeyValueCondition
predicate(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfNotEmpty
predicate(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfObjectFilter
predicate(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfPredicateBase: Evaluates a predicate condition on the input mask.
predicate(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfStackExists
PredicateAtCorner - Class in org.anchoranalysis.image.voxel.extracter.predicate: Projects a VoxelsPredicate to a corner in a larger global space
PredicateAtCorner(ReadableTuple3i, VoxelsPredicate) - Constructor for class org.anchoranalysis.image.voxel.extracter.predicate.PredicateAtCorner: Creates a new PredicateAtCorner instance.
PredicateBufferBinary<T> - Interface in org.anchoranalysis.image.voxel.iterator.predicate: Like ProcessBufferBinary but returns a boolean.
PredicateImplementation<T> - Class in org.anchoranalysis.image.voxel.extracter.predicate: Implementation of VoxelsPredicate for a particular Voxels.
PredicateImplementation(Voxels<T>, Predicate<T>) - Constructor for class org.anchoranalysis.image.voxel.extracter.predicate.PredicateImplementation: Creates a new PredicateImplementation instance.
PredicateKernelPointCursor - Interface in org.anchoranalysis.image.voxel.iterator.predicate: Processes a KernelPointCursor and evaluates a predicate on the current position.
PredicateTwoBytes - Interface in org.anchoranalysis.image.voxel.iterator.predicate: Like Predicate but takes two bytes as argument.
prefer(Class<? extends FeatureInput>, Class<? extends FeatureInput>) - Static method in class org.anchoranalysis.feature.input.FeatureInputType: Prefer to keep descriptor whose input-class is a sub-class rather than a super-class.
prefer(Feature<?>, Feature<?>) - Static method in class org.anchoranalysis.feature.input.FeatureInputType: Like FeatureInputType.prefer(Class, Class) but accepts features directly as input.
prefixPluralize(long, String) - Static method in class org.anchoranalysis.core.value.LanguageUtilities: Returns n somethings.
prefixPluralizeMaybe(long, String) - Static method in class org.anchoranalysis.core.value.LanguageUtilities: Returns 1 something or n somethings as is appropriate.
prefixWithDelimeter() - Method in class org.anchoranalysis.io.output.path.prefixer.DirectoryWithPrefix: The prefix concatenated with the delimeter.
Prepend - Class in org.anchoranalysis.bean.shared.color.scheme: Prepends a specific color to the list created by another ColorScheme.
Prepend() - Constructor for class org.anchoranalysis.bean.shared.color.scheme.Prepend
PrependName - Class in org.anchoranalysis.feature.bean.list: Prepends a string to the custom-name of each feature in a list.
PrependName() - Constructor for class org.anchoranalysis.feature.bean.list.PrependName
PreserveName - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming: Copies files to maintain the same relative-path from the destination file to the destination-directory, as existed from the source file to the source-directory.
PreserveName() - Constructor for class org.anchoranalysis.plugin.io.bean.file.copy.naming.PreserveName
prettyPath(String) - Static method in class org.anchoranalysis.launcher.executor.selectparam.path.convert.PrettyPathConverter: Converts a string path to either a normalized absolute-path or relative-path depending on which is prettier to the user.
prettyPath(Path) - Static method in class org.anchoranalysis.launcher.executor.selectparam.path.convert.PrettyPathConverter: Converts a Path to either a normalized absolute-path or relative-path depending on which is prettier to the user.
PrettyPathConverter - Class in org.anchoranalysis.launcher.executor.selectparam.path.convert: Utility class for converting paths to a more user-friendly representation.
previousEqualIndex(int) - Method in interface org.anchoranalysis.core.index.range.IndexRangeSeek: Finds the previous index in the range before index, or returns index itself if it's a valid index.
previousIndex(int) - Method in interface org.anchoranalysis.core.index.range.IndexRangeSeek: Finds the previous index in the range before index.
PrimitiveBeanCollection<T> - Interface in org.anchoranalysis.bean.primitive: A bean that provides a collection of primitive-types or Strings.
PrimitiveConverter - Class in org.anchoranalysis.image.voxel.buffer.primitive: Type conversion between primitive data types.
PrincipalAxisEccentricity - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.moments: Calculates the eccentricity of the Principal Axes (as defined by Image Moments).
PrincipalAxisEccentricity() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.PrincipalAxisEccentricity
PrincipalAxisLength - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.moments: The length of a principal-axis (as defined by Image Moments).
PrincipalAxisLength() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.PrincipalAxisLength
PrincipalAxisOrientation - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.moments: An element from orientation of a principal-axis (as defined by Image Moments).
PrincipalAxisOrientation() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.PrincipalAxisOrientation
printAllFilesFromTestDirectoryPath(String) - Method in class org.anchoranalysis.test.TestLoader: Prints the names of all files (recursively) in a test-folder to stdout.
printTasksToConsole(Path, Resources, PrintStream) - Static method in class org.anchoranalysis.launcher.run.tasks.PredefinedTasks: Prints names of the predefined tasks that are available to the application.
PrioritisedVertex - Class in org.anchoranalysis.plugin.image.object.merge.priority: A vertex with a priority attached, and a boolean flag as to whether it can be merged or not
PrioritisedVertex(ObjectMask, double, double, boolean) - Constructor for class org.anchoranalysis.plugin.image.object.merge.priority.PrioritisedVertex: Constructor
Prioritizer - Interface in org.anchoranalysis.plugin.image.object.merge.priority: Creates a priority between two vertices for object merging.
PriorityQueueIndexRangeDownhill<T> - Class in org.anchoranalysis.plugin.image.segment.watershed.encoding: Implements a priority queue based upon a range of values from 0 to maxValue.
PriorityQueueIndexRangeDownhill(int) - Constructor for class org.anchoranalysis.plugin.image.segment.watershed.encoding.PriorityQueueIndexRangeDownhill: Creates a new priority queue with a specified maximum value.
process(byte, byte) - Method in interface org.anchoranalysis.image.voxel.iterator.process.ProcessTwoBytes: Performs the processing.
process(InputBound<MultiInput, S>, DefineOutputter.Processor<ImageInitialization>) - Method in class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputter: Processes the input using the provided operation.
process(Channel, Channel) - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderBinary: Creates a Channel given the two entities provided by the delegates.
process(Channel, Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.TwoVoxelMappingBase
process(Channel, Channel, Channel) - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderTernary: Creates a Channel given the two entities provided by the delegates.
process(Channel, Channel, Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.MeanThreeChannels
process(VoxelBuffer<S>, VoxelBuffer<T>) - Method in interface org.anchoranalysis.image.voxel.iterator.process.voxelbuffer.ProcessVoxelBufferBinaryWithoutOffset: Processes a voxel location in a buffer
process(VoxelBuffer<S>, VoxelBuffer<T>, int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.voxelbuffer.ProcessVoxelBufferBinary: Processes a voxel location in a buffer
process(VoxelBuffer<T>, int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.voxelbuffer.ProcessVoxelBufferUnary: Processes a voxel location in a buffer.
process(KernelPointCursor) - Method in interface org.anchoranalysis.image.voxel.iterator.process.ProcessKernelPointCursor: Processes a particular point.
process(Point3i) - Method in interface org.anchoranalysis.image.voxel.iterator.process.ProcessPoint: Processes a particular point.
process(Point3i, int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.ProcessPointAndIndex: Processes a particular point.
process(Point3i, VoxelBuffer<S>, T, int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.voxelbuffer.ProcessVoxelBufferBinaryMixed: Processes a voxel location in a buffer
process(Point3i, VoxelBuffer<S>, T, int, int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.buffer.ProcessBufferBinaryMixed: Processes a voxel location in two buffers.
process(Point3i, VoxelBuffer<T>, int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.voxelbuffer.ProcessVoxelBufferUnaryWithPoint: Processes a voxel location in a buffer.
process(Point3i, S, T, int, int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.buffer.ProcessBufferBinary: Processes a voxel location in two buffers.
process(Point3i, T, int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.buffer.ProcessBufferUnary: Processes a voxel location in a buffer.
process(Point3i, T, T, T, int, int, int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.buffer.ProcessBufferTernary: Processes a voxel location in a buffer.
process(S, T) - Method in interface org.anchoranalysis.image.voxel.iterator.process.buffer.ProcessBufferBinaryWithoutOffset: Processes a voxel location in a buffer.
process(T) - Method in interface org.anchoranalysis.plugin.mpp.bean.define.DefineOutputter.Processor: Processes the initialization.
process(T, EnergyStack) - Method in interface org.anchoranalysis.plugin.mpp.bean.define.DefineOutputterWithEnergy.ProcessWithEnergyStack: Processes the initialization with an energy stack.
ProcessBufferBinary<S,T> - Interface in org.anchoranalysis.image.voxel.iterator.process.buffer: Processes a 3D point like ProcessPoint but also retrieves two Buffer for the current z-slice.
ProcessBufferBinaryMixed<S,T> - Interface in org.anchoranalysis.image.voxel.iterator.process.buffer: Processes a 3D point like ProcessPoint but also retrieves both one VoxelBuffer for the current z-slice and one Buffer for the current z-slice.
ProcessBufferBinaryWithoutOffset<S,T> - Interface in org.anchoranalysis.image.voxel.iterator.process.buffer: Processes two buffers for each z-slice jointly, without any offset or point.
ProcessBufferTernary<T> - Interface in org.anchoranalysis.image.voxel.iterator.process.buffer: Processes a 3D point like ProcessPoint but also retrieves three buffers for the current z-slice.
ProcessBufferUnary<T> - Interface in org.anchoranalysis.image.voxel.iterator.process.buffer: Processes a 3D point like ProcessPoint but also retrieves a buffer for the current z-slice.
ProcessChangedPointAbsoluteMasked<T> - Interface in org.anchoranalysis.image.voxel.iterator.neighbor: Processes a point which has been translated (changed) relative to another point - and includes global coordinates and includes an object-mask buffer.
ProcessCSVLine - Interface in org.anchoranalysis.io.input.csv: Called when a single line is read by a CSV-reader to determine how the entry is further processed.
processEachSlice(Channel, Consumer<ImageProcessor>) - Static method in class org.anchoranalysis.plugin.imagej.channel.provider.FilterHelper: Applies a Consumer to each slice independently of a Channel.
processEachSlice(BinaryVoxels<UnsignedByteBuffer>, Consumer<ImageProcessor>) - Static method in class org.anchoranalysis.plugin.imagej.channel.provider.FilterHelper: Applies a Consumer to each slice independently of a BinaryVoxels with UnsignedByteBuffer.
processElement(K, CheckedConsumer<V, OperationFailedException>) - Method in class org.anchoranalysis.core.collection.MapCreateCountdown: Runs an operation on the element, creating if necessary, without decrementing the count.
processElementDecrement(K, CheckedConsumer<V, OperationFailedException>) - Method in class org.anchoranalysis.core.collection.MapCreateCountdown: Runs an operation on the element, creating if necessary, and decrementing the count.
processIndividual(String, Channel, boolean, CheckedBiConsumer<String, Channel, OperationFailedException>, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.combine.AggregateChannelTask
processIndividual(String, Histogram, boolean, CheckedBiConsumer<String, Histogram, OperationFailedException>, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.histogram.ExportImageHistograms
processIndividual(String, S, boolean, CheckedBiConsumer<String, S, OperationFailedException>, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase: Processes each derived individual element from a Channel, calling consumeIndividual one or more times.
processInput(InitializationContext, SharedObjects, Optional<Dictionary>, DefineOutputterWithEnergy.ProcessWithEnergyStack<ImageInitialization, S>) - Method in class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputterWithEnergy: Processes the input with an energy stack and shared objects.
processInput(ExportSharedObjects, InitializationContext, DefineOutputterWithEnergy.ProcessWithEnergyStack<ImageInitialization, S>) - Method in class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputterWithEnergy: Processes the input with an energy stack.
ProcessKernelPointCursor - Interface in org.anchoranalysis.image.voxel.iterator.process: Processes a KernelPointCursor which includes a Point3i.
processLine(String[], boolean) - Method in interface org.anchoranalysis.io.input.csv.ProcessCSVLine: Called when a single line is read by a CSV-reader to determine how the entry is further processed.
processNeighborhoodPoints(boolean, ProcessVoxelNeighbor<?>) - Method in interface org.anchoranalysis.image.voxel.neighborhood.Neighborhood: Calls ProcessVoxelNeighbor for each voxel in the neighborhood of the current state of ProcessVoxelNeighbor.
processObjects(ObjectForReduction, ObjectForReduction, ReduceObjectsGraph) - Method in class org.anchoranalysis.image.inference.bean.reduce.ReduceElementsGreedy: Processes two objects.
processObjects(ObjectForReduction, ObjectForReduction, ReduceObjectsGraph) - Method in class org.anchoranalysis.image.inference.bean.reduce.RemoveOverlappingObjects
processPoint(int, int) - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighbor: Processes a particular point.
processPoint(int, int, int, int) - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsolute: Processes a particular point.
processPoint(int, int, int, int, int) - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.ProcessChangedPointAbsoluteMasked: Processes a particular point.
ProcessPoint - Interface in org.anchoranalysis.image.voxel.iterator.process: Processes a 3D point.
ProcessPointAndIndex - Interface in org.anchoranalysis.image.voxel.iterator.process: Processes a Point3i also including an index.
ProcessTwoBytes - Interface in org.anchoranalysis.image.voxel.iterator.process: Processes two bytes.
ProcessVoxelBufferBinary<S,T> - Interface in org.anchoranalysis.image.voxel.iterator.process.voxelbuffer: Processes a 3D point like ProcessPoint but also retrieves two VoxelBuffers for the current z-slice.
ProcessVoxelBufferBinaryMixed<S,T> - Interface in org.anchoranalysis.image.voxel.iterator.process.voxelbuffer: Processes a 3D point like ProcessVoxelBufferBinary but rather has one VoxelBuffer and one buffer, and also exposes a Point3i.
ProcessVoxelBufferBinaryWithoutOffset<S,T> - Interface in org.anchoranalysis.image.voxel.iterator.process.voxelbuffer: Processes two voxel-buffers for each z-slice jointly, without any offset or point.
ProcessVoxelBufferUnary<T> - Interface in org.anchoranalysis.image.voxel.iterator.process.voxelbuffer: Processes a 3D point like ProcessPoint but also retrieves a VoxelBuffer for the current z-slice.
ProcessVoxelBufferUnaryWithPoint<T,E> - Interface in org.anchoranalysis.image.voxel.iterator.process.voxelbuffer: Processes a 3D point like ProcessVoxelBufferUnary but also exposes a Point3i.
ProcessVoxelNeighbor<T> - Interface in org.anchoranalysis.image.voxel.iterator.neighbor: Processes a point that is an neighbor of another.
ProcessVoxelNeighborAbsolute<T> - Interface in org.anchoranalysis.image.voxel.iterator.neighbor: Processes a point that is a neighbor of another - includes global (absolute) coordinates for this point.
ProcessVoxelNeighborAbsoluteWithSlidingBuffer<T> - Class in org.anchoranalysis.image.voxel.iterator.neighbor: Like ProcessVoxelNeighborAbsolute but additionally includes a SlidingBuffer.
ProcessVoxelNeighborAbsoluteWithSlidingBuffer(SlidingBuffer<?>) - Constructor for class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsoluteWithSlidingBuffer: Creates for a particular sliding buffer.
ProcessVoxelNeighborFactory - Class in org.anchoranalysis.image.voxel.iterator.neighbor: Creates ProcessVoxelNeighbor to match certain circumstances.
ProjectableBuffer<T> - Interface in org.anchoranalysis.image.voxel.buffer: A buffer to which slices may be added to form a projection.
ProjectableBufferAggregator<T> - Class in org.anchoranalysis.plugin.image.bean.channel.aggregator: An aggregator that calculates the aggregation of every voxel across successive channels via a ProjectableBuffer.
ProjectableBufferAggregator() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.aggregator.ProjectableBufferAggregator
Projection - Class in org.anchoranalysis.image.voxel.projection: Base class for projections that map a 3D voxel-buffer to a 2D voxel-buffer.
Projection() - Constructor for class org.anchoranalysis.image.voxel.projection.Projection
projectMax() - Method in class org.anchoranalysis.image.core.channel.Channel: A maximum-intensity projection across the z-slices.
projectMax() - Method in class org.anchoranalysis.image.core.stack.DisplayStack: Creates a Maximum Intensity Projection of each channel.
projectMax() - Method in class org.anchoranalysis.image.core.stack.Stack: Creates a Maximum Intensity Projection of each channel.
projectMax() - Method in class org.anchoranalysis.image.core.stack.StackNotUniformSized: Creates a Maximum Intensity Projection of each channel.
projectMax() - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: A maximum-intensity projection (flattens in z dimension)
projectMax() - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter: A maximum intensity projection of all slices
projectMean() - Method in class org.anchoranalysis.image.core.channel.Channel: A mean-intensity projection across the z-slices.
projectMean() - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter: A mean intensity projection of all slices.
PROPERTIES_XML - Enum constant in enum class org.anchoranalysis.core.format.NonImageFileFormat: XML for storing properties (key/value pairs).
propertyValues() - Method in class org.anchoranalysis.bean.permute.property.PermuteProperty: An iterator with possible alternative values for the property.
propertyValues() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyDoubleSet
propertyValues() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequenceDouble
propertyValues() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequenceInteger
propertyValues() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyStringSet
ProposalAbnormalFailureException - Exception Class in org.anchoranalysis.mpp.proposer: An exception thrown when a proposal could not be made for an abnormal reason.
ProposalAbnormalFailureException(String) - Constructor for exception class org.anchoranalysis.mpp.proposer.ProposalAbnormalFailureException: Constructs a new exception with the specified detail message.
ProposalAbnormalFailureException(String, Throwable) - Constructor for exception class org.anchoranalysis.mpp.proposer.ProposalAbnormalFailureException: Constructs a new exception with the specified detail message and cause.
ProposalAbnormalFailureException(Throwable) - Constructor for exception class org.anchoranalysis.mpp.proposer.ProposalAbnormalFailureException: Constructs a new exception with the specified cause.
propose(RandomNumberGenerator, Optional<Resolution>) - Method in class org.anchoranalysis.mpp.bean.proposer.ScalarProposer: Proposes a scalar value based on the given parameters.
propose(MarkWithIdentifierFactory, ProposerContext) - Method in class org.anchoranalysis.mpp.bean.proposer.MarkCollectionProposer: Proposes a collection of marks.
propose(Mark, Dimensions, RandomNumberGenerator) - Method in class org.anchoranalysis.mpp.bean.proposer.OrientationProposer: Proposes an orientation for a given mark.
propose(VoxelizedMarkMemo, VoxelizedMarkMemo, ProposerContext) - Method in class org.anchoranalysis.mpp.bean.proposer.MarkMergeProposer: Proposes a merge between two marks.
propose(VoxelizedMarkMemo, ProposerContext) - Method in class org.anchoranalysis.mpp.bean.proposer.MarkProposer: Proposes changes to the input mark according to the internal rules of the proposer.
propose(VoxelizedMarkMemo, ProposerContext) - Method in class org.anchoranalysis.plugin.points.bean.FitPoints
propose(VoxelizedMarkMemo, ProposerContext, MarkWithIdentifierFactory) - Method in class org.anchoranalysis.mpp.bean.proposer.MarkSplitProposer: Proposes a split of the input mark into two new marks.
propose(ProposerContext) - Method in interface org.anchoranalysis.mpp.proposer.OptionalPointProposer: Proposes a position in 3D space.
propose(Point3d, RandomNumberGenerator, Dimensions, Orientation) - Method in class org.anchoranalysis.mpp.bean.proposer.RadiiProposer: Proposes a new point representing radii based on the given parameters.
propose(Point3d, Mark, Dimensions, RandomNumberGenerator, ErrorNode) - Method in class org.anchoranalysis.mpp.bean.proposer.PointsProposer: Proposes a list of points based on the given parameters.
ProposerBean<T> - Class in org.anchoranalysis.mpp.bean.proposer: An abstract base class for proposer beans in the MPP (Marked Point Process) framework.
ProposerBean() - Constructor for class org.anchoranalysis.mpp.bean.proposer.ProposerBean
ProposerContext - Class in org.anchoranalysis.mpp.proposer: Context for proposing operations in the MPP framework.
ProposerContext(RandomNumberGenerator, EnergyStack, RegionMap, OperationContext, ErrorNode) - Constructor for class org.anchoranalysis.mpp.proposer.ProposerContext: Creates a new ProposerContext instance.
ProposerException - Exception Class in org.anchoranalysis.mpp.proposer: An exception thrown when something goes wrong in a Proposer.
ProposerException(String) - Constructor for exception class org.anchoranalysis.mpp.proposer.ProposerException: Constructs a new exception with the specified detail message.
ProposerException(Throwable) - Constructor for exception class org.anchoranalysis.mpp.proposer.ProposerException: Constructs a new exception with the specified cause.
Provider<T> - Interface in org.anchoranalysis.bean: A class (usually an AnchorBean) that creates or otherwise supplies another object.
ProviderAsStack - Interface in org.anchoranalysis.image.core.stack: Provides a stack-representation of an entity.
ProvidesStackInput - Interface in org.anchoranalysis.image.io.stack.input: Base class for inputs which somehow eventually send up providing stacks, with or without names.
ProvisionFailedException - Exception Class in org.anchoranalysis.bean.xml.exception: If provisioning an object fails.
ProvisionFailedException(String) - Constructor for exception class org.anchoranalysis.bean.xml.exception.ProvisionFailedException: Creates with only a message.
ProvisionFailedException(String, Throwable) - Constructor for exception class org.anchoranalysis.bean.xml.exception.ProvisionFailedException: Creates with both a message and cause.
ProvisionFailedException(Throwable) - Constructor for exception class org.anchoranalysis.bean.xml.exception.ProvisionFailedException: Creates with only a cause.
put(String, double) - Method in class org.anchoranalysis.core.value.Dictionary: Inserts a key-value pair, after converting value to a String.
put(String, String) - Method in class org.anchoranalysis.core.value.Dictionary: Inserts a key-value pair.
put(ByteBuffer) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer: Relative put-method from an unsigned byte buffer, represented by a ByteBuffer.
put(ShortBuffer) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer: Relative put-method from an unsigned short buffer, represented by a ShortBuffer.
put(K, V) - Method in class org.anchoranalysis.core.cache.LRUCache: Puts a key-value pair irrespective of whether its already present or not.
put(UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer: Relative put-method from an unsigned byte buffer, represented by a UnsignedByteBuffer.
put(UnsignedShortBuffer) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer: Relative put-method from an unsigned short buffer, represented by a UnsignedShortBuffer.
put(T, int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.PriorityQueueIndexRangeDownhill: Adds an item to the priority queue with a specified index value.
put(U, S) - Method in class org.anchoranalysis.feature.calculate.part.CalculationPartMap: Assigns a evaluation result to the cache for a particular key.
putByte(int, byte) - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer: Puts a byte in the buffer at a particular position, converting, if necessary, to the buffer type.
putCheck(String, double) - Method in class org.anchoranalysis.core.value.Dictionary: Inserts a key/value pair, checking that the key doesn't already exist.
putCheck(String, String) - Method in class org.anchoranalysis.core.value.Dictionary: Inserts a key/value pair, checking that the key doesn't already exist.
putCheck(Dictionary) - Method in class org.anchoranalysis.core.value.Dictionary: Inserts all key/value pairs from another dictionary, checking that no key already exists.
putCode(int, int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedIntBuffer: Puts an encoded value at the given index.
putDouble(double) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer: Puts a double at the current buffer position.
putDouble(double) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
putDouble(double) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer
putDouble(double) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
putDouble(int, double) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer: Puts a double at a particular buffer position.
putDouble(int, double) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
putDouble(int, double) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer
putDouble(int, double) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
putDoubleClamped(double) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer: Puts a double at the current buffer position, clamping to ensure the value is within the range (0,255).
putFloat(float) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer: Puts a float at the current buffer position.
putFloat(float) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
putFloat(float) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer
putFloat(float) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
putFloat(int, float) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer: Puts a float at a particular buffer position.
putFloat(int, float) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
putFloat(int, float) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer
putFloat(int, float) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
putFloatClamped(float) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer: Puts a float at the current buffer position, clamping to ensure the value is within the range (0,255).
putFloatClamped(float) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer: Puts a float at the current buffer position, clamping to ensure the value is within the range (0,255).
putInstanceFor(Class<? extends T>, T) - Method in class org.anchoranalysis.bean.BeanInstanceMap: Assigns an instance to a particular family-type.
putInt(int, int) - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer: Puts a int in the buffer at a particular position, converting, if necessary, to the buffer type.
putInt(int, int) - Method in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsoluteWithSlidingBuffer: Assign a value to the buffer at a particular absolute position.
putLong(long) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer: Puts a long at the current buffer position.
putLong(long) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
putLong(long) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer
putLong(long) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
putLongClamped(long) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer: Puts a long at the current buffer position, clamping to ensure the value is within the range (0,255).
putRaw(byte) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer: Puts an unsigned-byte (represented as a byte) at the current buffer position.
putRaw(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer: Puts an unsigned-int (represented as a int) at the current buffer position.
putRaw(int, byte) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer: Puts an unsigned-byte (represented as a byte) a particular buffer position.
putRaw(int, int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer: Puts an unsigned-int (represented as a int) a particular buffer position.
putRaw(int, short) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer: Puts an unsigned-short (represented as a short) a particular buffer position.
putRaw(short) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer: Puts an unsigned-short (represented as a short) at the current buffer position.
putUnsigned(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBufferAsInt: Puts an unsigned-byte (represented by an int) at current buffer position.
putUnsigned(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
putUnsigned(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
putUnsigned(int, int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBufferAsInt: Puts an unsigned-byte (represented as a int) a particular buffer position.
putUnsigned(int, int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
putUnsigned(int, int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
putUnsigned(int, long) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer: Puts an unsigned-int (represented as a long) a particular buffer position.
putUnsigned(long) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer: Puts an unsigned-int (represented by a long) at current buffer position.
putUnsignedClamped(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer: Puts a long at the current buffer position, clamping to ensure the value is within the range (0,255).
putUnsignedInt(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer: Puts an unsigned-int (represented by a int) at current buffer position.
pyramid() - Method in interface org.anchoranalysis.image.io.stack.input.OpenedImageFile: Metadata to describe an image-pyramid, if it exists for this opened-image.
pyramid() - Method in class org.anchoranalysis.plugin.io.multifile.OpenedMultiFile

Q

QuadraticEquationSolver - Class in org.anchoranalysis.math.equation: Solves a Quadratic Equation by finding non-complex roots.
QuadraticEquationSolver.QuadraticRoots - Class in org.anchoranalysis.math.equation: Roots (solution) of a quadratic equation.
QuadraticRoots(double, double) - Constructor for class org.anchoranalysis.math.equation.QuadraticEquationSolver.QuadraticRoots: Creates a new QuadraticRoots instance.
quantile(double) - Method in interface org.anchoranalysis.image.voxel.statistics.VoxelStatistics: The voxel value corresponding to a particular quantile.
quantile(double) - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsCombined
quantile(double) - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsFromHistogram
quantile(double) - Method in class org.anchoranalysis.math.histogram.Histogram: Calculates the corresponding value for a particular quantile in the distribution of values in the histogram.
Quantile - Class in org.anchoranalysis.feature.bean.results: A quantile of the results from a particular feature.
Quantile - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold: Calculates the threshold value from a quantile of a histogram.
Quantile - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic: Calculates a specified quantile value from a Histogram.
Quantile() - Constructor for class org.anchoranalysis.feature.bean.results.Quantile
Quantile() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.Quantile
Quantile() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Quantile
QuantileAcrossConnectedComponents - Class in org.anchoranalysis.plugin.image.feature.bean.stack.object: Calculates the median of a feature applied to each connected component
QuantileAcrossConnectedComponents() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.stack.object.QuantileAcrossConnectedComponents
QuantileAcrossObjects<T> - Class in org.anchoranalysis.plugin.image.feature.bean.shared.object: Calculates the quantile of a feature applied to each connected component
QuantileAcrossObjects() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.shared.object.QuantileAcrossObjects
QuantileIntensity - Class in org.anchoranalysis.image.core.channel.convert.attached.channel: Converts a Channel to UnsignedByteBuffer by scaling against a quantile of the intensity values that appear in it.
QuantileIntensity(double) - Constructor for class org.anchoranalysis.image.core.channel.convert.attached.channel.QuantileIntensity: Scales against a particular quantile of the intensity values.
QuantileIntensityFromHistogram - Class in org.anchoranalysis.image.core.channel.convert.attached.histogram: Converts a Channel to UnsignedByteBuffer by scaling against a quantile of the intensity values from a corresponding histogram.
QuantileIntensityFromHistogram(double) - Constructor for class org.anchoranalysis.image.core.channel.convert.attached.histogram.QuantileIntensityFromHistogram: Scales against a particular quantile of the intensity values.
QuantileStretch - Class in org.anchoranalysis.plugin.image.bean.channel.provider.intensity: Changes the voxel values to map the range of 0th quantile to xth quantile across the entire voxel data range
QuantileStretch() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.QuantileStretch
quickOverlap() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
quickOverlap() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
quickOverlap() - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
quickOverlap() - Method in class org.anchoranalysis.mpp.mark.Mark: Provides an optional quick overlap calculation method.
QuickOverlapCalculation - Interface in org.anchoranalysis.mpp.mark: A method to quickly calculate overlap approximately

R

radiiOrdered() - Method in class org.anchoranalysis.mpp.mark.conic.ConicBase: Returns an ordered array of radii in their original units.
radiiOrderedResolved(Optional<Resolution>) - Method in class org.anchoranalysis.mpp.mark.conic.ConicBase: Returns an ordered array of radii resolved to the given resolution.
RadiiProposer - Class in org.anchoranalysis.mpp.bean.proposer: An abstract base class for proposing radii in a 3D space.
RadiiProposer() - Constructor for class org.anchoranalysis.mpp.bean.proposer.RadiiProposer
RadiiRandomizer - Class in org.anchoranalysis.mpp.mark.conic: Utility functions for generating random radii for ConicBase.
radiusForRegion(int) - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius: Calculates the radius for a specific region.
radiusForRegionSquared(int) - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius: Calculates the squared radius for a specific region.
RandomCollection<T> - Class in org.anchoranalysis.mpp.pair: An abstract collection of items from which one can randomly sample.
RandomCollection() - Constructor for class org.anchoranalysis.mpp.pair.RandomCollection
RandomCollectionWithAddCriteria<T> - Class in org.anchoranalysis.mpp.feature.addcriteria: An implementation of a RandomCollection that uses AddCriteria to determine which marks to add.
RandomCollectionWithAddCriteria(Class<?>) - Constructor for class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria: Creates a new instance with the specified pair type class.
randomIndex(RandomNumberGenerator) - Method in class org.anchoranalysis.mpp.mark.MarkCollection: Generates a random index within the collection.
randomizeRadii(Bound, RandomNumberGenerator, Optional<Resolution>, boolean) - Static method in class org.anchoranalysis.mpp.mark.conic.RadiiRandomizer: Generates random radii for a conic shape.
randomMark(RandomNumberGenerator) - Method in class org.anchoranalysis.mpp.mark.MarkCollection: Gets a random mark from the collection.
RandomNumberGenerator - Interface in org.anchoranalysis.core.random: Generates random numbers from various distributions.
RandomNumberGeneratorBean - Class in org.anchoranalysis.bean.shared.random: A bean that defines a type of RandomNumberGenerator.
RandomNumberGeneratorBean() - Constructor for class org.anchoranalysis.bean.shared.random.RandomNumberGeneratorBean
RandomNumberGeneratorMersenne - Class in org.anchoranalysis.core.random: Implements a random-number generator using the MersenneTwister algorithm.
RandomNumberGeneratorMersenne(boolean) - Constructor for class org.anchoranalysis.core.random.RandomNumberGeneratorMersenne: Creates indicating whether to use a fixed-seed or not.
RandomOrder - Class in org.anchoranalysis.plugin.io.bean.file.provider
RandomOrder() - Constructor for class org.anchoranalysis.plugin.io.bean.file.provider.RandomOrder
randomOrientation(RandomNumberGenerator, Optional<Resolution>) - Method in class org.anchoranalysis.mpp.bean.bound.rotation.BoundRotation: Generates a random orientation within the defined bounds.
randomOrientation(RandomNumberGenerator, Optional<Resolution>) - Method in class org.anchoranalysis.mpp.bean.bound.rotation.BoundRotation2D
randomOrientation(RandomNumberGenerator, Optional<Resolution>) - Method in class org.anchoranalysis.mpp.bean.bound.rotation.BoundRotation3D
randOpen(RandomNumberGenerator) - Method in class org.anchoranalysis.mpp.bean.bound.ResolvedBound: Generates a random value between the bounds (open interval).
Range - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic: The range (difference in values) between two quantiles
Range<T> - Class in org.anchoranalysis.plugin.operator.feature.bean.range: Calculates the statistical range between two feature values, with optional weighting.
Range() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Range
Range() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.range.Range
rangeChannelNum() - Method in class org.anchoranalysis.plugin.io.multifile.ParsedFilePathBag: Gets the range of channel numbers across all FileDetails.
RangeCompareBase<T> - Class in org.anchoranalysis.plugin.operator.feature.bean.range: A base class for features that compare a value against a range and return different results based on the comparison.
RangeCompareBase() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareBase
RangeCompareFromScalars<T> - Class in org.anchoranalysis.plugin.operator.feature.bean.range: A base class for setting the boundaries of a range using constant scalar values.
RangeCompareFromScalars() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareFromScalars
rangeCPresent() - Method in class org.anchoranalysis.plugin.io.multifile.SizeExtents
rangeSliceNum() - Method in class org.anchoranalysis.plugin.io.multifile.ParsedFilePathBag: Gets the range of slice numbers across all FileDetails.
rangeTimeIndex() - Method in class org.anchoranalysis.plugin.io.multifile.ParsedFilePathBag: Gets the range of time indices across all FileDetails.
rangeTPresent() - Method in class org.anchoranalysis.plugin.io.multifile.SizeExtents
RasterDirectoryObjectsGenerator - Class in org.anchoranalysis.image.io.object.output.mask: Writes each object as a binary Mask in a directory.
RasterGenerator<T> - Class in org.anchoranalysis.image.io.stack.output.generator: Transforms an entity to a Stack and writes it to the file-system.
RasterGenerator() - Constructor for class org.anchoranalysis.image.io.stack.output.generator.RasterGenerator
RasterGeneratorBridge<T,V> - Class in org.anchoranalysis.image.io.stack.output.generator: Allows us to call an RasterGenerator<S> as if it was an RasterGenerator<T> using an function to connect the two.
RasterGeneratorBridge(RasterGenerator<V>, CheckedFunction<T, V, ? extends Throwable>) - Constructor for class org.anchoranalysis.image.io.stack.output.generator.RasterGeneratorBridge: Creates with a delegate and a function to bridge the exposed element-type to the delegate element-type.
RasterGeneratorDelegateToDisplayStack<T> - Class in org.anchoranalysis.image.io.stack.output.generator: Delegates a RasterGeneratorSelectFormat to a SingleFileTypeGenerator<T, DisplayStack>.
RasterGeneratorDelegateToDisplayStack(SingleFileTypeGenerator<T, DisplayStack>, boolean) - Constructor for class org.anchoranalysis.image.io.stack.output.generator.RasterGeneratorDelegateToDisplayStack: Creates a new RasterGeneratorDelegateToDisplayStack instance.
RasterGeneratorDelegateToRaster<S,T> - Class in org.anchoranalysis.image.io.stack.output.generator: Uses a delegate raster-generator and optionally applies a conversions before calling RasterGeneratorDelegateToRaster.transform(T).
RasterGeneratorDelegateToRaster(RasterGenerator<S>) - Constructor for class org.anchoranalysis.image.io.stack.output.generator.RasterGeneratorDelegateToRaster: Creates a new RasterGeneratorDelegateToRaster instance.
RasterGeneratorSelectFormat<T> - Class in org.anchoranalysis.image.io.stack.output.generator: A RasterGenerator that selects an appropriate output-format based upon each generated image.
RasterGeneratorSelectFormat() - Constructor for class org.anchoranalysis.image.io.stack.output.generator.RasterGeneratorSelectFormat
RasterTask<S,U> - Class in org.anchoranalysis.plugin.image.task.bean: An experiment that takes (primarily) a series of raster images as an input.
RasterTask() - Constructor for class org.anchoranalysis.plugin.image.task.bean.RasterTask
RatioFirstToSecond - Class in org.anchoranalysis.image.feature.bean.object.pair: Ratio of first-object to second-object in a pair.
RatioFirstToSecond() - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.RatioFirstToSecond
RatioNonMode - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic: Calculates the ratio of non-mode pixels to total pixels in a Histogram.
RatioNonMode() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.RatioNonMode
RatioPrincipalAxisLength - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.moments: Calculates the ratio of prinicpal-axis length using Image Moments.
RatioPrincipalAxisLength() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.RatioPrincipalAxisLength
RatioThreshold - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.threshold: Calculates the ratio of values in a Histogram that satisfy a specified threshold condition.
RatioThreshold() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.RatioThreshold
read(Path) - Method in class org.anchoranalysis.io.input.csv.CSVReader: Opens a CSV for reading.
read(Path, OperationContext) - Method in interface org.anchoranalysis.annotation.io.AnnotationReader: Reads an annotation, if possible, from the file-system.
read(Path, OperationContext) - Method in class org.anchoranalysis.annotation.io.image.ImageLabelAnnotationReader
read(ProcessCSVLine) - Method in class org.anchoranalysis.io.input.csv.ReadByLine: Reads a CSV-file iterating through each row and passing it to lineProcessor
ReadableTuple3i - Interface in org.anchoranalysis.spatial.point: A tuple with three-values, respectively for the X, Y and Z dimensions.
readAcquisitionDate(Metadata) - Static method in class org.anchoranalysis.io.bioformats.metadata.AcquisitionDateReader: Reads an image acquisition-date from metadata, based on the present of EXIF data.
readAcquisitionDate(Path) - Static method in class org.anchoranalysis.io.bioformats.metadata.AcquisitionDateReader: Reads an image acquisition-date from a file identified by path, based on the present of EXIF data.
ReadAnnotationFromFile - Class in org.anchoranalysis.plugin.annotation.bean.strategy: Utility class for reading ImageLabelAnnotation from a file.
readAssumeExists(Path, OperationContext) - Static method in class org.anchoranalysis.plugin.annotation.bean.strategy.ReadAnnotationFromFile: Reads an ImageLabelAnnotation from a file, assuming the file exists.
ReadByLine - Class in org.anchoranalysis.io.input.csv: An opened-CSV file that is read line-by-line and processed.
ReadByLine(Path, CSVReader) - Constructor for class org.anchoranalysis.io.input.csv.ReadByLine: Creates a new ReadByLine instance.
readCheckExists(Path, OperationContext) - Static method in class org.anchoranalysis.plugin.annotation.bean.strategy.ReadAnnotationFromFile: Reads an ImageLabelAnnotation from a file if it exists.
readDate(Directory, int) - Static method in class org.anchoranalysis.io.bioformats.metadata.ReadMetadataUtilities: Reads a metadata entry of type Date from a Directory.
readDate(Metadata, Class<T>, int[], int[]) - Static method in class org.anchoranalysis.io.bioformats.metadata.ReadMetadataUtilities: Reads a metadata entry of type Date from the first directory of type directoryType.
readFromCSV(Path, boolean) - Static method in class org.anchoranalysis.plugin.image.task.labeller.FileLabelMap: Reads a FileLabelMap from a CSV file.
readFromFile(Path) - Static method in class org.anchoranalysis.core.value.Dictionary: Reads parameters from a Java properties file.
ReadFromFile - Class in org.anchoranalysis.io.input.bean.dictionary: Reads a Dictionary from a file in Java properties format.
ReadFromFile() - Constructor for class org.anchoranalysis.io.input.bean.dictionary.ReadFromFile
readFromWidthHeightTags(Directory, int, int) - Static method in class org.anchoranalysis.io.bioformats.metadata.ReadMetadataUtilities: Reads two metadata entries, representing width and height, and use them to form a Extent.
readFromWidthHeightTags(Metadata, Class<T>, int, int) - Static method in class org.anchoranalysis.io.bioformats.metadata.ReadMetadataUtilities: Reads two metadata entries, representing width and height, and use them to form a Extent.
readHistogramFromFile(Path) - Static method in class org.anchoranalysis.image.io.histogram.input.HistogramCSVReader: Reads a CSV file from the file-system that describes a histogram of voxel values.
readInt(Directory, int) - Static method in class org.anchoranalysis.io.bioformats.metadata.ReadMetadataUtilities: Reads a metadata entry of type int from a Directory.
readInt(Metadata, Class<T>, int) - Static method in class org.anchoranalysis.io.bioformats.metadata.ReadMetadataUtilities: Reads a metadata entry of type int from the first directory of type directoryType.
readLine() - Method in class org.anchoranalysis.io.input.csv.CSVReader.OpenedCSVFile: Reads the next-line from the open CSV file.
readMetadata(Path) - Static method in class org.anchoranalysis.io.bioformats.metadata.ReadMetadataUtilities: Reads metadata, if it exists, from an image.
readMetadata(Path, boolean) - Static method in class org.anchoranalysis.plugin.io.bean.stack.reader.ReadVoxelExtentXml: Looks for a metadata file describing the resolution
ReadMetadataUtilities - Class in org.anchoranalysis.io.bioformats.metadata: Reads various image properties from tags in Metadata.
ReadOptions - Class in org.anchoranalysis.io.bioformats.bean.options: Options that influence how stack is read in BioformatsReader.
ReadOptions() - Constructor for class org.anchoranalysis.io.bioformats.bean.options.ReadOptions
ReadOptionsDelegate - Class in org.anchoranalysis.io.bioformats.bean.options: Forces a particular settings, but otherwise uses settings from a delegate
ReadOptionsDelegate() - Constructor for class org.anchoranalysis.io.bioformats.bean.options.ReadOptionsDelegate
readResolutionXml(File) - Static method in class org.anchoranalysis.plugin.io.xml.ResolutionAsXML: Retrieves resolution from a XML file previously written by ResolutionAsXML.writeResolutionXML(Resolution, Path).
readStack(Path, OperationContext) - Method in class org.anchoranalysis.image.io.bean.stack.reader.StackReader: Opens a file at path that should contain only a single-stack.
ReadVoxelExtentXml - Class in org.anchoranalysis.plugin.io.bean.stack.reader: Reads Resolution from an XML file associated an image.
ReadVoxelExtentXml() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.reader.ReadVoxelExtentXml
reconstruction(VoxelsUntyped, VoxelsUntyped, Optional<ObjectMask>) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.grayscalereconstruction.GrayscaleReconstruction2DIJ
reconstruction(VoxelsUntyped, VoxelsUntyped, Optional<ObjectMask>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction.GrayscaleReconstructionByErosion: Performs grayscale reconstruction of a mask image from a marker image.
reconstruction(VoxelsUntyped, VoxelsUntyped, Optional<ObjectMask>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction.GrayscaleReconstructionRobinson
recordCopiedOutput(Path, Optional<Path>, int) - Method in class org.anchoranalysis.plugin.io.shared.RecordingCounter: Records an copy operation in the log / CSV path mapping.
RecordedExecutionTimes - Class in org.anchoranalysis.core.time: Recorded execution-times for operations.
RecordedExecutionTimes(Stream<RecordedExecutionTimes.RecordedOperation>) - Constructor for class org.anchoranalysis.core.time.RecordedExecutionTimes: Create with the running-times.
RecordedExecutionTimes.RecordedOperation - Class in org.anchoranalysis.core.time: A particular type of operation that has been recorded (en aggregate).
RecordedOperation(String, int, double, double, int) - Constructor for class org.anchoranalysis.core.time.RecordedExecutionTimes.RecordedOperation: Creates a new RecordedOperation instance.
recordedOutputs() - Method in class org.anchoranalysis.io.output.recorded.RecordingWriters: If defined, all output-names that are passed as arguments to both writers are recorded here.
RecordedOutputs - Class in org.anchoranalysis.io.output.recorded: Outputs recorded from RecordOutputNamesForWriter.
RecordedOutputs() - Constructor for class org.anchoranalysis.io.output.recorded.RecordedOutputs
RecordedOutputsWithRules - Class in org.anchoranalysis.io.output.recorded: Rules to determine what outputting occurs, together with maybe an entity that records the output-names that are used when writing / querying.
RecordedOutputsWithRules() - Constructor for class org.anchoranalysis.io.output.recorded.RecordedOutputsWithRules: Creates with no rules or outputs defined.
RecordedOutputsWithRules(MultiLevelRecordedOutputs, MultiLevelOutputEnabled, OutputEnabledDelta) - Constructor for class org.anchoranalysis.io.output.recorded.RecordedOutputsWithRules: Creates with all elements defined.
recordedTimes() - Method in class org.anchoranalysis.core.time.ExecutionTimeRecorder: The execution-times that have been recorded.
recordedTimes() - Method in class org.anchoranalysis.core.time.ExecutionTimeRecorderIgnore
recordError(Class<?>, String) - Method in interface org.anchoranalysis.core.log.error.ErrorReporter: Reports an error with a constant string error message.
recordError(Class<?>, String) - Method in class org.anchoranalysis.core.log.error.ErrorReporterBase
recordError(Class<?>, String) - Method in class org.anchoranalysis.experiment.task.ErrorReporterForTask
recordError(Class<?>, String, Throwable) - Method in interface org.anchoranalysis.core.log.error.ErrorReporter: Reports an error that occurred as an exception, with a message first introducing it.
recordError(Class<?>, String, Throwable) - Method in class org.anchoranalysis.core.log.error.ErrorReporterBase
recordError(Class<?>, String, Throwable) - Method in class org.anchoranalysis.experiment.task.ErrorReporterForTask
recordError(Class<?>, Throwable) - Method in interface org.anchoranalysis.core.log.error.ErrorReporter: Reports an error that occurred as an exception
recordError(Class<?>, Throwable) - Method in class org.anchoranalysis.core.log.error.ErrorReporterBase
recordError(Class<?>, Throwable) - Method in class org.anchoranalysis.experiment.task.ErrorReporterForTask
recordErrorFormatted(Class<?>, String, Object...) - Method in interface org.anchoranalysis.core.log.error.ErrorReporter: Reports an error with a string derived from a format-string.
recordExecutionTime(String, long) - Method in class org.anchoranalysis.core.time.ExecutionTimeRecorder: Records the execution-time of a particular operation.
recordExecutionTime(String, long) - Method in class org.anchoranalysis.core.time.ExecutionTimeRecorderIgnore
recordExecutionTime(String, CheckedRunnable<E>) - Method in class org.anchoranalysis.core.time.ExecutionTimeRecorder: Executes an operation while recording the execution-time - without a return type.
recordExecutionTime(String, CheckedSupplier<T, E>) - Method in class org.anchoranalysis.core.time.ExecutionTimeRecorder: Executes an operation while recording the execution-time - with a return type.
recordExecutionTimeUnchecked(String, Runnable) - Method in class org.anchoranalysis.core.time.ExecutionTimeRecorder: Executes an operation while recording the execution-time - without a return type, and without throwing an exception..
RecordingCounter<T> - Class in org.anchoranalysis.plugin.io.shared: A counter that also records outputs in a message-log and CSV file.
RecordingCounter(Counter, Outputter, T) - Constructor for class org.anchoranalysis.plugin.io.shared.RecordingCounter
RecordingWriters - Class in org.anchoranalysis.io.output.recorded: Two writers that record any output-names that are passed as arguments.
RecordingWriters(ElementOutputter, Optional<WriterExecuteBeforeEveryOperation>, Optional<MultiLevelRecordedOutputs>) - Constructor for class org.anchoranalysis.io.output.recorded.RecordingWriters: Creates the two writers.
recordTimeDifferenceBetween(String, long, long) - Method in class org.anchoranalysis.core.time.ExecutionTimeRecorder: Records the execution-time of a particular operation by subtracting the start-time from the end time.
recordWarning(String) - Method in interface org.anchoranalysis.core.log.error.ErrorReporter: Reports an warning with a constant string error message.
recordWarning(String) - Method in class org.anchoranalysis.core.log.error.ErrorReporterBase
recordWarning(String) - Method in class org.anchoranalysis.experiment.task.ErrorReporterForTask
recordWarningFormatted(String, Object...) - Method in interface org.anchoranalysis.core.log.error.ErrorReporter: Reports an warning with a string derived from a format-string.
RecursivelyDescribeExceptionStack - Class in org.anchoranalysis.core.exception.friendly: Generates a nice string representation of an Exception and its causes according to certain rules.
red() - Method in class org.anchoranalysis.image.core.stack.RGBStack: The red channel.
RED - Static variable in class org.anchoranalysis.image.core.stack.RGBChannelNames: Name for the red channel.
reduce() - Method in class org.anchoranalysis.math.optimization.HungarianAlgorithm: Reduce the cost matrix by subtracting the smallest element of each row from all elements of the row as well as the smallest element of each column from all elements of the column.
reduce(List<LabelledWithConfidence<ObjectMask>>, Extent, ExecutionTimeRecorder) - Method in class org.anchoranalysis.image.inference.bean.reduce.ReduceElementsGreedy
reduce(List<LabelledWithConfidence<ObjectMask>>, Extent, ExecutionTimeRecorder) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ThresholdConfidence
reduce(List<LabelledWithConfidence<T>>, Extent, ExecutionTimeRecorder) - Method in class org.anchoranalysis.image.inference.bean.segment.reduce.ReduceElements: Reduce a list of elements (each with a confidence score and a label) to a smaller-list.
reduce(ReduceElements<ObjectMask>, boolean, ExecutionTimeRecorder) - Method in class org.anchoranalysis.image.inference.segment.SegmentedObjects: Reduces the segmented-objects, applying a reduction algorithm separately to each object-class.
ReduceElements<T> - Class in org.anchoranalysis.image.inference.bean.segment.reduce: Reduces the number or spatial-extent of elements by favoring higher-confidence elements over lower-confidence elements.
ReduceElements() - Constructor for class org.anchoranalysis.image.inference.bean.segment.reduce.ReduceElements
ReduceElementsGreedy - Class in org.anchoranalysis.image.inference.bean.reduce: Reduces the number or spatial-extent of elements by favouring higher-confidence elements over lower-confidence elements.
ReduceElementsGreedy() - Constructor for class org.anchoranalysis.image.inference.bean.reduce.ReduceElementsGreedy
ReduceFirstAndSecond - Class in org.anchoranalysis.plugin.image.feature.bean.list.pair: Calculates the aggregate of a feature applied to both the first and second objects in a FeatureInputPairObjects.
ReduceFirstAndSecond() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.pair.ReduceFirstAndSecond
ReduceObjectsGraph - Class in org.anchoranalysis.image.inference.bean.reduce: Combines a PriorityQueue (ordering by highest confidence) and a graph-structure indicating which objects overlap with each other.
ReduceObjectsGraph(List<LabelledWithConfidence<ObjectMask>>) - Constructor for class org.anchoranalysis.image.inference.bean.reduce.ReduceObjectsGraph: Create with a list of elements.
ReduceRatioFirstAndSecond - Class in org.anchoranalysis.plugin.image.feature.bean.list.pair: Calculates the aggregate of the ratio of first:second and second:first for a FeatureInputPairObjects
ReduceRatioFirstAndSecond() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.pair.ReduceRatioFirstAndSecond
ReductionOutcome<T> - Class in org.anchoranalysis.image.inference.segment: The result of a reduction operation.
ReductionOutcome() - Constructor for class org.anchoranalysis.image.inference.segment.ReductionOutcome: Create with an empty list of retained-indices.
ReductionOutcome(List<Integer>) - Constructor for class org.anchoranalysis.image.inference.segment.ReductionOutcome: Creates a new ReductionOutcome instance.
ReductionOutcome(List<Integer>, List<T>) - Constructor for class org.anchoranalysis.image.inference.segment.ReductionOutcome: Creates a new ReductionOutcome instance.
Reference<T> - Class in org.anchoranalysis.feature.bean.operator: Uses another feature to calculate the value.
Reference - Class in org.anchoranalysis.plugin.image.bean.channel.provider: Provides a channel by referencing it from a a set of named-channels.
Reference - Class in org.anchoranalysis.plugin.image.bean.histogram.provider: A provider that references an existing Histogram by its identifier.
Reference - Class in org.anchoranalysis.plugin.image.bean.mask.provider: A provider that references an existing Mask by its identifier.
Reference - Class in org.anchoranalysis.plugin.image.bean.object.provider: An ObjectCollectionProvider that references an existing ObjectCollection by its identifier.
Reference - Class in org.anchoranalysis.plugin.image.bean.stack.provider: Retrieves an existing stack.
Reference - Class in org.anchoranalysis.plugin.mpp.bean.provider.collection: Provides a MarkCollection by referencing it from the initialization context using an ID.
Reference - Class in org.anchoranalysis.plugin.points.bean.fitter: A PointsFitter that references another PointsFitter by its ID.
Reference() - Constructor for class org.anchoranalysis.feature.bean.operator.Reference
Reference() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.Reference
Reference() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.provider.Reference
Reference() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.Reference
Reference() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.Reference
Reference() - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.Reference
Reference() - Constructor for class org.anchoranalysis.plugin.mpp.bean.provider.collection.Reference
Reference() - Constructor for class org.anchoranalysis.plugin.points.bean.fitter.Reference
Reference(String) - Constructor for class org.anchoranalysis.feature.bean.operator.Reference: Create with a specific identifier.
Reference(String) - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.Reference: Creates a new instance with a specified channel ID.
Reference(String) - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.provider.Reference: Creates a new Reference with the specified identifier.
Reference(String) - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.Reference: Creates a new Reference with the specified identifier.
Reference(String) - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.Reference: Creates a new Reference with the specified identifier.
Reference(String) - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.Reference: Creates a new Reference with a specified identifier.
Reference(String) - Constructor for class org.anchoranalysis.plugin.mpp.bean.provider.collection.Reference: Creates a new Reference instance.
ReferenceFactory - Class in org.anchoranalysis.plugin.image.provider: Creates reference (i.e.
ReferenceOrElse - Class in org.anchoranalysis.plugin.image.bean.object.provider: Returns a object-collection by name if it exists, or else calls objectsElse if it doesn't exist.
ReferenceOrElse() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.ReferenceOrElse
ReferenceOrEmpty - Class in org.anchoranalysis.plugin.mpp.bean.provider.collection: Returns an existing marks-collection or an empty set if it doesn't exist
ReferenceOrEmpty() - Constructor for class org.anchoranalysis.plugin.mpp.bean.provider.collection.ReferenceOrEmpty
ReferencingFeatureListProvider<T> - Class in org.anchoranalysis.feature.bean.list: A base class for implementations of FeatureListProvider that may reference features created elsewhere.
ReferencingFeatureListProvider() - Constructor for class org.anchoranalysis.feature.bean.list.ReferencingFeatureListProvider
ReflectInAxesWithinDistance - Class in org.anchoranalysis.plugin.points.bean.fitter: Reflects points in each axes if all points are within a certain distance from it
ReflectInAxesWithinDistance() - Constructor for class org.anchoranalysis.plugin.points.bean.fitter.ReflectInAxesWithinDistance
reflectThroughOrigin() - Method in class org.anchoranalysis.spatial.box.BoundingBox: Reflects the bounding box through the origin.
RegEx - Class in org.anchoranalysis.bean.shared.regex: The regular-expression to use for matching groups.
RegEx() - Constructor for class org.anchoranalysis.bean.shared.regex.RegEx
RegExList - Class in org.anchoranalysis.bean.shared.regex: Combines one or more RegEx together, by successively trying to match each RegEx until success.
RegExList() - Constructor for class org.anchoranalysis.bean.shared.regex.RegExList
RegExMatcher - Class in org.anchoranalysis.plugin.io.bean.file.namer
RegExMatcher() - Constructor for class org.anchoranalysis.plugin.io.bean.file.namer.RegExMatcher
RegExSimple - Class in org.anchoranalysis.bean.shared.regex: Matches a Java-style regular expression against the string.
RegExSimple() - Constructor for class org.anchoranalysis.bean.shared.regex.RegExSimple
RegExSimple(String) - Constructor for class org.anchoranalysis.bean.shared.regex.RegExSimple: Creates with an expression that should match one or more groups.
RegExSimple(String, Pattern) - Constructor for class org.anchoranalysis.bean.shared.regex.RegExSimple: Creates a new RegExSimple instance.
region() - Method in interface org.anchoranalysis.annotation.mark.AnnotationWithMarks: The region(s) of the marks that specifies the annotation.
region() - Method in class org.anchoranalysis.annotation.mark.DualMarksAnnotation
region(BoundingBox, boolean) - Method in class org.anchoranalysis.image.core.mask.Mask: Creates an ObjectMask corresponding to the on/off state in a bounding-box.
region(BoundingBox, boolean) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: A (sub-)region of the voxels.
region(BoundingBox, boolean) - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter: A (sub-)region of the voxels.
region(BoundingBox, boolean) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: A (sub-)region of the object-mask.
regionIntersecting(BoundingBox) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Creates an object-mask covering the a bounding-box (that is required to intersect at least partially)
regionIntersecting(BoundingBox, int) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: Like BoundedVoxels.region(org.anchoranalysis.spatial.box.BoundingBox, boolean) but only expects a bounding-box that intersects at least partially.
RegionMap - Class in org.anchoranalysis.mpp.bean.regionmap: Maps integer IDs to sub-regions in the map.
RegionMap() - Constructor for class org.anchoranalysis.mpp.bean.regionmap.RegionMap
RegionMap(int) - Constructor for class org.anchoranalysis.mpp.bean.regionmap.RegionMap: Creates a region map with a single entry mapping to a particular region.
RegionMapSingleton - Class in org.anchoranalysis.mpp.bean.regionmap: A singleton class providing a default RegionMap.
RegionMembership - Class in org.anchoranalysis.mpp.bean.regionmap: Abstract class representing membership of regions using a bit-flag system.
RegionMembership() - Constructor for class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
RegionMembership(int) - Constructor for class org.anchoranalysis.mpp.bean.regionmap.RegionMembership: Constructs a RegionMembership with a single region set.
RegionMembershipAnd - Class in org.anchoranalysis.mpp.bean.regionmap: A RegionMembership implementation that uses an AND operation to check membership.
RegionMembershipAnd() - Constructor for class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipAnd: Constructs a RegionMembershipAnd with no regions set.
RegionMembershipAnd(int) - Constructor for class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipAnd: Constructs a RegionMembershipAnd with a single region set.
RegionMembershipOr - Class in org.anchoranalysis.mpp.bean.regionmap: A RegionMembership implementation that uses an OR operation to check membership.
RegionMembershipOr() - Constructor for class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipOr: Constructs a RegionMembershipOr with no regions set.
RegionMembershipOr(int) - Constructor for class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipOr: Constructs a RegionMembershipOr with a single region set.
RegionMembershipUtilities - Class in org.anchoranalysis.mpp.bean.regionmap: Utility class for managing 8-bit region membership.
RegionMembershipWithFlags - Class in org.anchoranalysis.mpp.bean.regionmap: A wrapper for RegionMembership that includes pre-calculated flags and a region ID.
RegionMembershipWithFlags(RegionMembership, int) - Constructor for class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipWithFlags: Creates a new instance with the given region membership and region ID.
regionZ(int, int) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Creates an object-mask with a subrange of the slices.
regionZ(int, int, VoxelsFactoryTypeBound<T>) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: Creates an box with a subrange of the slices.
register(String, Function<List<T>, Object>) - Static method in class org.anchoranalysis.bean.xml.RegisterBeanFactories: Registers a bean that creates a {link java.util.List}.
register(String, AnchorBeanFactory) - Static method in class org.anchoranalysis.bean.xml.RegisterBeanFactories: Registers a specific factory.
registerAllPackageBeanFactories() - Static method in class org.anchoranalysis.bean.xml.RegisterBeanFactories: Registers the factories for the beans that exist in this package
registerBeanFactories() - Static method in class org.anchoranalysis.feature.bean.RegisterFeatureBeanFactories: Registers all custom feature-related beans.
RegisterBeanFactories - Class in org.anchoranalysis.bean.xml: Utility class for registering the Bean-factories that are found in anchor-bean (or any other).
RegisterFeatureBeanFactories - Class in org.anchoranalysis.feature.bean: Similar to RegisterBeanFactories but registers additional feature-related bean-factories.
RegularExpression - Class in org.anchoranalysis.plugin.io.bean.file.group.parser
RegularExpression() - Constructor for class org.anchoranalysis.plugin.io.bean.file.group.parser.RegularExpression
RegularExpressionBase - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming: A base class for CopyFilesNaming classes that use a regular-expression.
RegularExpressionBase() - Constructor for class org.anchoranalysis.plugin.io.bean.file.copy.naming.RegularExpressionBase
rejected() - Method in interface org.anchoranalysis.annotation.mark.DualMarks: The rejected marks.
RejectIfConditionXYResolution - Class in org.anchoranalysis.plugin.io.bean.stack.reader: If the XY resolution of an opened-image meets a certain condition then the resolution is scaled by a factor.
RejectIfConditionXYResolution() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.reader.RejectIfConditionXYResolution
RejectIfIntensityLessThan - Class in org.anchoranalysis.plugin.image.feature.bean.score: Rejects voxels with intensity less than a specified minimum, otherwise calculates a score using another VoxelScore.
RejectIfIntensityLessThan() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.RejectIfIntensityLessThan
RejectIfNotConnected - Class in org.anchoranalysis.plugin.image.bean.object.provider.connected: Rejects a set of objects, if any object is not fully connected (pixels form two or more separate connected components)
RejectIfNotConnected() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.connected.RejectIfNotConnected
relation() - Method in class org.anchoranalysis.bean.shared.relation.threshold.RelationToConstant
relation() - Method in class org.anchoranalysis.bean.shared.relation.threshold.RelationToThreshold: The relation to the threshold.
relation() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryNotOffVoxels
relation() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryNotOnVoxels
relation() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryOffVoxels
relation() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryOnVoxels
RelationBean - Class in org.anchoranalysis.bean.shared.relation: Base class that specifies a relation between two doubles.
RelationBean() - Constructor for class org.anchoranalysis.bean.shared.relation.RelationBean
RelationToConstant - Class in org.anchoranalysis.bean.shared.relation.threshold: Defines a constant threshold, and a relation to it.
RelationToConstant() - Constructor for class org.anchoranalysis.bean.shared.relation.threshold.RelationToConstant
RelationToConstant(RelationBean, double) - Constructor for class org.anchoranalysis.bean.shared.relation.threshold.RelationToConstant: Creates a new RelationToConstant instance.
RelationToThreshold - Class in org.anchoranalysis.bean.shared.relation.threshold: A base class specifying a threshold and a relation to it.
RelationToThreshold() - Constructor for class org.anchoranalysis.bean.shared.relation.threshold.RelationToThreshold
RelationWithMatches - Class in org.anchoranalysis.plugin.image.bean.object.filter.collective: Matches each object with others, and keeps only those where a relation holds true for all matches (in terms of features)
RelationWithMatches() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.collective.RelationWithMatches
relativeMaskTo(BoundingBox) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Creates a new object-mask with coordinates changed to be relative to another box.
relativePositionTo(BoundingBox) - Method in class org.anchoranalysis.spatial.box.BoundingBox: The relative position of the corner to another bounding box.
relativePositionToBox(BoundingBox) - Method in class org.anchoranalysis.spatial.box.BoundingBox: A new bounding-box using relative position coordinates to another box.
relativeScale(Extent, Extent) - Static method in class org.anchoranalysis.spatial.scale.RelativeScaleCalculator: Calculates a scaling factor so as to scale source to target.
relativeScale(Extent, Extent, boolean) - Static method in class org.anchoranalysis.spatial.scale.RelativeScaleCalculator: Multiplexes between RelativeScaleCalculator.relativeScalePreserveAspectRatio(Extent, Extent) and RelativeScaleCalculator.relativeScale(Extent, Extent).
RelativeScaleCalculator - Class in org.anchoranalysis.spatial.scale: Determine the scaling-factor needed to scale an Extent to become equal in size to another Extent.
relativeScalePreserveAspectRatio(Extent, Extent) - Static method in class org.anchoranalysis.spatial.scale.RelativeScaleCalculator: Calculates a scaling factor so as to maximally scale source to target - while preserving the aspect ratio.
RelativeToDirectory - Class in org.anchoranalysis.plugin.io.bean.file.namer: Constructs a name by finding the relative-path between the file and the input-directory.
RelativeToDirectory() - Constructor for class org.anchoranalysis.plugin.io.bean.file.namer.RelativeToDirectory
rememberConverted(NamedChannelsInput, U, StringBuilder) - Method in class org.anchoranalysis.plugin.mpp.shared.SharedStateRememberConverted: Remembers a converted input.
remove(double, double, T) - Method in class org.anchoranalysis.spatial.rtree.IntervalRTree: Removes a particular item from the r-tree, identified by its interval and payload.
remove(int) - Method in class org.anchoranalysis.core.color.ColorList: Remove an element at a particular index.
remove(int) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown: Removes a mark at a specific index from the collection.
remove(int) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy: Removes a mark at the specified index from the collection.
remove(int) - Method in class org.anchoranalysis.mpp.feature.mark.MemoList: Removes the element at the specified position in this list.
remove(int) - Method in class org.anchoranalysis.mpp.mark.ColoredMarks: Removes a mark and its associated color at the specified index.
remove(int) - Method in class org.anchoranalysis.mpp.mark.MarkCollection: Removes a mark at a specific index.
remove(Rectangle, T) - Method in class org.anchoranalysis.spatial.rtree.RTree: Removes a particular item from the r-tree, identified by its Rectangle and payload.
remove(K, V) - Method in class org.anchoranalysis.core.collection.MapCreate: Removes the entry for the specified key only if it is currently mapped to the specified value.
remove(EnergySavedIndividual, int) - Method in class org.anchoranalysis.mpp.feature.mark.EnergyMemoList: Removes a mark at a specific index and updates energies.
remove(EnergyMemoList, int, VoxelizedMarkMemo, EnergyStackWithoutParameters) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown: Removes a mark at a specific index from the collection and updates energies.
remove(EnergyMemoList, VoxelizedMarkMemo, EnergyStackWithoutParameters) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown: Removes a specific mark from the collection and updates energies.
remove(MemoForIndex, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
remove(MemoForIndex, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedPairs
remove(MemoForIndex, VoxelizedMarkMemo) - Method in interface org.anchoranalysis.mpp.mark.UpdatableMarks: Removes a mark from the existing set of marks.
remove(VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.mark.MemoList: Removes the first occurrence of the specified element from this list, if it is present.
remove(BoundingBox, T) - Method in class org.anchoranalysis.spatial.rtree.BoundingBoxRTree: Removes a particular item from the r-tree, identified by its bounding-box and payload.
remove(T) - Method in class org.anchoranalysis.image.voxel.object.IntersectingObjects: Removes an object-mask, so that it is no longer considered in queries.
removeAnyLeadingPeriod(String) - Static method in class org.anchoranalysis.core.format.FormatExtensions: Removes a single leading period from a string, if one exists.
removeBelowThreshold(int) - Method in class org.anchoranalysis.math.histogram.Histogram: All values less than threshold are removed.
removeClosestToUnitZ() - Method in class org.anchoranalysis.math.statistics.moment.ImageMoments: Removes the entry that is closest to having an eigenVector in direction (0,0,1).
removeEdge(ObjectForReduction, ObjectForReduction) - Method in class org.anchoranalysis.image.inference.bean.reduce.ReduceObjectsGraph: Remove an edge between two vertices.
removeEdge(V, V) - Method in class org.anchoranalysis.core.graph.GraphWithoutPayload: Remove an edge between two vertices.
removeEdge(V, V) - Method in class org.anchoranalysis.core.graph.GraphWithPayload: Remove an edge between two vertices.
removeExtension(String) - Static method in class org.anchoranalysis.core.system.path.ExtensionUtilities: Removes an extension from a filename or path.
removeExtension(Path) - Static method in class org.anchoranalysis.core.system.path.ExtensionUtilities: Like ExtensionUtilities.removeExtension(String) but accepts and returns a Path.
RemoveExtension - Class in org.anchoranalysis.plugin.io.bean.file.namer: Removes extensions from the identifier (but not from the file) and only if the extension hasn't already been removed upstream.
RemoveExtension() - Constructor for class org.anchoranalysis.plugin.io.bean.file.namer.RemoveExtension
RemoveExtension(FileNamer) - Constructor for class org.anchoranalysis.plugin.io.bean.file.namer.RemoveExtension
removeIfExists(FeatureList<FeatureInput>) - Method in class org.anchoranalysis.feature.shared.SharedFeatures: Remove all features, if they currently exist, from features.
removeIfExists(T) - Method in class org.anchoranalysis.core.identifier.provider.NameValueMap: Removes an element from the set, if it exists.
removeInstanceFor(Class<? extends T>) - Method in class org.anchoranalysis.bean.BeanInstanceMap: Removes any instance in the map of a particular family-type.
removeIntersectingVoxels(ObjectCollection, Dimensions, boolean) - Static method in class org.anchoranalysis.plugin.image.object.ObjectIntersectionRemover: Removes intersecting voxels from a collection of objects.
RemoveIntersectingVoxels - Class in org.anchoranalysis.plugin.image.bean.object.provider.split: Considers all possible pairs of objects in a provider, and removes any intersecting pixels
RemoveIntersectingVoxels() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.split.RemoveIntersectingVoxels
RemoveLastElement - Class in org.anchoranalysis.plugin.io.bean.grouper: Splits an identifier into elements by the directory separator, and removes the final element.
RemoveLastElement() - Constructor for class org.anchoranalysis.plugin.io.bean.grouper.RemoveLastElement
RemoveMatching - Class in org.anchoranalysis.plugin.io.bean.file.provider
RemoveMatching() - Constructor for class org.anchoranalysis.plugin.io.bean.file.provider.RemoveMatching
removeNonMatching(List<T>) - Method in class org.anchoranalysis.plugin.io.input.filter.FilterDescriptiveNameEqualsContains: Removes items from the input list that don't match the filter criteria.
RemoveOverlappingObjects - Class in org.anchoranalysis.image.inference.bean.reduce: Intersecting objects are removed if they have sufficient overlap.
RemoveOverlappingObjects() - Constructor for class org.anchoranalysis.image.inference.bean.reduce.RemoveOverlappingObjects
removeStackWriter() - Static method in class org.anchoranalysis.test.image.io.BeanInstanceMapFixture: Removes any StackWriter that may exist in the underlying BeanInstanceMap.
RemoveTouchingBorder - Class in org.anchoranalysis.plugin.image.bean.object.provider.filter: Considers all possible pairs of objects in a provider, and removes those that touch the border.
RemoveTouchingBorder() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.filter.RemoveTouchingBorder
removeTouchingBorderXY(Extent) - Method in class org.anchoranalysis.annotation.io.assignment.OverlappingObjects: Removes any objects from the assignment if they touch the X or Y scene border.
RemoveTrailingDirectory - Class in org.anchoranalysis.plugin.io.bean.path.derive
RemoveTrailingDirectory() - Constructor for class org.anchoranalysis.plugin.io.bean.path.derive.RemoveTrailingDirectory
removeTwo(int, int) - Method in class org.anchoranalysis.mpp.mark.MarkCollection: Removes two marks at specified indices.
removeTwo(EnergySavedIndividual, int, int) - Method in class org.anchoranalysis.mpp.feature.mark.EnergyMemoList: Removes two marks at specific indices and updates energies.
removeTwo(EnergyMemoList, int, int, EnergyStackWithoutParameters) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown: Removes two marks at specific indices from the collection and updates energies.
removeVertex(ObjectForReduction) - Method in class org.anchoranalysis.image.inference.bean.reduce.ReduceObjectsGraph: Removes a vertex and any edges connected to it.
removeVertex(V) - Method in class org.anchoranalysis.core.graph.GraphWithoutPayload: Removes a vertex and any edges connected to it.
removeVertex(V) - Method in class org.anchoranalysis.core.graph.GraphWithPayload: Removes a vertex and any edges connected to it.
RemoveWhitespace - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming: Removes any whitespace characters from the path
RemoveWhitespace() - Constructor for class org.anchoranalysis.plugin.io.bean.file.copy.naming.RemoveWhitespace
repeat(int, Supplier<T>) - Static method in class org.anchoranalysis.core.functional.FunctionalList: Creates a list of elements, by repeatedly calling the same operation.
repeat(int, CheckedRunnable<E>) - Static method in class org.anchoranalysis.core.functional.FunctionalIterate: Repeats an operation a number of times.
Repeat - Class in org.anchoranalysis.bean.shared.color.scheme: Duplicates a ColorList produced by another ColorScheme a certain number of times.
Repeat - Class in org.anchoranalysis.plugin.image.bean.segment.binary: Repeats a binary segmentation operation for a specified number of iterations.
Repeat() - Constructor for class org.anchoranalysis.bean.shared.color.scheme.Repeat
Repeat() - Constructor for class org.anchoranalysis.plugin.image.bean.segment.binary.Repeat
REPEAT - Static variable in class org.anchoranalysis.image.bean.nonbean.spatial.align.PositionChoicesConstants: The choice which will cause a single-slice in the z-dimension to be duplicated across the z-dimension to match the z-size onto which it is projected.
repeatAsStream(int, Class<? extends E>, CheckedSupplier<T, E>) - Static method in class org.anchoranalysis.core.functional.FunctionalIterate: Repeats an operation a number of times, to form a Stream.
repeatCountSuccessful(int, CheckedBooleanSupplier<E>) - Static method in class org.anchoranalysis.core.functional.FunctionalIterate: Repeats an operation a number of times, counting the number of times the operation returns true.
RepeatSlice - Class in org.anchoranalysis.plugin.image.bean.channel.provider.slice: Creates a new channel with specific dimensions that repeatedly duplicates a slice from an existing channel
RepeatSlice - Class in org.anchoranalysis.plugin.image.bean.mask.provider.slice: Creates a new mask with specific dimensions that repeatedly duplicates a slice from an existing mask
RepeatSlice() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.slice.RepeatSlice
RepeatSlice() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.slice.RepeatSlice
repeatUntil(int, CheckedBooleanSupplier<E>) - Static method in class org.anchoranalysis.core.functional.FunctionalIterate: Repeats an operation until a true value is returned.
repeatWithIndex(int, CheckedIntConsumer<E>) - Static method in class org.anchoranalysis.core.functional.FunctionalIterate: Repeats an operation a number of times, passing an increment index to operation each time.
Replace - Class in org.anchoranalysis.plugin.io.bean.path.derive: Generates a file-path by replacing all occurrences of a string-pattern with another
Replace() - Constructor for class org.anchoranalysis.plugin.io.bean.path.derive.Replace
replaceBy(BinaryVoxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.image.core.mask.Mask: Replaces the underlying voxels in the mask with new voxels.
replaceError(ErrorNode) - Method in class org.anchoranalysis.mpp.proposer.ProposerContext: Creates a new ProposerContext with a replaced error node.
ReplaceInfinity<T> - Class in org.anchoranalysis.plugin.operator.feature.bean.replace: Replaces infinite values in a feature's result with a specified replacement value.
ReplaceInfinity() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.replace.ReplaceInfinity
replaceInput(T) - Method in class org.anchoranalysis.feature.session.SessionInputSequential: Replaces existing input with new input
replaceInputManager(InputManager<T>) - Method in class org.anchoranalysis.experiment.bean.io.InputOutputExperiment
replaceInputManager(InputManager<T>) - Method in interface org.anchoranalysis.experiment.io.ReplaceInputManager: Replace the existing @{link InputManager} associated with this class.
ReplaceInputManager<T> - Interface in org.anchoranalysis.experiment.io: Indicates and provides a mechanism that the InputManager can be replaced.
ReplaceNaN<T> - Class in org.anchoranalysis.plugin.operator.feature.bean.replace: Replaces NaN (Not a Number) values in a feature's result with a specified replacement value.
ReplaceNaN() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.replace.ReplaceNaN
replaceOutputManager(OutputManager) - Method in class org.anchoranalysis.experiment.bean.io.InputOutputExperiment
replaceOutputManager(OutputManager) - Method in interface org.anchoranalysis.experiment.io.ReplaceOutputManager: Replace the currently-assigned OutputManager with another.
ReplaceOutputManager - Interface in org.anchoranalysis.experiment.io: Indicates and provides a mechanism that the OutputManager can be replaced.
ReplacePropertyBeanFactory<T> - Class in org.anchoranalysis.bean.xml.factory: Replaces a property (an XML element of attribute) on a bean before loading it.
ReplacePropertyBeanFactory(BeanInstanceMap) - Constructor for class org.anchoranalysis.bean.xml.factory.ReplacePropertyBeanFactory: Creates a new ReplacePropertyBeanFactory instance.
replaceSlice(int, VoxelBuffer<FloatBuffer>) - Method in class org.anchoranalysis.image.voxel.buffer.slice.FromFloat
replaceSlice(int, VoxelBuffer<UnsignedByteBuffer>) - Method in class org.anchoranalysis.image.voxel.buffer.slice.FromByte
replaceSlice(int, VoxelBuffer<UnsignedIntBuffer>) - Method in class org.anchoranalysis.image.voxel.buffer.slice.FromInt
replaceSlice(int, VoxelBuffer<UnsignedShortBuffer>) - Method in class org.anchoranalysis.image.voxel.buffer.slice.FromShort
replaceSlice(int, VoxelBuffer<T>) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: Assigns a new buffer for a slice.
replaceSlice(int, VoxelBuffer<T>) - Method in interface org.anchoranalysis.image.voxel.buffer.slice.SliceBufferIndex: Replaces the voxels for a particular z-slice.
replaceSlice(int, VoxelBuffer<T>) - Method in class org.anchoranalysis.image.voxel.Voxels: Assigns a new buffer for a particular slice.
replaceSlice(int, VoxelsUntyped, int, boolean) - Method in class org.anchoranalysis.image.voxel.VoxelsUntyped: Copies one particular z-slice of voxels from a source into the current voxels.
ReplaceStrategy<T> - Interface in org.anchoranalysis.feature.session.replace: Different strategies on associating a FeatureCalculationInput with a particular input.
replaceTask(Task<T, S>) - Method in class org.anchoranalysis.experiment.bean.io.InputOutputExperiment
replaceTask(Task<T, S>) - Method in class org.anchoranalysis.experiment.bean.processor.JobProcessor
replaceTask(Task<T, S>) - Method in interface org.anchoranalysis.experiment.io.ReplaceTask: Replace the currently-assigned Task with another.
replaceTask(Task<U, S>) - Method in class org.anchoranalysis.plugin.mpp.bean.convert.ConvertNamedChannels
ReplaceTask<T,S> - Interface in org.anchoranalysis.experiment.io: Indicates and provides a mechanism that the Task can be replaced.
ReplaceUnusualValue<T> - Class in org.anchoranalysis.plugin.operator.feature.bean.replace: Calculates the underlying feature, but replaces the result with a constant if it is an "unusual" value.
ReplaceUnusualValue() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.replace.ReplaceUnusualValue
replaceVoxels(Voxels<?>) - Method in class org.anchoranalysis.image.core.channel.Channel: Assigns new voxels to replace the existing voxels.
replaceVoxels(Voxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Replaces the voxels in the object-mask.
replaceVoxels(Voxels<T>) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: Replaces the voxels in the box.
requestOmitExperimentIdentifier() - Method in class org.anchoranalysis.io.output.path.prefixer.OutputPrefixerSettings: Requests that the experiment-identifier (name and index) is not included in the output-directory path.
requestOmitExperimentIdentifier(String) - Method in class org.anchoranalysis.experiment.arguments.OutputArguments: Requests that the experiment-identifier (name and index) is not included in the output-directory path.
requestOutputIncrementingNumberSequence() - Method in class org.anchoranalysis.experiment.arguments.OutputArguments: Requests outputting with an incrementing number sequence, rather than the usual outputter (normally based upon input filenames).
requestOutputIncrementingNumberSequence() - Method in class org.anchoranalysis.io.output.path.prefixer.OutputPrefixerSettings: Requests outputting with an incrementing number sequence, rather than the usual outputter (normally based upon input filenames).
requestOutputSuppressDirectories() - Method in class org.anchoranalysis.experiment.arguments.OutputArguments: Requests suppressing directories (replacing subdirectory separators with an underscore) in the identifiers that are outputted.
requestOutputSuppressDirectories() - Method in class org.anchoranalysis.io.output.path.prefixer.OutputPrefixerSettings: Requests suppressing directories (replacing subdirectory separators with an underscore) in the identifiers that are outputted.
RequireArguments - Class in org.anchoranalysis.experiment.bean.require: A predicate on whether all necessary arguments exist for some purpose.
RequireArguments() - Constructor for class org.anchoranalysis.experiment.bean.require.RequireArguments
RequireDebugMode - Class in org.anchoranalysis.experiment.bean.require: Require that debug-mode has been enabled.
RequireDebugMode() - Constructor for class org.anchoranalysis.experiment.bean.require.RequireDebugMode
requiresImageMetadata() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.image.SummarizerImageMetadata
requiresImageMetadata() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.input.ExtractIdentifier
requiresImageMetadata() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.input.ExtractIdentifierAndPath
requiresImageMetadata() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.input.ExtractPath
requiresImageMetadata() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.path.SummarizerPath
requiresImageMetadata() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.Summarizer: Whether a ImageMetadataInput is required as an input.
requiresImageMetadata() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerAggregate
requiresImageMetadata() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerCount
requiresImageMetadata() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerListMultiline
requiresImageMetadata() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerSplitMoreThan
reset() - Method in class org.anchoranalysis.core.cache.CachedSupplierBase: Ensures the object is unevaluated, deleting any cached result if it exists.
reset() - Method in class org.anchoranalysis.math.arithmetic.RunningSum: Reset the sum and count to zero.
reset() - Method in class org.anchoranalysis.math.arithmetic.RunningSumCollection: Resets all items to zero.
reset() - Method in class org.anchoranalysis.math.histogram.Histogram: Sets the count for all values to 0.
reset() - Method in class org.anchoranalysis.mpp.mark.voxelized.memo.VoxelizedMarkMemo: Resets the cached voxelized mark.
resetInd() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedIndividual: Resets the list of individual energy totals.
ResettableCalculation - Interface in org.anchoranalysis.feature.calculate.cache: A calculation that be invalidated (resetted), removing any existing cached value.
resize(VoxelsUntyped, VoxelsUntyped) - Method in class org.anchoranalysis.image.voxel.resizer.VoxelsResizer: Copies voxels slice-by-slice from source to destination performing necessary interpolation.
resizeByte(VoxelBuffer<UnsignedByteBuffer>, VoxelBuffer<UnsignedByteBuffer>, Extent, Extent) - Method in class org.anchoranalysis.image.voxel.resizer.VoxelsResizer: Interpolates from voxelsSource to voxelsDestination for unsigned 8-bit buffers.
resizeByte(VoxelBuffer<UnsignedByteBuffer>, VoxelBuffer<UnsignedByteBuffer>, Extent, Extent) - Method in class org.anchoranalysis.image.voxel.resizer.VoxelsResizerExecutionTime
resizeByte(VoxelBuffer<UnsignedByteBuffer>, VoxelBuffer<UnsignedByteBuffer>, Extent, Extent) - Method in class org.anchoranalysis.image.voxel.resizer.VoxelsResizerImgLib2
resizeByte(VoxelBuffer<UnsignedByteBuffer>, VoxelBuffer<UnsignedByteBuffer>, Extent, Extent) - Method in class org.anchoranalysis.image.voxel.resizer.VoxelsResizerNone
resizeByte(VoxelBuffer<UnsignedByteBuffer>, VoxelBuffer<UnsignedByteBuffer>, Extent, Extent) - Method in class org.anchoranalysis.io.imagej.resizer.VoxelsResizerImageJ
resizeByte(VoxelBuffer<UnsignedByteBuffer>, VoxelBuffer<UnsignedByteBuffer>, Extent, Extent) - Method in class org.anchoranalysis.plugin.opencv.resizer.VoxelsResizerOpenCV
resizedXY(int, int, VoxelsResizer) - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter: Creates a new voxels that are a resized version of the current voxels (only in X and Y dimensions), interpolating as needed.
resizeFloat(VoxelBuffer<FloatBuffer>, VoxelBuffer<FloatBuffer>, Extent, Extent) - Method in class org.anchoranalysis.image.voxel.resizer.VoxelsResizer: Interpolates from voxelsSource to voxelsDestination for float buffers.
resizeFloat(VoxelBuffer<FloatBuffer>, VoxelBuffer<FloatBuffer>, Extent, Extent) - Method in class org.anchoranalysis.image.voxel.resizer.VoxelsResizerExecutionTime
resizeFloat(VoxelBuffer<FloatBuffer>, VoxelBuffer<FloatBuffer>, Extent, Extent) - Method in class org.anchoranalysis.image.voxel.resizer.VoxelsResizerImgLib2
resizeFloat(VoxelBuffer<FloatBuffer>, VoxelBuffer<FloatBuffer>, Extent, Extent) - Method in class org.anchoranalysis.image.voxel.resizer.VoxelsResizerNone
resizeFloat(VoxelBuffer<FloatBuffer>, VoxelBuffer<FloatBuffer>, Extent, Extent) - Method in class org.anchoranalysis.io.imagej.resizer.VoxelsResizerImageJ
resizeFloat(VoxelBuffer<FloatBuffer>, VoxelBuffer<FloatBuffer>, Extent, Extent) - Method in class org.anchoranalysis.plugin.opencv.resizer.VoxelsResizerOpenCV
resizeShort(VoxelBuffer<UnsignedShortBuffer>, VoxelBuffer<UnsignedShortBuffer>, Extent, Extent) - Method in class org.anchoranalysis.image.voxel.resizer.VoxelsResizer: Interpolates from voxelsSource to voxelsDestination for unsigned 16-bit buffers.
resizeShort(VoxelBuffer<UnsignedShortBuffer>, VoxelBuffer<UnsignedShortBuffer>, Extent, Extent) - Method in class org.anchoranalysis.image.voxel.resizer.VoxelsResizerExecutionTime
resizeShort(VoxelBuffer<UnsignedShortBuffer>, VoxelBuffer<UnsignedShortBuffer>, Extent, Extent) - Method in class org.anchoranalysis.image.voxel.resizer.VoxelsResizerImgLib2
resizeShort(VoxelBuffer<UnsignedShortBuffer>, VoxelBuffer<UnsignedShortBuffer>, Extent, Extent) - Method in class org.anchoranalysis.image.voxel.resizer.VoxelsResizerNone
resizeShort(VoxelBuffer<UnsignedShortBuffer>, VoxelBuffer<UnsignedShortBuffer>, Extent, Extent) - Method in class org.anchoranalysis.io.imagej.resizer.VoxelsResizerImageJ
resizeShort(VoxelBuffer<UnsignedShortBuffer>, VoxelBuffer<UnsignedShortBuffer>, Extent, Extent) - Method in class org.anchoranalysis.plugin.opencv.resizer.VoxelsResizerOpenCV
resizeXY(int, int) - Method in class org.anchoranalysis.image.core.dimensions.Dimensions: Resizes the dimensions to have new sizes in the X and Y dimension.
resizeXY(int, int, VoxelsResizer) - Method in class org.anchoranalysis.image.core.channel.Channel: Like Channel.resizeXY(Extent, VoxelsResizer) but specifies the size via int parameters.
resizeXY(Extent, VoxelsResizer) - Method in class org.anchoranalysis.image.core.channel.Channel: Resizes the dimensions of the channel, interpolating the existing voxel values to match.
resolution() - Method in class org.anchoranalysis.feature.energy.EnergyStack: The image-resolution associated with the energy-stack.
resolution() - Method in class org.anchoranalysis.image.core.channel.Channel: The resolution of the voxel that describes a physical size for each voxel.
resolution() - Method in class org.anchoranalysis.image.core.dimensions.Dimensions: Resolution of voxels to physical measurements.
resolution() - Method in class org.anchoranalysis.image.core.mask.Mask: Resolution of voxels to physical measurements.
resolution() - Method in class org.anchoranalysis.image.core.stack.DisplayStack: Resolution of voxels to physical measurements.
resolution() - Method in class org.anchoranalysis.image.core.stack.Stack: Resolution of voxels to physical measurements.
resolution(Resolution) - Method in enum class org.anchoranalysis.image.core.dimensions.OrientationChange: A Resolution that describes resolution after the orientation change.
Resolution - Class in org.anchoranalysis.image.core.dimensions: The resolution of an image.
Resolution() - Constructor for class org.anchoranalysis.image.core.dimensions.Resolution: Creates with a default resolution with value 1.0 in each dimension.
Resolution(double, double, double) - Constructor for class org.anchoranalysis.image.core.dimensions.Resolution: Creates with a resolution from three double values for each dimension.
Resolution(Tuple3d) - Constructor for class org.anchoranalysis.image.core.dimensions.Resolution: Constructs a resolution from a tuple.
ResolutionAsXML - Class in org.anchoranalysis.plugin.io.xml: Reads and writes a metadata XML file specifying the image-resolution.
ResolutionFixture - Class in org.anchoranalysis.test.image: Provides a pre-created Resolution instance for use in tests.
resolutionRequired() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeBase: Gets the required Resolution.
resolve(String) - Method in class org.anchoranalysis.image.inference.bean.segment.instance.SegmentStackIntoObjectsPooled: Resolves a relative filename for a model into a path, relative to the model directory.
resolve(Path, Path) - Static method in class org.anchoranalysis.core.system.path.ResolvePathAbsolute: Like Path.resolve(java.nio.file.Path) but with some additional quirks.
resolve(Optional<Resolution>, boolean) - Method in class org.anchoranalysis.mpp.bean.bound.Bound: Resolves the bound based on the given resolution and dimensionality.
resolve(Optional<UnitConverter>, DirectionVector) - Method in class org.anchoranalysis.image.bean.unitvalue.distance.DistancePhysical
resolve(Optional<UnitConverter>, DirectionVector) - Method in class org.anchoranalysis.image.bean.unitvalue.distance.DistanceVoxels
resolve(Optional<UnitConverter>, DirectionVector) - Method in class org.anchoranalysis.image.bean.unitvalue.distance.UnitValueDistance: Resolves the distance using a DirectionVector.
resolve(Optional<UnitConverter>, Point3d, Point3d) - Method in class org.anchoranalysis.image.bean.unitvalue.distance.UnitValueDistance: Resolves the distance using the direction between two points of type Point3d.
resolve(Optional<UnitConverter>, Point3i, Point3i) - Method in class org.anchoranalysis.image.bean.unitvalue.distance.UnitValueDistance: Resolves the distance using the direction between two points of type Point3i.
ResolvedBound - Class in org.anchoranalysis.mpp.bean.bound: A bound resolved into pixel units.
ResolvedBound() - Constructor for class org.anchoranalysis.mpp.bean.bound.ResolvedBound
ResolvedBound(double, double) - Constructor for class org.anchoranalysis.mpp.bean.bound.ResolvedBound
ResolvedBound(ResolvedBound) - Constructor for class org.anchoranalysis.mpp.bean.bound.ResolvedBound: Creates a new instance by copying another ResolvedBound.
ResolvedPart<S,T> - Class in org.anchoranalysis.feature.calculate.cache.part: Like a CalculationPart but has been resolved against a cache to reuse any existing identical instance.
ResolvedPart(CalculationPart<S, T>) - Constructor for class org.anchoranalysis.feature.calculate.cache.part.ResolvedPart: Creates a new ResolvedPart instance.
ResolvedPartMap<S,T,U> - Class in org.anchoranalysis.feature.calculate.cache.part: A CalculationPartMap that has been resolved against a cache.
ResolvedPartMap(CalculationPartMap<S, T, U, FeatureCalculationException>) - Constructor for class org.anchoranalysis.feature.calculate.cache.part.ResolvedPartMap: Creates with a map.
resolveFeatureIdentifier(String) - Method in interface org.anchoranalysis.feature.calculate.cache.FeatureSymbolCalculator: Resolves an identifier to a unique-string, suitable for FeatureSymbolCalculator.calculateFeatureByIdentifier(String, FeatureCalculationInput).
resolveForAxis(Optional<UnitConverter>, Axis) - Method in class org.anchoranalysis.image.bean.unitvalue.distance.UnitValueDistance: Resolves the distance in a direction aligned to a particular axis.
resolveName(String) - Method in class org.anchoranalysis.bean.define.adder.DefineAdderWithPrefixBean: Prepends a prefix before the name.
resolvePath(String) - Method in class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixer: Like PathPrefixer.resolvePath(Path) but accepts a String as the path.
resolvePath(Path) - Method in class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixer: Converts a relative-path to an absolute-path (relative to the file-path associated with this current bean)
ResolvePathAbsolute - Class in org.anchoranalysis.core.system.path: More advanced implementation of Path.resolve(java.nio.file.Path).
resolver() - Method in interface org.anchoranalysis.feature.calculate.FeatureCalculationInput: A resolver for calculations.
resolver() - Method in class org.anchoranalysis.feature.session.SessionInputSequential
resolveTestPath(String) - Method in class org.anchoranalysis.test.image.io.TestLoaderImage: Resolves a test path to an actual file system path.
resolveTestPath(String) - Method in class org.anchoranalysis.test.TestLoader: Resolves a path to test-data (relative path to the test-data root) to an absolute path on the file system.
resolveToVoxels(Optional<UnitConverter>) - Method in class org.anchoranalysis.image.bean.unitvalue.extent.area.AreaPhysical
resolveToVoxels(Optional<UnitConverter>) - Method in class org.anchoranalysis.image.bean.unitvalue.extent.area.AreaPixels
resolveToVoxels(Optional<UnitConverter>) - Method in class org.anchoranalysis.image.bean.unitvalue.extent.UnitValueExtent: Resolves a measurement of area/volume (in whatever units) to units corresponding to the image pixels/voxels.
resolveToVoxels(Optional<UnitConverter>) - Method in class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumePhysical
resolveToVoxels(Optional<UnitConverter>) - Method in class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumeVoxels
resources() - Method in class org.anchoranalysis.launcher.config.LauncherConfig
Resources - Class in org.anchoranalysis.launcher.resources: Accesses resource-files associated with this application.
Resources(ClassLoader, String, String, String, String, Optional<String>) - Constructor for class org.anchoranalysis.launcher.resources.Resources: Creates a new Resources instance.
ResultsVector - Class in org.anchoranalysis.feature.results: A vector of results of applying a feature-calculations to many entities.
ResultsVector(int) - Constructor for class org.anchoranalysis.feature.results.ResultsVector: Creates with a particular size.
ResultsVectorList - Class in org.anchoranalysis.feature.results: A list of elements of type ResultsVector.
ResultsVectorList() - Constructor for class org.anchoranalysis.feature.results.ResultsVectorList
ResultsVectorList(ResultsVector) - Constructor for class org.anchoranalysis.feature.results.ResultsVectorList: Creates with the list containing a single item.
ResultsVectorTestUtilities - Class in org.anchoranalysis.test.feature.plugins: Utility class for testing ResultsVector objects.
ResultsVectorWithThumbnail - Class in org.anchoranalysis.plugin.image.task.feature: A results-vector with an optional thumbnail associated with it.
ResultsVectorWithThumbnail(CheckedSupplier<ResultsVector, OperationFailedException>) - Constructor for class org.anchoranalysis.plugin.image.task.feature.ResultsVectorWithThumbnail: Creates a new instance with a results vector and no thumbnail.
ResultsVectorWithThumbnail(CheckedSupplier<ResultsVector, OperationFailedException>, CheckedSupplier<Optional<DisplayStack>, OperationFailedException>) - Constructor for class org.anchoranalysis.plugin.image.task.feature.ResultsVectorWithThumbnail: Creates a new ResultsVectorWithThumbnail instance.
retrieveCreateAggregatedChannel() - Method in class org.anchoranalysis.image.bean.channel.ChannelAggregator: Retrieve or create an aggregated-channel of type outputType.
retrieveCreateAggregatedChannel() - Method in class org.anchoranalysis.plugin.image.bean.channel.aggregator.ProjectableBufferAggregator
reuseByte(Voxels<UnsignedByteBuffer>) - Static method in class org.anchoranalysis.image.voxel.binary.BinaryVoxelsFactory: Like BinaryVoxelsFactory.reuseByte(org.anchoranalysis.image.voxel.Voxels<org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer>) but uses default binary-values for off (0) and on (255).
reuseByte(Voxels<UnsignedByteBuffer>, BinaryValuesInt) - Static method in class org.anchoranalysis.image.voxel.binary.BinaryVoxelsFactory: Reuses an existing voxel-buffer (of type unsigned byte) as a binary-version which should have only two intensity-values representing off and on.
reuseInt(Voxels<UnsignedIntBuffer>, BinaryValuesInt) - Static method in class org.anchoranalysis.image.voxel.binary.BinaryVoxelsFactory: Reuses an existing voxel-buffer (of type unsigned int) as a binary-version which should have only two intensity-values representing off and on.
ReuseSingletonStrategy<T> - Class in org.anchoranalysis.feature.session.replace: Always re-use an existing SessionInputSequential, invalidating it each time a new call occurs.
ReuseSingletonStrategy(CacheCreator) - Constructor for class org.anchoranalysis.feature.session.replace.ReuseSingletonStrategy: Constructor with default means of creating a FeatureCalculationInput.
ReuseSingletonStrategy(CacheCreator, ChildCacheFinder) - Constructor for class org.anchoranalysis.feature.session.replace.ReuseSingletonStrategy: Constructor with custom means of creating a FeatureCalculationInput
reverseIterateArray(T[], CheckedConsumer<T, E>) - Static method in class org.anchoranalysis.core.functional.FunctionalIterate: Iterates through every element in an array in reverse order
rewind() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer: Rewinds the buffer ala ByteBuffer.rewind().
rgb(boolean) - Method in class org.anchoranalysis.image.io.stack.output.StackWriteAttributes: Derives a StackWriteAttributes that will be RGB or RGB-A, but is otherwise unchanged.
rgb(boolean, boolean) - Static method in class org.anchoranalysis.image.io.stack.output.StackWriteAttributesFactory: A StackWriteAttributes which is always RGB, and depending on a flag, may be guaranteed to be 2D.
RGB_WITH_ALPHA - Enum constant in enum class org.anchoranalysis.image.io.stack.output.StackRGBState: RGB with a alpha channel.
RGB_WITHOUT_ALPHA - Enum constant in enum class org.anchoranalysis.image.io.stack.output.StackRGBState: RGB without any alpha channel.
RGBChannelNames - Class in org.anchoranalysis.image.core.stack: Constants for referring to the channels in a RGB-stack or RGBA-stack.
RGBColor - Class in org.anchoranalysis.core.color: A color encoded in RGB color space.
RGBColor() - Constructor for class org.anchoranalysis.core.color.RGBColor: Create with black color.
RGBColor(int) - Constructor for class org.anchoranalysis.core.color.RGBColor: Creates with an RGB value encoded as an int, as in the constructor for Color.
RGBColor(int, int, int) - Constructor for class org.anchoranalysis.core.color.RGBColor: Creates with specific values for the red, green and blue components.
RGBColor(Color) - Constructor for class org.anchoranalysis.core.color.RGBColor: Create from a Color.
RGBColorBean - Class in org.anchoranalysis.bean.shared.color: A bean describing a color in the RGB color space.
RGBColorBean() - Constructor for class org.anchoranalysis.bean.shared.color.RGBColorBean: Creates with a completely black color.
RGBColorBean(int, int, int) - Constructor for class org.anchoranalysis.bean.shared.color.RGBColorBean: Create from values for red, green and blue.
RGBColorBean(Color) - Constructor for class org.anchoranalysis.bean.shared.color.RGBColorBean: Create from a Color.
RGBColorBean(RGBColor) - Constructor for class org.anchoranalysis.bean.shared.color.RGBColorBean: Create from a RGBColor.
RGBIfNamesMatch - Class in org.anchoranalysis.plugin.image.task.bean.format.convertstyle: Converts a set of channels to a single RGB-stack if the channel-names match, otherwise uses fallback.
RGBIfNamesMatch() - Constructor for class org.anchoranalysis.plugin.image.task.bean.format.convertstyle.RGBIfNamesMatch
rgbMaybe3D(boolean) - Static method in class org.anchoranalysis.image.io.stack.output.StackWriteAttributesFactory: A StackWriteAttributes which is always RGB/RGBA, and is not guaranteed to be 2D.
RGBStack - Class in org.anchoranalysis.image.core.stack: A stack with exactly three channels, respectively for red, green and blue colors.
RGBStack(Channel, Channel, Channel) - Constructor for class org.anchoranalysis.image.core.stack.RGBStack: Create with Channels for each color.
RGBStack(Dimensions, ChannelFactorySingleType) - Constructor for class org.anchoranalysis.image.core.stack.RGBStack: Creates a particularly-sized stack with all channels initialized to 0.
RGBStack(Stack) - Constructor for class org.anchoranalysis.image.core.stack.RGBStack: Creates from an existing stack (which must have 1 or 3 channels).
RGBStack(Extent) - Constructor for class org.anchoranalysis.image.core.stack.RGBStack: Creates a particularly-sized stack with unsigned byte voxel data type, with all voxels initialized to 0.
RGBStack(Extent, Color) - Constructor for class org.anchoranalysis.image.core.stack.RGBStack: Creates a particularly-sized stack with unsigned byte voxel data type, with all voxels initialized to a specific Color.
RGBStack(Extent, RGBColor) - Constructor for class org.anchoranalysis.image.core.stack.RGBStack: Creates a particularly-sized stack with unsigned byte voxel data type, with all voxels initialized to a specific RGBColor.
RGBStack(Extent, ChannelFactorySingleType) - Constructor for class org.anchoranalysis.image.core.stack.RGBStack: Creates a particularly-sized stack with all channels initialized to 0.
RIGHT - Static variable in class org.anchoranalysis.image.bean.nonbean.spatial.align.PositionChoicesConstants: Align to the right in the X-dimension/
rightPad(String, int) - Static method in class org.anchoranalysis.core.value.StringUtilities: Right-pad a string with whitespace, so it reaches a fixed length.
rightSize() - Method in class org.anchoranalysis.annotation.io.assignment.OverlappingObjects: The total number of objects in the right set.
rmv(int) - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedIndividual: Removes an energy total at a specific index and updates the total energy.
rootDirectory(InputContextParameters) - Method in class org.anchoranalysis.io.input.bean.files.FilesProvider: A root directory for these files, if it exists.
rootDirectory(InputContextParameters) - Method in class org.anchoranalysis.io.input.bean.files.FilesProviderUnary
rootDirectory(InputContextParameters) - Method in class org.anchoranalysis.io.input.bean.files.FilesProviderWithDirectory
rootDirectory(InputContextParameters) - Method in class org.anchoranalysis.io.input.bean.files.FilesProviderWithoutDirectory
rootDirectory(InputContextParameters) - Method in class org.anchoranalysis.io.input.bean.files.SpecificPathList
rootDirectoryPrefix(Optional<String>, PathPrefixerContext) - Method in class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixer: Provides a prefix that becomes the root-folder.
rootDirectoryPrefix(Optional<String>, PathPrefixerContext) - Method in class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixerAvoidResolve
rootDirectoryPrefix(Optional<String>, PathPrefixerContext) - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.HomeSubdirectory
rootDirectoryPrefix(Optional<String>, PathPrefixerContext) - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.Rooted
rootDirectoryPrefixAvoidResolve(Optional<String>) - Method in class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixerAvoidResolve: Provides a prefix that becomes the root-folder.
Rooted - Class in org.anchoranalysis.plugin.io.bean.file.path.prefixer: Prepend a 'root' before the file-path-prefix obtained from a delegate
Rooted - Class in org.anchoranalysis.plugin.io.bean.file.provider: Represents a set of files, with a different path-root depending on context.
Rooted - Class in org.anchoranalysis.plugin.io.bean.path.derive
Rooted() - Constructor for class org.anchoranalysis.plugin.io.bean.file.path.prefixer.Rooted
Rooted() - Constructor for class org.anchoranalysis.plugin.io.bean.file.provider.Rooted
Rooted() - Constructor for class org.anchoranalysis.plugin.io.bean.path.derive.Rooted
Rooted(PathPrefixerAvoidResolve, String) - Constructor for class org.anchoranalysis.plugin.io.bean.file.path.prefixer.Rooted: Creates a new Rooted instance.
RootedFilePath - Class in org.anchoranalysis.plugin.io.bean.file.path
RootedFilePath() - Constructor for class org.anchoranalysis.plugin.io.bean.file.path.RootedFilePath
RootedFilePathUtilities - Class in org.anchoranalysis.plugin.io.input.path
RootPath - Class in org.anchoranalysis.bean.shared.path: Defines a root path.
RootPath() - Constructor for class org.anchoranalysis.bean.shared.path.RootPath
RootPathMap - Class in org.anchoranalysis.plugin.io.input.path: A collection of root-paths indexed by their name.
RotatableBoundingBox - Class in org.anchoranalysis.mpp.mark.points: A two-dimensional bounding-box rotated at arbitrary angle in XY plane around a point.
RotatableBoundingBox() - Constructor for class org.anchoranalysis.mpp.mark.points.RotatableBoundingBox: Creates a new RotatableBoundingBox with default values.
RotatableBoundingBoxFactory - Class in org.anchoranalysis.mpp.mark.points: Creates instances of RotatableBoundingBox.
ROTATE_180 - Enum constant in enum class org.anchoranalysis.image.core.dimensions.OrientationChange: Pixels should appear 180 degrees rotated in the clockwise direction.
ROTATE_180_MIRROR - Enum constant in enum class org.anchoranalysis.image.core.dimensions.OrientationChange: Pixels should appear 180 degrees rotated in the clockwise direction, and then mirrored across the X-dimension.
ROTATE_90_ANTICLOCKWISE - Enum constant in enum class org.anchoranalysis.image.core.dimensions.OrientationChange: Pixels should appear 90 degrees rotated in the anti-clockwise direction.
ROTATE_90_ANTICLOCKWISE_MIRROR - Enum constant in enum class org.anchoranalysis.image.core.dimensions.OrientationChange: Pixels should appear 90 degrees rotated in the anticlockwise direction, and then mirrored across the X-dimension.
ROTATE_90_CLOCKWISE - Enum constant in enum class org.anchoranalysis.image.core.dimensions.OrientationChange: Pixels should appear 90 degrees rotated in the clockwise direction.
ROTATE_90_CLOCKWISE_MIRROR - Enum constant in enum class org.anchoranalysis.image.core.dimensions.OrientationChange: Pixels should appear 90 degrees rotated clockwise, and then mirrored across the X-dimension.
RotateImageToMatchEXIFOrientation - Class in org.anchoranalysis.plugin.io.bean.stack.reader: Rotates an image to match any EXIF orientation information, if it exists.
RotateImageToMatchEXIFOrientation() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.reader.RotateImageToMatchEXIFOrientation
RotateImageToMatchEXIFOrientation(StackReaderOrientationCorrection) - Constructor for class org.anchoranalysis.plugin.io.bean.stack.reader.RotateImageToMatchEXIFOrientation: Creates a new RotateImageToMatchEXIFOrientation instance.
rotatePoint(Tuple3d) - Method in class org.anchoranalysis.spatial.orientation.RotationMatrix: Performs a rotation on a single point, encoded as a Point3d.
rotatePointInplace(Point3d) - Method in class org.anchoranalysis.spatial.orientation.RotationMatrix: Performs a rotation on a single point, replacing the existing value of the point.
RotationMatrix - Class in org.anchoranalysis.spatial.orientation: A matrix that performs a rotation in Euclidean space.
RotationMatrix(int) - Constructor for class org.anchoranalysis.spatial.orientation.RotationMatrix: Creates a rotation-matrix populated only with zeros.
RotationMatrix(DoubleMatrix2D) - Constructor for class org.anchoranalysis.spatial.orientation.RotationMatrix: Creates a rotation-matrix from an existing DoubleMatrix2D.
RowLabels - Class in org.anchoranalysis.feature.io.csv.metadata: Labels for each row of feature-results in the outputted CSV row.
RowLabels(String) - Constructor for class org.anchoranalysis.feature.io.csv.metadata.RowLabels: Creates with a single string as an identifier.
RowLabels(Optional<String[]>, Optional<MultiName>) - Constructor for class org.anchoranalysis.feature.io.csv.metadata.RowLabels: Creates a new RowLabels instance.
RTree<T> - Class in org.anchoranalysis.spatial.rtree: Bases class for implementations of R-Trees that store objects with associated geometry.
RTree(int) - Constructor for class org.anchoranalysis.spatial.rtree.RTree: Creates an empty R-Tree.
RTree(int, int) - Constructor for class org.anchoranalysis.spatial.rtree.RTree: Creates an empty R-Tree with a specified number of children.
run() - Method in interface org.anchoranalysis.core.functional.checked.CheckedRunnable: Runs an operation like with Runnable.run().
runCommandLineApplication(String[], LauncherConfig, Logger) - Static method in class org.anchoranalysis.launcher.Launch: Runs a command-line application, by parsing arguments, and then executing an experiment.
runExperiment(String) - Method in class org.anchoranalysis.test.experiment.launcher.ExperimentLauncherFromShell: Runs an experiment identified by an XML found in the resources
runExperiment(String, Optional<String>, Optional<String>) - Method in class org.anchoranalysis.test.experiment.launcher.ExperimentLauncherFromShell: Runs an experiment identified by an XML found in the resources
runExperimentInTemporaryDirectory(String, Path) - Method in class org.anchoranalysis.test.experiment.launcher.ExperimentLauncherFromShell: Creates a temporary-folder, copies data all data from the associated test-loader, and runs an experiment
runExperimentInTemporaryDirectory(String, Optional<String>, Optional<String>, Path, String[]) - Method in class org.anchoranalysis.test.experiment.launcher.ExperimentLauncherFromShell: Creates a temporary-folder, copies data all data from the associated test-loader, and runs an experiment
RunningSum - Class in org.anchoranalysis.math.arithmetic: Mutable class that allows for incrementing jointly sum and count variables, so as to eventually calculate the mean.
RunningSum() - Constructor for class org.anchoranalysis.math.arithmetic.RunningSum
RunningSum(double, long) - Constructor for class org.anchoranalysis.math.arithmetic.RunningSum: Creates a new RunningSum instance.
RunningSumCollection - Class in org.anchoranalysis.math.arithmetic: A collection of RunningSum where an operation is executed on all objects in the collection.
RunningSumCollection(int) - Constructor for class org.anchoranalysis.math.arithmetic.RunningSumCollection: Constructor.
RunningSumExtrema - Class in org.anchoranalysis.math.arithmetic: Like a RunningSum but also remembers the mean and max across all the added values.
RunningSumExtrema() - Constructor for class org.anchoranalysis.math.arithmetic.RunningSumExtrema
RunningSumParented - Class in org.anchoranalysis.experiment.time: Wraps a RunningSum with an additional variable, indicating the total number of parent operations.
RunningSumParented(int) - Constructor for class org.anchoranalysis.experiment.time.RunningSumParented: Creates a new RunningSumParented instance.
RunningSumPoint - Class in org.anchoranalysis.spatial.point: A running sum for tracking points separately in each dimension.
RunningSumPoint() - Constructor for class org.anchoranalysis.spatial.point.RunningSumPoint

S

sampleDoubleFromRange(double) - Method in interface org.anchoranalysis.core.random.RandomNumberGenerator: Generates a uniformly random floating-point number within a range from 0 (exclusive) to endExclusive.
sampleDoubleFromRange(double, double) - Method in interface org.anchoranalysis.core.random.RandomNumberGenerator: Generates a uniformly random floating-point number within a range.
sampleDoubleFromZeroCenteredRange(double) - Method in interface org.anchoranalysis.core.random.RandomNumberGenerator: Generates a uniformly random floating-point number centered around 0 ranging from [-halfWidth,+halfWidth] (both exclusive).
sampleDoubleZeroAndOne() - Method in interface org.anchoranalysis.core.random.RandomNumberGenerator: Samples from a uniformly-distributed range between 0.0 (exclusive) and 1.0 (exclusive).
sampleDoubleZeroAndOne() - Method in class org.anchoranalysis.core.random.RandomNumberGeneratorMersenne
sampleFromList(List<T>) - Method in interface org.anchoranalysis.core.random.RandomNumberGenerator: Samples uniformly an element from a list.
sampleInteger(int) - Method in class org.anchoranalysis.mpp.proposer.ProposerContext: Samples an integer uniformly between [0..maxValExclusive).
sampleIntFromRange(int) - Method in interface org.anchoranalysis.core.random.RandomNumberGenerator: Generates a uniformly random discrete number within a range from 0 (inclusive) to endExclusive.
sampleIntFromRange(int, int) - Method in interface org.anchoranalysis.core.random.RandomNumberGenerator: Samples from a uniformly random discrete number within a range.
sampleLongFromRange(long) - Method in interface org.anchoranalysis.core.random.RandomNumberGenerator: Generates a uniformly random discrete number within a range from 0 (inclusive) to endExclusive.
sampleRandomPairNonUniform(RandomNumberGenerator) - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
sampleRandomPairNonUniform(RandomNumberGenerator) - Method in class org.anchoranalysis.mpp.pair.RandomCollection: Samples a random pair of items from the collection using a non-uniform distribution.
SampleWithDirectory - Class in org.anchoranalysis.plugin.io.bean.file.provider
SampleWithDirectory() - Constructor for class org.anchoranalysis.plugin.io.bean.file.provider.SampleWithDirectory
SavedFiles - Class in org.anchoranalysis.test.image.stackwriter: Access previously saved-files in resources.
ScalarProposer - Class in org.anchoranalysis.mpp.bean.proposer: An abstract base class for proposing scalar values.
ScalarProposer() - Constructor for class org.anchoranalysis.mpp.bean.proposer.ScalarProposer
ScalarThreeDimensionalConsumer - Interface in org.anchoranalysis.spatial.point.consumer: Like a IntConsumer but accepts three coordinates of a point as scalar arguments.
ScalarTwoDimensionalConsumer - Interface in org.anchoranalysis.spatial.point.consumer: Like a IntConsumer but accepts two coordinates of a point as scalar arguments.
scale(double) - Method in class org.anchoranalysis.mpp.bean.bound.Bound: Scales the bound by a multiplication factor.
scale(double) - Method in class org.anchoranalysis.mpp.bean.bound.BoundMinMax
scale(double) - Method in class org.anchoranalysis.mpp.bean.bound.ResolvedBound: Scales the bound by a multiplication factor.
scale(double) - Method in class org.anchoranalysis.spatial.point.Point2d: Arithmetically multiplies each dimension's value by a factor.
scale(double) - Method in class org.anchoranalysis.spatial.point.Point2f: Multiplies each dimension's component by a factor.
scale(double) - Method in class org.anchoranalysis.spatial.point.Tuple3d: Arithmetically multiply values across each dimension.
scale(double) - Method in class org.anchoranalysis.spatial.point.Tuple3i: Arithmetically multiplies by a value across each dimension.
scale(int) - Method in class org.anchoranalysis.spatial.point.Tuple3i: Arithmetically multiplies by a value across each dimension.
scale(int, int) - Method in class org.anchoranalysis.spatial.scale.ScaleFactorInt: Multiplies a point by the respective scaling-factor in each dimension.
scale(Extent) - Method in class org.anchoranalysis.spatial.scale.ScaleFactorInt: Multiplies an Extent by the respective scaling-factor in each dimension.
scale(Point2i) - Method in class org.anchoranalysis.spatial.scale.ScaleFactorInt: Multiplies a Point2i by the respective scaling-factor in each dimension.
scale(Point3d) - Method in class org.anchoranalysis.spatial.scale.ScaleFactor: Multiplies a Point3d by the respective scaling-factor in each X and Y dimensions.
scale(ScaleFactor) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Produces a scaled-version of an object-mask.
scale(ScaleFactor) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
scale(ScaleFactor) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
scale(ScaleFactor) - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius: Objects are scaled in pre-rotated position.
scale(ScaleFactor) - Method in class org.anchoranalysis.mpp.mark.Mark: Scales the mark in X and Y dimensions.
scale(ScaleFactor) - Method in class org.anchoranalysis.mpp.mark.MarkWithPosition
scale(ScaleFactor) - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
scale(ScaleFactor) - Method in class org.anchoranalysis.mpp.mark.points.PointList: Scales the points in the list by a given scale factor.
scale(ScaleFactor) - Method in class org.anchoranalysis.mpp.mark.points.Polygon
scale(ScaleFactor) - Method in class org.anchoranalysis.mpp.mark.points.PolygonCurve
scale(ScaleFactor) - Method in class org.anchoranalysis.mpp.mark.points.RotatableBoundingBox
scale(ScaleFactor) - Method in class org.anchoranalysis.spatial.box.BoundingBox: Scales the bounding-box, both the corner-point and the extent.
scale(ScaleFactor, Optional<Extent>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Produces a scaled-version of an object-mask.
scale(ScaleFactor, VoxelsResizer, Optional<Extent>) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: Creates a scaled-version (in XY dimensions only) of the current bounding-box.
scale(ScaleFactor, Extent) - Method in class org.anchoranalysis.spatial.box.BoundingBox: Scales the bounding-box corner-point, and assigns a new extent.
scale(ScaleFactor, Point3i) - Static method in class org.anchoranalysis.spatial.scale.Scaler: Scales a point in XY by multiplying each dimension by its corresponding scaling-factor.
Scale - Class in org.anchoranalysis.plugin.image.bean.object.provider: Scales all the objects in the collection by a particular scale-factor.
Scale() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.Scale
ScaleableBackground - Class in org.anchoranalysis.image.io.stack.output.box: A stack that can be used as a background (and maybe scaled).
scaleAndThreshold(Voxels<FloatBuffer>, Extent, VoxelsResizer, float) - Static method in class org.anchoranalysis.image.inference.segment.ScaleAndThresholdVoxels: Scales voxels representing a mask to a target size, and then thresholds.
ScaleAndThresholdVoxels - Class in org.anchoranalysis.image.inference.segment: Scales the size of a Voxels<FloatBuffer> and then thresholds it.
scaleBy(DisplayStack, ScaleFactor, VoxelsResizer) - Static method in class org.anchoranalysis.image.io.stack.output.box.ScaleableBackground: Creates a background from a stack with scaling.
ScaleByDictionary - Class in org.anchoranalysis.plugin.image.bean.channel.convert: Scales by compressing a certain range of values into the 8-bit signal.
ScaleByDictionary() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByDictionary
ScaleByMinMaxValue - Class in org.anchoranalysis.plugin.image.bean.channel.convert: Scales by compressing a certain range of values into the 8-bit signal
ScaleByMinMaxValue() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByMinMaxValue
ScaleByTypeToByte - Class in org.anchoranalysis.plugin.image.bean.channel.convert: Converts a channel to unsigned byte format, scaling the values based on the original voxel type.
ScaleByTypeToByte() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByTypeToByte
scaleCalculator - Variable in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage: Calculates what scale-factor to apply on the image.
ScaleCalculator - Class in org.anchoranalysis.image.bean.spatial: Calculating a scaling-factor from dimensions.
ScaleCalculator() - Constructor for class org.anchoranalysis.image.bean.spatial.ScaleCalculator
scaleCeil(double, int) - Static method in class org.anchoranalysis.spatial.scale.Scaler: Multiplies a quantity (integer) by a scaling-factor, returning it as an integer via ceil.
scaleCeil(ScaleFactor, Point3i) - Static method in class org.anchoranalysis.spatial.scale.Scaler: Scales a point in XY by multiplying each dimension by its corresponding scaling-factor.
scaleClampTo(ScaleFactor, Extent) - Method in class org.anchoranalysis.spatial.box.BoundingBox: Scales the bounding-box, both the corner-point and the extent - ensuring it remains inside a containing-extent.
ScaledElements<T> - Class in org.anchoranalysis.image.core.object.scale: A list of elements, with an ObjectMask representation, that have been scaled.
ScaledElements(List<T>, ScaleFactor, ObjectScalingMethod, Optional<UnaryOperator<T>>, Optional<UnaryOperator<T>>, AccessObjectMask<T>) - Constructor for class org.anchoranalysis.image.core.object.scale.ScaledElements: Creates elements to be scaled.
scaledObjectFor(T) - Method in class org.anchoranalysis.image.core.object.scale.ScaledElements: Gets the scaled version of an element given the unscaled element.
scaleElements(List<T>, ScaleFactor, boolean, Extent, AccessObjectMask<T>) - Static method in class org.anchoranalysis.image.core.object.scale.Scaler: Scales every element in a list collectively, ensuring the results remain inside a particular region.
scaleElements(List<T>, ScaleFactor, Optional<UnaryOperator<T>>, Optional<UnaryOperator<T>>, AccessObjectMask<T>) - Method in interface org.anchoranalysis.image.core.object.scale.method.ObjectScalingMethod: Applies a scaling factor to elements, where each element is associated with a unique ObjectMask.
scaleElements(List<T>, ScaleFactor, AccessObjectMask<T>) - Method in interface org.anchoranalysis.image.core.object.scale.method.ObjectScalingMethod: Applies a scaling factor to elements, where each element is associated with a unique ObjectMask.
ScaleFactor - Class in org.anchoranalysis.spatial.scale: What to scale X and Y dimensions by.
ScaleFactor(double) - Constructor for class org.anchoranalysis.spatial.scale.ScaleFactor: Create with an identical scaling-factor for all dimensions.
ScaleFactor(double, double) - Constructor for class org.anchoranalysis.spatial.scale.ScaleFactor: Create with specific scaling-factors for each dimension.
ScaleFactorInt - Class in org.anchoranalysis.spatial.scale: Like ScaleFactor but only allows integer scaling-factors in each dimension.
ScaleFactorInt(int, int) - Constructor for class org.anchoranalysis.spatial.scale.ScaleFactorInt: Creates a new ScaleFactorInt instance.
scaleFactorUpscale() - Method in class org.anchoranalysis.image.inference.ImageInferenceContext: The scaling-factors needed to upscale the model output to match the desired scale.
scaleFloor(double, int) - Static method in class org.anchoranalysis.spatial.scale.Scaler: Multiplies a quantity (integer) by a scaling-factor, returning it as an integer via floor.
ScaleImage<S> - Class in org.anchoranalysis.plugin.image.task.bean.scale: Base class for tasks whose primary aim is to scale (resize) an image.
ScaleImage() - Constructor for class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage
ScaleImageCommonSize - Class in org.anchoranalysis.plugin.image.task.bean.scale: Creates a scaled copy of images, ensuring all images have identical output size.
ScaleImageCommonSize() - Constructor for class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImageCommonSize
ScaleImageIndependently - Class in org.anchoranalysis.plugin.image.task.bean.scale: Creates a scaled copy of images, treating each image independently, and without any padding or alignment.
ScaleImageIndependently() - Constructor for class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImageIndependently
scaleMultiplex(double, int, boolean) - Static method in class org.anchoranalysis.spatial.scale.Scaler: Multiplexes between Scaler.scaleRound(double, int) and Scaler.scaleCeil(org.anchoranalysis.spatial.scale.ScaleFactor, org.anchoranalysis.spatial.point.Point3i).
scaleObjects(ObjectCollection, ScaleFactor) - Static method in class org.anchoranalysis.image.core.object.scale.Scaler: Scales every object-mask in a collection collectively.
scaleObjects(ObjectCollection, ScaleFactor, boolean, Optional<UnaryOperator<ObjectMask>>, Optional<UnaryOperator<ObjectMask>>) - Static method in class org.anchoranalysis.image.core.object.scale.Scaler: Scales every object-mask in a collection collectively (if not overlappjng), allowing for additional manipulation before and after scaling.
scaleObjects(ObjectCollection, ScaleFactor, boolean, Extent) - Static method in class org.anchoranalysis.image.core.object.scale.Scaler: Scales every object-mask in a collection collectively, ensuring the results remain inside a particular region.
Scaler - Class in org.anchoranalysis.image.core.object.scale: Scales object-masks (or other more generic elements) collectively to avoid undesired overlap.
Scaler - Class in org.anchoranalysis.spatial.scale: Scales different types of entities with a ScaleFactor.
scaleRadii(double) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse: Scales the radii of the ellipse.
scaleRound(double, int) - Static method in class org.anchoranalysis.spatial.scale.Scaler: Multiplies a quantity (integer) by a scaling-factor, returning it as an integer via rounding.
scaleStack(Stack, Optional<ImageSizeSuggestion>, VoxelsResizer, NoSharedState) - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImageIndependently
scaleStack(Stack, Optional<ImageSizeSuggestion>, VoxelsResizer, CommonSize) - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImageCommonSize
scaleStack(Stack, Optional<ImageSizeSuggestion>, VoxelsResizer, S) - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage: Produce a scaled version of a Stack, mapping each channel to a scaled version of itself.
scaleToMatchRow(double, int) - Method in class org.anchoranalysis.image.bean.spatial.arrange.fill.ExtentToArrange: Changes the size of the image to match a row that has a total width of rowWidth, preserving aspect-ratio.
ScaleToSize - Class in org.anchoranalysis.plugin.image.bean.thumbnail.stack: Create a thumbnail by scales an image to a particular size.
ScaleToSize() - Constructor for class org.anchoranalysis.plugin.image.bean.thumbnail.stack.ScaleToSize
scaleToWidth(List<List<ExtentToArrange>>, boolean, int) - Static method in class org.anchoranalysis.image.bean.spatial.arrange.fill.FitCombinedScaler: Calculates the size of the combined image to use for the montage, and scales the associated Extent each to match.
scaleX(double) - Method in class org.anchoranalysis.spatial.point.Tuple3i: Arithmetically multiplies the X-axis component by a value.
scaleXY(double) - Method in class org.anchoranalysis.spatial.point.Tuple3d: Arithmetically multiply values by a factor only in X and Y dimensions.
scaleXY(double) - Method in class org.anchoranalysis.spatial.point.Tuple3i: Arithmetically multiplies the X- and Y-axis components by a value.
scaleXY(ScaleFactor) - Method in class org.anchoranalysis.annotation.mark.DualMarksAnnotation: Scales the marks in the annotation in X and Y dimensions.
scaleXY(ScaleFactor) - Method in class org.anchoranalysis.image.core.dimensions.Resolution: Multiplies the X and Y components of the resolution by a factor.
scaleXY(ScaleFactor) - Method in class org.anchoranalysis.image.core.mask.Mask: Creates a new Mask whose X- and Y- dimensions are scaled by scaleFactor.
scaleXY(ScaleFactor) - Method in class org.anchoranalysis.mpp.mark.MarkCollection: Scales all marks in the collection in X and Y dimensions.
scaleXY(ScaleFactor, VoxelsResizer) - Method in class org.anchoranalysis.image.core.channel.Channel: Resizes the dimensions of the channel, by scaling the existing size by a factor.
ScaleXY - Class in org.anchoranalysis.plugin.image.bean.channel.provider.intensity: Scales the channel in the X and Y dimensions.
ScaleXY - Class in org.anchoranalysis.plugin.image.bean.mask.provider: Scales the mask in XY dimensions, but not in Z dimension.
ScaleXY - Class in org.anchoranalysis.plugin.mpp.bean.provider.collection: Scales the X and Y coordinates of marks in a MarkCollection using a ScaleCalculator.
ScaleXY() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.ScaleXY
ScaleXY() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.ScaleXY
ScaleXY() - Constructor for class org.anchoranalysis.plugin.mpp.bean.provider.collection.ScaleXY
scaleXYBy(double, boolean) - Method in class org.anchoranalysis.spatial.box.Extent: Scales all dimensions by a scaling-factor.
scaleXYBy(ScaleFactor) - Method in class org.anchoranalysis.image.core.dimensions.Dimensions: Scales the X- and Y- dimensions by a scaling-factor.
scaleXYBy(ScaleFactor) - Method in class org.anchoranalysis.plugin.image.task.size.SizeMapping: Scales the XY dimensions the factor.
scaleXYBy(ScaleFactor, boolean) - Method in class org.anchoranalysis.spatial.box.Extent: Scales the X- and Y- dimensions by a scaling-factor.
scaleY(double) - Method in class org.anchoranalysis.spatial.point.Tuple3i: Arithmetically multiplies the Y-axis component by a value.
scaling - Variable in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.ToUnsignedByteWithScaling: The additional scaling that is applied during conversion.
sceneContains(Point2i) - Static method in class org.anchoranalysis.test.feature.plugins.objects.CircleObjectFixture: Checks if a given 2D point is within the scene dimensions.
ScoreObjects - Class in org.anchoranalysis.plugin.image.bean.channel.provider.score: Creates a channel by scoring objects based on a feature calculation.
ScoreObjects() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreObjects
ScoreVoxels - Class in org.anchoranalysis.plugin.image.bean.channel.provider.score: Assigns a score (a value indicating how probable something is) to each voxel
ScoreVoxels() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
search(CalculationPart<S, T>) - Method in interface org.anchoranalysis.feature.calculate.part.CalculationPartResolver: Searches for an equivalent calculation to calculation.
search(CalculationPartMap<S, T, U, FeatureCalculationException>) - Method in interface org.anchoranalysis.feature.calculate.part.CalculationPartResolver: Searches for an equivalent calculation to calculation.
SearchClosestValueMonoticallyIncreasing - Class in org.anchoranalysis.math.optimization: Given a monotonically increasing function of an integer, determine the input value that provides an output value as close to target as possible.
SearchClosestValueMonoticallyIncreasing(double, SearchClosestValueMonoticallyIncreasing.ValueFunction) - Constructor for class org.anchoranalysis.math.optimization.SearchClosestValueMonoticallyIncreasing: Create without an upper bound.
SearchClosestValueMonoticallyIncreasing(double, SearchClosestValueMonoticallyIncreasing.ValueFunction, IntPredicate) - Constructor for class org.anchoranalysis.math.optimization.SearchClosestValueMonoticallyIncreasing: Creates a new SearchClosestValueMonoticallyIncreasing instance.
SearchClosestValueMonoticallyIncreasing.ValueFunction - Interface in org.anchoranalysis.math.optimization: The function that calculates the output value for a particular input int.
SearchDirectory - Class in org.anchoranalysis.io.input.bean.files: Searches a directory for files whose paths match a particular predicate.
SearchDirectory() - Constructor for class org.anchoranalysis.io.input.bean.files.SearchDirectory
SearchDirectory(String) - Constructor for class org.anchoranalysis.io.input.bean.files.SearchDirectory: Create for a specific directory.
second(String) - Method in class org.anchoranalysis.io.output.enabled.multi.MultiLevelBinary
second(String) - Method in class org.anchoranalysis.io.output.enabled.multi.MultiLevelNot
second(String) - Method in interface org.anchoranalysis.io.output.enabled.multi.MultiLevelOutputEnabled: A second-level of OutputEnabled for a particular outputName as used in first-level.
second(String) - Method in class org.anchoranalysis.io.output.enabled.OutputEnabledMutable
second(String) - Method in class org.anchoranalysis.io.output.recorded.MultiLevelRecordedOutputs: A RecordedOutputs for recording second-level outputs for a given outputName from the first-level.
Second - Class in org.anchoranalysis.image.feature.bean.object.pair: Evaluates a feature on the second object in a pair of objects.
Second() - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.Second
Second(Feature<FeatureInputSingleObject>) - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.Second: Creates a new instance that will evaluate the given feature on the second object of a pair.
SECOND - Enum constant in enum class org.anchoranalysis.image.feature.calculation.CalculateInputFromPair.Extract: Extract the second object from the pair.
secondEntries() - Method in class org.anchoranalysis.io.output.recorded.MultiLevelRecordedOutputs: All second-level recorded output entries.
secondLevel(String) - Method in class org.anchoranalysis.io.output.recorded.RecordingWriters: A writer that performs a second-level check on which outputs occur, but writes to the top-level directory.
secondLevelOutputs(String, OutputEnabled) - Method in class org.anchoranalysis.io.output.bean.rules.OutputEnableRulesSpecify: Retrieves a second-level SingleLevelOutputEnabled corresponding to a first-level output-name.
secondPart() - Method in class org.anchoranalysis.feature.io.name.CombinedName
secondPart() - Method in interface org.anchoranalysis.feature.io.name.MultiName: The second part of the name.
secondPart() - Method in class org.anchoranalysis.feature.io.name.SimpleName
seek(int) - Method in class org.anchoranalysis.image.voxel.buffer.SlidingBuffer: Moves buffer to a particular z-slice.
segment(Channel, Optional<ObjectMask>, Optional<ObjectCollection>) - Method in class org.anchoranalysis.image.bean.segment.object.SegmentChannelIntoObjects: Segments a channel to produce an object-collection.
segment(Channel, Optional<ObjectMask>, Optional<ObjectCollection>) - Method in class org.anchoranalysis.image.bean.segment.object.SegmentChannelIntoObjectsUnary
segment(Channel, Optional<ObjectMask>, Optional<ObjectCollection>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.ConnectedComponentsFromBinarySegmentation
segment(Channel, Optional<ObjectMask>, Optional<ObjectCollection>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Mser
segment(Channel, Optional<ObjectMask>, Optional<ObjectCollection>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong.WatershedYeong
segment(Channel, Optional<ObjectMask>, Optional<ObjectCollection>) - Method in class org.anchoranalysis.plugin.imagej.bean.object.segment.FloodFillEachIntensityLevel
segment(Channel, Optional<ObjectMask>, Optional<ObjectCollection>, SegmentChannelIntoObjects) - Method in class org.anchoranalysis.image.bean.segment.object.SegmentChannelIntoObjectsUnary: Creates an ObjectCollection given the segmentation-results provided by the delegate.
segment(Channel, Optional<ObjectMask>, Optional<ObjectCollection>, SegmentChannelIntoObjects) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.AtScale
segment(Channel, Optional<ObjectMask>, Optional<ObjectCollection>, SegmentChannelIntoObjects) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Filter
segment(Channel, Optional<ObjectMask>, Optional<ObjectCollection>, SegmentChannelIntoObjects) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.ImposeMinima
segment(Channel, Optional<ObjectMask>, Optional<ObjectCollection>, SegmentChannelIntoObjects) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.SegmentOnMaximumIntensityAndExpandInZ
segment(Stack, ExecutionTimeRecorder) - Method in class org.anchoranalysis.image.inference.bean.segment.instance.SegmentStackIntoObjectsPooled: Segments individually using a pool of size 1 just for one stack.
segment(Stack, ConcurrentModelPool<S>, ExecutionTimeRecorder) - Method in class org.anchoranalysis.image.inference.bean.segment.instance.SegmentStackIntoObjectsScaleDecode
segment(Stack, ConcurrentModelPool<T>, ExecutionTimeRecorder) - Method in class org.anchoranalysis.image.inference.bean.segment.instance.SegmentStackIntoObjectsPooled: Segments a stack to produce an object-collection.
segment(Stack, ConcurrentModelPool<T>, ExecutionTimeRecorder) - Method in class org.anchoranalysis.image.inference.bean.segment.instance.SuppressNonMaximum
segment(VoxelsUntyped, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class org.anchoranalysis.image.bean.segment.binary.BinarySegmentation: Performs a segmentation on voxels so that each voxel has an on or off state after the operation.
segment(VoxelsUntyped, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationReference
segment(VoxelsUntyped, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationThreshold
segment(VoxelsUntyped, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationUnary
segment(VoxelsUntyped, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.Sequence
segment(VoxelsUntyped, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.ThresholdAgainstChannel
segmentAll(Voxels<?>, Voxels<?>, Voxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.plugin.image.segment.thresholder.slice.SliceThresholder: Segments all slices in the input voxels.
segmentAll(Voxels<?>, Voxels<?>, Voxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.plugin.image.segment.thresholder.slice.SliceThresholderMask
segmentAll(Voxels<?>, Voxels<?>, Voxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.plugin.image.segment.thresholder.slice.SliceThresholderWithoutMask
SegmentationBean<T> - Class in org.anchoranalysis.image.bean.segment: Performs some kind of segmentation on an image.
SegmentationBean() - Constructor for class org.anchoranalysis.image.bean.segment.SegmentationBean
SegmentationFailedException - Exception Class in org.anchoranalysis.image.bean.nonbean.segment: When a segmentation cannot successfully complete.
SegmentationFailedException(String) - Constructor for exception class org.anchoranalysis.image.bean.nonbean.segment.SegmentationFailedException: Create with a message only.
SegmentationFailedException(String, Throwable) - Constructor for exception class org.anchoranalysis.image.bean.nonbean.segment.SegmentationFailedException: Create with a message and a cause.
SegmentationFailedException(Throwable) - Constructor for exception class org.anchoranalysis.image.bean.nonbean.segment.SegmentationFailedException: Create with a cause only.
SegmentChannel - Class in org.anchoranalysis.plugin.image.bean.mask.provider.segment: Applies a BinarySegmentation algorithm to derive a mask from a channel
SegmentChannel - Class in org.anchoranalysis.plugin.image.bean.object.provider.segment: Segments a channel into objects using a specified segmentation algorithm.
SegmentChannel() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.segment.SegmentChannel
SegmentChannel() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentChannel
SegmentChannelByObject - Class in org.anchoranalysis.plugin.image.bean.object.provider.segment: Performs segmentation of a channel using each object in the upstream collection as a mask.
SegmentChannelByObject() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentChannelByObject
SegmentChannelIntoObjects - Class in org.anchoranalysis.image.bean.segment.object: A base class for algorithms to segment a channel into one or more objects.
SegmentChannelIntoObjects() - Constructor for class org.anchoranalysis.image.bean.segment.object.SegmentChannelIntoObjects
SegmentChannelIntoObjectsUnary - Class in org.anchoranalysis.image.bean.segment.object: Implementation of SegmentChannelIntoObjects that calls a single delegate SegmentChannelIntoObjects.
SegmentChannelIntoObjectsUnary() - Constructor for class org.anchoranalysis.image.bean.segment.object.SegmentChannelIntoObjectsUnary
SegmentedBackground - Class in org.anchoranalysis.image.inference.segment: The background to a segmentation.
SegmentedBackground(DualScale<Stack>, StackDisplayer) - Constructor for class org.anchoranalysis.image.inference.segment.SegmentedBackground: Creates a new SegmentedBackground instance.
SegmentedObjects - Class in org.anchoranalysis.image.inference.segment: Objects that are a result of an instance-segmentation.
SegmentedObjects(String, Collection<WithConfidence<MultiScaleObject>>, SegmentedBackground, ExecutionTimeRecorder) - Constructor for class org.anchoranalysis.image.inference.segment.SegmentedObjects: Create for a collection of objects with an identical label.
SegmentedObjects(List<LabelledWithConfidence<MultiScaleObject>>, SegmentedBackground, ExecutionTimeRecorder) - Constructor for class org.anchoranalysis.image.inference.segment.SegmentedObjects: Create for a collection of objects with potentially differing labels.
SegmentedObjectsAtScale - Class in org.anchoranalysis.image.inference.segment: Exposes a particular set of segmented-objects at a particular scale.
SegmentedObjectsAtScale(List<LabelledWithConfidence<MultiScaleObject>>, Function<MultiScaleObject, ObjectMask>, Stack, StackDisplayer, ExecutionTimeRecorder, String) - Constructor for class org.anchoranalysis.image.inference.segment.SegmentedObjectsAtScale: Creates a new SegmentedObjectsAtScale instance.
segmentFromExistingSegmentation(VoxelsUntyped, BinarySegmentationParameters, Optional<ObjectMask>, BinarySegmentation) - Method in class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationUnary: Performs a binary-segmentation, in a similar manner to BinarySegmentation.segment(org.anchoranalysis.image.voxel.VoxelsUntyped, org.anchoranalysis.image.bean.nonbean.segment.BinarySegmentationParameters, java.util.Optional<org.anchoranalysis.image.voxel.object.ObjectMask>) but with the delegate as additional argument.
segmentFromExistingSegmentation(VoxelsUntyped, BinarySegmentationParameters, Optional<ObjectMask>, BinarySegmentation) - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.Invert
segmentFromExistingSegmentation(VoxelsUntyped, BinarySegmentationParameters, Optional<ObjectMask>, BinarySegmentation) - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.Repeat
SegmentInstanceWithModel<T> - Class in org.anchoranalysis.plugin.image.task.bean.segment: Using a model-pool, performs instance segmentation on an image producing zero, one or more objects per image.
SegmentInstanceWithModel() - Constructor for class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel
SegmentObjectsFromONNXModel - Class in org.anchoranalysis.plugin.onnx.bean.object.segment.stack: Performs instance-segmentation using the ONNX Runtime and an .onnx model file.
SegmentObjectsFromONNXModel() - Constructor for class org.anchoranalysis.plugin.onnx.bean.object.segment.stack.SegmentObjectsFromONNXModel
SegmentObjectsFromTensorFlowModel - Class in org.anchoranalysis.plugin.opencv.bean.object.segment.stack: Performs instance-segmentation using OpenCV's DNN module and a TensorFlow .pb SavedModel file.
SegmentObjectsFromTensorFlowModel() - Constructor for class org.anchoranalysis.plugin.opencv.bean.object.segment.stack.SegmentObjectsFromTensorFlowModel
SegmentOnMaximumIntensityAndExpandInZ - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel: Perform a segmentation in a MIP instead of z-stacks, and fits the result back into a 3D segmentation.
SegmentOnMaximumIntensityAndExpandInZ() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.channel.SegmentOnMaximumIntensityAndExpandInZ
SegmentStack<T> - Class in org.anchoranalysis.plugin.image.bean.object.provider.segment: Segments a stack into objects.
SegmentStack() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentStack
SegmentStackIntoObjectsPooled<T> - Class in org.anchoranalysis.image.inference.bean.segment.instance: A base class for algorithms to segment a stack into one or more objects - using a pool of models
SegmentStackIntoObjectsPooled() - Constructor for class org.anchoranalysis.image.inference.bean.segment.instance.SegmentStackIntoObjectsPooled
SegmentStackIntoObjectsScaleDecode<T,S> - Class in org.anchoranalysis.image.inference.bean.segment.instance: A SegmentStackIntoObjectsScaleDecode that scales the input image, before performing inference, and then decodes the output.
SegmentStackIntoObjectsScaleDecode() - Constructor for class org.anchoranalysis.image.inference.bean.segment.instance.SegmentStackIntoObjectsScaleDecode
SegmentWithSeeds - Class in org.anchoranalysis.plugin.image.bean.object.provider.segment: Takes each object one-by-one from objectsSource, and finds matching seeds from objectsSeeds
SegmentWithSeeds() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentWithSeeds
select(ExecutionArguments) - Method in interface org.anchoranalysis.launcher.executor.selectparam.SelectParam: Retrieves the parameter.
select(ExecutionArguments) - Method in class org.anchoranalysis.launcher.executor.selectparam.UseDefaultManager
selectChannels(ChannelSource, boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.All
selectChannels(ChannelSource, boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.FromStacks: Takes a stack-collection and extracts a set of references to particular channels (each with a name).
selectChannels(ChannelSource, boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.One
selectChannels(ChannelSource, boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.SpecificAndRename
selectDelegate(StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchChannels
selectDelegate(StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchStack
selectDelegate(StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchSuggestedFormat
selectDelegate(StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.StackWriterDelegateBase: Selects a StackWriter to use as a delegate.
selectDerivePath() - Method in class org.anchoranalysis.io.input.bean.grouper.FromDerivePath: Selects the DerivePath to use for deriving a key.
selectDerivePath() - Method in class org.anchoranalysis.plugin.io.bean.grouper.RemoveLastElement
selectFileExtension(Stack, StackWriteOptions, OutputWriteSettings, Optional<Logger>) - Method in class org.anchoranalysis.image.io.stack.output.generator.RasterGenerator: Selects the file-extension to use for a particular stack.
selectFileExtension(Stack, StackWriteOptions, OutputWriteSettings, Optional<Logger>) - Method in class org.anchoranalysis.image.io.stack.output.generator.RasterGeneratorSelectFormat: Combines stack-write-options derived for a particular stack with the general write-options associated with the RasterGenerator.
selectFileExtension(OutputWriteSettings, Optional<Logger>) - Method in class org.anchoranalysis.image.io.object.output.hdf5.HDF5ObjectsGenerator
selectFileExtension(OutputWriteSettings, Optional<Logger>) - Method in class org.anchoranalysis.io.generator.serialized.DictionaryGenerator
selectFileExtension(OutputWriteSettings, Optional<Logger>) - Method in class org.anchoranalysis.io.generator.serialized.SerializedGenerator
selectFileExtension(OutputWriteSettings, Optional<Logger>) - Method in class org.anchoranalysis.io.generator.SingleFileTypeGenerator: Selects the file/extension to be used for outputting the file.
selectFileExtension(OutputWriteSettings, Optional<Logger>) - Method in class org.anchoranalysis.io.generator.SingleFileTypeGeneratorBridge
selectFileExtension(OutputWriteSettings, Optional<Logger>) - Method in class org.anchoranalysis.io.generator.tabular.CSVGenerator
selectFileExtension(OutputWriteSettings, Optional<Logger>) - Method in class org.anchoranalysis.io.generator.text.StringGenerator
selectFileExtension(OutputWriteSettings, Optional<Logger>) - Method in class org.anchoranalysis.io.generator.xml.XMLGenerator
selective() - Method in class org.anchoranalysis.io.output.recorded.RecordingWriters: A writer that allows only certain selected output-names, and records the written output-names.
selectMarkFrom(MarkCollection, ProposerContext) - Method in class org.anchoranalysis.mpp.bean.proposer.MarkFromCollectionProposer: Selects a mark from a collection of marks.
selectOutputEnabled(Optional<OutputEnabledRules>) - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputsWithRules: Selects which OutputEnabledRules to employ.
SelectParam<T> - Interface in org.anchoranalysis.launcher.executor.selectparam: Different methods of selecting an object T that is used as a parameter for an experiment.
SelectParamFactory - Class in org.anchoranalysis.launcher.executor.selectparam: Creates an appropriate SelectParam based upon the options passed to the command-line.
separate(Collection<T>) - Method in class org.anchoranalysis.spatial.rtree.SpatiallySeparate: Splits a collection of elements into spatially separate clusters, without consuming all elements in elements.
Sequence - Class in org.anchoranalysis.plugin.image.bean.segment.binary: Performs a sequence of succesive segmentations
Sequence() - Constructor for class org.anchoranalysis.plugin.image.bean.segment.binary.Sequence
SequenceInteger - Class in org.anchoranalysis.bean.permute.property: A sequence of integers.
SequenceInteger() - Constructor for class org.anchoranalysis.bean.permute.property.SequenceInteger
sequenceIterator() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequence: Iterates each element in sequence.
SequentialProcessor<T,S> - Class in org.anchoranalysis.experiment.bean.processor: Executes jobs sequentially, without any parallelism.
SequentialProcessor() - Constructor for class org.anchoranalysis.experiment.bean.processor.SequentialProcessor
SequentialSession<T> - Class in org.anchoranalysis.feature.session: Calculates features with successively different inputs, without caching any results from one input to the next.
SERIALIZED_BINARY - Enum constant in enum class org.anchoranalysis.core.format.NonImageFileFormat: Binary serialization format from Java native serialization.
SERIALIZED_XML - Enum constant in enum class org.anchoranalysis.core.format.NonImageFileFormat: XML for storing serialized XML (via XStream).
SerializedGenerator<T> - Class in org.anchoranalysis.io.generator.serialized: A generator that writes binary serialized files to the file-system.
SerializedGenerator() - Constructor for class org.anchoranalysis.io.generator.serialized.SerializedGenerator
serializeObjectToFile(T, Path) - Static method in class org.anchoranalysis.core.serialize.XStreamSerializer: Writes a file with a serialized representation of an object.
SessionInputSequential<T> - Class in org.anchoranalysis.feature.session: A feature-input that will be used in a SequentialSession
SessionInputSequential(T, CacheCreator) - Constructor for class org.anchoranalysis.feature.session.SessionInputSequential: Creates for a particular input and CacheCreator, otherwise using defaults.
SessionInputSequential(T, CacheCreator, ChildCacheFinder) - Constructor for class org.anchoranalysis.feature.session.SessionInputSequential: Creates for a particular input, CacheCreator and ChildCacheFinder.
set() - Method in class org.anchoranalysis.bean.primitive.DoubleSet: The underlying set of values.
set() - Method in class org.anchoranalysis.bean.primitive.IntegerSet: The underlying set of values.
set() - Method in class org.anchoranalysis.bean.primitive.StringSet: The underlying set of values.
set(int, double) - Method in class org.anchoranalysis.feature.results.ResultsVector: Assigns a result at a particular position.
set(int, ResultsVector) - Method in class org.anchoranalysis.feature.results.ResultsVector: Assigns many results, starting at a particular position, and incrementing thereafter.
set(int, Mark) - Method in class org.anchoranalysis.mpp.mark.MarkCollection: Replaces the mark at a specific index.
set(int, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.mark.MemoList: Replaces the element at the specified position in this list with the specified element.
setAboveMaxValue(double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareBase: Constant to return if outside the range (above the maximum allowed)
setAcceptDirectoryErrors(boolean) - Method in class org.anchoranalysis.io.input.bean.files.SearchDirectory: If true, continues when a directory-access-error occurs (logging it), otherwise throws an exception.
setAcceptMissingResolution(boolean) - Method in class org.anchoranalysis.image.feature.bean.physical.WithResolutionBase: Whether to return Double.NaN (if true) or throw an exception (if false) when image resolution is missing.
setAcceptMissingResolution(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.VoxelPhysicalSize: Whether to throw an exception (if true) if image-resolution is missing, or return Double.Nan (if false).
setAcceptNoResolution(boolean) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ReadVoxelExtentXml: If false, an exception is thrown if the resolution file is missing for a particular image.
setAdd(DefineAdderBean) - Method in class org.anchoranalysis.plugin.mpp.bean.define.VisualizeOnBackground
setAddCriteria(AddCriteria<T>) - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria: The criteria used to determine which marks to add.
setAdditionalBackgrounds(List<DerivePath>) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy: Additional background-stacks that are possible to use while annotating.
setAdditionalPropertyPaths(StringSet) - Method in class org.anchoranalysis.bean.permute.property.PermuteProperty: Additional property paths that are also changed, together with propertyPath.
setAddName(boolean) - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
setAddOne(boolean) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Quantile
setAddSum(int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientBaseAddSum: Added to all gradients (so we can store negative gradients).
setAggregator(ChannelAggregator) - Method in class org.anchoranalysis.plugin.image.task.bean.combine.AggregateChannelTask: How to aggregate the Channels.
setAlign(Align) - Method in class org.anchoranalysis.image.bean.spatial.arrange.align.Grow: How to align the box after it is grown, as much as possible.
setAlign(Align) - Method in class org.anchoranalysis.image.bean.spatial.arrange.overlay.Overlay: Indicates how to align the image across the three axes.
setAlign(Align) - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImageCommonSize: How a smaller image (after scaling) is aligned to the larger image (with the common size).
setAligner(BoxAligner) - Method in class org.anchoranalysis.image.bean.spatial.arrange.tile.Tile: How to align a smaller image inside a larger cell.
setAligner(BoxAligner) - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage: When varyImageSize==false and varyImageLocation==false, how to align a smaller image inside a larger cell.
setAlignerLabel(BoxAligner) - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage: When label==false and varyImageLocation==false, how to align the label with its associated image.
setAlignX(String) - Method in class org.anchoranalysis.image.bean.spatial.arrange.align.Align: Indicates how to align the image across the X-axis (i.e. horizontally): one of left, right, center.
setAlignY(String) - Method in class org.anchoranalysis.image.bean.spatial.arrange.align.Align: Indicates how to align the image across the Y-axis (i.e. vertically): one of top, bottom, center.
setAlignZ(String) - Method in class org.anchoranalysis.image.bean.spatial.arrange.align.Align: Indicates how to align the image across the Z-axis: one of top, bottom, center, repeat.
setAll(EnergySavedAll) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown: Certain features are stored for every object, so that we can reference them in our calculations for the 'all' component.
setAnnotations(AnnotationInputManager<NamedChannelsInputPart, T>) - Method in class org.anchoranalysis.plugin.annotation.bean.file.FromAnnotations: The annotation input manager.
setAnnotatorStrategy(S) - Method in class org.anchoranalysis.annotation.io.bean.AnnotationInputManager: The strategy to be used for annotating.
setAppendDictionary(List<NamedBean<DerivePath>>) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager: List of dictionaries to append.
setAppendFilePath(List<NamedBean<DerivePath>>) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager: List of file paths to append.
setAppendHistogram(List<NamedBean<DerivePath>>) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager: List of histograms to append.
setAppendMarks(List<NamedBean<DerivePath>>) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager: List of marks to append.
setAppendMarksFromAnnotation(List<NamedBean<DerivePath>>) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager: List of marks from annotations (both accepted and rejected) to append.
setAppendMarksFromAnnotationAcceptedOnly(List<NamedBean<DerivePath>>) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager: List of marks from annotations (accepted only) to append.
setAppendMarksFromAnnotationRejectedOnly(List<NamedBean<DerivePath>>) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager: List of marks from annotations (rejected only) to append.
setAppendObjects(List<NamedBean<DerivePath>>) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager: List of object-collections to append to the MultiInput.
setAppendStack(List<NamedBean<DerivePath>>) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager: List of additional stacks to append.
setApplyResolution(boolean) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D: If true, multiplies the values by the x-resolution, if it exists.
setApplyToPath(boolean) - Method in class org.anchoranalysis.io.input.bean.path.matcher.MatchRegularExpression: If true, the filter is applied to the path, not just the filename (using forward slashes as directory separators)
setArrange(StackArranger) - Method in class org.anchoranalysis.image.bean.provider.stack.Arrange: Determines how the stacks in list are arranged.
setArrange(StackArranger) - Method in class org.anchoranalysis.image.bean.spatial.arrange.tile.Cell: How to arrange any RGBStacks in this particular cell.
setAsMemberFlag(byte, byte) - Static method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipUtilities: Sets a membership flag.
setAsPercentage(boolean) - Method in class org.anchoranalysis.feature.bean.results.Quantile: If true, the quantile is interpreted as a percentage rather than a decimal.
setAssigner(AnnotationComparisonAssigner<T>) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations: The assigner used for annotation comparison.
setAvoidBulletOnFirst(boolean) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerAggregate: Iff true no bullet is added for the very first-item in the list
setAvoidDivideByZero(boolean) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.Divide: If true, returns a predefined value when division by zero occurs instead of throwing an exception.
setAvoidOverlappingObjects(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors: If true, no overlapping objects are treated as pairs
setAxis(String) - Method in class org.anchoranalysis.image.bean.spatial.direction.AxisAlignedUnitVector: Which axis the unit-vector will align with.
setAxis(String) - Method in class org.anchoranalysis.image.feature.bean.object.single.CenterOfGravity: The axis along which to calculate the center of gravity.
setAxis(String) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientForAxis: Which axis?
setAxis(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.ForSpecificAxis: The axis to perform the calculation on.
setAxis(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.ArbitraryInsidePoint: The axis to output.
setAxis(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxAlongAxisBase: The axis along which to calculate the feature value ("x", "y", or "z").
setAxis(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.GradientMeanForAxis
setAxis(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.PrincipalAxisOrientation: Which axis to read from (x,y,z)
setBackground(Either<Dimensions, DisplayStack>) - Method in class org.anchoranalysis.image.io.object.output.rgb.ObjectsAsRGBGenerator: A background image or dimensions to define an empty background.
setBackground(String) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations: The name of the stack to use as background to the annotations.
setBackground(AnnotationBackground) - Method in class org.anchoranalysis.annotation.io.bean.AnnotatorStrategy: The visual background to use while annotating.
setBackground(ProviderAsStack) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase: The background.
setBackgroundChannelIndex(int) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize: Uses only this channel (identified by an index in the stack) as the background, -1 disables.
setBackgroundChannelProvider(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.MorphologicalOperatorBase: Optional provider for a background channel to use in intensity-based conditions.
setBackgroundID(String) - Method in class org.anchoranalysis.plugin.mpp.bean.define.VisualizeOnBackground
setBackgroundIntensity(int) - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImageCommonSize: The background intensity to use in each channel when the scaled image does not cover the entire canvas.
setBackgroundStackMap(StringMap) - Method in class org.anchoranalysis.annotation.io.bean.AnnotationBackground: If non-null, maps underlying stack-name to a background.
setBelowMinValue(double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareBase: Constant to return if outside the range (below the minimum allowed)
setBigNeighborhood(boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Dilate
setBigNeighborhood(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.ConnectedComponentsFromMask: If true uses 8 neighborhood rather than 4 neighborhood etc. in 2D, and similar in 3D
setBigNeighborhood(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.DecomposeIntoConnectedComponents: if true, uses 8 neighborhood instead of 4, and similarly in 3d
setBigNeighborhood(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Dilate
setBinary(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage: Iff true the image to be scaled is treated as a binary-mask, and interpolation during scaling ensures only two binary-values are outputted.
setBinarySgmn(BinarySegmentation) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.BinarySegmentByObject
setBit0(boolean) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership: Flag for region 0.
setBit1(boolean) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership: Flag for region 1.
setBit2(boolean) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership: Flag for region 2.
setBit3(boolean) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership: Flag for region 3.
setBit4(boolean) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership: Flag for region 4.
setBit5(boolean) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership: Flag for region 5.
setBit6(boolean) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership: Flag for region 6.
setBit7(boolean) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership: Flag for region 7.
setBitsPerPixel(int) - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceBitsPerPixel: The assigned bits per pixels.
setBlockSize(SizeXY) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters: The block-size as per OpenCV implementation (identical default-size).
setBlockStride(SizeXY) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters: The block-stride as per OpenCV implementation (identical default-size).
setBlue(int) - Method in class org.anchoranalysis.bean.shared.color.RGBColorBean: Sets the blue component value.
setBlue(int) - Method in class org.anchoranalysis.core.color.RGBColor: Sets the blue component value.
setBlue(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeChannels: Provider for the blue channel.
setBold(boolean) - Method in class org.anchoranalysis.image.io.bean.stack.combine.TextStyle: Whether to bold the drawn text
setBorderWidth(int) - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices: Adds a border around each part of the montage.
setBridgeMatcher(ObjectMatcher) - Method in class org.anchoranalysis.plugin.image.bean.object.match.Bridge: Used to match each input-object to an intermediary-object
setBySlices(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.ConnectedComponentsFromMask
setCacheSize(int) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.collective.RelationWithMatches: Size of feature evaluation cache for featureEvaluatorMatch
setCalculateLevel(CalculateLevel) - Method in class org.anchoranalysis.image.bean.threshold.CalculateLevelUnary: The delegate CalculateLevel.
setCalculateLevel(CalculateLevel) - Method in class org.anchoranalysis.image.bean.threshold.ThresholderGlobal
setCalculateLevel(CalculateLevel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectBase: Method to calculate the level for a particular object.
setCalculateLevel(CalculateLevel) - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.GreaterThanThreshold: Calculates the level for the threshold
setCalculateLevel(CalculateLevel) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.LevelFromHistogram
setCalculateLevel(CalculateLevel) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.ThresholdHistogram
setCalculateLevel(CalculateLevel) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevelBase: The method to calculate the threshold level.
setCalculateLevelElse(CalculateLevel) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelRelativeToThreshold: Alternative CalculateLevel to use when the condition in CalculateLevelRelativeToThreshold.useElseInstead(int, int) is met.
setCalculations(EnergyMemoList) - Method in class org.anchoranalysis.mpp.feature.input.FeatureInputAllMemo: The list of memoized energy calculations for all marks.
setCaseSensitive(boolean) - Method in class org.anchoranalysis.plugin.io.bean.file.namer.patternspan.PatternSpan: Iff true, a case sensitive search is used to match patterns.
setCellDefault(StackArranger) - Method in class org.anchoranalysis.image.bean.spatial.arrange.tile.Tile: Used to define an individual cell, when no specific entry is found in cells for a particular cell.
setCells(List<Cell>) - Method in class org.anchoranalysis.image.bean.spatial.arrange.tile.Tile: Defines the corresponding StackArranger for an individual cell in table.
setCellSize(SizeXY) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters: The cell-size as per OpenCV implementation (identical default-size).
setCenterPoint(Point3d) - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult: The center point of the fitted ellipsoid.
setChangeExisting(boolean) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.convert.ConvertBase: If true, the existing channel can be changed.
setChannel(ChannelProvider) - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderUnary: The delegate ChannelProvider that is called.
setChannel(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.dimensions.provider.FromChannel: The ChannelProvider to use for dimensions.
setChannel(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.FromChannel: The provider for the channel from which to create the histogram.
setChannel(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.FromChannelBase: The provider for the channel from which to create the mask.
setChannel(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntensityGreaterEqualThan
setChannel(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.UnaryWithChannelBase: Provider for the channel to be used in object creation.
setChannel(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithChannelBase: Provider for the channel from which objects will be created.
setChannel(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.FromChannelOrMask: A channel that is provided to the stack.
setChannel1(ChannelProvider) - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderBinary: The first delegate ChannelProvider that is called.
setChannel1(ChannelProvider) - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderTernary: The first delegate ChannelProvider that is called.
setChannel2(ChannelProvider) - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderBinary: The second delegate ChannelProvider that is called.
setChannel2(ChannelProvider) - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderTernary: The second delegate ChannelProvider that is called.
setChannel3(ChannelProvider) - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderTernary: The third delegate ChannelProvider that is called.
setChannelAssignFrom(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromChannel: The channel provider from which pixels will be assigned.
setChannelConversionStyle(ChannelConvertStyle) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat: To convert as RGB or independently or in another way.
setChannelConverter(ConvertChannelTo<?>) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat: Optionally, how to convert from one bit-depth to another (scaling, clamping etc.)
setChannelConverter(ConvertChannelTo<T>) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.convert.Convert
setChannelElse(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.IfParamEquals: The channel provider to use if the condition is false.
setChannelFirst(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Difference: Index of first channel
setChannelGroupID(int) - Method in class org.anchoranalysis.plugin.io.bean.file.group.parser.RegularExpression
setChannelID(String) - Method in class org.anchoranalysis.plugin.imagej.bean.define.AddEdgeFilters: The ID of the channel that provides the input to the filter.
setChannelIfVoxelZero(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.IfVoxelZero: If a pixel is zero in the input-channel, the output is formed from the corresponding pixel in this channel instead
setChannelIndex(int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromStack: The index of the channel to extract from the stack.
setChannelIndex(int) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromStackChannel: The index of the channel to use from the stack.
setChannelIndex(int) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.One: The index of the channel to retrieve from stackName.
setChannelLookup(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.NormalizeDifferenceToMedian
setChannelMap(ChannelMapCreator) - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannels
setChannelMask(String) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.histogram.ExportImageHistograms: If defined, this is the name of channel used as a mask over the values which are fed into the histogram
setChannelName(String) - Method in class org.anchoranalysis.plugin.io.bean.channel.map.SingleChannel
setChannelName(String) - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertNamedChannelsToStack: By default all channels are converted into a stack.
setChannelSecond(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Difference: Index of second channel
setChannelsExtra(List<ChannelProvider>) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
setChannelThreshold(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.ThresholdAgainstChannel
setCheckParsedFilePathBag(CheckParsedFilePathBag) - Method in class org.anchoranalysis.plugin.io.bean.file.group.GroupFiles: Imposes a condition on each parsed-file-path-bag which must be-fulfilled if a file is to be included.
setClassifierProvider(FeatureListProvider<FeatureInputStack>) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.BinaryClassifierImageLabeller: Provider for the classifier feature list.
setClassLabelsPath(String) - Method in class org.anchoranalysis.image.inference.bean.segment.instance.SegmentStackIntoObjectsScaleDecode: Relative-path to the class-labels file, a text file where each line specifies a class label in order, relative to the models/ directory in the Anchor distribution.
setClearOutsideMask(boolean) - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.ThresholdAgainstChannel
setColor(RGBColorBean) - Method in class org.anchoranalysis.bean.shared.color.scheme.FromSingle: The single color to repeat.
setColor(RGBColorBean) - Method in class org.anchoranalysis.plugin.annotation.bean.label.AnnotationLabel: An optional color associated with the label when displayed via GUI.
setColor(RGBColorBean) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredMask
setColors(List<RGBColorBean>) - Method in class org.anchoranalysis.bean.shared.color.scheme.FromList: The list of colors to specify.
setColors(ColorScheme) - Method in class org.anchoranalysis.bean.shared.color.scheme.ColorSchemeUnary: The delegate that creates the color-list before subsequent processing.
setColors(ColorScheme) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBaseWithGenerator: Colors to use for drawing objects.
setColorScheme(ColorScheme) - Method in class org.anchoranalysis.plugin.image.bean.color.provider.GenerateToMatchObjects
setColorsUnpaired(ColorScheme) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations: The color scheme for unpaired objects.
setColorUnselectedObjects(RGBColorBean) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize: Optionally outline the other (unselected for the thumbnail) objects in this particular color.
setColumn(int) - Method in class org.anchoranalysis.image.bean.spatial.arrange.tile.Cell: The column in the table that the cell refers to (zero-indexed).
setColumns(int) - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices: How many columns to use in the montage, or 0 to guess an approximately square output.
setCommand(String) - Method in class org.anchoranalysis.plugin.imagej.bean.mask.provider.MorphologicalOperation: One of: open, close, fill, erode, dilate, skel, outline
setComparerLeft(ComparableSource) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager: The comparable source for the left side of the comparison.
setComparerRight(ComparableSource) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager: The comparable source for the right side of the comparison.
setCondition(DictionaryCondition) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.IfParamEquals: The condition to evaluate from the dictionary.
setCondition(DictionaryCondition) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfKeyValueCondition
setContains(String) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.DescriptiveNameContainsImageLabeller: The string to search for in the image's descriptive name.
setContains(String) - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterDescriptiveName: A descriptive-name must contain (case-sensitive) this string.
setConvert(ConvertChannelToWithHistogram<T>) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.convert.ConvertWithHistogram
setConvexHull(boolean) - Method in class org.anchoranalysis.plugin.points.bean.FitPointsFromObjects: If true, reduces the set of points by applying a convex-hull operation.
setCopyFilesNaming(CopyFilesNaming<NoSharedState>) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.CopyFilesNamingOne
setCountThreshold(int) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerSplitMoreThan: If there are more than countThreshold elements, use summarizerGreaterThan, else summarizerElse.
setCov(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shape.ObjectRadiusStandardDeviation: If true, returns the coefficient of variation (stdDev/mean) instead of standard deviation.
setCreateShort(boolean) - Method in class org.anchoranalysis.image.bean.provider.stack.Arrange: If true, the created raster has unsigned short voxel data type.
setCreateShort(boolean) - Method in class org.anchoranalysis.image.io.bean.stack.combine.TileWithLabels: When true, the voxel-data-type of the created image is unsigned short, otherwise unsigned byte.
setCreateShort(boolean) - Method in class org.anchoranalysis.image.io.bean.stack.combine.WriteText: When true, text is drawn across all z-slices in the stack. when false, it appears on only one z-slice.
setCreateShort(boolean) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D: If true, creates a short (16-bit) output instead of byte (8-bit).
setCreateShort(boolean) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransformForEachObject3D
setCreateShort(boolean) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.CreateNew: If True creates an unsigned short-image
setCsvFilePath(DerivePath) - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterCSVColumn
setCsvIgnoreZeros(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.histogram.ExportImageHistograms: Iff true, bins with zero-counts are not written as a row in the CSV file.
setCustomName(String) - Method in class org.anchoranalysis.feature.bean.Feature: An optional additional name that be associated with the feature (defaults to an empty string).
setDay(boolean) - Method in class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierAuto: If true, the current day (yyyy.MM.dd) is included in the output.
setDebug(boolean) - Method in class org.anchoranalysis.bean.shared.path.RootPath: If true this root is preferred, when executing a job in debugging mode.
setDebug(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedFeature
setDebugModeParameters(Optional<DebugModeParameters>) - Method in class org.anchoranalysis.io.input.InputContextParameters: Parameters for debug-mode (only defined if we are in debug mode).
setDecode(DecodeInstanceSegmentation<T>) - Method in class org.anchoranalysis.image.inference.bean.segment.instance.SegmentStackIntoObjectsScaleDecode: Decodes inference output into segmented objects.
setDefaultBehaviourString(Optional<String>) - Method in class org.anchoranalysis.launcher.executor.ExperimentExecutor: If present, a string is printed in the description if the default-experiment is used, otherwise ignored.
setDefaultColors(ColorScheme) - Method in class org.anchoranalysis.io.output.bean.OutputWriteSettings: The default color-scheme used for outputs, if no other scheme is specified.
setDefaultStackReaderForMetadata(StackReader) - Method in class org.anchoranalysis.plugin.mpp.bean.convert.ConvertNamedChannels: Supplies to the imageMetadataReader to use, if no other reader is specified.
setDefine(Define) - Method in class org.anchoranalysis.mpp.feature.bean.mark.MarkEvaluator: Defines additional configuration for the evaluation process.
setDefine(Define) - Method in class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputter: The Define to be applied on inputs.
setDefine(DefineOutputter) - Method in class org.anchoranalysis.plugin.mpp.bean.define.Develop: Defines entities (chanels, stacks etc.) that are derived from inputs and other entities.
setDelegate(ResolvedBound) - Method in class org.anchoranalysis.mpp.bean.bound.BoundMinMax
setDelimiter(String) - Method in class org.anchoranalysis.io.output.path.prefixer.DirectoryWithPrefix: Added between prefix and the filename, if the filename is defined.
setDelimiter(String) - Method in class org.anchoranalysis.plugin.io.bean.file.namer.SubsetRangeIfRequested: Character used to split the name into groups.
setDelimiter(String) - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.LastDirectoryAsPrefix
setDelta(double) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Mser
setDeltat(double) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.AnisotropicDiffusion: the integration constant for the numerical integration scheme.
setDepth(double) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ImposeResolution: Physical pixel size of a voxel in z-dimension.
setDerivePath(DerivePath) - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.MaskAsObject: Where to find the Mask to compare, as a function of the source file-path.
setDerivePath(DerivePath) - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.Objects: Where to find the objects to compare, as a function of the source file-path.
setDerivePath(DerivePath) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.CollapseFileName: Called as a delegate to provide a source Path.
setDerivePath(DerivePath) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.RemoveTrailingDirectory
setDictionary(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.ParamFromCollection: The name of the Dictionary that will be retrieved from SharedObjects.
setDictionary(String) - Method in class org.anchoranalysis.plugin.mpp.bean.define.Develop: If non-empty, the identifier for a dictionary that is treated as part of the energy-stack.
setDictionary(DictionaryProvider) - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureEvaluator: Parameters to optionally associated with stackEnergy, and meaningless if stackEnergy is not specified.
setDictionary(DictionaryProvider) - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement: Optional dictionary provider.
setDictionary(DictionaryProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByDictionary
setDictionary(DictionaryProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromDictionary: The dictionary from which an assignment will occur.
setDictionary(DictionaryProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
setDictionary(DictionaryProvider) - Method in class org.anchoranalysis.plugin.image.bean.dictionary.DictionaryCondition: The dictionary to provide a value to check.
setDictionary(DictionaryProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.IfParamEqual
setDictionary(DictionaryProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputterWithEnergy: An optional dictionary provider.
setDimensions(DimensionsProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromDimensionsBase: The provider for the dimensions of the channel to be created.
setDimensions(DimensionsProvider) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.FromDimensionsBase: Provider for the dimensions used to create the mask.
setDimensions(DimensionsProvider) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.slice.RepeatSlice: Dimensions to create new mask
setDimensions(DimensionsProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeBase: Provider for image dimensions.
setDimensions(DimensionsProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithDimensionsBase: Provider for the dimensions to be used.
setDimensions(DimensionsProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithOptionalDimensionsBase: Optional provider for dimensions.
setDimensions(DimensionsProvider) - Method in class org.anchoranalysis.plugin.image.bean.scale.ToDimensions: The dimensions the source image/entity is desired to be scaled to.
setDimensions(DimensionsProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.object.provider.FromMarks
setDimensions(DimensionsProvider) - Method in class org.anchoranalysis.plugin.points.bean.fitter.PointsFitterToMark: Provides the Dimensions for the fitting operation.
setDimensionsSourceFallback(DimensionsProvider) - Method in class org.anchoranalysis.plugin.image.bean.scale.ToDimensions: Source dimensions used as a fallback, if they are not passed as parameter to ToDimensions.calculate(java.util.Optional<org.anchoranalysis.image.core.dimensions.Dimensions>, java.util.Optional<org.anchoranalysis.image.core.dimensions.size.suggestion.ImageSizeSuggestion>).
setDirection(DirectionVectorBean) - Method in class org.anchoranalysis.image.feature.bean.physical.ConvertToPhysicalDistance: Direction of the distance being converted, defaults to a unit vector along the X-axis.
setDirectory(String) - Method in class org.anchoranalysis.io.input.bean.files.FilesProviderWithDirectoryString: A directory in which to look for files.
setDirectory(String) - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.HomeSubdirectory: A relative-path (to the user home directory) which is used as an output directory
setDirectory(Path) - Method in class org.anchoranalysis.io.output.path.prefixer.DirectoryWithPrefix: Assigns a new directory, replacing the existing directory.
setDisableDebugMode(boolean) - Method in class org.anchoranalysis.plugin.io.bean.file.path.RootedFilePath
setDisableDebugMode(boolean) - Method in class org.anchoranalysis.plugin.io.bean.file.provider.Rooted
setDisplayer(StackDisplayer) - Method in class org.anchoranalysis.image.inference.bean.segment.instance.SegmentStackIntoObjectsScaleDecode: How to convert an image to be displayed to the user.
setDisplayer(StackDisplayer) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations: How to convert an image to be displayed to the user.
setDisplayer(StackDisplayer) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase: How to convert an image to be displayed to the user.
setDisplayer(StackDisplayer) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize: How to convert an image so that it can be displayed.
setDisplayer(StackDisplayer) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.stack.ScaleToSize: How to convert an image to be displayed to the user.
setDisplayer(StackDisplayer) - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage: How to convert an image to be displayed to the user.
setDistance(int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectNeighbors: How many neighbors to include by distance (distance==1 implies all directly touching neighbors, distance==2 implies those touching the directly touching etc.)
setDistanceMax(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevel: The maximum distance from the threshold level to consider.
setDistanceX(double) - Method in class org.anchoranalysis.plugin.points.bean.fitter.ReflectInAxesWithinDistance
setDistanceY(double) - Method in class org.anchoranalysis.plugin.points.bean.fitter.ReflectInAxesWithinDistance
setDistanceZ(double) - Method in class org.anchoranalysis.plugin.points.bean.fitter.ReflectInAxesWithinDistance
setDivideByZeroValue(double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.Divide: The value to return when division by zero occurs and Divide.avoidDivideByZero is true.
setDivisor(double) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequenceDouble: What to divide the integer-sequence by.
setDo3D(boolean) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.AnisotropicDiffusion: Whether to perform the diffusion in 3D direction, or rather only in the 2D plane.
setDo3D(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.ObjectCollectionProviderMorphological: Whether to perform the operation in 3D (true) or 2D (false).
setDo3D(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations: Whether to perform the morphological dimensions in 3D or 2D.
setDo3D(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
setDo3D(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.TouchingVoxels: Whether to perform calculations in 3D (true) or 2D (false).
setDo3D(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.Erode: If true, performs 3D erosion; if false, performs 2D erosion on each z-slice separately.
setDo3D(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.NumberRemovedVoxelsAfterClosing
setDo3D(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.OutlineKernelBase: If true, applies the kernel in 3D; otherwise, applies it in 2D.
setDuplicate(boolean) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.Reference: If true, the channel is duplicated after it is retrieved, to prevent overwriting existing data.
setDuplicate(boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.Reference: If true, the mask is duplicated after it is retrieved, to prevent overwriting existing data.
setElemAllCreator(FeatureListProvider<FeatureInputAllMemo>) - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement: Optional creator for features considering all elements.
setElemIndCreator(FeatureListProvider<FeatureInputSingleMemo>) - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement: Creates features for individual elements.
setElemPairCreator(FeatureListProvider<FeatureInputPairMemo>) - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement: Creates features for pairs of elements.
setEmptyValue(double) - Method in class org.anchoranalysis.image.feature.bean.object.single.CenterOfGravity: The value to return if the center of gravity calculation results in NaN.
setEmptyValue(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.Intersection
setEmptyValue(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.ArbitraryInsidePoint: The value to return if no point is found inside the object-mask.
setEmptyValue(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase: The value to return when the resulting object is empty.
setEmptyValue(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.DerivedObject: The value to return when the derived object is empty.
setEmptyValue(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanMaxSlice: The value to return when the object has no voxels in any slice.
setEnd(int) - Method in class org.anchoranalysis.bean.permute.property.SequenceInteger: An index beyond which we cannot iterate (inclusive).
setEnergyChannelIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Identity: The index of the energy channel to use for calculations.
setEnergyChannelIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.RejectIfIntensityLessThan: The index of the energy channel to check for intensity.
setEnergyChannelIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.SingleChannel: The index of the energy channel to use for score calculation.
setEnergyChannelIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.QuantileAcrossConnectedComponents
setEnergyChannelIndexCheck(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram: The index of the energy channel to check.
setEnergyChannelIndexFail(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram: The index of the energy channel to use if the relation check fails.
setEnergyIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.NumberNeighboringVoxels: Index of which channel in the energy-stack to select
setEnergyIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.SpecificEnergyChannelBase: Index of which channel in the energy-stack to select. 0 represents the first channel, 1 the second, and so on.
setEnergyIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.FeatureEnergyChannel: Index of channel to use in the energy-stack (0 is the first channel, 1 is second etc.)
setEnergyIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.OutsideRange: The index of the energy channel to use for intensity values.
setEnergyIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.intensity.Intensity: The channel that that forms the histogram.
setEnergyIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.AsObjectMask: The channel that that forms an object-mask with the bounding-box set to entire channel's dimensions
setEnergyIndexGradient(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.TextureScore
setEnergyIndexMask(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase: A channel of the energyStack that is used as an additional mask using default byte values for on and off.
setEnergyIndexMask(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.intensity.Intensity: Optionally, index of another channel that masks the histogram. -1 disables.
setEnergyIndexX(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.IntensityGradientBase: Index of the channel in the energy stack to use for the X-component of the gradient.
setEnergyIndexY(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.IntensityGradientBase: Index of the channel in the energy stack to use for the Y-component of the gradient.
setEnergyIndexZ(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.IntensityGradientBase: Index of the channel in the energy stack to use for the Z-component of the gradient.
setEnergySchemeCreator(EnergySchemeCreator) - Method in class org.anchoranalysis.mpp.feature.bean.mark.MarkEvaluator: Creator for the energy scheme used in mark evaluation.
setEnergyStack(Optional<EnergyStack>) - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy: Assigns an optional EnergyStack to be associated with the input.
setEnergyStack(EnergyStack) - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy: Assigns an EnergyStack to be associated with the input.
setEnergyTotal(double) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy: The pre-annealed total energy.
setEnergyTotal(double) - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedIndividual: The total energy of all individual marks.
setEquals(String) - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterDescriptiveName: A descriptive-name must be exactly equal to (case-sensitive) this string.
setErodeAtBoundary(boolean) - Method in class org.anchoranalysis.plugin.points.bean.convexhull.ConvexHullBase: Whether to erode the mask at the boundary before finding the contour.
setError(int, Exception) - Method in class org.anchoranalysis.feature.results.ResultsVector: Set an error state at a particular position.
setErrorAll(Exception) - Method in class org.anchoranalysis.feature.results.ResultsVector: Set an error state at all positions.
setErrorDisconnectedObjects(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.split.RemoveIntersectingVoxels: If true, throws an error if there is a disconnected object after the erosion
setExactDepth(int) - Method in class org.anchoranalysis.plugin.io.bean.input.files.provider.DirectoryDepth
setExceptionIfEmpty(boolean) - Method in class org.anchoranalysis.image.feature.bean.histogram.FeatureHistogramStatistic: If true, then an exception is thrown if the histogram is empty, otherwise FeatureHistogramStatistic.valueIfEmpty is returned.
setExcludeZero(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.Intensity: Iff true, zero-valued voxels are excluded from the histogram
setExcludeZero(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanMaxSlice: If true, zero-valued voxels are excluded from the mean intensity calculation.
setExitWithMinima(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong.WatershedYeong: If true, exits early and just returns the minima, without any further segmentation
setExpandLabelZ(boolean) - Method in class org.anchoranalysis.image.io.bean.stack.combine.TileWithLabels: When true, the label is repeated across all z-slices in the stack. when false, it appears on only one z-slice.
setExperimentIdentifier(ExperimentIdentifier) - Method in class org.anchoranalysis.experiment.bean.io.OutputExperiment: A name for the experiment.
setExpression(String) - Method in class org.anchoranalysis.bean.shared.regex.RegExSimple: A Java-style regular expression containing groups.
setExpression(String) - Method in class org.anchoranalysis.io.input.bean.path.matcher.MatchRegularExpression: The regular-expression, Java-style as described in Pattern.
setExpression(String) - Method in class org.anchoranalysis.plugin.io.bean.file.group.parser.RegularExpression
setExtension(String) - Method in class org.anchoranalysis.image.io.bean.stack.writer.OneOrThreeChannelsWriter: Which extension to use to write the image (without any leading period).
setExtensions(StringSet) - Method in class org.anchoranalysis.io.input.bean.path.matcher.MatchExtensions: A set of file-extensions (without the period), one of which must match the end of a path.
setExtensions(StringSet) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.BranchExtension: Any extensions to match (case insensitive) excluding any leading period.
setFactor(double) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreObjects: Factor to multiply the feature value by before assigning it to the output channel.
setFactorHigh(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Identity: The factor to apply for values above 0.5 when normalizing.
setFactorLow(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Identity: The factor to apply for values below 0.5 when normalizing.
setFallback(ScaleCalculator) - Method in class org.anchoranalysis.plugin.image.bean.scale.ToSuggested: Used as a delegate to calculate the scale if suggestedSize is empty when passed to ToSuggested.calculate(java.util.Optional<org.anchoranalysis.image.core.dimensions.Dimensions>, java.util.Optional<org.anchoranalysis.image.core.dimensions.size.suggestion.ImageSizeSuggestion>).
setFallback(ImageMetadataReader) - Method in class org.anchoranalysis.plugin.io.bean.metadata.reader.InferFromHeader: Fallback to use if EXIF information is non-existing or absent.
setFallback(FilesProvider) - Method in class org.anchoranalysis.io.input.bean.files.SpecificPathList: If no paths can be found either from listPaths or the input-context, then the fallback is called if exists, otherwise an error is thrown
setFallback(ChannelConvertStyle) - Method in class org.anchoranalysis.plugin.image.task.bean.format.convertstyle.ExtractToRGB: If a channel doesn't match an RGB pattern, this conversion-style can be used instead.
setFallback(ChannelConvertStyle) - Method in class org.anchoranalysis.plugin.image.task.bean.format.convertstyle.RGBIfNamesMatch: If a channel doesn't match an RGB pattern, this conversion-style can be used instead.
setFallbackName(String) - Method in class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierAuto: If there's no task-name, then this constant is used as a fallback name.
setFeature(Feature<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreObjects: Feature that calculates the score for an object.
setFeature(Feature<T>) - Method in class org.anchoranalysis.feature.bean.provider.FeatureProviderDefine: The feature to provide.
setFeature(Feature<T>) - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureEvaluator: The single feature that will be calculated (possibly repeatedly) in the session.
setFeature(Feature<T>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureBase: The feature to be permuted.
setFeature(FeatureListEvaluator<FeatureInputSingleObject>) - Method in class org.anchoranalysis.image.io.bean.object.feature.OutputFeatureTable: A list of features to calculate in an evaluation context.
setFeatureCondition(Feature<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.conditional.IfCondition
setFeatureCondition(Feature<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.IfConditionWithinRange: Calculates value for the condition - which is checked if it lies within a certain range
setFeatureElse(Feature<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.conditional.IfCondition
setFeatureEvaluator(FeatureEvaluator<FeatureInputPairObjects>) - Method in class org.anchoranalysis.annotation.io.bean.comparer.MultipleComparer: Calculates the cost used when making assignments.
setFeatureEvaluator(FeatureEvaluator<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner
setFeatureEvaluator(FeatureEvaluator<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.collective.DiscardOutliers
setFeatureEvaluator(FeatureEvaluator<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.collective.RelationWithMatches
setFeatureEvaluator(FeatureEvaluator<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedFeature
setFeatureEvaluator(FeatureEvaluator<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.feature.ObjectCollectionProviderWithFeature: The feature evaluator used to calculate features for single objects.
setFeatureEvaluator(FeatureEvaluator<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeGreedyToIncreaseObjectFeature
setFeatureEvaluator(FeatureEvaluator<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeToIncreaseObjectFeature
setFeatureEvaluatorMatch(FeatureEvaluator<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.collective.RelationWithMatches
setFeatureEvaluatorMerge(FeatureEvaluator<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergePairs
setFeatureEvaluatorThreshold(FeatureEvaluator<FeatureInputNull>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergePairs: Allows merge only if the feature-value satisfies a relation to this threshold
setFeatureProvider(FeatureProvider<T>) - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureEvaluator: The single feature that will be calculated (possibly repeatedly) in the session
setFeatures(List<NamedBean<FeatureListProvider<FeatureInputSingleObject>>>) - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel: Features to calculate for objects in the features output.
setFeatures(List<NamedBean<FeatureListProvider>>) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures: The features to be exported (after possibly some manipulation or augmentation).
setFeatures(List<FeatureProvider<T>>) - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureListEvaluator: A list of providers, combined together to form a list of features, to be calculated in a session.
setFeaturesAggregate(List<NamedBean<FeatureListProvider<FeatureInputResults>>>) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures: Features applied to each group to aggregate values (accepting FeatureInputResults).
setFeaturesImage(List<NamedBean<FeatureListProvider<FeatureInputStack>>>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors: Additional features that only depend on the image, so do not need to be replicated for every object.
setFeaturesPair(List<NamedBean<FeatureListProvider<FeatureInputPairObjects>>>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors: Additional features that are processed on the pair of images (i.e.
setFeatureTables(List<OutputFeatureTable>) - Method in class org.anchoranalysis.plugin.mpp.bean.define.Develop: Specifies a feature-table that can also be outputted.
setFileFilterAndDirectory(Path) - Method in class org.anchoranalysis.io.input.bean.files.SearchDirectory: Sets both the directory and the glob from a string containing both.
setFileInput(InputManager<FileInput>) - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannels
setFileInput(InputManager<FileInput>) - Method in class org.anchoranalysis.plugin.io.bean.input.stack.Stacks
setFileInput(NamedFiles) - Method in class org.anchoranalysis.plugin.io.bean.file.group.GroupFiles
setFilePath(String) - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetSlice
setFilePathParser(FilePathParser) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader
setFiles(FilesProvider) - Method in class org.anchoranalysis.io.input.bean.dictionary.ReadFromFile: Provides a single file containing a dictionary.
setFiles(FilesProvider) - Method in class org.anchoranalysis.io.input.bean.files.FilesProviderUnary
setFiles(FilesProvider) - Method in class org.anchoranalysis.io.input.bean.path.provider.FromFiles: A provider that should return exactly one File whose path is employed.
setFiles(FilesProvider) - Method in class org.anchoranalysis.plugin.io.bean.input.files.NamedFiles: The files to use as inputs.
setFiles(FilesProviderWithDirectory) - Method in class org.anchoranalysis.io.input.bean.files.FilesProviderWithDirectoryUnary
setFiles(FilesProviderWithDirectory) - Method in class org.anchoranalysis.plugin.io.bean.file.provider.Rooted
setFiles(FilesProviderWithDirectory) - Method in class org.anchoranalysis.plugin.io.bean.input.files.NamedFilesWithDirectory: The files to use as inputs.
setFilter(ObjectFilter) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfObjectFilter
setFilter(ObjectFilter) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.ObjectCollectionProviderFilterBase: The filter to apply to the object collection.
setFilter(ObjectFilter) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Filter
setFilter(ImageLabeller<T>) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageLabellerStringMap
setFindMaxima(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice: If true, the maxima of the score is searched for.
setFirst(boolean) - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.AsSingle: Iff true, first object is used, otherwise the second
setFirst(StringSet) - Method in class org.anchoranalysis.io.output.bean.rules.OutputEnableRulesSpecify: Output-names in the first-level.
setFirstLineHeaders(boolean) - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
setFixedSizeScaler(ScaleCalculator) - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage: How to calculate the size of each image, when varyImageSize==false.
setFlatten(boolean) - Method in class org.anchoranalysis.annotation.io.bean.comparer.MultipleComparer: If true, a maximum-intensity-projection is first applied to any 3D objects into a 2D plane, before comparison.
setFlatten(boolean) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations: If true, a maximum-intensity-projection is first applied to any 3D objects into a 2D plane, before comparison.
setFlatten(boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.ExteriorContour: If true, any 3D mask is flattened in the z-dimension (maximum intensity projection) to make it 2D
setFlatten(boolean) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase: If true, objects and the background are flattened in the z dimension (via maximum intensity projection), so that a 2D image is produced.
setFontColor(RGBColorBean) - Method in class org.anchoranalysis.image.io.bean.stack.combine.TextStyle: Font-color of drawn text
setFontName(String) - Method in class org.anchoranalysis.image.io.bean.stack.combine.TextStyle: Font-name of drawn text
setFontSize(int) - Method in class org.anchoranalysis.image.io.bean.stack.combine.TextStyle: Font-size of drawn text
setForceChangeBytes(boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.Invert: If true, rather than modifying the binary-values (an index) bytes are modified in the buffer to reflect the existing binary-values.
setForceDetailedLogging(boolean) - Method in class org.anchoranalysis.experiment.bean.io.OutputExperiment: Whether more detailed log-messages around each experiment occur.
setForceEagerEvaluation(boolean) - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
setForceRGB(boolean) - Method in class org.anchoranalysis.image.bean.provider.stack.Arrange: Iff true, ensures every stack is converted into 3 channels.
setFormats(List<HeaderFormat>) - Method in class org.anchoranalysis.plugin.io.bean.metadata.reader.InferFromHeader: The formats whose headers will be searched, to find sufficient metadata to populate ImageMetadata.
setFrom3i(ObjectMask) - Static method in class org.anchoranalysis.image.core.points.PointsFromObject: A sorted-set of three-dimensional integer points from the entire object-mask
setFromContour(ObjectMask) - Static method in class org.anchoranalysis.image.core.points.PointsFromObject: A set of points from the contour of object in three dimensions.
setGaussian(boolean) - Method in class org.anchoranalysis.plugin.imagej.bean.define.AddEdgeFilters: If true, the Gaussian filter is included.
setGaussianSigmaMeters(double) - Method in class org.anchoranalysis.plugin.imagej.bean.define.AddEdgeFilters: The sigma value for the Gaussian filter in meters.
setGlob(String) - Method in class org.anchoranalysis.io.input.bean.path.matcher.MatchGlob: The string describing a glob e.g. "*.jpg".
setGradient(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
setGrayscaleReconstruction(GrayscaleReconstructionByErosion) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.MinimaImpositionGrayscaleReconstruction: The grayscale reconstruction algorithm to be used.
setGreen(int) - Method in class org.anchoranalysis.bean.shared.color.RGBColorBean: Sets the green component value.
setGreen(int) - Method in class org.anchoranalysis.core.color.RGBColor: Sets the green component value.
setGreen(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeChannels: Provider for the green channel.
setGroup(String) - Method in class org.anchoranalysis.plugin.annotation.bean.label.AnnotationLabel: Specifies a group for the label (similar labels that are displayed together).
setGroup(Grouper) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures: Includes an additional group column in CSVs, and creates group-specific feature files.
setGroup(Grouper) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase: How to partition the inputs into groups.
setGroup(Grouper) - Method in class org.anchoranalysis.plugin.io.bean.grouper.IfGroupIndexRange: Fallback to use when no group-index-range is specified.
setHeight(double) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ImposeResolution: Physical pixel size of a voxel in y-dimension.
setHeight(int) - Method in class org.anchoranalysis.image.bean.spatial.SizeXY: Size in Y dimension.
setHistogram(HistogramProvider) - Method in class org.anchoranalysis.image.bean.provider.HistogramProviderUnary: The delegate HistogramProvider that is called.
setHistogram(HistogramProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.convert.ConvertWithHistogram: If set, a histogram used in conversion to describe input intensities (across perhaps multiple images).
setHistogram(HistogramProvider) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.segment.SegmentChannel: An optional histogram of voxel intensity values which can be used by segment
setHistogram(HistogramProvider) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromHistogram: If non-null, a histogram is extracted from this provider rather than the histogram from the inputted CSV.
setHistogramChannelIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevelBase: The index of the histogram channel to use for calculations.
setHistogramIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram: The index of the histogram to use for comparison.
setHistogramsExtra(List<HistogramProvider>) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
setId(int) - Method in class org.anchoranalysis.mpp.mark.Mark: Sets the identifier of the mark.
setId(String) - Method in class org.anchoranalysis.bean.shared.dictionary.DictionaryProviderReference: Unique identifier for the Dictionary to retrieve.
setId(String) - Method in class org.anchoranalysis.feature.bean.operator.Reference: The identifier that uniquely determines the other feature to reference.
setId(String) - Method in class org.anchoranalysis.feature.bean.provider.FeatureProviderReference: The name of the feature to reference.
setId(String) - Method in class org.anchoranalysis.feature.bean.results.FeatureResultsStatistic: The name of the feature, whose results will provide the statistic.
setId(String) - Method in class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationReference: The identifier of the existing BinarySegmentation to use.
setId(String) - Method in class org.anchoranalysis.io.input.bean.path.provider.FilePathProviderReference: A unique identifer for another FilePathProvider that is referenced.
setId(String) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.Reference: The ID of the channel to retrieve from the named-provider.
setId(String) - Method in class org.anchoranalysis.plugin.image.bean.dimensions.provider.FromChannel: An shared-objects identifier for a ChannelProvider to use for dimensions.
setId(String) - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.Reference: The identifier of the histogram to reference.
setId(String) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.Reference: The identifier of the mask to reference.
setId(String) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Reference: The identifier of the object collection to reference.
setId(String) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.ReferenceOrElse
setId(String) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.Reference: The identifier of the stack to retrieve.
setId(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjects: ID for the particular object-collection
setId(String) - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.Reference: The ID of the MarkCollection to retrieve from the initialization context.
setId(String) - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.ReferenceOrEmpty
setId(String) - Method in class org.anchoranalysis.plugin.points.bean.fitter.Reference: The ID of the referenced PointsFitter.
setId(DerivePath) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures: Translates an input file name to a unique ID.
setIdentifierSubrange(Optional<IndexRangeNegative>) - Method in class org.anchoranalysis.io.input.InputContextParameters: If defined, this indicates and specifies only a subset of the naming-elements to use.
setIgnoreAtThreshold(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.OutlineKernelBase: If true, ignores voxels at the threshold when applying the kernel.
setIgnoreCase(boolean) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.path.FilePathPattern: if true, case is ignored in the pattern matching.
setIgnoreContains(String) - Method in class org.anchoranalysis.annotation.io.bean.AnnotationBackground: If non-empty, to not display any stacks in backgroundStackMap whose name contains this string.
setIgnoreFileNotFoundAppend(boolean) - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
setIgnoreFittingFailure(boolean) - Method in class org.anchoranalysis.plugin.points.bean.FitPointsFromObjects: If true, ignores fitting failures and continues processing.
setIgnoreHidden(boolean) - Method in class org.anchoranalysis.io.input.bean.files.SearchDirectory: If true, case is ignored in the pattern matching.
setIgnoreHidden(boolean) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.path.FilePathPattern: Iff true, any hidden-path is not considered, and simply ignored
setIgnoreHigherSide(boolean) - Method in class org.anchoranalysis.plugin.operator.feature.bean.statistics.GaussianCumulative: If true, always returns 1.0 for values higher than the mean.
setIgnoreLowerSide(boolean) - Method in class org.anchoranalysis.plugin.operator.feature.bean.statistics.GaussianCumulative: If true, always returns 1.0 for values lower than the mean.
setIgnoreMissingChannel(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.format.convertstyle.IndependentChannels: Iff true and we cannot find a channel in the file, we ignore it and carry on
setIgnoreNaN(boolean) - Method in class org.anchoranalysis.feature.bean.operator.Sum: If true, we ignore any NaN values.
setIgnoreNoObjects(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel: When true, then the outputs (outline, mask, image etc.) are not written for images that produce no objects.
setIgnoreZero(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.RatioNonMode: Whether to ignore the zero value when calculating the ratio.
setIgnoreZeros(boolean) - Method in class org.anchoranalysis.image.io.histogram.output.HistogramCSVGenerator: Iff true bins in the histogram with a zero count are not written
setIgnoreZIfNaN(boolean) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D: If true and the z-resolution is undefined, the z dimension is ignored.
setImageLabeller(ImageLabeller<T>) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageAssignLabel: Maps a label to an image
setImageMetadataReader(ImageMetadataReader) - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage: How to read the ImageMetadata from the file-system.
setImageMetadataReader(ImageMetadataReader) - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImageCommonSize: How to read the ImageMetadata from the file-system.
setImageMetadataReader(ImageMetadataReader) - Method in class org.anchoranalysis.plugin.mpp.bean.convert.ConvertNamedChannels: How to read the ImageMetadata from the file-system.
setImgChannelMapCreator(ChannelMapCreator) - Method in class org.anchoranalysis.plugin.io.bean.file.group.GroupFiles
setIncludeBatchDimension(boolean) - Method in class org.anchoranalysis.plugin.onnx.bean.object.segment.stack.SegmentObjectsFromONNXModel: If true, a 4-dimensional tensor is created (with the first dimension describing a batch-size of 1), instead of the usual 3-dimensional tensor describing channel, height, width.
setIncludeDirectories(boolean) - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.DirectoryStructure: If false, the folders are ignored, and only the file-name is used in the output
setIncludeFeatureNames(boolean) - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement: If true, the names of the imageFeatures are taken as a combination of the namedItem and the actual features.
setIncludeFirst(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors: Include features for the First-object of the pair
setIncludeMerged(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors: Include features for the Merged-object of the pair
setIncludeSecond(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors: Include features for the Second-object of the pair
setIncludeZ(boolean) - Method in class org.anchoranalysis.image.io.bean.object.draw.Outline: If true the outline is also applied in the z-dimension, otherwise this is ignored as possible boundary
setIncludeZ(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.NotTouchingSceneBorder
setIncrement(int) - Method in class org.anchoranalysis.bean.permute.property.SequenceInteger: Size of step to use when incrementing.
setIndex(int) - Method in class org.anchoranalysis.image.io.bean.channel.IndexedChannel: The index (starting at zero) of this Channel relative to others.
setIndex(int) - Method in class org.anchoranalysis.image.voxel.kernel.KernelPointCursor: The index in the buffer that the kernel currently is focussed on.
setIndex(int) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.AtIndex
setIndex(int) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.slice.SliceAt: Index in z-dimension of slice to extract.
setIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.SpecificAxisBase: Specifies which principal-axis to use for calculations (0=largest eigenvalue, 1=second-largest eigenvalue etc.)
setIndex(int) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGFeature: Which index to return from the HOG descriptor.
setIndex(int, double) - Method in class org.anchoranalysis.spatial.orientation.DirectionVector: Sets an element of the vector by the index of its position.
setIndexDay(int) - Method in class org.anchoranalysis.plugin.io.bean.file.pattern.TimestampPattern: The index of the group in regularExpression that encodes the day, starting from 0 for the first group.
setIndexEnd(int) - Method in class org.anchoranalysis.io.input.bean.path.NameElementRange: The index of the last element (inclusive) for the range.
setIndexEnd(int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.slice.ExtractSliceRange: Slice index to end extracting from (inclusive).
setIndexHours(int) - Method in class org.anchoranalysis.plugin.io.bean.file.pattern.TimestampPattern: The index of the group in regularExpression that encodes the hours, starting from 0 for the first group.
setIndexMinutes(int) - Method in class org.anchoranalysis.plugin.io.bean.file.pattern.TimestampPattern: The index of the group in regularExpression that encodes the minutes, starting from 0 for the first group.
setIndexMonth(int) - Method in class org.anchoranalysis.plugin.io.bean.file.pattern.TimestampPattern: The index of the group in regularExpression that encodes the month, starting from 0 for the first group.
setIndexSeconds(int) - Method in class org.anchoranalysis.plugin.io.bean.file.pattern.TimestampPattern: The index of the group in regularExpression that encodes the seconds, starting from 0 for the first group.
setIndexStart(int) - Method in class org.anchoranalysis.io.input.bean.path.NameElementRange: The index of the first element (inclusive) for the range.
setIndexStart(int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.slice.ExtractSliceRange: Slice index to start extracting from (inclusive).
setIndexYear(int) - Method in class org.anchoranalysis.plugin.io.bean.file.pattern.TimestampPattern: The index of the group in regularExpression that encodes the year, starting from 0 for the first group.
setInnerCoreDistance(double) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid: The distance to the inner core, expressed as a ratio of the radii.
setInput(InputManager<? extends ProvidesStackInput>) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager: The input manager for the main stack.
setInput(InputManager<NamedChannelsInput>) - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertNamedChannelsToStack
setInput(InputManager<NamedChannelsInputPart>) - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
setInput(InputManager<T>) - Method in class org.anchoranalysis.annotation.io.bean.AnnotationInputManager: The inputs to be annotated.
setInput(InputManager<T>) - Method in class org.anchoranalysis.experiment.bean.io.InputOutputExperiment: The input-manager to specify where/which/how necessary inputs for the experiment occur.
setInput(InputManager<T>) - Method in class org.anchoranalysis.io.input.bean.InputManagerUnary: The delegate input-manager which will be circumstantially called by the current input-manager.
setInput(InputManager<T>) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager: The input manager for the base input type T.
setInput(SelectParam<Optional<Path>>) - Method in class org.anchoranalysis.launcher.executor.ExperimentExecutor: The input selection parameter.
setInputDebug(InputManager<T>) - Method in class org.anchoranalysis.plugin.io.bean.input.BranchIfDebug: If defined, this provides an input to the manager when in debug-mode, rather than than otherwise inputs.
setInputDirectory(Optional<Path>) - Method in class org.anchoranalysis.io.input.InputContextParameters: If defined, a directory which can be used by beans to find input.
setInputFilterExtensions(Optional<StringSetTrie>) - Method in class org.anchoranalysis.io.input.InputContextParameters: A trie of extensions that can be used filter inputs.
setInputFilterGlob(Optional<String>) - Method in class org.anchoranalysis.io.input.InputContextParameters: A glob that can be used by beans to filter input.
setInputName(String) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager: The name of the input to be used in the MultiInput.
setInputName(String) - Method in class org.anchoranalysis.plugin.onnx.bean.object.segment.stack.SegmentObjectsFromONNXModel: The name of the input in the ONNX model.
setInputPaths(Optional<List<Path>>) - Method in class org.anchoranalysis.io.input.InputContextParameters: A list of paths referring to specific inputs.
setInputPointShift(float) - Method in class org.anchoranalysis.plugin.points.bean.fitter.ConicFitterBase: The shift to apply to input points before fitting.
setIntensity(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
setInterleaveChannels(boolean) - Method in class org.anchoranalysis.plugin.onnx.bean.object.segment.stack.SegmentObjectsFromONNXModel: If true, the channels are placed as the final position of the tensor (**after** width/height) instead of **before** width/height.
setInterpolator(Interpolator) - Method in class org.anchoranalysis.image.bean.provider.stack.Arrange: The interpolator to use for scaling images, if needed.
setInterpolator(Interpolator) - Method in class org.anchoranalysis.image.inference.bean.segment.instance.SegmentStackIntoObjectsScaleDecode: The interpolator to use for scaling images.
setInterpolator(Interpolator) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.ScaleXY: The interpolator to use for scaling images.
setInterpolator(Interpolator) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.AtScale: The interpolator to use.
setInterpolator(Interpolator) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize: Interpolator used when scaling the background
setInterpolator(Interpolator) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.stack.ScaleToSize
setInterpolator(Interpolator) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.CombineObjectsForFeatures: Interpolator used to resize images in thumbnail generation.
setInterpolator(Interpolator) - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage: How to resize images.
setInterpolator(Interpolator) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase: The interpolator to use for scaling images.
setInterpolator(Interpolator) - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage: The interpolator to use for scaling images.
setInterpolator(Interpolator) - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel: The interpolator to use for scaling images.
setInterpolator(Interpolator) - Method in class org.anchoranalysis.plugin.onnx.bean.object.segment.decode.instance.maskrcnn.DecodeMaskRCNN: The interpolator to use for scaling images.
setInterpolator(Interpolator) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters: The interpolator to use for scaling images.
setInverse(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.IntersectsWithContainer
setInverse(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase: If true, calculates instead on the inverse of the object-mask (what's left when the shell is removed).
setInverseMask(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase: If true, uses the inverse of the passed mask.
setInvert(boolean) - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.MaskAsObject: If true the Mask is inverted before conversion into an ObjectCollection.
setInvert(boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromObjects
setInvert(boolean) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.FilterWithRegularExpression: Iff true, then a file is rejected if the regular-expression matches and vice-versa.
setItem(Feature<FeatureInputHistogram>) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.ThresholdHistogram
setItem(Feature<FeatureInputHistogram>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.Intensity: Feature to apply to the histogram
setItem(Feature<FeatureInputHistogram>) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.intensity.Intensity: Feature to apply to the histogram.
setItem(Feature<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjectsSingleElement: The feature to calculate for each intersecting object pair.
setItem(Feature<FeatureInputSingleObject>) - Method in class org.anchoranalysis.image.feature.bean.object.pair.FeatureDeriveFromPair: The feature to be applied to individual objects.
setItem(Feature<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.DerivedObject: The feature to calculate on the derived object.
setItem(Feature<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.FeatureSingleObjectFromShared: The feature to be calculated on a single object.
setItem(Feature<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.AsObjectMask
setItem(Feature<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.QuantileAcrossConnectedComponents
setItem(Feature<S>) - Method in class org.anchoranalysis.feature.bean.operator.FeatureUnary
setItem(Feature<T>) - Method in class org.anchoranalysis.feature.bean.list.DefineSingle: The sole feature that forms the list.
setItem(FeatureListProvider<FeatureInput>) - Method in class org.anchoranalysis.feature.bean.list.PrependName: Provides the features and names before any prepending.
setItem(FeatureListProvider<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.DeriveFromPair
setItem(FeatureListProvider<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.FeatureListProviderAggregatePair: For each feature in the list, a corresponding aggregate feature is created in the output list.
setItem(FeaturePairObjects) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.PairedWithMask
setItem(VoxelScore) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.RejectIfIntensityLessThan: The VoxelScore to use for calculating the score if the intensity is not rejected.
setItem(DerivePath) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Rooted
setItem(T) - Method in class org.anchoranalysis.bean.NamedBean: The item that is to be named, the underlying bean.
setItem1(Feature<T>) - Method in class org.anchoranalysis.feature.bean.operator.FeatureBinary: Provides the first value for the binary-function.
setItem2(Feature<T>) - Method in class org.anchoranalysis.feature.bean.operator.FeatureBinary: Provides the second value for the binary-function.
setItemMean(Feature<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.statistics.StatisticalBase: The Feature used to calculate the mean.
setItemStdDev(Feature<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.statistics.StatisticalBase: The Feature used to calculate the standard deviation.
setIterations(int) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.AnisotropicDiffusion: How many iterations to perform diffusion.
setIterations(int) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.MorphologicalOperatorBase: Number of iterations to apply the morphological operation.
setIterations(int) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.ObjectCollectionProviderMorphological: The number of iterations to apply the morphological operation.
setIterations(int) - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.Repeat: The maximum number of iterations.
setIterations(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.Erode: The number of iterations to perform the erosion operation.
setIterations(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.NumberRemovedVoxelsAfterClosing
setIterations(int) - Method in class org.anchoranalysis.plugin.imagej.bean.mask.provider.MorphologicalOperation: iterations for erode, dilate, open, close
setIterations(MorphologicalIterations) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.Intersection: The number of dilations and erosions to apply to determine if two objects intersect
setIterations(MorphologicalIterations) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase: The number of dilations and erosions to apply and whether to do in the Z dimension.
setIterations(MorphologicalIterations) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.Shell: The number of dilations and erosions to apply and whether to do so in the Z dimension.
setIterationsDilation(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations: Number of times to perform morphological dilation.
setIterationsErosion(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations: Number of times to perform morphological erosion.
setKappa(double) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.AnisotropicDiffusion: A parameter kappa associated with the diffusion functions.
setKeepExtension(boolean) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.CollapseFileName: When true, the extension is appended to the directory.
setKeepExtremes(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Identity: Whether to keep extreme values (0 and 1) unchanged when normalizing.
setKeepProcessorsFree(int) - Method in class org.anchoranalysis.experiment.bean.processor.DebugDependentProcessor: How many processors to avoid using for the tasks.
setKeepProcessorsFree(int) - Method in class org.anchoranalysis.experiment.bean.processor.ParallelProcessor: How many processors to avoid using for the tasks.
setKeepZ(boolean) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ImposeResolution: Keep the z-resolution if it is already defined
setKernelHalfWidth(int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.Median: Kernel will be a square kernel of size (2*kernelHalfWidth+1)x(2*kernelHalfWidth+1)
setKey(String) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromDictionary: The key of the value in the dictionary that will be assigned.
setKey(String) - Method in class org.anchoranalysis.plugin.image.bean.dictionary.DictionaryCondition: The key in the dictionary whose value is checked.
setKey(String) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.IfParamEqual
setKey(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.ParamFromCollection: The name of the key in the dictionary, whose corresponding value will be returned.
setKey(String) - Method in class org.anchoranalysis.plugin.operator.feature.bean.FromDictionary
setKeyGroupID(int) - Method in class org.anchoranalysis.plugin.io.bean.file.group.parser.RegularExpression
setKeyLower(String) - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByDictionary
setKeyPrefix(String) - Method in class org.anchoranalysis.plugin.operator.feature.bean.FromDictionary: Prefix prepended to key
setKeyRequired(boolean) - Method in class org.anchoranalysis.plugin.io.bean.file.group.parser.RegularExpression
setKeySuffix(String) - Method in class org.anchoranalysis.plugin.operator.feature.bean.FromDictionary
setKeyUpper(String) - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByDictionary
setLabel(boolean) - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices: If true, a label is added beside every image showing the slice index.
setLabel(String) - Method in class org.anchoranalysis.image.io.bean.stack.combine.StackProviderWithLabel: The label associated with stack.
setLabels(List<AnnotationLabel>) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.ImageLabelStrategy: List of AnnotationLabels available for annotation.
setLevel(int) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Constant
setLimitUpper(Optional<Either<Integer, Double>>) - Method in class org.anchoranalysis.io.input.InputContextParameters: If defined, an upper limit that is imposed on the number of inputs.
setList(List<DefineAdderBean>) - Method in class org.anchoranalysis.bean.define.adder.Concatenate
setList(List<NamedBean<FeatureListProvider<T>>>) - Method in class org.anchoranalysis.feature.bean.list.DefinedNamed: A list of FeatureListProviders with an associated name.
setList(List<NamedBean<FromStack>>) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.SpecificAndRename
setList(List<Provider<Stack>>) - Method in class org.anchoranalysis.image.bean.provider.stack.Arrange: The stacks that are passed in respect order into arrange.
setList(List<RegEx>) - Method in class org.anchoranalysis.bean.shared.regex.RegExList: The list of RegExes that are successively tried to be matched.
setList(List<StringMapItem>) - Method in class org.anchoranalysis.bean.shared.StringMap: A list of mappings between a single-items in the respective sets.
setList(List<LoggingDestination>) - Method in class org.anchoranalysis.experiment.bean.log.ToMultiple: The list of loggers to log to
setList(List<Feature<T>>) - Method in class org.anchoranalysis.feature.bean.list.Define: The list that specifies features.
setList(List<Feature<T>>) - Method in class org.anchoranalysis.feature.bean.list.FeatureList: The list of features.
setList(List<Feature<T>>) - Method in class org.anchoranalysis.feature.bean.operator.FeatureFromList: Assigns the list of features to use.
setList(List<ObjectFilter>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.combine.ObjectFilterCombine: A list of other filters from which the sub-classes implement filtering behaviour.
setList(List<ColorProvider>) - Method in class org.anchoranalysis.plugin.image.bean.color.provider.Concatenate: A list of ColorProvider to be concatenated.
setList(List<ObjectCollectionProvider>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Concatenate: List of ObjectCollectionProviders whose ObjectCollections will be concatenated.
setList(List<BinarySegmentation>) - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.Sequence: A list of binary-segmentations that are applied successively (the output of the predecessor becomes the input of the sucecssor)
setList(List<CalculateLevel>) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelListBase: List of CalculateLevel objects to be used in the calculation.
setList(List<ProviderAsStack>) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.Concatenate
setList(List<IndexedChannel>) - Method in class org.anchoranalysis.plugin.io.bean.channel.map.FromEntries
setList(List<StackProviderWithLabel>) - Method in class org.anchoranalysis.image.io.bean.stack.combine.TileWithLabels: The list of StackProviderWithLabels that are tiled.
setList(List<FilesProvider>) - Method in class org.anchoranalysis.plugin.io.bean.file.provider.Combine
setList(List<InputManager<T>>) - Method in class org.anchoranalysis.plugin.io.bean.input.Concatenate: The list of InputManagers that will be concatenated.
setList(List<RegionMembership>) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMap: List of region memberships.
setList(List<AddCriteriaPair>) - Method in class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaOr: List of AddCriteriaPair to be combined with OR operation.
setList(List<Summarizer<T>>) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerAggregate
setList(FeatureList<T>) - Method in class org.anchoranalysis.feature.bean.operator.FeatureFromList: Assigns the list of features to use.
setListAdditionalChannelProviders(List<ChannelProvider>) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreObjects: Additional channels to be included in the EnergyStack for feature calculation.
setListAppend(List<NamedBean<DerivePath>>) - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
setListFeatures(List<NamedBean<FeatureListProvider<FeatureInputStack>>>) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.BinaryClassifierImageLabeller: List of named feature list providers for additional features.
setListImageFeatures(List<NamedBean<FeatureListProvider<FeatureInputStack>>>) - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement: List of named feature providers for image-based features.
setListPaths(StringList) - Method in class org.anchoranalysis.io.input.bean.files.SpecificPathList: If specified, this forms the list of paths which is provided as input.
setLocalized(boolean) - Method in class org.anchoranalysis.io.input.bean.files.FilesProviderWithDirectoryString: When true paths are resolved against the location of the associated BeanXML file.
setLog(LoggingDestination) - Method in class org.anchoranalysis.experiment.bean.log.OnlyIf: The logger to use if conditions are fulfilled
setLogExperiment(LoggingDestination) - Method in class org.anchoranalysis.experiment.bean.io.OutputExperiment: Where log messages that do not pertain to a specific job (input) appear.
setLoggerTaskCreator(LoggingDestination) - Method in class org.anchoranalysis.experiment.task.ParametersExperiment: This is a means to create new log-reporters for each task.
setLogPath(boolean) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Rooted: if true, the pathIn and pathOut are logged.
setLogTask(LoggingDestination) - Method in class org.anchoranalysis.experiment.bean.io.InputOutputExperiment: Where log messages that do pertain to a specific job (input) appear.
setMap(StringMap) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageLabellerStringMap
setMarkEvaluator(NamedBean<MarkEvaluator>) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy: A mark-evaluator that is added to the GUI to support this annotation
setMarkFactory(MarkFactory) - Method in class org.anchoranalysis.plugin.points.bean.FitPointsFromObjects: The MarkFactory used to create new marks.
setMarkFactory(MarkWithIdentifierFactory) - Method in class org.anchoranalysis.mpp.feature.bean.mark.MarkEvaluator: Factory for creating marks with identifiers.
setMarkProposer(String) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy: Name of the MarkProposer to use.
setMarkProvider(SingleMarkProvider) - Method in class org.anchoranalysis.mpp.bean.points.CreateMarkFromPoints: Provides the mark to be fitted.
setMarkProvider(SingleMarkProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.FromSingleMark: The provider for a single mark.
setMarks(MarkCollectionProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.object.provider.FromMarks
setMarks(MarkCollectionProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.ScaleXY: The provider for the MarkCollection to be scaled.
setMarks(MarkCollectionProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.stack.provider.ColoredMarks
setMarks(MarkCollection) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy: The marks in the collection.
setMarks(Point2d, Orientation) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse: Sets the marks with radii and orientation.
setMarksExplicit(Point3d) - Method in class org.anchoranalysis.mpp.mark.conic.ConicBase: Sets the mark's position explicitly.
setMarksExplicit(Point3d) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
setMarksExplicit(Point3d) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
setMarksExplicit(Point3d, Orientation) - Method in class org.anchoranalysis.mpp.mark.conic.ConicBase: Sets the mark's position and orientation explicitly.
setMarksExplicit(Point3d, Orientation) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
setMarksExplicit(Point3d, Orientation) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
setMarksExplicit(Point3d, Orientation, Point2d) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse: Sets the marks explicitly with position, orientation, and radii.
setMarksExplicit(Point3d, Orientation, Point3d) - Method in class org.anchoranalysis.mpp.mark.conic.ConicBase: Sets the mark's properties explicitly.
setMarksExplicit(Point3d, Orientation, Point3d) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
setMarksExplicit(Point3d, Orientation, Point3d) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
setMask(Provider<Mask>) - Method in class org.anchoranalysis.image.bean.provider.MaskProviderUnary: The delegate Provider<Mask> that is called.
setMask(Provider<Mask>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.ConnectedComponentsFromMask
setMask(Provider<Mask>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.mask.FromMask
setMask(Provider<Mask>) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.FromChannelOrMask: A mask that is provided to the stack.
setMask(MaskProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.mask.FromMaskBase: The MaskProvider used to create the binary mask.
setMask(MaskProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.mask.UnaryWithMaskBase: The MaskProvider used to create the binary mask.
setMask(MaskProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
setMask(MaskProvider) - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.FromChannel: An optional mask provider to restrict the histogram creation to specific areas.
setMask(MaskProvider) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.segment.SegmentChannel: An optional mask which restricts the algorithm to only parts of the channel where the mask has an on voxel
setMask(MaskProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.mask.AndObjectsWithMasks
setMask(MaskProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentChannel: Optional mask to restrict the segmentation area.
setMask(MaskProvider) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredMask
setMask(MaskProvider) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.PairedWithMask
setMask(MaskProvider) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.MaskAsSingleObject: The provider for the mask to be treated as a single object.
setMask(MaskProvider) - Method in class org.anchoranalysis.plugin.imagej.bean.object.provider.FillHoles
setMaskElse(MaskProvider) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfPredicateBase: Returned instead of mask if the predicate is not satisfied.
setMaskValue(int) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.histogram.ExportImageHistograms: What voxel value to read as "On" in the mask above.
setMatch(String) - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterCSVColumn
setMatcher(ObjectMatcher) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.collective.RelationWithMatches
setMatcher(ObjectMatcher) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.feature.ObjectWithMaximumFeatureFromEachMatchedCollection
setMatcher(ObjectMatcher) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.Match: The ObjectMatcher used to find matches in the input object collection.
setMatcher(FilePathMatcher) - Method in class org.anchoranalysis.io.input.bean.files.SearchDirectory
setMatcher(FilePathMatcher) - Method in class org.anchoranalysis.io.input.bean.path.matcher.MatchExtensions: A secondary matcher, which is required additionally match (as well as the extension).
setMax(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram: Whether to use the maximum (true) or minimum (false) value from the histogram.
setMax(double) - Method in class org.anchoranalysis.mpp.bean.bound.BoundMinMax: Sets the maximum value of the bound.
setMax(double) - Method in class org.anchoranalysis.mpp.bean.bound.ResolvedBound
setMax(double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.InvertedMax
setMax(double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareFromScalars: Boundary value indicating the maximally-allowed range value.
setMax(int) - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByMinMaxValue
setMax(int) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.ClampHistogramMax
setMax(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.OutsideRange: The maximum value of the range (exclusive).
setMax(Feature<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.CompareWithRangeFeature: Calculates maximally-allowed range boundary
setMax(UnitValueExtent) - Method in class org.anchoranalysis.plugin.image.feature.bean.physical.UnitsWithinRange: Maximum-boundary for acceptable range
setMaxCost(double) - Method in class org.anchoranalysis.annotation.io.bean.comparer.MultipleComparer: The maximum cost (as calculated by featureEvaluator) to accept when creating an assignment between objects.
setMaxCost(double) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner
setMaxDirectoryDepth(int) - Method in class org.anchoranalysis.io.input.bean.files.SearchDirectory: If non-negative the max depth of directories.
setMaxDistance(UnitValueDistance) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithOptionalDistanceConstraint: An optional maximum distance between objects that can be merged.
setMaxDistance(UnitValueDistance) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.CostOverlapWithinMidpointDistance
setMaximumNumberChannels(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.IntensityMoments: An upper limit on the number of channels in the energy-stack for which we create features.
setMaxNumberItems(int) - Method in class org.anchoranalysis.plugin.io.bean.file.provider.Limit
setMaxNumberItems(int) - Method in class org.anchoranalysis.plugin.io.bean.input.Limit
setMaxNumberProcessors(int) - Method in class org.anchoranalysis.experiment.bean.processor.DebugDependentProcessor: An upper limit on the number of the processors that can be simultaneously used in parallel, if they are available.
setMaxNumberProcessors(int) - Method in class org.anchoranalysis.experiment.bean.processor.ParallelProcessor: Theoretical maximum number of (CPU) processors to use in parallel.
setMaxNumItems(int) - Method in class org.anchoranalysis.plugin.io.bean.file.provider.LimitWithDirectory
setMaxPathWidth(int) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.input.ExtractIdentifierAndPath: The maximum width permitted for an identifier, so that it is printed as one line.
setMaxSize(long) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Mser
setMaxSplitGroups(int) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations: The maximum number of groups to split the identifier into.
setMaxValue(long) - Method in class org.anchoranalysis.image.voxel.convert.ToUnsignedByteScaleByMaxValue: Assigns the maximum-value that will be represented in the scaled-values.
setMaxVar(double) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Mser
setMaxVolume(UnitValueExtent) - Method in class org.anchoranalysis.plugin.imagej.bean.mask.provider.FillHoles: The maximum volume of a hole to be filled.
setMaxX(int) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Box: Maximum X coordinate inclusive.
setMaxY(int) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Box: Maximum Y coordinate inclusive.
setMaxZ(int) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Box: Maximum Z coordinate inclusive.
setMean(double) - Method in class org.anchoranalysis.math.statistics.MeanScale: The mean.
setMedian(boolean) - Method in class org.anchoranalysis.plugin.imagej.bean.define.AddEdgeFilters: If true, the median filter is included.
setMedianRadiusMeters(double) - Method in class org.anchoranalysis.plugin.imagej.bean.define.AddEdgeFilters: The radius of the median filter in meters.
setMemo(VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.input.FeatureInputSingleMemo: The memoized voxelized mark.
setMerge(boolean) - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.CutBelowThreshold
setMessageNoInputs(String) - Method in class org.anchoranalysis.experiment.bean.io.InputOutputExperiment: A message written to the logger if no inputs exist for the experiment, and it thus ends early.
setMethod(String) - Method in class org.anchoranalysis.plugin.fiji.bean.mask.provider.AutoLocalThreshold
setMethod(String) - Method in class org.anchoranalysis.plugin.fiji.bean.threshold.ThresholderAutoIJ: The thresholding method to use.
setMethod(CopyFilesMethod) - Method in class org.anchoranalysis.plugin.io.bean.task.CopyFiles: How the copying occurs from source to destination file.
setMin(double) - Method in class org.anchoranalysis.mpp.bean.bound.BoundMinMax: Sets the minimum value of the bound.
setMin(double) - Method in class org.anchoranalysis.mpp.bean.bound.ResolvedBound
setMin(double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareFromScalars: Boundary value indicating the minimally-allowed range value.
setMin(int) - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByMinMaxValue
setMin(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.OutsideRange: The minimum value of the range (inclusive).
setMin(Feature<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.CompareWithRangeFeature: Calculates minimally-allowed range boundary
setMin(UnitValueExtent) - Method in class org.anchoranalysis.plugin.image.feature.bean.physical.UnitsWithinRange: Minimum-boundary for acceptable range
setMinConfidence(double) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ThresholdConfidence: The minimum confidence of an element for its object-mask to be initially included for consideration (before merging).
setMinConfidence(double) - Method in class org.anchoranalysis.plugin.onnx.bean.object.segment.decode.instance.text.DecodeEAST: Proposed bounding boxes below this confidence interval are removed from consideration.
setMinConfidence(float) - Method in class org.anchoranalysis.plugin.onnx.bean.object.segment.decode.instance.maskrcnn.DecodeMaskRCNN: Only proposals outputted from the model with a score greater or equal to this threshold are considered.
setMinDifference(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Difference: A minimum difference, below which 0.0 is returned
setMinDifference(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.DifferenceCalculateLevelStandardDeviation
setMinDiversity(double) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Mser
setMinimaImposition(MinimaImposition) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.ImposeMinima
setMinimumBoundingBoxVolume(int) - Method in class org.anchoranalysis.plugin.imagej.bean.object.segment.FloodFillEachIntensityLevel: Only objects whose bounding-box volume is greater or equal to this threshold are included.
setMinimumPerCluster(int) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster.ClusterByTimestamp: The minimum number of files that must exist for a cluster.
setMinIntensity(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.RejectIfIntensityLessThan: The minimum intensity threshold.
setMinIntensity(int) - Method in class org.anchoranalysis.plugin.imagej.bean.threshold.ThresholderSimpleFillHoles2D: The minimum intensity value for thresholding.
setMinIntensityValue(int) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.MorphologicalOperatorBase: Minimum intensity value for voxels to be considered in the operation.
setMinMaskValue(float) - Method in class org.anchoranalysis.plugin.onnx.bean.object.segment.decode.instance.maskrcnn.DecodeMaskRCNN: Only voxels with a value greater or equal to this threshold are considered as part of the mask.
setMinMaxValues(long, long) - Method in class org.anchoranalysis.image.voxel.convert.ToUnsignedByteScaleByMinMaxValue: Assigns the minimum- and maximum-values which existing values are scaled against.
setMinNumberObjects(int) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.collective.DiscardOutliers
setMinNumberPoints(int) - Method in class org.anchoranalysis.plugin.points.bean.SplitContourAtSaddlePoints: If a contour has less than this number of points, we don't split it, and return it as-is
setMinNumberVoxels(int) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.split.SplitIntoSquares: Only includes squares that have at least this number of voxels.
setMinNumberVoxels(int) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.ConnectedComponentsFromBinarySegmentation
setMinNumberVoxels(int) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ThresholdConfidence: The minimum number of voxels that must exist in a connected-component to be included.
setMinNumPoints(int) - Method in class org.anchoranalysis.mpp.bean.points.CreateMarkFromPoints: Minimum number of points required to create a mark.
setMinNumPoints(int) - Method in class org.anchoranalysis.plugin.points.bean.fitter.PointsFitterToMark: The minimum number of points required for fitting.
setMinNumZSlices(int) - Method in class org.anchoranalysis.plugin.io.bean.file.group.check.AtLeastZSlices
setMinOverlap(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.CostOverlapWithinMidpointDistance
setMinRadius(double) - Method in class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresEllipseFitter
setMinRadius(double) - Method in class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresEllipsoidFitter
setMinRatio(double) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.collective.DiscardOutliers
setMinResolution(double) - Method in class org.anchoranalysis.plugin.image.bean.scale.MinimumXYResolution: The minimum resolution to achieve in meters.
setMinSize(long) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Mser
setMinVolume(UnitValueExtent) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.ConnectedComponentsFromMask
setMinX(int) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Box: Minimum X coordinate inclusive.
setMinY(int) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Box: Minimum Y coordinate inclusive.
setMinZ(int) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Box: Minimum Z coordinate inclusive.
setMip(boolean) - Method in class org.anchoranalysis.image.feature.bean.object.single.NumberVoxels: If true, calculates the number of voxels in the maximum intensity projection (MIP) of the object.
setMip(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.surface.SurfaceNumberVoxelsBase: If true, calculates the surface on a maximum intensity projection rather than the 3D object.
setModelBinaryPath(String) - Method in class org.anchoranalysis.plugin.opencv.bean.object.segment.stack.SegmentObjectsFromTensorFlowModel: Relative-path to the TensorFlow model file, likely with .pb extension, relative to the models/ directory in the Anchor distribution.
setModelPath(String) - Method in class org.anchoranalysis.plugin.onnx.bean.object.segment.stack.SegmentObjectsFromONNXModel: Relative-path to the model file in ONNX form, relative to the models/ directory in the Anchor distribution.
setModelTextGraphPath(String) - Method in class org.anchoranalysis.plugin.opencv.bean.object.segment.stack.SegmentObjectsFromTensorFlowModel: Relative-path to the TensorFlow model file, likely with .pb.txt extension, relative to the models/ directory in the Anchor distribution.
setMultipleComparer(MultipleComparer) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy: Multiple comparer for comparing annotations.
setMultipleOf(int) - Method in class org.anchoranalysis.plugin.image.bean.scale.FitTo: The eventual width and height of the image must be a multiple of this number.
setMultiplyBy(float) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D: A factor to multiply the distance values by.
setName(String) - Method in class org.anchoranalysis.bean.define.adder.FromXMLList: The name of the file in the current working directory WITHOUT THE .xml EXTENSION
setName(String) - Method in class org.anchoranalysis.bean.NamedBean: The name associated with item.
setName(String) - Method in class org.anchoranalysis.bean.shared.path.RootPath: The name of the root-path, which need not be unique in itself.
setName(String) - Method in interface org.anchoranalysis.core.identifier.name.NameValue: Assigns the associated name.
setName(String) - Method in class org.anchoranalysis.core.identifier.name.SimpleNameValue
setName(String) - Method in class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierConstant
setName(String) - Method in class org.anchoranalysis.image.io.bean.channel.IndexedChannel: The name of the Channel this entry represents.
setNameLeft(String) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager: The name of the left side in the comparison.
setNamer(FileNamer) - Method in class org.anchoranalysis.plugin.io.bean.file.group.GroupFiles
setNamer(FileNamer) - Method in class org.anchoranalysis.plugin.io.bean.file.namer.RemoveExtension
setNamer(FileNamer) - Method in class org.anchoranalysis.plugin.io.bean.file.namer.SubsetRangeIfRequested: The namer that is called to provide names that are subsetted.
setNamer(FileNamer) - Method in class org.anchoranalysis.plugin.io.bean.input.files.NamedFilesBase
setNameRight(String) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager: The name of the right side in the comparison.
setNaming(CopyFilesNaming<T>) - Method in class org.anchoranalysis.plugin.io.bean.task.CopyFiles: How an output name (and path) is selected for an input file.
setNavigateHigherDirectories(int) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader: Search x number directories higher than file.
setNoBlack(boolean) - Method in class org.anchoranalysis.plugin.fiji.bean.threshold.ThresholderAutoIJ: If true, the thresholding algorithm will not consider black pixels (value 0) in its calculations.
setNormalize(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Identity: Whether to normalize the voxel intensity values.
setNumberBins(int) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters: The number of bins in each histogram for a cell.
setNumberChannels(int) - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceNumberChannels: The assigned number of channels.
setNumberColumns(int) - Method in class org.anchoranalysis.image.bean.spatial.arrange.tile.Tile: The number of columns to use in the table produced when tiling.
setNumberColumns(int) - Method in class org.anchoranalysis.io.input.csv.CSVReader.OpenedCSVFile: Sets the number of columns, if it is already known from elsewhere.
setNumberDecimalPlaces(int) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner
setNumberDigits(int) - Method in class org.anchoranalysis.io.output.bean.path.prefixer.IncrementingNumber: Number of digits in the number, with leading zeros as necessary.
setNumberDilations(int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectIndependently
setNumberFrames(int) - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceNumberFrames: The assigned number of frames.
setNumberGPUProcessors(int) - Method in class org.anchoranalysis.experiment.bean.processor.ParallelProcessor: How many GPU processors to use when this is possible as a substitute for a CPU processor
setNumberLevelsGrouping(int) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations: The number of levels for grouping.
setNumberLoopPoints(int) - Method in class org.anchoranalysis.plugin.points.bean.SplitContourAtSaddlePoints
setNumberRows(int) - Method in class org.anchoranalysis.image.bean.spatial.arrange.fill.Fill: The number of rows to use the montage, when sufficient images are available.
setNumberRows(int) - Method in class org.anchoranalysis.image.bean.spatial.arrange.tile.Tile: The number of rows to use in the table produced when tiling.
setNumberSubdirectories(int) - Method in class org.anchoranalysis.plugin.io.bean.file.namer.LastDirectories: How many directories to include in the name.
setNumColumns(int) - Method in class org.anchoranalysis.image.io.bean.stack.combine.TileWithLabels: How many columns when tiling, so long as there are sufficient StackProviderWithLabels.
setObjectMatcher(ObjectMatcher) - Method in class org.anchoranalysis.plugin.image.bean.object.match.Bridge: Used to match each intermediary-object to a final-object
setObjects(Provider<ObjectCollection>) - Method in class org.anchoranalysis.image.bean.provider.ObjectCollectionProviderUnary: The delegate Provider<ObjectCollection> that is called.
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.image.io.bean.object.feature.OutputFeatureTable: The objects for which features are calculated.
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransformForEachObject3D
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectBase: The objects for whom a level is calculated.
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.UnaryWithObjectsBase: The provider for the collection of objects to be used in channel creation.
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.color.provider.GenerateToMatchObjects
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromObjects
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntersectsWith
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.match.Always
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.match.Intersection: Provider for the objects to intersect with the source objects.
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Permute
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredObjects: Objects to draw on a background
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.ObjectAggregationBase: The provider for the collection of objects to calculate features on.
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.PointsFromObjects: Provider for the object collection from which to create point marks.
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.points.bean.fitter.PointsFitterToMark: Provides the ObjectCollection to be used in the fitting process.
setObjects1(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeTwoCollectionsItemwise: First collection with items to be merged
setObjects2(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeTwoCollectionsItemwise: Second collection with items to be merged
setObjectsBlue(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeColoredObjects
setObjectsContainer(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithContainerBase: Optional provider for a container of objects.
setObjectsElse(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.ReferenceOrElse
setObjectsGreater(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.GreaterIntersectionWith
setObjectsGreen(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeColoredObjects
setObjectsGrouped(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.FilterByGroup: Provides the ObjectCollection used for grouping the objects to be filtered.
setObjectsLesser(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.GreaterIntersectionWith
setObjectsRed(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeColoredObjects
setObjectsSeeds(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentChannel: Optional provider for seed objects to guide the segmentation.
setObjectsSeeds(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentWithSeeds
setObjectsSource(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromIntersectingObjects
setObjectsSource(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentWithSeeds
setObjectsSplitBy(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.split.SplitByObjects: Provider for the collection of objects used to split the input objects.
setObjectsTarget(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromIntersectingObjects
setOfConnectedComponentIDs() - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels: Gets a set of all connected component IDs in the voxels.
setOff(int, int, int) - Method in interface org.anchoranalysis.image.voxel.binary.BinaryOnOffSetter: Assigns an off state to a voxel at a particular point.
setOff(Point3i) - Method in interface org.anchoranalysis.image.voxel.binary.BinaryOnOffSetter: Assigns an off state to a voxel at a particular point.
setOn(int, int, int) - Method in interface org.anchoranalysis.image.voxel.binary.BinaryOnOffSetter: Assigns an on state to a voxel at a particular point.
setOn(Point3i) - Method in interface org.anchoranalysis.image.voxel.binary.BinaryOnOffSetter: Assigns an on state to a voxel at a particular point.
setOpenInDesktop(boolean) - Method in class org.anchoranalysis.launcher.executor.ExperimentExecutor: Whether to open the output directory in the desktop GUI after execution (if supported on the O/S).
SetOperationFailedException - Exception Class in org.anchoranalysis.core.index: When a set operation fails for a particular key.
SetOperationFailedException(String) - Constructor for exception class org.anchoranalysis.core.index.SetOperationFailedException: Creates with only a message.
SetOperationFailedException(Throwable) - Constructor for exception class org.anchoranalysis.core.index.SetOperationFailedException: Creates with only a cause.
setOptions(ReadOptions) - Method in class org.anchoranalysis.io.bioformats.bean.BioformatsReader: Options that influence how stack is read.
setOptions(ReadOptions) - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptionsDelegate: Options can be specified to alter how an image file is read.
setOtherwise(FileNamer) - Method in class org.anchoranalysis.plugin.io.bean.file.namer.IfRelativeToDirectory: The namer to use if the relative-to-directory option is not selected.
setOutline(boolean) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase: If true, an outline is drawn around the entries.
setOutlineAtBoundary(boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.ExteriorContour
setOutlineColor(RGBColorBean) - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel: The color of the outline.
setOutlineWidth(int) - Method in class org.anchoranalysis.image.io.bean.object.draw.Outline: The size of the outline, in terms of the number of voxels.
setOutlineWidth(int) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations: How many pixels should the outline be around objects.
setOutlineWidth(int) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.AtScale
setOutlineWidth(int) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase: The width of the outline (only relevant if outline==true).
setOutlineWidth(int) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize: The width of the outline.
setOutlineWidth(int) - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel: The width of the outline.
setOutlineWidth(int) - Method in class org.anchoranalysis.plugin.mpp.bean.define.VisualizeOnBackground
setOutPath(String) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.InsertRegExGroups: Constructs a path as an output, replacing $1, $2 etc. with the respective group from the matched regular-expression.
setOutput(OutputManager) - Method in class org.anchoranalysis.experiment.bean.io.OutputExperiment: The output-manager that specifies how/where/which elements occur duing outputting.
setOutput(SelectParam<Optional<Path>>) - Method in class org.anchoranalysis.launcher.executor.ExperimentExecutor: The output selection parameter.
setOutputName(String) - Method in class org.anchoranalysis.experiment.bean.log.ToTextFileBase: The name to use (without extension) for the text-file log
setOutputName(String) - Method in class org.anchoranalysis.io.output.namestyle.OutputNameStyle: An identifier used in rules to determine if an output is enabled or not.
setOutputName(String) - Method in class org.anchoranalysis.plugin.image.task.bean.combine.AggregateChannelTask: How to name the aggregated channel in the output.
setOutputNameStyle(IndexableOutputNameStyle) - Method in class org.anchoranalysis.plugin.io.bean.file.namer.FromOutputName
setOutputsDisabled(StringSet) - Method in class org.anchoranalysis.io.output.bean.enabled.SpecificDisabled: The names of the outputs that are disbled.
setOutputsEnabled(StringSet) - Method in class org.anchoranalysis.io.output.bean.enabled.SpecificEnabled: The names of the outputs that are enabled.
setOutputsEnabled(OutputEnabledRules) - Method in class org.anchoranalysis.io.output.bean.OutputManager: Which outputs are enabled or not enabled.
setOutputShort(boolean) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientBase: If true, outputs a short channel, otherwise byte channel.
setOutputStackProvider(StackProvider) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageAssignLabel: If it's set, a stack is generated that is outputted into subdirectory corresponding to the groupIdentifier.
setOutputWriteSettings(OutputWriteSettings) - Method in class org.anchoranalysis.io.output.bean.OutputManager: General settings (default file extensions, colors etc.) for outputting files.
setOutside(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.physical.UnitsWithinRange: Returned as a constant if a value lies otside the range
setOutsideAtThreshold(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.OutlineKernelBase: If true, considers voxels outside the object at the threshold as part of the object.
setOverlappingObjects(boolean) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize: Whether objects may overlap or not when unscaled.
setPaddingXY(int) - Method in class org.anchoranalysis.image.bean.spatial.Padding: Padding placed on each side of the outputted image (if it's within the image) in XY directions
setPaddingZ(int) - Method in class org.anchoranalysis.image.bean.spatial.Padding: Padding placed on each side of the outputted image (if it's within the image) in Z direction
setPairAddCriteria(AddCriteriaPair) - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement: Criteria for adding pairs of elements.
setPairTypeClass(Class<?>) - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria: The class type of the pair.
setParam(P) - Method in class org.anchoranalysis.bean.initializable.property.BeanInitializer: Sets the current parameters used for propagation.
setParameters(Dictionary) - Method in class org.anchoranalysis.feature.energy.EnergyStack: The associated parameters.
setParameters(HOGParameters) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGDescriptor: Parameters used for calculating HOG
setParameters(HOGParameters) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGFeature: Parameters used for calculating HOG.
setParamPrefix(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureSequenceInteger: Prefix for the parameter key.
setParamPrefixAppendNumber(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFirstSecondOrder: If true, the constant is appended to the param prefix (a dot and a number).
setPath(String) - Method in class org.anchoranalysis.bean.shared.path.RootPath: A path on a file-system to the directory, that defines the root.
setPath(String) - Method in class org.anchoranalysis.plugin.io.bean.file.path.RootedFilePath
setPath(String) - Method in class org.anchoranalysis.plugin.io.bean.file.path.StaticFilePath
setPathAnnotation(DerivePath) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.SinglePathStrategy: Derives the path to the corresponding annotation files, given a path to the image to be annotated.
setPathDefaultMarks(DerivePath) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy: Path to derive default marks from.
setPathDictionary(DerivePath) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy: Path to derive dictionary from.
setPathLabel(DerivePath) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageCSVLabeller: Path to a CSV label file (comma-separated, with header, no quotes).
setPathParser(FilePathParser) - Method in class org.anchoranalysis.plugin.io.bean.file.group.GroupFiles
setPaths(List<DerivePath>) - Method in class org.anchoranalysis.plugin.io.bean.input.files.provider.FilterForExistingFiles: All files need to be present
setPaths(StringSet) - Method in class org.anchoranalysis.plugin.io.bean.file.provider.FileSetFromStringSet
setPermutation(PermuteProperty<S>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeature: A permutation to apply.
setPermutations(List<PermuteProperty<S>>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeature: A list of permutations to apply.
setPermuteProperty(PermuteProperty<?>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Permute
setPermuteProperty(PermutePropertySequenceInteger) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureSequenceInteger: Defines how to permute the property with a sequence of integers.
setPoint(Point3i, int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels: Sets the encoded value for a specific point.
setPointConnectedComponentID(Point3i, int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels: Sets the connected component ID for a specific point.
setPointDirection(Point3i, int, int, int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels: Sets the direction for a specific point.
setPoints(Point3d, Point3d) - Method in class org.anchoranalysis.mpp.mark.points.LineSegment: Sets the start and end points of the line segment.
setPoints(Point3i, Point3i) - Method in class org.anchoranalysis.mpp.mark.points.LineSegment: Sets the start and end points of the line segment.
setPointsFitter(String) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy: Name of the PointsFitter to use.
setPointsFitter(PointsFitter) - Method in class org.anchoranalysis.mpp.bean.points.CreateMarkFromPoints: Fits the provided mark to the extracted points.
setPointsFitter(PointsFitter) - Method in class org.anchoranalysis.plugin.points.bean.FitPoints: The PointsFitter used to fit points to a mark.
setPointsFitter(PointsFitter) - Method in class org.anchoranalysis.plugin.points.bean.fitter.PointsFitterToMark: The PointsFitter used to fit points to a mark.
setPointsFitter(PointsFitter) - Method in class org.anchoranalysis.plugin.points.bean.fitter.ReflectInAxesWithinDistance
setPointsFitter(PointsFitterToMark) - Method in class org.anchoranalysis.plugin.points.bean.FitPointsFromObjects: The PointsFitterToMark used to fit points to marks.
setPointsProposer(PointsProposer) - Method in class org.anchoranalysis.plugin.points.bean.FitPoints: The PointsProposer used to generate points.
setPosition(Point3d) - Method in class org.anchoranalysis.mpp.mark.MarkWithPosition: The position of the mark in 3D space.
setPower(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.MeanRaisedToPower: The power to which the mean value is raised.
setPrefix(boolean) - Method in class org.anchoranalysis.bean.define.adder.FromXMLList: If true, a prefix is prepended to the name of each added bean.
setPrefix(String) - Method in class org.anchoranalysis.bean.define.adder.DefineAdderWithPrefixBean: A prefix that is placed before the name of every bean created.
setPrefix(String) - Method in class org.anchoranalysis.feature.bean.list.PrependName: The string to prepend to the custom-name of each feature.
setPrefix(String) - Method in class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixerAvoidResolve: A string prefixed to each output-path.
setPrefix(String) - Method in class org.anchoranalysis.io.output.path.prefixer.DirectoryWithPrefix: Always prepended to outputted filenames.
setPrefix(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.DeriveFromPair
setPrefix(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.FeatureListProviderAggregatePair: The string to prepend.
setPrefixer(PathPrefixer) - Method in class org.anchoranalysis.io.output.bean.OutputManager: Determines a prefix to use when outputting a file based upon an input-path.
setPrefixer(PathPrefixerAvoidResolve) - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.LastDirectoryAsPrefix
setPrefixer(PathPrefixerAvoidResolve) - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.Rooted
setPrefixerElse(PathPrefixerAvoidResolve) - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.IfIncrementingNumberRequested: Called if the requested condition is not true.
setPrefixerIf(PathPrefixerAvoidResolve) - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.IfIncrementingNumberRequested: Called if the requested condition is true.
setPrefixToRemove(String) - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.DirectoryStructure
setPrependColor(RGBColorBean) - Method in class org.anchoranalysis.bean.shared.color.scheme.Prepend: The color to prepend.
setPreserveAspectRatio(boolean) - Method in class org.anchoranalysis.image.bean.spatial.arrange.align.Grow: Whether to preserve the aspect-ratio of the smaller image when growing.
setPreserveAspectRatio(boolean) - Method in class org.anchoranalysis.plugin.image.bean.scale.FitTo: If true, the aspect-ratio is preserved between width and height.
setPreserveAspectRatio(boolean) - Method in class org.anchoranalysis.plugin.image.bean.scale.ToDimensions: If true, the ratio between x and y is kept constant when scaling.
setPreserveExtensionIfDuplicate(boolean) - Method in class org.anchoranalysis.plugin.io.bean.file.namer.RemoveExtension: Keeps the extension if the file-name (without the extension) becomes duplicated with another.
setPreserveSubdirectories(boolean) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster.ClusterByTimestamp: If true, the entire relative-path is used when copying files into the cluster directory.
setPrioritizeInputContext(boolean) - Method in class org.anchoranalysis.io.input.bean.path.matcher.MatchExtensions: When true, any extensions available in the input-context are prioritized ahead of extensions.
setProperty(String, T) - Method in class org.anchoranalysis.image.core.object.properties.ObjectWithProperties: Assigns a value to a property with a particular name.
setPropertyPath(String) - Method in class org.anchoranalysis.bean.permute.property.PermuteProperty: Either a direct property of a bean or a nested-property with the children separated by full-stops.
setQuantile(double) - Method in class org.anchoranalysis.feature.bean.results.Quantile: The quantile.
setQuantile(double) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.QuantileStretch
setQuantile(double) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Quantile
setQuantile(double) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.collective.DiscardOutliers
setQuantile(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Quantile: The quantile to calculate from the histogram.
setQuantile(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.QuantileAcrossObjects
setQuantile(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.QuantileAcrossConnectedComponents
setQuantileHigh(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Range
setQuantileLow(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Range
setQuantileLower(double) - Method in class org.anchoranalysis.image.bean.displayer.IntensityQuantiles: The lower quantile to use as the lower-limit for the intensity range to display.
setQuantileLower(double) - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ToByteUpperLowerQuantileIntensity: The lower quantile value for intensity scaling.
setQuantileUpper(double) - Method in class org.anchoranalysis.image.bean.displayer.IntensityQuantiles: The lower quantile to use as the upper-limit for the intensity range to display.
setQuantileUpper(double) - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ToByteUpperLowerQuantileIntensity: The upper quantile value for intensity scaling.
setRadius(double) - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius: Sets the radius of the mark.
setRadius(double) - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.WithRadiusBase: The radius of the operation.
setRadius(int) - Method in class org.anchoranalysis.plugin.fiji.bean.mask.provider.AutoLocalThreshold
setRadiusInMeters(boolean) - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.WithRadiusBase: If true, treats the radius as being in meters.
setRadiusX(double) - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult: The radius of the ellipsoid along the X-axis.
setRadiusY(double) - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult: The radius of the ellipsoid along the Y-axis.
setRadiusZ(double) - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult: The radius of the ellipsoid along the Z-axis.
setRatioHeightForLabel(double) - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage: When label==true, this determines the height of the label.
setRatioRowsToColumns(double) - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage: An ideal approximate ratio of the number of rows to the number of columns.
setReader(StackReaderOrientationCorrection) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.RotateImageToMatchEXIFOrientation: Reads the image that is subsequently flattened.
setReaderMatching(StackReader) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.BranchExtension: The reader to use if the extension matches.
setReaderNotMatching(StackReader) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.BranchExtension: The reader to use if the extension does not match.
setReadFromResources(boolean) - Method in class org.anchoranalysis.plugin.onnx.bean.object.segment.stack.SegmentObjectsFromONNXModel: When true, rather than reading modelPath from the file-system, it is read from Java resources on the class-path.
setReceive(MaskProvider) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.combine.CombineBase: The MaskProvider for the second mask to be combined.
setRecurseSubfolders(boolean) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader
setRecursive(boolean) - Method in class org.anchoranalysis.io.input.bean.files.SearchDirectory: If true the search is applied recursively over sub-directories.
setRed(int) - Method in class org.anchoranalysis.bean.shared.color.RGBColorBean: Sets the red component value.
setRed(int) - Method in class org.anchoranalysis.core.color.RGBColor: Sets the red component value.
setRed(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeChannels: Provider for the red channel.
setReduce(FeatureFromList<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.FeatureListProviderAggregatePair: Method for reducing all pairs into a single value e.g.
setReduce(ReduceElements<ObjectMask>) - Method in class org.anchoranalysis.image.inference.bean.segment.instance.SuppressNonMaximum: The algorithm for reducing the number of object-masks.
setReferencePoissonIntensity(double) - Method in class org.anchoranalysis.mpp.bean.mark.factory.MarkWithIdentifierFactory: The reference Poisson intensity for mark creation.
setReferences(StringSet) - Method in class org.anchoranalysis.feature.bean.list.ReferencingFeatureListProvider: The names of other feature-lists, whose features may be referenced by this feature.
setReferencesFeatureListCreator(StringSet) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeature: Makes sure a particular feature list creator is evaluated
setReferencesList(String) - Method in class org.anchoranalysis.feature.bean.provider.FeatureProviderReference: The name of the list in which the feature referenced by id resides.
setRegex(String) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.RegularExpressionBase
setRegex(String) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Replace: Regular expression to match against string
setRegEx(RegEx) - Method in class org.anchoranalysis.plugin.io.bean.file.namer.RegExMatcher
setRegEx(RegEx) - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.PathRegEx: Regular expression to use to match path with at least one group in it.
setRegEx(RegEx) - Method in class org.anchoranalysis.plugin.io.bean.file.provider.RemoveMatching: If a path matches a regular expression it is removed.
setRegEx(RegEx) - Method in class org.anchoranalysis.plugin.io.bean.input.Exclude: A regular-expression to be matched against the identifiers of inputs.
setRegEx(RegEx) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.InsertRegExGroups: The regular-expression to use for matching groups.
setRegEx(RegEx) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.JoinRegExGroups
setRegExDirectory(String) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader: If non-empty a regular-expression is applied to directories.
setRegExFile(String) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader: If non-empty a regular-expression is applied to files.
setRegExString(String) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.InsertRegExGroups: The regular-expression to use for matching groups, overloaded to handle legacy situations where a string is supplied.
setRegionID(int) - Method in class org.anchoranalysis.plugin.mpp.bean.object.provider.FromMarks
setRegionID(int) - Method in class org.anchoranalysis.plugin.mpp.bean.stack.provider.ColoredMarks
setRegionMap(RegionMap) - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement: Mapping of regions.
setRegionMap(RegionMap) - Method in class org.anchoranalysis.plugin.mpp.bean.object.provider.FromMarks
setRegularExpression(String) - Method in class org.anchoranalysis.plugin.io.bean.file.pattern.TimestampPattern: The regular-expression that checks a match and specifies groups for the encoded date-time.
setRejectIterationIfAllLow(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Erode
setRejectIterationIfDisconnected(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Erode
setRelation(RelationBean) - Method in class org.anchoranalysis.bean.shared.relation.threshold.RelationToConstant: The relation to the threshold, where the threshold forms the second operand.
setRelation(RelationBean) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterRelation: The relation to be used in the filter predicate.
setRelation(RelationBean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergePairs: Relation to threshold
setRelation(RelationBean) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram: The relation to test between the voxel value and the histogram value.
setRelation(RelationToThreshold) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.RejectIfConditionXYResolution: A predicate defined by the relationship of the XY-resolution to a constant threshold.
setRelativeForIdentifier(boolean) - Method in class org.anchoranalysis.io.input.InputContextParameters: If true, the entire filename or relative path (excluding extension) is used to determine a unique identifier.
setRemoveExtension(boolean) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.path.FilePathPattern: if true, the extension is removed from paths before finding the pattern.
setRemoveExtensionInDescription(boolean) - Method in class org.anchoranalysis.plugin.io.bean.file.namer.LastDirectories: Whether to remove the file-extension from the filename.
setRemoveNaNColumns(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeaturesStyle: When true, columns containing all Double.NaN values are removed before outputting.
setRemoveTouchingBorderXY(boolean) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner
setRepeatZProvider(Provider<Stack>) - Method in class org.anchoranalysis.image.io.bean.stack.combine.WriteText: Repeats the generated (2D) string in z, so it's the same z-size as intensityProvider
setReplaceMatchesWithSolids(boolean) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations: If true, matched objects are replaced with solid colors.
setReplacement(String) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.SubstituteRegularExpression
setReplacement(String) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Replace: What to replace in the path
setReplaceWithMidpoint(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeGreedyToIncreaseObjectFeature
setReportFitterErrors(boolean) - Method in class org.anchoranalysis.plugin.points.bean.FitPoints: Whether to report fitter errors.
setRequireAllFilesMatch(boolean) - Method in class org.anchoranalysis.plugin.io.bean.file.group.GroupFiles
setRequireArguments(RequireArguments) - Method in class org.anchoranalysis.experiment.bean.log.OnlyIf: The conditions that must be fulfilled
setRequireBBoxNeighbors(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithFeature: Requires for any potential merge that the bounding-boxes of the two objects must intersect or touch.
setRequireTouching(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithFeature: Requires the object-masks to touch.
setResizeTo(SizeXY) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase: If set, each channel is scaled to a specific size before aggregation (useful for combining different sized images).
setResizeTo(SizeXY) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGDescriptor: The input-image is rescaled to this width/height before calculating HOG descriptors
setResizeTo(SizeXY) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGFeature: The input is rescaled to this width/height before calculating HOG descriptors.
setRestrictTo(MaskProvider) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.Invert: If set, the inversion only occurs on a particular region of the mask, as determined by this mask
setRewardHigherSide(boolean) - Method in class org.anchoranalysis.plugin.operator.feature.bean.statistics.GaussianCumulative: If true, treats the higher side as if it's the full CDF.
setRewardLowerSide(boolean) - Method in class org.anchoranalysis.plugin.operator.feature.bean.statistics.GaussianCumulative: If true, treats the lower side as if it's 1 minus the full CDF.
setRgb(boolean) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.FromChannelOrMask: If true, the output contains three channels (the input and two duplicates) instead of one.
setRoot1(double) - Method in class org.anchoranalysis.math.equation.QuadraticEquationSolver.QuadraticRoots: The first root.
setRoot2(double) - Method in class org.anchoranalysis.math.equation.QuadraticEquationSolver.QuadraticRoots: The second root.
setRootName(String) - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.Rooted: The name of the root-path to associate with this fileset.
setRootName(String) - Method in class org.anchoranalysis.plugin.io.bean.file.path.RootedFilePath
setRootName(String) - Method in class org.anchoranalysis.plugin.io.bean.file.provider.Rooted
setRootName(String) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Rooted
setRotationAngle(Bound) - Method in class org.anchoranalysis.mpp.bean.bound.rotation.BoundRotation2D
setRotationX(Bound) - Method in class org.anchoranalysis.mpp.bean.bound.rotation.BoundRotation3D
setRotationY(Bound) - Method in class org.anchoranalysis.mpp.bean.bound.rotation.BoundRotation3D
setRotationZ(Bound) - Method in class org.anchoranalysis.mpp.bean.bound.rotation.BoundRotation3D
setRotMatrix(DoubleMatrix2D) - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult: The rotation matrix, which must be considered immutable to be used here.
setRow(int) - Method in class org.anchoranalysis.image.bean.spatial.arrange.tile.Cell: The row in the table that the cell refers to (zero-indexed).
setSampleEvery(int) - Method in class org.anchoranalysis.plugin.io.bean.file.provider.SampleWithDirectory
setScale(double) - Method in class org.anchoranalysis.math.statistics.MeanScale: The scale, typically the standard-deviation.
setScale(double) - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices: Whether to increase or reduce the size of the images.
setScaleCalculator(ScaleCalculator) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.ScaleXY
setScaleCalculator(ScaleCalculator) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.ScaleXY: Determines how much to scale by.
setScaleCalculator(ScaleCalculator) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Scale
setScaleCalculator(ScaleCalculator) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.AtScale
setScaleCalculator(ScaleCalculator) - Method in class org.anchoranalysis.plugin.image.bean.scale.Invert: The delegate ScaleCalculator whose calculation will be inverted.
setScaleCalculator(ScaleCalculator) - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage: Calculates what scale-factor to apply on the image.
setScaleCalculator(ScaleCalculator) - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.ScaleXY: The ScaleCalculator used to determine the scaling factor.
setScaleFactor(double) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientBase: Scale factor applied to the gradient values.
setScaleInput(ScaleCalculator) - Method in class org.anchoranalysis.image.inference.bean.segment.instance.SegmentStackIntoObjectsScaleDecode: Any scaling to be applied to the input-image before being input to the model for inference.
setScaleLower(double) - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByDictionary
setScaleLower(double) - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ToByteUpperLowerQuantileIntensity: Sets the min by multiplying the quantileLower by this constant.
setScaleRadii(double) - Method in class org.anchoranalysis.plugin.points.bean.fitter.ConicFitterBase: The scale factor to apply to the radii of the conic.
setScaleUpper(double) - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByDictionary
setScaleUpper(double) - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ToByteUpperLowerQuantileIntensity: Sets the max by multiplying the quantileUpper by this constant.
setScore(VoxelScore) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
setScoreProvider(FeatureListProvider<FeatureInputStack>) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice
setScoreThreshold(double) - Method in class org.anchoranalysis.image.inference.bean.reduce.RemoveOverlappingObjects: Bounding boxes with scores above this threshold are removed.
setSecond(boolean) - Method in class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierAuto: Only relevant if time==true.
setSecond(List<NamedBean<StringSet>>) - Method in class org.anchoranalysis.io.output.bean.rules.OutputEnableRulesSpecify: Output-names in the second-level (for all first level output-names).
setSegment(BinarySegmentation) - Method in class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationUnary: The delegate BinarySegmentation that may be called.
setSegment(BinarySegmentation) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.segment.SegmentChannel: Segmentation algorithm
setSegment(BinarySegmentation) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.ConnectedComponentsFromBinarySegmentation
setSegment(SegmentChannelIntoObjects) - Method in class org.anchoranalysis.image.bean.segment.object.SegmentChannelIntoObjectsUnary: The delegate SegmentChannelIntoObjects that is called.
setSegment(SegmentChannelIntoObjects) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentChannel: The segmentation algorithm to use.
setSegment(SegmentChannelIntoObjects) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentChannelByObject
setSegment(SegmentChannelIntoObjects) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentWithSeeds
setSegment(SegmentStackIntoObjectsPooled<T>) - Method in class org.anchoranalysis.image.inference.bean.segment.instance.SuppressNonMaximum: The segmentation algorithm that is applied as an input to non-maximum suppression.
setSegment(SegmentStackIntoObjectsPooled<T>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentStack: The segmentation procedure.
setSegment(SegmentStackIntoObjectsPooled<T>) - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel: The segmentation algorithm.
setSegmentStack(BinarySegmentation) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.SegmentOnMaximumIntensityAndExpandInZ
setSelect(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.DeriveFromPair: Either "merged" or "first" or "second" indicating which feature to delegate from
setSelectChannels(FromStacks) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase: Selects which channels are included, optionally renaming.
setSeparateEachLabel(boolean) - Method in class org.anchoranalysis.image.inference.bean.segment.instance.SuppressNonMaximum: If true, each label is reduced separately. if false, all labels are reduced together.
setSeperator(String) - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
setSequence(SequenceInteger) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequence: A sequence of integers, with each element assigned assigned directly during the permutation, or after further manipulation.
setSequence(OutputSequenceIndexed<T, S>) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ChangeableOutputSequence: The current output sequence.
setSeriesIndex(int) - Method in class org.anchoranalysis.image.io.bean.stack.metadata.reader.FromStackReader: The series to open to the read the metadata (zero-indexed).
setSharedState(S) - Method in class org.anchoranalysis.plugin.mpp.shared.SharedStateRememberConverted: The shared state.
setShell(double) - Method in class org.anchoranalysis.mpp.bean.mark.factory.MarkEllipseFactory: The shell thickness of the ellipse.
setShell(double) - Method in class org.anchoranalysis.mpp.bean.mark.factory.MarkEllipsoidFactory: The shell thickness of the ellipsoid.
setShell(double) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse: The size of the shell, expressed as a ratio of the radius.
setShell(double) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid: The size of the shell, expressed as a ratio of the radii.
setShell(double) - Method in class org.anchoranalysis.plugin.points.bean.fitter.ConicFitterBase: The shell thickness of the conic.
setShowOngoingJobsLessThan(int) - Method in class org.anchoranalysis.experiment.bean.processor.ParallelProcessor: When the number of ongoing jobs is less than this threshold, they are shown in event logs. 0 disables.
setShuffle(boolean) - Method in class org.anchoranalysis.io.input.InputContextParameters: If true, the order of the inputs are shuffled (randomized).
setSigma(double) - Method in class org.anchoranalysis.plugin.image.bean.blur.BlurStrategy: The sigma value for the blur operation.
setSigma(double) - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.GaussianBlur2D: The standard deviation of the Gaussian distribution used for blurring.
setSigmaInMeters(boolean) - Method in class org.anchoranalysis.plugin.image.bean.blur.BlurStrategy: If true, treats sigma as if it's in meters (physical units).
setSilentlyDeleteExisting(boolean) - Method in class org.anchoranalysis.io.output.bean.OutputManager: Whether to silently first delete any existing output at the intended path, or rather throw an error.
setSize(SizeXY) - Method in class org.anchoranalysis.image.io.bean.stack.combine.WriteText: Explicit size of the image the string is draw on.
setSize(SizeXY) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize: Size of all created thumbnails
setSize(SizeXY) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.stack.ScaleToSize
setSizeXY(SizeXY) - Method in class org.anchoranalysis.plugin.image.bean.dimensions.provider.SpecifyDimensions: Length of X and Y dimensions.
setSizeZ(int) - Method in class org.anchoranalysis.plugin.image.bean.dimensions.provider.SpecifyDimensions: Length of Z dimension.
setSkipAtBorder(boolean) - Method in class org.anchoranalysis.plugin.imagej.bean.mask.provider.FillHoles: If true, holes that touch the border of the mask are not filled.
setSkipFileName(boolean) - Method in class org.anchoranalysis.plugin.io.bean.file.namer.LastDirectories: Iff true the filename is not considered, only the subdirectories.
setSkipFirstTrim(int) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.RemoveTrailingDirectory
setSkipMissingChannels(boolean) - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
setSkipNumberSubdirectories(int) - Method in class org.anchoranalysis.plugin.io.bean.file.namer.LastDirectories: Initially skip this number of directories before including them in the description.
setSlice(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.slice.RepeatSlice
setSliceFirst(int) - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices: First slice to include in the montage.
setSliceIndex(int) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.slice.RepeatSlice: Which slice to use from mask
setSliceLast(int) - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices: Last slice to include in the montage.
setSlicesSeparately(boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.FitBoxToOnVoxels
setSlicewise(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.combine.AggregateChannelTask: When true, a 3D image is added slice-by-slice to the aggregation, treating each slice as a separate image.
setSmoothingFactor(double) - Method in class org.anchoranalysis.plugin.points.bean.SplitContourAtSaddlePoints
setSortIfNotRequested(boolean) - Method in class org.anchoranalysis.plugin.io.bean.input.ShuffleIfRequested: When true, the inputs are sorted alphabetically, if a shuffle is not requested.
setSource(String) - Method in class org.anchoranalysis.bean.shared.StringMapItem: The origin of the mapping.
setSource(FeatureSource<T, S, U>) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures: Source of feature-values to be exported.
setSources(List<NamedBean<ComparableSource>>) - Method in class org.anchoranalysis.annotation.io.bean.comparer.MultipleComparer: The other entities to compare with the annotation.
setSplitIdentifierRegex(String) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations: If non-empty, the string (a regular-expression) is used to split the file's identifier into groups.
setSquareSize(int) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.split.SplitIntoSquares
setStack(Provider<Stack>) - Method in class org.anchoranalysis.image.bean.provider.stack.StackProviderUnary: The delegate Provider<Stack> that is called.
setStack(Provider<Stack>) - Method in class org.anchoranalysis.image.io.bean.stack.combine.StackProviderWithLabel: Provides the stack.
setStack(ProviderAsStack) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromStack: Provides a stack.
setStack(ProviderAsStack) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentStack: The stack to segment
setStackBackground(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.define.VisualizeOnBackground
setStackEnergy(Provider<Stack>) - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureEvaluator: Optionally specifies an energy-stack to be associated with every calculation input.
setStackEnergy(StackProvider) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromImage: Optionally defines an energy-stack for feature calculation (if not set, the energy-stack is considered to be the input stacks).
setStackEnergy(StackProvider) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.BinaryClassifierImageLabeller: Provider for the energy stack.
setStackEnergy(StackProvider) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice
setStackEnergy(StackProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputterWithEnergy: The stack provider for the energy stack.
setStackID(String) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfStackExists
setStackName(String) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.One: If defined, processing only occurs the stack with this specific name and index.
setStackNameDefault(String) - Method in class org.anchoranalysis.annotation.io.bean.AnnotationBackground: The name of the default stack from backgroundStackMap to display as background when annotating.
setStackProviderID(String) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromStack: Specifies the ID of an existing stack.
setStackProviderID(String) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromStackChannel: The identifier of the stack provider to retrieve the stack from.
setStackReader(StackReader) - Method in class org.anchoranalysis.annotation.io.bean.AnnotatorStrategy: How to read raster Stacks from the file-system.
setStackReader(StackReader) - Method in class org.anchoranalysis.image.io.bean.stack.metadata.reader.FromStackReader: The StackReader to use to read the image metadata.
setStackReader(StackReader) - Method in class org.anchoranalysis.image.io.bean.stack.reader.InputManagerWithStackReader: How to read an image from the file-system.
setStackReader(StackReader) - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.MaskAsObject: How to read the Mask from the file-system.
setStackReader(StackReader) - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage: Fallback for imageMetadataReader to read image files without a directy metadata reader.
setStackReader(StackReader) - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImageCommonSize: Fallback for imageMetadataReader to read image files without a direct metadata reader.
setStackReader(StackReader) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.FlattenAsChannel: Reads the image that is subsequently flattened.
setStackReader(StackReader) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ImposeResolution: Reads an image before a resolution is imposed.
setStackReader(StackReader) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader
setStackReader(StackReader) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ReadVoxelExtentXml: Reads an image before a resolution is imposed.
setStackReader(StackReader) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.RejectIfConditionXYResolution: Reads an image before a resolution is imposed.
setStart(int) - Method in class org.anchoranalysis.bean.permute.property.SequenceInteger: The index to begin iteration from.
setStartingIntensity(int) - Method in class org.anchoranalysis.plugin.imagej.bean.object.segment.FloodFillEachIntensityLevel: The first intensity-value to consider as a valid object (e.g. usually 0 is ignored as background).
setStrategy(BlurStrategy) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.Blur
setStrongEdgeEnhancer(boolean) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.AnisotropicDiffusion: If true uses, the strong-edge-enhancer diffusion function, otherwise the wide-region-enhancer.
setStyle(TextStyle) - Method in class org.anchoranalysis.image.io.bean.stack.combine.WriteText
setStyle(ExportFeaturesStyle) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures: Visual style for how feature export occurs.
setStyle(ExportFeaturesStyle) - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel: Visual style for how feature export occurs.
setSubtractConstant(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.IntensityGradientBase: A constant value to subtract from each voxel intensity before calculating the gradient.
setSubtractFromMaskOnly(boolean) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.SubtractMean: Whether to subtract the mean only from voxels within the mask.
setSubtractMean(DoubleList) - Method in class org.anchoranalysis.image.inference.bean.segment.instance.SegmentStackIntoObjectsScaleDecode: A constant intensity for each respective channel to be subtracted before performing inference.
setSubtractRadii(double) - Method in class org.anchoranalysis.plugin.points.bean.fitter.ConicFitterBase: The value to subtract from the radii of the conic.
setSummarizer(Summarizer<S>) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.input.SummarizerInputFromManager
setSummarizer(Summarizer<S>) - Method in class org.anchoranalysis.plugin.io.bean.task.SummarizeBase
setSummarizerElse(Summarizer<T>) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerSplitMoreThan: Used for summary if count(elements) <= countThreshold
setSummarizerGreaterThan(Summarizer<T>) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerSplitMoreThan: Used for summary if count(elements) > countThreshold
setSuppress3D(boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.MorphologicalOperatorBase: Whether to suppress 3D operations and only perform 2D operations.
setSuppress3D(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.surface.SurfaceNumberVoxelsBase: If true, suppresses 3D calculations and treats the object as 2D.
setSuppressDirectories(boolean) - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.FromDescriptiveName: If true, any directory separators in the identifier in a descriptive-name are replaced by underscores.
setSuppressErrors(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeaturesStyle: When false, an image is reported as errored, if any exception is thrown during calculation.
setSuppressExceptions(boolean) - Method in class org.anchoranalysis.experiment.bean.processor.JobProcessor: When true, any exception thrown processing and input is caught and logged.
setSuppressOutlineZ(boolean) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase: If true, the outline is suppressed in the z-dimension i.e. a boundary only in z-dimension is not outlined (only relevant if outline==true).
setSuppressRootOut(boolean) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Rooted: if true, the root is not added to the outFilePath, and the path is instead localized against the location of the BeanXML. if false, nothing is changed
setSuppressSeries(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat: If true, the series index is not included in the outputted file-names.
setSuppressSubfolders(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputter: If true, suppresses the creation of subfolders for outputs.
setSuppressZ(boolean) - Method in class org.anchoranalysis.mpp.feature.addcriteria.BoundingBoxIntersection: If true, the Z dimension is ignored when checking for intersection.
setSuppressZ(boolean) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D: If true, suppresses the z-dimension in distance calculations.
setSuppressZ(boolean) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransformForEachObject3D
setSuppressZ(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithOptionalDistanceConstraint: If true, suppresses the Z-dimension when calculating distances between objects.
setSuppressZ(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.CostOverlapWithinMidpointDistance
setSuppressZ(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.ImageMomentsBase: If true co-variance is suppressed in z-dimension.
setSuppressZ(boolean) - Method in class org.anchoranalysis.plugin.points.bean.feature.EllipsoidBase: If true, suppresses covariance in the z-direction.
setSuppressZCovariance(boolean) - Method in class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresEllipsoidFitter
setTarget(String) - Method in class org.anchoranalysis.bean.shared.StringMapItem: The destination of the mapping.
setTargetSize(SizeXY) - Method in class org.anchoranalysis.plugin.image.bean.scale.FitTo: The target size.
setTask(Task<T, S>) - Method in class org.anchoranalysis.experiment.bean.processor.JobProcessor: The task to be applied to inputs.
setTask(Task<U, S>) - Method in class org.anchoranalysis.plugin.mpp.bean.convert.ConvertNamedChannels: The underlying task that will be called, perhaps with a different input-type.
setTask(SelectParam<Optional<Path>>) - Method in class org.anchoranalysis.launcher.executor.ExperimentExecutor: The task selection parameter.
setTaskProcessor(JobProcessor<T, S>) - Method in class org.anchoranalysis.experiment.bean.io.InputOutputExperiment: What task is associated with the experiment, and how it is processed.
setTemplateMark(MarkFactory) - Method in class org.anchoranalysis.mpp.bean.mark.factory.MarkWithIdentifierFactory: A template mark factory from which all new marks are created.
setText(String) - Method in class org.anchoranalysis.image.io.bean.stack.combine.WriteText: Text to draw on an image.
setThreshold(double) - Method in class org.anchoranalysis.bean.shared.relation.threshold.RelationToConstant: The constant threshold.
setThreshold(double) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedFeature
setThreshold(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjectsThreshold: The threshold value for considering intersecting objects.
setThreshold(int) - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.CutBelowThreshold
setThreshold(int) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelRelativeToThreshold: Threshold value to compare against when deciding whether to use the alternative calculation.
setThreshold(RelationToThreshold) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Count
setThreshold(RelationToThreshold) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.RatioThreshold: The threshold condition to be applied to the histogram values.
setThreshold(RelationToThreshold) - Method in class org.anchoranalysis.plugin.operator.feature.bean.conditional.IfCondition
setThreshold(UnitValueDistance) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntensityGreaterEqualThan
setThreshold(UnitValueVolume) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedVolume
setThresholder(Thresholder) - Method in class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationThreshold: Performs the global thresholding.
setThresholder(Thresholder) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.segment.Threshold: The thresholder that will convert a channel into a binary-channel
setThresholdHours(double) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster.ClusterByTimestamp: Files whose creation-time differs <= this parameter are joined into the same cluster.
setThresholdNumberObjectsGlobal(int) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ThresholdConfidence: When the number of objects is greater or equal than this, they are reduced globally, without separation.
setThrowExceptionForInsufficientPoints(boolean) - Method in class org.anchoranalysis.mpp.bean.points.CreateMarkFromPoints: Whether to throw an exception when there are insufficient points.
setThumbnail(ThumbnailFromObjects) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.CombineObjectsForFeatures: Generates a thumbnail representation of one or more combined objects, as form a single input.
setThumbnail(ThumbnailFromStack) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromImage: Method to generate a thumbnail for images.
setTime(boolean) - Method in class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierAuto: If true, the current time (HH.mm.ss) is included in the output.
setTimeIndex(int) - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertNamedChannelsToStack
setTimeIndexGroupID(int) - Method in class org.anchoranalysis.plugin.io.bean.file.group.parser.RegularExpression
setTimes(int) - Method in class org.anchoranalysis.bean.shared.color.scheme.Repeat: How many times to duplicate the list.
setTimestampPatterns(List<TimestampPattern>) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster.ClusterByTimestamp: The patterns which can be used to extract a date-time from a filename.
setTimeZoneOffset(int) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster.ClusterByTimestamp: If >= 0, sets a specific time-offset in hours.
setTransposed(boolean) - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
setTrimTrailingDirectory(int) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.RemoveTrailingDirectory
setUniqueLabel(String) - Method in class org.anchoranalysis.plugin.annotation.bean.label.AnnotationLabel: Label that uniquely identifies the ID (for machine purposes).
setUnitType(String) - Method in class org.anchoranalysis.image.bean.unitvalue.distance.DistancePhysical: A string indicating type of units to use, as per SpatialUnits.
setUnitType(String) - Method in class org.anchoranalysis.image.bean.unitvalue.extent.area.AreaPhysical: How much each value represents e.g. square nanometers, squares millimeters etc.
setUnitType(String) - Method in class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumePhysical: How much each value represents e.g. cubic nanometers, cubic millimeters etc.
setUnitType(String) - Method in class org.anchoranalysis.image.feature.bean.physical.FeatureConvertUnits: The type of unit to convert to, represented as a string (e.g., "um" for micrometers).
setUnitTypeFrom(String) - Method in class org.anchoranalysis.plugin.operator.feature.physical.ConvertUnits: The unit type to convert from.
setUnitTypeTo(String) - Method in class org.anchoranalysis.plugin.operator.feature.physical.ConvertUnits: The unit type to convert to.
setupBefore(Dimensions, ImageFileEncoding) - Method in class org.anchoranalysis.io.bioformats.copyconvert.ConvertTo: Always called before any batch of calls to ConvertTo.convertSliceOfSingleChannel(java.nio.ByteBuffer, int, org.anchoranalysis.image.core.dimensions.OrientationChange).
setupBefore(Dimensions, ImageFileEncoding) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tofloat.FloatFromUnsignedByte
setupDictionary(Dictionary) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.FromDictionaryBase: Sets up the feature using the provided dictionary.
setUseLastSeriesIndexOnly(boolean) - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannels
setUseLastSeriesIndexOnly(boolean) - Method in class org.anchoranalysis.plugin.io.bean.input.stack.Stacks
setUserFriendlyLabel(String) - Method in class org.anchoranalysis.plugin.annotation.bean.label.AnnotationLabel: Descriptive user-friendly label displayed via GUI.
setUseZ(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.RemoveTouchingBorder
setValue(double) - Method in class org.anchoranalysis.feature.bean.operator.Constant: The constant value.
setValue(double) - Method in class org.anchoranalysis.image.bean.unitvalue.distance.DistancePhysical: The value in units of type unitType.
setValue(double) - Method in class org.anchoranalysis.image.bean.unitvalue.distance.DistanceVoxels: The distance in units of voxels.
setValue(double) - Method in class org.anchoranalysis.image.bean.unitvalue.extent.area.AreaPhysical: The volume in units of meters, with the unit described by unitType.
setValue(double) - Method in class org.anchoranalysis.image.bean.unitvalue.extent.area.AreaPixels: The volume in pixels.
setValue(double) - Method in class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumePhysical: The volume in units of meters, with the unit described by unitType.
setValue(double) - Method in class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumeVoxels: The volume in voxels.
setValue(double) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignValue
setValue(double) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.UnaryWithValueBase: The scalar value to be used in channel creation.
setValue(double) - Method in class org.anchoranalysis.plugin.image.bean.scale.ConstantScaleFactor: The constant floating-point value to scale each dimension by.
setValue(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram: The value to return if the relation test passes.
setValue(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.NormalizeByConstant: The constant value to divide the voxel intensity by.
setValue(double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.WithValueBase: The constant value to be used in the operation.
setValue(int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.CreateNew
setValue(int) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.EmptyHistogramConstant
setValue(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.CountEqual: The intensity value to count.
setValue(String) - Method in class org.anchoranalysis.plugin.image.bean.dictionary.DictionaryCondition: The value the key should have in the dictionary, in order for the condition to be fulfilled.
setValue(String) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.IfParamEqual
setValue(String) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Constant
setValue(T) - Method in class org.anchoranalysis.bean.NamedBean
setValue(T) - Method in interface org.anchoranalysis.core.identifier.name.NameValue: Assigns the associated value.
setValue(V) - Method in class org.anchoranalysis.core.identifier.name.SimpleNameValue
setValueByDimension(int, double) - Method in class org.anchoranalysis.spatial.point.Tuple3d: Assigns a value to a component of the tuple corresponding to a particular dimension by index.
setValueByDimension(int, float) - Method in class org.anchoranalysis.spatial.point.Tuple3f: Assigns a value to a component of a tuple corresponding to a particular dimension by index.
setValueIfEmpty(double) - Method in class org.anchoranalysis.image.feature.bean.histogram.FeatureHistogramStatistic: The value to return iff exceptionifEmpty is false.
setValueIfTooFewVoxels(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.ImageMomentsBase: A value to return if there are too few voxels (less than MIN_NUM_VOXELS) to calculate moments.
setValueNoObject(int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreObjects: The value assigned to voxels that do not belong to any object.
setValueNoObjects(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjects: The value to return when there are no objects in the search collection.
setValues(DoubleSet) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyDoubleSet: The respect double values to assign during the permutation.
setValues(StringSet) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyStringSet: The respect string values to assign during the permutation.
setVaryColors(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel: When true, the colors change for different objects in the image (using a default color set).
setVaryImageLocation(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage: When true, the location of an image in the grid, as well as the number of images in each row are both allowed to vary to fill space.
setVaryImageSize(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage: When true, the images may vary in width/height in their respective rows to fill space, while preserving the aspect-ratio of each image.
setVaryingSizeWidth(int) - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage: If no specific width or scaling-factor is suggested, this determines the default width that the combined-montage should have, when varyImageSize==true.
setVaryingSizeWidthRatio(double) - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage: If no specific width or scaling-factor is suggested, this determines the default percentage of the existing size, the combined-montage should have, when varyImageSize==true.
setVaryNumberImagesPerRow(boolean) - Method in class org.anchoranalysis.image.bean.spatial.arrange.fill.Fill: When true the number of Extents per row is allowed vary, to sensibly fill space.
setVersion(String) - Method in class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierConstant
setVisuallyShortenDecimals(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeaturesStyle: When true, feature-values are shown as visually compressed as possible, including suppressing decimal places.
setWeightBackground(double) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.OtsuWeighted
setWeightForeground(double) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.OtsuWeighted
setWeightItem1Greater(double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.Range: Weight applied when the first item's value is greater than the second.
setWeightItem2Greater(double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.Range: Weight applied when the second item's value is greater than the first.
setWeightWidthDescription(int) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.ImageLabelStrategy: The weight to use for the width of the description.
setWhenBinaryChannel(StackWriter) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchChannels: Writer employed if a stack is a single-channeled binary image.
setWhenDetailed(LoggingDestination) - Method in class org.anchoranalysis.experiment.bean.log.SwitchDetailedLogging: Logger to use when detailed-logging is on
setWhenEqual(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.IfParamEqual
setWhenFalse(DrawObject) - Method in class org.anchoranalysis.image.io.bean.object.draw.IfElse: The DrawObject that is used when condition==false.
setWhenNot(LoggingDestination) - Method in class org.anchoranalysis.experiment.bean.log.SwitchDetailedLogging: Logger to use when detailed-logging is off
setWhenNotEightBit(StackWriter) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchChannels: Writer employed if a stack contains channels that are not 8-bit.
setWhenNotEqual(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.IfParamEqual
setWhenRelative(FileNamer) - Method in class org.anchoranalysis.plugin.io.bean.file.namer.IfRelativeToDirectory: The namer to use if the relative-to-directory option is selected.
setWhenRGB(StackWriter) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchChannels: Writer employed if a stack is a three-channeled RGB image.
setWhenRGBAlpha(StackWriter) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchChannels: Writer employed if a stack is a four-channeled RGBA image.
setWhenSingleChannel(StackWriter) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchChannels: Writer employed if a stack is a single-channeled image, not guaranteed to be binary.
setWhenThreeChannels(StackWriter) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchChannels: Writer employed if a stack is a three-channeled non-RGB image.
setWhenTrue(DrawObject) - Method in class org.anchoranalysis.image.io.bean.object.draw.IfElse: The DrawObject that is used when condition==true.
setWidth(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Difference: Width (what the difference is divided by)
setWidth(double) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ImposeResolution: Physical pixel size of a voxel in x-dimension.
setWidth(int) - Method in class org.anchoranalysis.image.bean.spatial.arrange.fill.Fill: The width of the combined image in pixels.
setWidth(int) - Method in class org.anchoranalysis.image.bean.spatial.SizeXY: Size in X dimension.
setWidthFactor(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.DifferenceCalculateLevelStandardDeviation
setWidthRatio(double) - Method in class org.anchoranalysis.image.bean.spatial.arrange.fill.Fill: What fraction of the natural width of the elements should be used to determine the final width.
setWindowSize(SizeXY) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters: The window-size as per OpenCV implementation.
setWithin(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.physical.UnitsWithinRange: Returned as a constant if a value lies within the range
setWithinValue(double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.CompareWithRange: Constant to return if value lies within the range
setWithinValue(double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.CompareWithRangeFeature: Constant to return if value lies within the range
setWriter(StackWriter) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchChannels: Default writer, if a more specific writer is not specified for a condition.
setWriter(StackWriter) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.WriteResolutionXml
setWriter(DrawObject) - Method in class org.anchoranalysis.image.io.bean.object.draw.Flatten
setWriterAlways2D(StackWriter) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchStack: Writer to use if it is guaranteed that the image will always be 2D.
setWriterElse(StackWriter) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchStack: Otherwise the writer to use.
setWriterIfNoSuggestion(StackWriter) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchSuggestedFormat: The writer to use if there is no suggested file-format.
setWriters(List<NamedBean<?>>) - Method in class org.anchoranalysis.io.output.bean.OutputWriteSettings: Specifies a writer bean instance for a particular type of writer (identified by the writer bean class)
setWritersIfSuggested(List<StackWriter>) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchSuggestedFormat: A list of writers to select if a given format is used
setX(double) - Method in class org.anchoranalysis.image.bean.spatial.direction.SpecifyVector: Component of the vector along the x-axis.
setX(double) - Method in class org.anchoranalysis.spatial.point.Tuple3d: X-axis component of the tuple.
setX(int) - Method in class org.anchoranalysis.spatial.point.Point2i: X-axis component of point.
setX(int) - Method in class org.anchoranalysis.spatial.point.Tuple3d: X-axis component of the tuple.
setX(int) - Method in class org.anchoranalysis.spatial.point.Tuple3i: X-axis component of the tuple.
setY(double) - Method in class org.anchoranalysis.image.bean.spatial.direction.SpecifyVector: Component of the vector along the y-axis.
setY(double) - Method in class org.anchoranalysis.spatial.point.Tuple3d: Y-axis component of the tuple.
setY(int) - Method in class org.anchoranalysis.spatial.point.Point2i: Y-axis component of point.
setY(int) - Method in class org.anchoranalysis.spatial.point.Tuple3d: Y-axis component of the tuple.
setY(int) - Method in class org.anchoranalysis.spatial.point.Tuple3i: Y-axis component of the tuple.
setZ(double) - Method in class org.anchoranalysis.image.bean.spatial.direction.SpecifyVector: Component of the vector along the z-axis.
setZ(double) - Method in class org.anchoranalysis.spatial.point.Tuple3d: Z-axis component of the tuple.
setZ(int) - Method in class org.anchoranalysis.spatial.point.Tuple3d: Z-axis component of the tuple.
setZ(int) - Method in class org.anchoranalysis.spatial.point.Tuple3i: Z-axis component of the tuple.
setZSliceGroupID(int) - Method in class org.anchoranalysis.plugin.io.bean.file.group.parser.RegularExpression
setZSliceNum(int) - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetSlice
shallowCopy() - Method in class org.anchoranalysis.core.color.ColorList: Creates a new list, containing the same elements as the current list.
shallowCopy() - Method in class org.anchoranalysis.core.graph.GraphWithPayload: Creates a new graph with identical elements and structure, reusing the existing vertice and edge data objects.
shallowCopy() - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria: Creates a shallow copy of this RandomCollectionWithAddCriteria.
shallowCopy() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown: Creates a shallow copy of this instance.
shallowCopy() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy: Makes a shallow copy of this instance.
shallowCopy() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedAll: Creates a shallow copy of this instance.
shallowCopy() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedIndividual: Creates a shallow copy of this instance.
shallowCopy() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedPairs: Creates a shallow copy of this instance.
shallowCopy() - Method in class org.anchoranalysis.mpp.mark.ColoredMarks: Creates a shallow copy of this ColoredMarks instance.
shallowCopy() - Method in class org.anchoranalysis.mpp.mark.MarkCollection: Creates a shallow copy of the collection.
shallowDuplicate() - Method in class org.anchoranalysis.feature.bean.list.FeatureList: Creates a new feature-list which contains identical elements.
ShapeRegularityCenterSlice - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shape: Calculates the shape regularity of the center slice of an ObjectMask.
ShapeRegularityCenterSlice() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.shape.ShapeRegularityCenterSlice
ShapeRegularityMaximumIntensityProjection - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shape: Calculates the shape regularity of the maximum intensity projection of an ObjectMask.
ShapeRegularityMaximumIntensityProjection() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.shape.ShapeRegularityMaximumIntensityProjection
SharedFeatures - Class in org.anchoranalysis.feature.shared: A group of features made available to other features to reference.
SharedFeatures() - Constructor for class org.anchoranalysis.feature.shared.SharedFeatures: Create empty, without any features.
SharedFeaturesSubset<T> - Class in org.anchoranalysis.feature.shared: A subset of features from SharedFeatures that share a common feature input-type.
SharedFeaturesSubset(NameValueMap<Feature<T>>) - Constructor for class org.anchoranalysis.feature.shared.SharedFeaturesSubset: Creates a new SharedFeaturesSubset instance.
sharedObjects() - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitialization: Objects shared between different components, a form of shared memory between them.
SharedObjects - Class in org.anchoranalysis.core.identifier.provider.store: Objects shared between different components.
SharedObjects(CommonContext) - Constructor for class org.anchoranalysis.core.identifier.provider.store.SharedObjects: Creates a new SharedObjects instance.
sharedObjectsRequired() - Method in class org.anchoranalysis.feature.initialization.FeatureInitialization: Retrieves the shared-objects associated with the initialization, or throws an an exception if they do not exist.
SharedStateFilteredImageOutput<T> - Class in org.anchoranalysis.plugin.image.task.labeller: Manages filtered image output with shared state across multiple images.
SharedStateFilteredImageOutput(Outputter, ImageLabeller<T>, String, String) - Constructor for class org.anchoranalysis.plugin.image.task.labeller.SharedStateFilteredImageOutput: Creates a new SharedStateFilteredImageOutput.
SharedStateRememberConverted<U,S> - Class in org.anchoranalysis.plugin.mpp.shared: Shared-state that remembers converted inputs for corresponding unconverted inputs.
SharedStateRememberConverted() - Constructor for class org.anchoranalysis.plugin.mpp.shared.SharedStateRememberConverted
SharedStateSegmentInstance<T> - Class in org.anchoranalysis.plugin.image.task.segment: Shared-state for instance segmentation.
SharedStateSegmentInstance(ConcurrentModelPool<T>, FeatureTableCalculator<FeatureInputSingleObject>, LabelHeaders, String, FeatureExporterContext) - Constructor for class org.anchoranalysis.plugin.image.task.segment.SharedStateSegmentInstance: Creates a new instance of SharedStateSegmentInstance.
SharedStateSelectedSlice - Class in org.anchoranalysis.plugin.image.task.stack: Shared state for writing selected slice information to a CSV file.
SharedStateSelectedSlice(Outputter) - Constructor for class org.anchoranalysis.plugin.image.task.stack.SharedStateSelectedSlice: Creates a new instance of SharedStateSelectedSlice.
Shell - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.morphological: Creates a shell around an ObjectMask by applying morphological operations.
Shell() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.Shell
shift() - Method in class org.anchoranalysis.image.voxel.buffer.SlidingBuffer: Increments the slice number by one.
shiftBackBy(VoxelsAssigner, ReadableTuple3i) - Static method in class org.anchoranalysis.image.voxel.assigner.VoxelsAssignerFactory: Shifts all coordinates backwards before passing to another VoxelsAssigner.
shiftBackBy(ReadableTuple3i) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Shifts the object-mask by moving its bounding-box backwards.
shiftBackBy(ReadableTuple3i) - Method in class org.anchoranalysis.spatial.box.BoundingBox: Shifts the bounding-box backwards.
shiftBy(ObjectMask, ReadableTuple3i) - Method in class org.anchoranalysis.image.core.object.scale.AccessObjectMaskSimple
shiftBy(ReadableTuple3i) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection: Shifts the bounding-box of each object by adding to it.
shiftBy(ReadableTuple3i) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Shifts the object-mask by moving its bounding-box forwards.
shiftBy(ReadableTuple3i) - Method in class org.anchoranalysis.spatial.box.BoundingBox: Shifts the bounding-box forwards.
shiftBy(T, ReadableTuple3i) - Method in interface org.anchoranalysis.image.core.object.scale.AccessObjectMask: Positionally-shifts an element by a given quantity in the positive direction.
shiftTo(ReadableTuple3i) - Method in class org.anchoranalysis.spatial.box.BoundingBox: Assigns a new corner-location to the bounding-box.
shiftToOrigin() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Creates a new object-mask with identical voxels but with the bounding-box beginning at the origin (0,0,0).
shiftToOrigin() - Method in class org.anchoranalysis.spatial.box.BoundingBox: Moves the bounding-box to the origin (0,0,0) but preserves the extent.
shiftToZ(int) - Method in class org.anchoranalysis.spatial.box.BoundingBox: Assigns a new z-slice corner-location to the bounding-box.
SHORT_OPTION_DEBUG - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions: Enables debug-mode: runs only the first available input [whose name contains string].
SHORT_OPTION_GROUP - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions: Activates grouping from a subset of the identifier's elements.
SHORT_OPTION_HELP - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions: Displays help message with all command-line options.
SHORT_OPTION_INPUT - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions: Changes inputs.
SHORT_OPTION_INPUT_COPY_NON_INPUTS - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions: Additionally copies any files in the input directory, unused as inputs.
SHORT_OPTION_INPUT_LIMIT - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions: Imposes an upper limit on the number of inputs.
SHORT_OPTION_INPUT_RANDOM_SAMPLE - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions: Randomly samples a number of inputs.
SHORT_OPTION_INPUT_RELATIVE_PATH - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions: Derives the unique identifier from the **entire relative filename or path** (excluding file extension).
SHORT_OPTION_INPUT_SHUFFLE - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions: Shuffles the order of the inputs.
SHORT_OPTION_INPUT_SUBSET_IDENTIFIER - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions: Subsets the identifier.
SHORT_OPTION_LOG_ERROR - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions: Logs initial BeanXML errors in greater detail to a file-path.
SHORT_OPTION_OUTPUT - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions: Changes output manager.
SHORT_OPTION_OUTPUT_CONSOLE_ONLY - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions: Output console only.
SHORT_OPTION_OUTPUT_DISABLE_ADDITIONAL - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions: Disables specific output(s).
SHORT_OPTION_OUTPUT_ENABLE_ADDITIONAL - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions: Enables specific output(s).
SHORT_OPTION_OUTPUT_ENABLE_ALL - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions: Enables all outputs.
SHORT_OPTION_OUTPUT_IMAGE_FILE_FORMAT - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions: Suggests an output image file format: e.g -of jpg or -of ome.xml.
SHORT_OPTION_OUTPUT_INCREMENTING_NUMBER - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions: Outputs with an incrementing number instead of the input identifier.
SHORT_OPTION_OUTPUT_OMIT_EXPERIMENT_IDENTIFIER - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions: Ignores the experiment identifier, when forming an output-path.
SHORT_OPTION_OUTPUT_SUPPRESS_DIRECTORIES - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions: Suppressed the subdirectory structure when outputting file identifiers.
SHORT_OPTION_SHOW_EXPERIMENT_ARGUMENTS - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions: Shows additional argument information, otherwise executes as normal.
SHORT_OPTION_SHOW_TASKS - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions: Prints the names of predefined tasks that can be easily used with -t.
SHORT_OPTION_TASK - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions: Changes task.
SHORT_OPTION_TASK_NUMBER_PROCESSORS - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions: Suggests a maximum number of processors to use for the task.
SHORT_OPTION_TASK_SIZE - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions: Suggests dimensions or a scaling factor for certain tasks.
SHORT_OPTION_VERSION - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions: Displays version and authorship information.
shouldObjectsBeProcessed(ObjectMask, ObjectMask) - Method in class org.anchoranalysis.image.inference.bean.reduce.ReduceElementsGreedy: Whether to include another (possibly-overlapping with source) element in processing?
shouldObjectsBeProcessed(ObjectMask, ObjectMask) - Method in class org.anchoranalysis.image.inference.bean.reduce.RemoveOverlappingObjects
shouldOverwriteVoxelWithConstant(int, int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.ArithmeticWithConstantConditionallyWriteBase: Determines whether to overwrite the current voxel value with the constant.
shouldOverwriteVoxelWithConstant(int, int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.MaxWithConstant
shouldOverwriteVoxelWithConstant(int, int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.MinWithConstant
shrinkBy(ReadableTuple3i) - Method in class org.anchoranalysis.spatial.box.Extent: Creates a new Extent with toSubtract size subtracted from each respective dimension.
shuffle() - Method in class org.anchoranalysis.core.color.ColorList: Randomize the order of the colors in the list.
Shuffle - Class in org.anchoranalysis.bean.shared.color.scheme: Randomizes the order of colors in a list created by another ColorScheme.
Shuffle<T> - Class in org.anchoranalysis.plugin.io.bean.input: Randomly shuffles the order of the inputs.
Shuffle() - Constructor for class org.anchoranalysis.bean.shared.color.scheme.Shuffle
Shuffle() - Constructor for class org.anchoranalysis.plugin.io.bean.input.Shuffle
Shuffle(ColorScheme) - Constructor for class org.anchoranalysis.bean.shared.color.scheme.Shuffle: Creates with a specific delegate ColorScheme.
ShuffleIfRequested<T> - Class in org.anchoranalysis.plugin.io.bean.input: Like Shuffle if requested in the InputContextParameters otherwise makes no change to the inputs.
ShuffleIfRequested() - Constructor for class org.anchoranalysis.plugin.io.bean.input.ShuffleIfRequested
SignedShortVoxelType - Class in org.anchoranalysis.image.voxel.datatype: A 16-bit voxel data-type representing signed-short numbers.
SignedVoxelType - Class in org.anchoranalysis.image.voxel.datatype: Base class for voxel-data-types that are signed and integral.
SignedVoxelType(int, String, long, long) - Constructor for class org.anchoranalysis.image.voxel.datatype.SignedVoxelType: Construct for a particular number of bits, with a unique identifier, and with bounds on the values.
SimpleAnnotationDeleter - Class in org.anchoranalysis.annotation.io: Deletes any annotation when it is represented by a single file.
SimpleAnnotationDeleter() - Constructor for class org.anchoranalysis.annotation.io.SimpleAnnotationDeleter
SimpleName - Class in org.anchoranalysis.feature.io.name: A name with only one part, and is always unique.
SimpleName(String) - Constructor for class org.anchoranalysis.feature.io.name.SimpleName
SimpleNameValue<V> - Class in org.anchoranalysis.core.identifier.name: A simple container expressing a name-value pair.
SimpleNameValue(String, V) - Constructor for class org.anchoranalysis.core.identifier.name.SimpleNameValue: Creates a new SimpleNameValue instance.
SimpleOutputNameStyle - Class in org.anchoranalysis.io.output.namestyle: A constant filename that is identical to the output-name plus extension.
SimpleOutputNameStyle(String) - Constructor for class org.anchoranalysis.io.output.namestyle.SimpleOutputNameStyle: Creates with an output-name.
Single - Class in org.anchoranalysis.image.bean.spatial.arrange: A single Stack arranged as-is.
Single() - Constructor for class org.anchoranalysis.image.bean.spatial.arrange.Single
SingleChannel - Class in org.anchoranalysis.plugin.image.feature.bean.score: A score that is calculated on a single channel only.
SingleChannel - Class in org.anchoranalysis.plugin.io.bean.channel.map: For an image with a single channel
SingleChannel() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.SingleChannel
SingleChannel() - Constructor for class org.anchoranalysis.plugin.io.bean.channel.map.SingleChannel
SingleChannel(String) - Constructor for class org.anchoranalysis.plugin.io.bean.channel.map.SingleChannel
singleChannelMaybe3D(boolean) - Static method in class org.anchoranalysis.image.io.stack.output.StackWriteAttributesFactory: A StackWriteAttributes which is always a single-channel, and depending on a flag, may be guaranteed to be 2D.
SingleColor - Class in org.anchoranalysis.core.color: An index that always uses the same single color
SingleColor(Color) - Constructor for class org.anchoranalysis.core.color.SingleColor: Creates with a particular color.
SingleColor(RGBColor) - Constructor for class org.anchoranalysis.core.color.SingleColor
singleCPUProcessor() - Static method in class org.anchoranalysis.inference.concurrency.ConcurrencyPlan: Creates a plan for a single-CPU processor with the default number of GPUs.
singleCPUProcessor(int) - Static method in class org.anchoranalysis.inference.concurrency.ConcurrencyPlan: Creates a plan for a single-CPU processor - with a maximum number of GPUs.
SingleFile - Class in org.anchoranalysis.io.input.bean.files: Provides a single file only.
SingleFile() - Constructor for class org.anchoranalysis.io.input.bean.files.SingleFile
SingleFile(String) - Constructor for class org.anchoranalysis.io.input.bean.files.SingleFile: Creates with a path for the single-file.
SingleFileInputBase - Class in org.anchoranalysis.io.input.file: A base class for inputs that refer to a single file.
SingleFileInputBase(NamedFile) - Constructor for class org.anchoranalysis.io.input.file.SingleFileInputBase: Creates for a particular file.
SingleFileTypeGenerator<T,S> - Class in org.anchoranalysis.io.generator: A Generator that eventually writes only a single file to the filesystem.
SingleFileTypeGenerator() - Constructor for class org.anchoranalysis.io.generator.SingleFileTypeGenerator
SingleFileTypeGeneratorBridge<S,T,V> - Class in org.anchoranalysis.io.generator: Allows us to call an SingleFileTypeGenerator<V,S> as if it was an SingleFileTypeGenerator<T,S> using an function to connect the two.
SingleFileTypeGeneratorBridge(SingleFileTypeGenerator<V, S>, CheckedFunction<T, V, ? extends Throwable>) - Constructor for class org.anchoranalysis.io.generator.SingleFileTypeGeneratorBridge: Creates a new SingleFileTypeGeneratorBridge instance.
SingleLevelAnd - Class in org.anchoranalysis.io.output.enabled.single: Outputs are enabled if they are contained in both of two SingleLevelOutputEnabled.
SingleLevelAnd(SingleLevelOutputEnabled, SingleLevelOutputEnabled) - Constructor for class org.anchoranalysis.io.output.enabled.single.SingleLevelAnd: Creates using two SingleLevelOutputEnableds.
SingleLevelBinary - Class in org.anchoranalysis.io.output.enabled.single: Base class for a SingleLevelOutputEnabled that combines two existing such classes.
SingleLevelBinary(SingleLevelOutputEnabled, SingleLevelOutputEnabled) - Constructor for class org.anchoranalysis.io.output.enabled.single.SingleLevelBinary: Creates a new SingleLevelBinary instance.
SingleLevelInSet - Class in org.anchoranalysis.io.output.enabled.single: Outputs are enabled if they are contained in a set.
SingleLevelInSet(Set<String>) - Constructor for class org.anchoranalysis.io.output.enabled.single.SingleLevelInSet: Creates a new SingleLevelInSet instance.
SingleLevelNot - Class in org.anchoranalysis.io.output.enabled.single: The complement of an existing SingleLevelOutputEnabled where disabled outputs are enabled, and vice-versa.
SingleLevelNot(SingleLevelOutputEnabled) - Constructor for class org.anchoranalysis.io.output.enabled.single.SingleLevelNot: Creates a new SingleLevelNot instance.
SingleLevelOr - Class in org.anchoranalysis.io.output.enabled.single: Outputs are enabled if they are contained in either of two SingleLevelOutputEnabled.
SingleLevelOr(SingleLevelOutputEnabled, SingleLevelOutputEnabled) - Constructor for class org.anchoranalysis.io.output.enabled.single.SingleLevelOr: Creates using two SingleLevelOutputEnableds.
SingleLevelOutputEnabled - Interface in org.anchoranalysis.io.output.enabled.single: An interface for any class that defines whether a top-level output is enabled.
SingleMarkProvider - Class in org.anchoranalysis.mpp.bean.provider: Provides (maybe) a single mark
SingleMarkProvider() - Constructor for class org.anchoranalysis.mpp.bean.provider.SingleMarkProvider
SinglePathStrategy - Class in org.anchoranalysis.plugin.annotation.bean.strategy: A base class for implementations of AnnotatorStrategy where a single unique path exists for every annotation.
SinglePathStrategy() - Constructor for class org.anchoranalysis.plugin.annotation.bean.strategy.SinglePathStrategy
SingleRowPerInput<T,S> - Class in org.anchoranalysis.plugin.image.task.bean.feature.source: Base class for exporting features, where features are calculated per-image using a NamedFeatureStore.
SingleRowPerInput(String) - Constructor for class org.anchoranalysis.plugin.image.task.bean.feature.source.SingleRowPerInput: Creates with a single non-group header that should be describe an identifier.
SingleRowPerInput(String[]) - Constructor for class org.anchoranalysis.plugin.image.task.bean.feature.source.SingleRowPerInput: Creates a new SingleRowPerInput instance.
SingleTableCalculator - Class in org.anchoranalysis.image.feature.calculator: A feature table calculator for single objects.
SingleTableCalculator(NamedFeatureStore<FeatureInputSingleObject>) - Constructor for class org.anchoranalysis.image.feature.calculator.SingleTableCalculator: Creates a new SingleTableCalculator instance.
size() - Method in class org.anchoranalysis.core.color.ColorList: The number of elements (colors) in the list.
size() - Method in class org.anchoranalysis.core.identifier.provider.NameValueMap: The number of elements in the set.
size() - Method in class org.anchoranalysis.feature.bean.list.FeatureList: Returns the number of elements in this list.
size() - Method in class org.anchoranalysis.feature.io.results.LabelledResultsVector: The number of calculations stored in the vector.
size() - Method in class org.anchoranalysis.feature.name.FeatureNameList: The number of names in the list.
size() - Method in class org.anchoranalysis.feature.results.ResultsVector: The number of calculations stored in the vector.
size() - Method in class org.anchoranalysis.feature.results.ResultsVectorList: The number of ResultsVectors in the list.
size() - Method in class org.anchoranalysis.feature.store.NamedFeatureStore: The total number of Features in the store.
size() - Method in class org.anchoranalysis.image.core.object.properties.ObjectCollectionWithProperties: Number of objects in the collection.
size() - Method in class org.anchoranalysis.image.core.object.scale.ScaledElements: Number of scaled-elements.
size() - Method in class org.anchoranalysis.image.core.stack.named.NamedStacks: Number of stacks.
size() - Method in class org.anchoranalysis.image.inference.segment.SegmentedObjects: The total number of segmented objects.
size() - Method in class org.anchoranalysis.image.inference.segment.SegmentedObjectsAtScale: A count of the total number of elements in each representation.
size() - Method in class org.anchoranalysis.image.io.stack.time.TimeSeries: The number of frames in the time-series.
size() - Method in class org.anchoranalysis.image.voxel.object.IntersectingObjects: Number of items in the r-tree.
size() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection: The number of objects in the collection.
size() - Method in interface org.anchoranalysis.image.voxel.statistics.VoxelStatistics: The total count.
size() - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsCombined
size() - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsFromHistogram
size() - Method in class org.anchoranalysis.math.histogram.Histogram: The size of the range of values in the histogram.
size() - Method in class org.anchoranalysis.mpp.bean.bound.BoundUnitless: Calculates the size of the bound range.
size() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown: Gets the number of marks in the collection.
size() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy: Gets the number of marks in the collection.
size() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedIndividual: Gets the number of individual energy totals stored.
size() - Method in class org.anchoranalysis.mpp.feature.mark.EnergyMemoList
size() - Method in class org.anchoranalysis.mpp.feature.mark.MemoList: Returns the number of elements in this list.
size() - Method in class org.anchoranalysis.mpp.index.IndexByChannel: Gets the number of channels in the index.
size() - Method in class org.anchoranalysis.mpp.mark.ColoredMarks: Returns the number of marks in the collection.
size() - Method in class org.anchoranalysis.mpp.mark.MarkCollection: Returns the number of marks in the collection.
size() - Method in interface org.anchoranalysis.mpp.mark.voxelized.memo.MemoForIndex: Returns the total number of memos available.
size() - Method in class org.anchoranalysis.overlay.collection.ColoredOverlayCollection: The total number of elements in the list.
size() - Method in class org.anchoranalysis.overlay.collection.OverlayCollection: The total number of elements in the list.
size() - Method in class org.anchoranalysis.plugin.image.feature.object.ListWithThumbnails: Gets the size of the list.
size() - Method in class org.anchoranalysis.plugin.io.multifile.ParsedFilePathBag: Gets the number of FileDetails objects in the collection.
size() - Method in class org.anchoranalysis.spatial.box.BoundedList: The number of elements.
size() - Method in class org.anchoranalysis.spatial.rtree.RTree: The total number of items stored in the tree.
sizeAfter() - Method in class org.anchoranalysis.image.inference.segment.ReductionOutcome: The total number of elements after reduction.
sizeAfterAnyScaling() - Method in class org.anchoranalysis.image.io.stack.output.box.ScaleableBackground: The size of the background after any scaling has occurred.
sizeC(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.Default
sizeC(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceNumberChannels
sizeC(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptions: Number of channels.
sizeC(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptionsDelegate
sizeCurrentLoad() - Method in class org.anchoranalysis.core.cache.LRUCache: Number of items currently in the cache.
sizeDescriptor(Extent) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters: Calculates the size of the descriptor will be for a given image.
SizeExtents - Class in org.anchoranalysis.plugin.io.multifile: Remembers the different sizes among the files
SizeExtents(ParsedFilePathBag) - Constructor for class org.anchoranalysis.plugin.io.multifile.SizeExtents
sizeFeatures() - Method in interface org.anchoranalysis.feature.calculate.bound.FeatureCalculatorMulti: The number of features that is calculated on each call to FeatureCalculatorMulti.calculate(T), and therefore the size of the returned ResultsVector.
sizeFeatures() - Method in class org.anchoranalysis.feature.calculate.bound.FeatureCalculatorMultiChangeInput
sizeFeatures() - Method in class org.anchoranalysis.feature.session.SequentialSession
sizeFeatures() - Method in class org.anchoranalysis.image.feature.calculator.merged.PairsTableCalculator
sizeFeatures() - Method in class org.anchoranalysis.image.feature.calculator.SingleTableCalculator
sizeFirst() - Method in class org.anchoranalysis.annotation.io.assignment.CostMatrix: The number of elements in the first list.
SizeMapping - Class in org.anchoranalysis.plugin.image.task.size: Maps a Path to a particular image-size and orientation-change.
SizeMapping(Path, Extent) - Constructor for class org.anchoranalysis.plugin.image.task.size.SizeMapping: Creates a new SizeMapping instance.
sizeSecond() - Method in class org.anchoranalysis.annotation.io.assignment.CostMatrix: The number of elements in the second list.
sizeT(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.Default
sizeT(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceNumberFrames
sizeT(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceTimeSeriesToStack
sizeT(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptions: Number of time-points (frames in a time series).
sizeT(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptionsDelegate
sizeT(Logger) - Method in class org.anchoranalysis.image.io.channel.map.NamedChannelsConcatenate
sizeT(Logger) - Method in interface org.anchoranalysis.image.io.channel.map.NamedChannelsMap: The number of frames along the time-axis.
sizeT(Logger) - Method in class org.anchoranalysis.image.io.channel.map.OpenedNamedChannels
SizeXY - Class in org.anchoranalysis.image.bean.spatial: The size of an entity in the X and Y dimensions.
SizeXY() - Constructor for class org.anchoranalysis.image.bean.spatial.SizeXY
SizeXY(int, int) - Constructor for class org.anchoranalysis.image.bean.spatial.SizeXY: Creates a new SizeXY instance.
SizeXY(Extent) - Constructor for class org.anchoranalysis.image.bean.spatial.SizeXY: Create form an Extent.
sizeZ(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.Default
sizeZ(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceTimeSeriesToStack
sizeZ(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptions: Number of z-slices (slices in a 3D image).
sizeZ(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptionsDelegate
skewness(Histogram) - Static method in class org.anchoranalysis.math.histogram.HistogramStatistics: Calculates the skewness of a distribution of values, represented by their histogram.
Skewness - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic: Calculates the skewness of all the values in the histogram.
Skewness() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Skewness
SkipInit - Annotation Interface in org.anchoranalysis.bean.annotation: Indicates that this particular bean-field should be ignored during (recursive) initialization.
slice(int) - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels: A VoxelBuffer corresponding to a particular z-slice.
slice(int) - Method in class org.anchoranalysis.image.voxel.buffer.slice.FromByte
slice(int) - Method in class org.anchoranalysis.image.voxel.buffer.slice.FromFloat
slice(int) - Method in class org.anchoranalysis.image.voxel.buffer.slice.FromInt
slice(int) - Method in class org.anchoranalysis.image.voxel.buffer.slice.FromShort
slice(int) - Method in interface org.anchoranalysis.image.voxel.buffer.slice.SliceBufferIndex: A VoxelBuffer corresponding to a particular z-slice.
slice(int) - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter: Creates a new Voxels with only particular slice.
slice(int) - Method in class org.anchoranalysis.image.voxel.Voxels: A VoxelBuffer corresponding to a particular z-slice.
slice(int) - Method in class org.anchoranalysis.image.voxel.VoxelsUntyped: A VoxelBuffer corresponding to a particular z-slice.
SliceAt - Class in org.anchoranalysis.plugin.image.bean.object.provider.slice: Extracts a specific slice from a collection of 3D objects.
SliceAt() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.slice.SliceAt
sliceBinary(int) - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels: A particular z-slice, wrapped into a BinaryVoxels.
sliceBuffer(int) - Method in class org.anchoranalysis.image.core.mask.Mask: A buffer corresponding to a particular z-slice.
sliceBuffer(int) - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels: A buffer corresponding to a particular z-slice.
sliceBuffer(int) - Method in interface org.anchoranalysis.image.voxel.buffer.slice.SliceBufferIndex: The underlying buffer corresponding to a particular z-slice.
sliceBuffer(int) - Method in class org.anchoranalysis.image.voxel.Voxels: A buffer corresponding to a particular z-slice.
sliceBuffer(int, int) - Method in class org.anchoranalysis.image.core.stack.RGBStack: A buffer corresponding to a particular z-slice of a particular channel.
sliceBufferGlobal(int) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: A slice buffer with global coordinates.
sliceBufferGlobal(int) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: A slice buffer with global coordinates.
SliceBufferIndex<T> - Interface in org.anchoranalysis.image.voxel.buffer.slice: A container with voxel-buffers for each z-slice.
sliceBufferLocal(int) - Method in class org.anchoranalysis.image.core.object.properties.ObjectWithProperties: A slice buffer with local coordinates.
sliceBufferLocal(int) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: A slice buffer with local coordinates.
sliceBufferLocal(int) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: A slice buffer with local coordinates.
slices() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels: An index mapping slice of voxels (in the z dimension) to a particular buffer with the corresponding voxel intensities.
slices() - Method in class org.anchoranalysis.image.voxel.Voxels: An index mapping slice of voxels (in the z dimension) to a particular buffer with the corresponding voxel intensities.
SliceThresholder - Class in org.anchoranalysis.plugin.image.segment.thresholder.slice: Segmenting a z-Stack slice-by-slice.
SliceThresholder(BinaryValuesByte) - Constructor for class org.anchoranalysis.plugin.image.segment.thresholder.slice.SliceThresholder: Creates a new SliceThresholder instance.
SliceThresholderMask - Class in org.anchoranalysis.plugin.image.segment.thresholder.slice: A slice thresholder that applies thresholding within a mask region.
SliceThresholderMask(boolean, ObjectMask, BinaryValuesByte) - Constructor for class org.anchoranalysis.plugin.image.segment.thresholder.slice.SliceThresholderMask: Creates a new SliceThresholderMask.
SliceThresholderWithoutMask - Class in org.anchoranalysis.plugin.image.segment.thresholder.slice: A slice thresholder that applies thresholding to the entire image without using a mask.
SliceThresholderWithoutMask(BinaryValuesByte) - Constructor for class org.anchoranalysis.plugin.image.segment.thresholder.slice.SliceThresholderWithoutMask: Creates a new SliceThresholderWithoutMask.
SlidingBuffer<T> - Class in org.anchoranalysis.image.voxel.buffer: An index that places a particular z-slice in local context.
SlidingBuffer(Voxels<T>) - Constructor for class org.anchoranalysis.image.voxel.buffer.SlidingBuffer: Create for particular voxels.
SMALL_2D - Static variable in class org.anchoranalysis.test.image.ChannelFixture: Small 2D extent for testing.
SMALL_3D - Static variable in class org.anchoranalysis.test.image.ChannelFixture: Small 3D extent for testing.
Sobel - Class in org.anchoranalysis.plugin.image.bean.channel.provider.gradient: 3x3 Sobel Filter
Sobel() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.Sobel
solveQuadraticEquation(double, double, double) - Static method in class org.anchoranalysis.math.equation.QuadraticEquationSolver: Solves a quadratic equation in form x^2 + b^x + c = 0.
sort(Comparator<Feature<T>>) - Method in class org.anchoranalysis.feature.bean.list.FeatureList: Creates a new feature-list sorted in a particular order.
SortAlphabetically - Class in org.anchoranalysis.plugin.io.bean.file.provider
SortAlphabetically<T> - Class in org.anchoranalysis.plugin.io.bean.input: Sorts the input-items in alphabetical order of their input-name.
SortAlphabetically() - Constructor for class org.anchoranalysis.plugin.io.bean.file.provider.SortAlphabetically
SortAlphabetically() - Constructor for class org.anchoranalysis.plugin.io.bean.input.SortAlphabetically
SortAlphabeticallyWithDirectory - Class in org.anchoranalysis.plugin.io.bean.file.provider
SortAlphabeticallyWithDirectory() - Constructor for class org.anchoranalysis.plugin.io.bean.file.provider.SortAlphabeticallyWithDirectory
SortByFeature - Class in org.anchoranalysis.plugin.image.bean.object.provider.feature: Creates a new object-collection with objects sorted by a derived feature-value (in ascending order)
SortByFeature() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.feature.SortByFeature
SortedSetChannel - Class in org.anchoranalysis.plugin.io.multifile
SortedSetChannel() - Constructor for class org.anchoranalysis.plugin.io.multifile.SortedSetChannel
SortedSetSlice - Class in org.anchoranalysis.plugin.io.multifile
SortedSetSlice(String, int) - Constructor for class org.anchoranalysis.plugin.io.multifile.SortedSetSlice
sourceIncrement - Variable in class org.anchoranalysis.io.bioformats.copyconvert.ConvertTo: The number of elements (bytes) to increment by, when iterating through the source buffer.
sourceSize - Variable in class org.anchoranalysis.io.bioformats.copyconvert.ConvertTo: The total number of elements (always bytes) in the source buffer.
sourceValue - Variable in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsoluteWithSlidingBuffer: The intensity value of the source voxel.
spatiallySeparate() - Method in class org.anchoranalysis.image.voxel.object.IntersectingObjects: Splits the collection of objects into spatially separate clusters.
SpatiallySeparate<T> - Class in org.anchoranalysis.spatial.rtree: Splits a collection of elements into spatially separate clusters.
SpatiallySeparate(Function<T, BoundingBox>) - Constructor for class org.anchoranalysis.spatial.rtree.SpatiallySeparate: Creates a new SpatiallySeparate instance.
SpatialUnits - Class in org.anchoranalysis.image.core.dimensions: Units to describe spatial quantities.
SpatialUnits.UnitSuffix - Enum Class in org.anchoranalysis.image.core.dimensions: Suffix that describes a particular quantity of units (micron, nano, square microns etc.)
SpecificAndRename - Class in org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels: Selects a specific set of channels from stacks, each identified by a stack-name and channel index
SpecificAndRename() - Constructor for class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.SpecificAndRename
SpecificAxisBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.moments: A feature based on one specific principal-axis as identified by image moments.
SpecificAxisBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.SpecificAxisBase
SpecificDisabled - Class in org.anchoranalysis.io.output.bean.enabled: Only specific outputs, identified by a textual name, are disabled, and all others are enabled.
SpecificDisabled() - Constructor for class org.anchoranalysis.io.output.bean.enabled.SpecificDisabled
SpecificDisabled(StringSet) - Constructor for class org.anchoranalysis.io.output.bean.enabled.SpecificDisabled: Creates a new SpecificDisabled instance.
SpecificEnabled - Class in org.anchoranalysis.io.output.bean.enabled: Only specific outputs, identified by a textual name, are enabled.
SpecificEnabled() - Constructor for class org.anchoranalysis.io.output.bean.enabled.SpecificEnabled
SpecificEnabled(String) - Constructor for class org.anchoranalysis.io.output.bean.enabled.SpecificEnabled: Create with a single output-enabled.
SpecificEnabled(StringSet) - Constructor for class org.anchoranalysis.io.output.bean.enabled.SpecificEnabled: Creates a new SpecificEnabled instance.
SpecificEnergyChannelBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.energy: A base class for features that operate on a specific channel from the energy stack.
SpecificEnergyChannelBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.SpecificEnergyChannelBase
SpecificPathList - Class in org.anchoranalysis.io.input.bean.files: A specific list of paths which form the input.
SpecificPathList() - Constructor for class org.anchoranalysis.io.input.bean.files.SpecificPathList
SpecificPathList(List<String>) - Constructor for class org.anchoranalysis.io.input.bean.files.SpecificPathList: Creates by reusing an existing list.
SpecificPathList(StringList) - Constructor for class org.anchoranalysis.io.input.bean.files.SpecificPathList: Creates by reusing an existing list.
SpecifyDimensions - Class in org.anchoranalysis.plugin.image.bean.dimensions.provider: Specifies dimensions explicitly via bean properties.
SpecifyDimensions() - Constructor for class org.anchoranalysis.plugin.image.bean.dimensions.provider.SpecifyDimensions
SpecifyDimensions(int, int) - Constructor for class org.anchoranalysis.plugin.image.bean.dimensions.provider.SpecifyDimensions: Create with specific lengths for X and Y dimensions.
SpecifyDimensions(SizeXY) - Constructor for class org.anchoranalysis.plugin.image.bean.dimensions.provider.SpecifyDimensions: Create with specific lengths for X and Y dimensions.
SpecifyVector - Class in org.anchoranalysis.image.bean.spatial.direction: Specifies each axis-component of a vector in a particular direction.
SpecifyVector() - Constructor for class org.anchoranalysis.image.bean.spatial.direction.SpecifyVector
SpecifyVector(double, double, double) - Constructor for class org.anchoranalysis.image.bean.spatial.direction.SpecifyVector: Creates a new SpecifyVector instance.
SpecifyVector(DirectionVector) - Constructor for class org.anchoranalysis.image.bean.spatial.direction.SpecifyVector: Create from a DirectionVector.
Sphere - Class in org.anchoranalysis.mpp.mark.conic: Represents a 3D sphere mark.
Sphere() - Constructor for class org.anchoranalysis.mpp.mark.conic.Sphere
Sphere(Bound) - Constructor for class org.anchoranalysis.mpp.mark.conic.Sphere: Creates a sphere with a radius within particular bounds.
Sphere(Sphere) - Constructor for class org.anchoranalysis.mpp.mark.conic.Sphere: Copy constructor.
split(Path) - Method in class org.anchoranalysis.bean.shared.path.RootPath: It splits the root portion of a path from the remainder.
split(Path, String, boolean) - Method in class org.anchoranalysis.plugin.io.input.path.RootPathMap: Given a path, it splits the *root* portion of the path from the remainder, trying a root identified by the rootName and debugMode (and if this fails, also trying with debugMode==false)
SplitByObjects - Class in org.anchoranalysis.plugin.image.bean.object.provider.split: Splits objects in a collection based on intersections with another set of objects.
SplitByObjects() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.split.SplitByObjects
SplitContourAtSaddlePoints - Class in org.anchoranalysis.plugin.points.bean: Splits a 2D contour represented by an object-mask into several contours, splitting at "turn" points.
SplitContourAtSaddlePoints() - Constructor for class org.anchoranalysis.plugin.points.bean.SplitContourAtSaddlePoints
splitFilename(String) - Static method in class org.anchoranalysis.core.system.path.ExtensionUtilities: Splits the file-name of a path into a base part and an extension part.
SplitIntoSquares - Class in org.anchoranalysis.plugin.image.bean.object.provider.split: Splits objects into sub-objects by cutting by an orthogonal square lattice (like a chessboard).
SplitIntoSquares() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.split.SplitIntoSquares
SplitPath - Class in org.anchoranalysis.core.system.path: A path that has been split into two components: a root and a remainder.
SplitPath(Path, Path) - Constructor for class org.anchoranalysis.core.system.path.SplitPath: Creates a new SplitPath instance.
SQUARE_MICRO - Enum constant in enum class org.anchoranalysis.image.core.dimensions.SpatialUnits.UnitSuffix: 1e-6 squared.
SQUARE_MILLI - Enum constant in enum class org.anchoranalysis.image.core.dimensions.SpatialUnits.UnitSuffix: 1e-3 squared.
SQUARE_NANO - Enum constant in enum class org.anchoranalysis.image.core.dimensions.SpatialUnits.UnitSuffix: 1e-9 squared.
stack() - Method in class org.anchoranalysis.mpp.io.input.MultiInput: Gets the map of TimeSeries (stacks).
stack(String) - Static method in class org.anchoranalysis.plugin.image.provider.ReferenceFactory: Creates a reference to a stack.
Stack - Class in org.anchoranalysis.image.core.stack: One or more single-channel images that all have the same dimensions.
Stack() - Constructor for class org.anchoranalysis.image.core.stack.Stack: Creates a new empty Stack that will not become an RGB image after adding channels.
Stack(boolean) - Constructor for class org.anchoranalysis.image.core.stack.Stack: Creates a new empty Stack and whether it will become an RGB image or not.
Stack(boolean, Stream<Channel>) - Constructor for class org.anchoranalysis.image.core.stack.Stack: Like Stack(Stream) but allows explicitly setting whether it should be interpreted as RGB or not.
Stack(boolean, Channel...) - Constructor for class org.anchoranalysis.image.core.stack.Stack: Creates from a varying number of channels, and a flag to indicate if they represent an RGB image or not.
Stack(Stream<Channel>) - Constructor for class org.anchoranalysis.image.core.stack.Stack: Create a Stack from a stream of Channels.
Stack(Channel) - Constructor for class org.anchoranalysis.image.core.stack.Stack: Creates a Stack with a single channel.
Stack(Dimensions, ChannelFactorySingleType, int, boolean) - Constructor for class org.anchoranalysis.image.core.stack.Stack: Create with a particular number of empty Channels.
Stack(Extent) - Constructor for class org.anchoranalysis.image.core.stack.Stack: Creates a Stack with a single unsigned-byte channel of size channel.
StackArrangement - Class in org.anchoranalysis.image.bean.nonbean.spatial.arrange: A list of BoundingBoxes that indicate where to locate corresponding Stacks on a unified larger image.
StackArrangement(Extent) - Constructor for class org.anchoranalysis.image.bean.nonbean.spatial.arrange.StackArrangement: Create with the overall Extent and no boxes.
StackArrangement(Extent, List<BoundingBoxEnclosed>) - Constructor for class org.anchoranalysis.image.bean.nonbean.spatial.arrange.StackArrangement: Creates a new StackArrangement instance.
StackArrangement(Extent, BoundingBox) - Constructor for class org.anchoranalysis.image.bean.nonbean.spatial.arrange.StackArrangement: Create with a single BoundingBox.
StackArranger - Class in org.anchoranalysis.image.bean.spatial.arrange: Base class for a method that determines positions for RGBStacks when combined onto a single plane.
StackArranger() - Constructor for class org.anchoranalysis.image.bean.spatial.arrange.StackArranger
StackCopierAtBox - Class in org.anchoranalysis.image.bean.nonbean.spatial.arrange: Copies a source stack into a destination stack at a particular BoundingBox.
StackDisplayer - Class in org.anchoranalysis.image.bean.displayer: Converts from a Channel or Stack to a DisplayStack so that it can be displayed.
StackDisplayer() - Constructor for class org.anchoranalysis.image.bean.displayer.StackDisplayer
StackFixture - Class in org.anchoranalysis.test.image: Creates stacks of 1 or more channels using ChannelFixture.
StackFixture() - Constructor for class org.anchoranalysis.test.image.StackFixture
StackFixture(Optional<VoxelDataType>) - Constructor for class org.anchoranalysis.test.image.StackFixture: Create with a voxel-type for the first channel.
StackGenerator - Class in org.anchoranalysis.image.io.stack.output.generator: Writes a stack to the filesystem.
StackGenerator(boolean) - Constructor for class org.anchoranalysis.image.io.stack.output.generator.StackGenerator: Creates a generator that performs no padding.
StackGenerator(boolean, boolean) - Constructor for class org.anchoranalysis.image.io.stack.output.generator.StackGenerator: Creates the generator from a stack, inferring whether all stacks will be 2D from this stack's dimensions.
StackGenerator(boolean, StackWriteAttributes) - Constructor for class org.anchoranalysis.image.io.stack.output.generator.StackGenerator: Creates a new StackGenerator instance.
stackGrayscale() - Method in class org.anchoranalysis.test.image.segment.InstanceSegmentationTestBase: Provides the grayscale stack to be tested.
StackIdentifiers - Class in org.anchoranalysis.image.io.stack: Common identifiers used for storing particular types of images.
StackNotUniformSized - Class in org.anchoranalysis.image.core.stack: A list of Channels that are permitted to vary in size.
StackNotUniformSized() - Constructor for class org.anchoranalysis.image.core.stack.StackNotUniformSized: Creates an empty with no channels.
StackNotUniformSized(Stream<Channel>) - Constructor for class org.anchoranalysis.image.core.stack.StackNotUniformSized: Creates from a stream of Channels.
StackNotUniformSized(Channel) - Constructor for class org.anchoranalysis.image.core.stack.StackNotUniformSized: Creates from a single Channel.
StackProvider - Class in org.anchoranalysis.image.bean.provider.stack: Base class for beans that implement Provider to provide a Stack.
StackProvider() - Constructor for class org.anchoranalysis.image.bean.provider.stack.StackProvider
StackProviderUnary - Class in org.anchoranalysis.image.bean.provider.stack: Implementation of StackProvider that calls a single delegate Provider<Stack>.
StackProviderUnary() - Constructor for class org.anchoranalysis.image.bean.provider.stack.StackProviderUnary
StackProviderWithLabel - Class in org.anchoranalysis.image.io.bean.stack.combine: Combines a Provider<Stack> with a label.
StackProviderWithLabel() - Constructor for class org.anchoranalysis.image.io.bean.stack.combine.StackProviderWithLabel
StackProviderWithLabel(Stack, String) - Constructor for class org.anchoranalysis.image.io.bean.stack.combine.StackProviderWithLabel: Create for a particular Stack and label.
StackReader - Class in org.anchoranalysis.image.io.bean.stack.reader: Reads an image-Stack from the file-system.
StackReader() - Constructor for class org.anchoranalysis.image.io.bean.stack.reader.StackReader
StackReaderOrientationCorrection - Class in org.anchoranalysis.image.io.bean.stack.reader: A StackReader that supports the correction of orientation as images are read from the file-system.
StackReaderOrientationCorrection() - Constructor for class org.anchoranalysis.image.io.bean.stack.reader.StackReaderOrientationCorrection
stackRGB() - Method in class org.anchoranalysis.test.image.segment.InstanceSegmentationTestBase: Provides the RGB stack to be tested.
StackRGBState - Enum Class in org.anchoranalysis.image.io.stack.output: Whether a stack is RGB or RGBA or neither.
stacks() - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitialization: A collection of Stacks, indexed by name.
stacks(Logger) - Method in class org.anchoranalysis.annotation.io.AnnotationWithStrategy: All stacks associated with the input, lazily evaluated.
Stacks - Class in org.anchoranalysis.plugin.io.bean.input.stack: An InputManager where each file provides one or more Stacks.
Stacks() - Constructor for class org.anchoranalysis.plugin.io.bean.input.stack.Stacks
Stacks(InputManager<FileInput>) - Constructor for class org.anchoranalysis.plugin.io.bean.input.stack.Stacks
StackSequenceInput - Interface in org.anchoranalysis.image.io.stack.input: Provides a single stack (or a time series of such stacks) as an input
StackTester - Class in org.anchoranalysis.test.image.stackwriter: A utility class for testing stack writers by writing stacks and optionally comparing them.
StackTester(StackWriter, Path, String, boolean) - Constructor for class org.anchoranalysis.test.image.stackwriter.StackTester: Creates a new StackTester instance.
stackTrace() - Method in exception class org.anchoranalysis.core.exception.friendly.AnchorFriendlyCheckedException: Prints a stack trace of the current exception to a string.
StackWithMap - Class in org.anchoranalysis.mpp.io.input: Combines a Stack with a map of other stacks.
StackWithMap(String, ProvidesStackInput) - Constructor for class org.anchoranalysis.mpp.io.input.StackWithMap: Creates a new StackWithMap instance.
StackWriteAttributes - Class in org.anchoranalysis.image.io.stack.output: Attributes describing stack which may determine which writer is used.
StackWriteAttributes(boolean, boolean, boolean, StackRGBState, boolean) - Constructor for class org.anchoranalysis.image.io.stack.output.StackWriteAttributes: Alternative constructor that assumes each channel is 8-bits.
StackWriteAttributesFactory - Class in org.anchoranalysis.image.io.stack.output: Creates StackWriteAttributes to describe certain attributes.
StackWriteOptions - Class in org.anchoranalysis.image.io.stack.output: A combination of attributions describing how to write a particular stack and any suggestions from the user.
StackWriteOptions(StackWriteAttributes, Optional<ImageFileFormat>) - Constructor for class org.anchoranalysis.image.io.stack.output.StackWriteOptions: Creates a new StackWriteOptions instance.
StackWriter - Class in org.anchoranalysis.image.io.bean.stack.writer: Writes a stack (i.e. raster) to the filesystem.
StackWriter() - Constructor for class org.anchoranalysis.image.io.bean.stack.writer.StackWriter
StackWriterDelegateBase - Class in org.anchoranalysis.plugin.io.bean.stack.writer: A base class for a StackWriter delegates to another StackWriter based on values of a StackWriteAttributes.
StackWriterDelegateBase() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.writer.StackWriterDelegateBase
StackWriterTestBase - Class in org.anchoranalysis.test.image.stackwriter: Base class for testing various implementations of StackWriter.
StackWriterTestBase(ImageFileFormat, boolean, ComparisonPlan) - Constructor for class org.anchoranalysis.test.image.stackwriter.StackWriterTestBase: Creates a new StackWriterTestBase instance.
standardDeviation() - Method in class org.anchoranalysis.math.histogram.Histogram: Calculates the standard-deviation of the distribution represented by the histogram.
StandardDeviation - Class in org.anchoranalysis.feature.bean.results: The standard-deviation of the results from a particular feature.
StandardDeviation - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic: Calculates the standard deviation of values in a Histogram.
StandardDeviation() - Constructor for class org.anchoranalysis.feature.bean.results.StandardDeviation
StandardDeviation() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.StandardDeviation
StandardDeviationIntensityProjection - Class in org.anchoranalysis.image.voxel.projection: Creates buffers for projecting the standard-deviation.
StandardDeviationIntensityProjection() - Constructor for class org.anchoranalysis.image.voxel.projection.StandardDeviationIntensityProjection
StandardDeviationProjection<T> - Class in org.anchoranalysis.plugin.image.bean.channel.aggregator: Projection of the standard-deviation of voxels values across all inputs.
StandardDeviationProjection() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.aggregator.StandardDeviationProjection
start() - Method in class org.anchoranalysis.experiment.bean.log.StatefulNullMessageLogger
start() - Method in class org.anchoranalysis.experiment.log.ConsoleMessageLogger
start() - Method in class org.anchoranalysis.experiment.log.FailureOnlyMessageLogger
start() - Method in class org.anchoranalysis.experiment.log.MultipleLoggers
start() - Method in interface org.anchoranalysis.experiment.log.StatefulMessageLogger: Starts logging.
start() - Method in class org.anchoranalysis.experiment.log.TextFileMessageLogger
start() - Method in class org.anchoranalysis.feature.io.csv.results.LabelledResultsCSVWriter: Starts writing the CSV file.
start() - Method in class org.anchoranalysis.io.generator.text.TextFileOutput: This should be called once before subsequently writing content with TextFileOutput.getWriter()
start() - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.stack.ScaleToSize
start() - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.stack.ThumbnailFromStack: Initializes the thumbnail creation process.
start(Optional<Dimensions>, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.collective.DiscardOutliers
start(Optional<Dimensions>, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.collective.RelationWithMatches
start(Optional<Dimensions>, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.GreaterIntersectionWith
start(Optional<Dimensions>, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntensityGreaterEqualThan
start(Optional<Dimensions>, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntersectsWith
start(Optional<Dimensions>, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedFeature
start(Optional<Dimensions>, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedVolume
start(Optional<Dimensions>, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterPredicate: Performs any necessary initialization before filtering begins.
start(Optional<Dimensions>, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterRelation
start(FeatureInitialization, SharedFeatures, Logger) - Method in class org.anchoranalysis.feature.session.SequentialSession: Starts the session.
start(ImageInitialization, Optional<EnergyStack>, Logger) - Method in interface org.anchoranalysis.image.feature.calculator.FeatureTableCalculator: Initializes a feature store that has the same structure as that previously created by createFeatures() from the same object.
start(ImageInitialization, Optional<EnergyStack>, Logger) - Method in class org.anchoranalysis.image.feature.calculator.merged.PairsTableCalculator
start(ImageInitialization, Optional<EnergyStack>, Logger) - Method in class org.anchoranalysis.image.feature.calculator.SingleTableCalculator
start(ObjectCollection, StreamableCollection<BoundingBox>, Optional<Stack>, ExecutionTimeRecorder) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize
start(ObjectCollection, StreamableCollection<BoundingBox>, Optional<Stack>, ExecutionTimeRecorder) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.ThumbnailFromObjects: Initializes a batch to create thumbnails.
startBatchDeriveInputs(ObjectCollection, EnergyStack, Logger) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.CombineObjectsForFeatures: Derives a list of inputs from an object-collection.
startBatchDeriveInputs(ObjectCollection, EnergyStack, Logger) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.EachObjectIndependently
startBatchDeriveInputs(ObjectCollection, EnergyStack, Logger) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
startSeries(NoSharedState, OutputSequenceIndexed<Stack, String>, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat
startSeries(S, U, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.RasterTask: Starts processing of a series.
StatefulMessageLogger - Interface in org.anchoranalysis.experiment.log: A MessageLogger that can be started and stopped, and is aware of this state.
StatefulNullMessageLogger - Class in org.anchoranalysis.experiment.bean.log: Does nothing (i.e. simply ignores) with any messages logged.
StatefulNullMessageLogger() - Constructor for class org.anchoranalysis.experiment.bean.log.StatefulNullMessageLogger
StaticFilePath - Class in org.anchoranalysis.plugin.io.bean.file.path
StaticFilePath() - Constructor for class org.anchoranalysis.plugin.io.bean.file.path.StaticFilePath
StatisticalBase<T> - Class in org.anchoranalysis.plugin.operator.feature.bean.statistics: Calculates a score based upon the statistical mean and standard deviation.
StatisticalBase() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.statistics.StatisticalBase
statisticFromFeatureValue(DoubleArrayList) - Method in class org.anchoranalysis.feature.bean.results.FeatureResultsStatistic: Calculates the statistic for a given list of result-value.
statisticFromFeatureValue(DoubleArrayList) - Method in class org.anchoranalysis.feature.bean.results.Maximum
statisticFromFeatureValue(DoubleArrayList) - Method in class org.anchoranalysis.feature.bean.results.Mean
statisticFromFeatureValue(DoubleArrayList) - Method in class org.anchoranalysis.feature.bean.results.Minimum
statisticFromFeatureValue(DoubleArrayList) - Method in class org.anchoranalysis.feature.bean.results.Quantile
statisticFromFeatureValue(DoubleArrayList) - Method in class org.anchoranalysis.feature.bean.results.StandardDeviation
statisticFromFeatureValue(DoubleArrayList) - Method in class org.anchoranalysis.feature.bean.results.Sum
statistics() - Method in interface org.anchoranalysis.annotation.io.assignment.Assignment: The statistics associated with the assignment.
statistics() - Method in class org.anchoranalysis.annotation.io.assignment.ObjectVoxelIntersection
statistics() - Method in class org.anchoranalysis.annotation.io.assignment.OverlappingObjects
statisticsFor(int, int, int) - Method in interface org.anchoranalysis.mpp.mark.voxelized.VoxelizedMark: Calculates statistics for a specific slice in a specific channel and region.
statisticsForAllGroups() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.ComparisonSharedState: Retrieves statistics for all groups.
statisticsForAllSlices(int, int) - Method in interface org.anchoranalysis.mpp.mark.voxelized.VoxelizedMark: Calculates statistics for all slices in a specific channel and region.
statisticsForAllSlicesMaskSlice(int, int, int) - Method in interface org.anchoranalysis.mpp.mark.voxelized.VoxelizedMark: Calculates statistics for all slices in a specific channel and region, using a mask from another channel.
StatisticsToExport - Class in org.anchoranalysis.annotation.io.comparer: Statistics to be exported, comprised of name-value pairs.
StatisticsToExport() - Constructor for class org.anchoranalysis.annotation.io.comparer.StatisticsToExport
stdDev() - Method in interface org.anchoranalysis.image.voxel.statistics.VoxelStatistics: The standard-deviation of all voxel values.
Steepest - Class in org.anchoranalysis.plugin.image.segment.watershed.encoding: Calculates the steepest descent direction for voxels in a watershed segmentation.
Steepest(SlidingBuffer<?>, WatershedEncoding, boolean, boolean, Optional<ObjectMask>) - Constructor for class org.anchoranalysis.plugin.image.segment.watershed.encoding.Steepest: Creates a Steepest instance for a specific buffer.
steepestDescent(Point3i, int, int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.Steepest: Calculates the steepest descent direction for a given point.
StoreSupplier<T> - Interface in org.anchoranalysis.core.identifier.provider.store: Supplier of an object for a store.
stream() - Method in class org.anchoranalysis.bean.primitive.DoubleSet: Creates a stream of elements in the set.
stream() - Method in class org.anchoranalysis.bean.primitive.IntegerSet: Creates a stream of elements in the set.
stream() - Method in class org.anchoranalysis.bean.primitive.StringSet: Creates a stream of elements in the set.
stream() - Method in class org.anchoranalysis.core.functional.StreamableCollection: A single instance of the stream from the supplier.
stream() - Method in class org.anchoranalysis.core.identifier.provider.NameValueMap: Exposes the elements in the set as a stream.
stream() - Method in class org.anchoranalysis.feature.results.ResultsVectorList: A stream of ResultsVectors.
stream() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection: Provides various functional-programming operations on the object-collection.
stream() - Method in class org.anchoranalysis.plugin.annotation.counter.ImageCounterList: Returns a sequential Stream with this list as its source.
stream() - Method in class org.anchoranalysis.spatial.box.BoundedList: A stream of elements in the list.
StreamableCollection<T> - Class in org.anchoranalysis.core.functional: As a stream can only be used once, this data-structure allows for repeatedly getting streams from a collection.
StreamableCollection(Collection<T>) - Constructor for class org.anchoranalysis.core.functional.StreamableCollection: Create for a particular collection
StreamableCollection(Supplier<Stream<T>>) - Constructor for class org.anchoranalysis.core.functional.StreamableCollection: Creates a new StreamableCollection instance.
streamIndices(Collection<Integer>) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection: Streams only objects at specific indices.
streamObjectWithProperties() - Method in class org.anchoranalysis.plugin.image.object.ColoredObjectCollection: Creates a stream of ObjectWithProperties derived from the collection.
streamOverZ() - Method in class org.anchoranalysis.spatial.box.Extent: Streams over the range of z values.
streamStandardJava() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection: A stream of object-masks as per Java's standard collections interface.
StringGenerator - Class in org.anchoranalysis.io.generator.text: A generator that writes the contents of a String to the file-system as text-file.
StringGenerator() - Constructor for class org.anchoranalysis.io.generator.text.StringGenerator
StringList - Class in org.anchoranalysis.bean.primitive: A bean defining a list of Strings.
StringList() - Constructor for class org.anchoranalysis.bean.primitive.StringList: Constructs with an empty list.
StringList(String...) - Constructor for class org.anchoranalysis.bean.primitive.StringList: Constructs, populated with one or more values.
StringList(List<String>) - Constructor for class org.anchoranalysis.bean.primitive.StringList: Constructs, populated with a list of strings.
StringListFactory - Class in org.anchoranalysis.bean.xml.factory.primitive: Creates a StringList from a XML element.
StringListFactory() - Constructor for class org.anchoranalysis.bean.xml.factory.primitive.StringListFactory
StringMap - Class in org.anchoranalysis.bean.shared: A bean that defines a mapping between a set of Strings to another set of Strings.
StringMap() - Constructor for class org.anchoranalysis.bean.shared.StringMap
StringMapItem - Class in org.anchoranalysis.bean.shared: A bean with a pair of strings, representing a mapping from one string to the other.
StringMapItem() - Constructor for class org.anchoranalysis.bean.shared.StringMapItem
StringSet - Class in org.anchoranalysis.bean.primitive: A bean defining a set of Strings.
StringSet() - Constructor for class org.anchoranalysis.bean.primitive.StringSet
StringSet(String...) - Constructor for class org.anchoranalysis.bean.primitive.StringSet: Constructs with one or more values added to the list.
StringSet(Set<String>) - Constructor for class org.anchoranalysis.bean.primitive.StringSet: Creates a new StringSet instance.
StringSetFactory - Class in org.anchoranalysis.bean.xml.factory.primitive: Creates a StringSet from a XML element.
StringSetFactory() - Constructor for class org.anchoranalysis.bean.xml.factory.primitive.StringSetFactory
StringSetTrie - Class in org.anchoranalysis.core.collection: A Trie / Prefix Tree that stores Strings efficiently.
StringSetTrie() - Constructor for class org.anchoranalysis.core.collection.StringSetTrie: Create with no elements.
StringSetTrie(Collection<String>) - Constructor for class org.anchoranalysis.core.collection.StringSetTrie: Create from existing collection.
StringSetTrie(Stream<String>) - Constructor for class org.anchoranalysis.core.collection.StringSetTrie: Create from existing collection.
StringSuffixOutputNameStyle - Class in org.anchoranalysis.io.output.namestyle: Outputs a file-name involving a string suffix.
StringSuffixOutputNameStyle() - Constructor for class org.anchoranalysis.io.output.namestyle.StringSuffixOutputNameStyle: Empty constructor, as needed for deserialization.
StringSuffixOutputNameStyle(String, Optional<String>) - Constructor for class org.anchoranalysis.io.output.namestyle.StringSuffixOutputNameStyle: Creates with an output-name.
StringUtilities - Class in org.anchoranalysis.core.value: Utility functions for manipualting strings.
strMarks() - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius: Returns a string representation of the mark's attributes.
subdirectory(String, boolean) - Method in interface org.anchoranalysis.io.output.outputter.InputOutputContext: Creates a new context that writes instead to a subdirectory.
subdirectoryForGroupOutputs() - Method in class org.anchoranalysis.plugin.image.task.bean.combine.AggregateChannelTask
subdirectoryForGroupOutputs() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase: An optional subdirectory where the group outputs are placed.
subdirectoryForGroupOutputs() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.histogram.ExportImageHistograms
SUBMARK_CORE - Static variable in class org.anchoranalysis.mpp.mark.GlobalRegionIdentifiers: Identifier for the core region of a submark.
SUBMARK_CORE_INNER - Static variable in class org.anchoranalysis.mpp.mark.GlobalRegionIdentifiers: Identifier for the inner core region of a submark.
SUBMARK_INSIDE - Static variable in class org.anchoranalysis.mpp.mark.GlobalRegionIdentifiers: Identifier for the inside region of a submark.
SUBMARK_OUTSIDE - Static variable in class org.anchoranalysis.mpp.mark.GlobalRegionIdentifiers: Identifier for the outside region of a submark.
SUBMARK_SHELL - Static variable in class org.anchoranalysis.mpp.mark.GlobalRegionIdentifiers: Identifier for the shell region of a submark.
SUBMARK_SHELL_OUTSIDE - Static variable in class org.anchoranalysis.mpp.mark.GlobalRegionIdentifiers: Identifier for the outer shell region of a submark.
SubmittedJob - Class in org.anchoranalysis.experiment.task.processor: A job that has been submitted for execution.
SubmittedJob(JobDescription, JobStateMonitor) - Constructor for class org.anchoranalysis.experiment.task.processor.SubmittedJob: Creates a new SubmittedJob instance.
subset(StringSet) - Method in class org.anchoranalysis.image.core.stack.named.NamedStacks: Creates a new collection containing only items whose keys exist in a particular set.
subsetCompatibleWith(Class<? extends FeatureInput>) - Method in class org.anchoranalysis.feature.shared.SharedFeatures: Extracts the subset of inputs that are compatible with a particular input-type.
SubsetRangeIfRequested - Class in org.anchoranalysis.plugin.io.bean.file.namer: If specified in the context, the existing name if subsetted according to an index range.
SubsetRangeIfRequested() - Constructor for class org.anchoranalysis.plugin.io.bean.file.namer.SubsetRangeIfRequested
subsetWhereBBoxIntersects(Dimensions, int, List<BoundingBox>) - Method in class org.anchoranalysis.mpp.mark.ColoredMarks: Creates a subset of marks whose bounding boxes intersect with given boxes.
subsetWhereBoxIntersects(Dimensions, DrawOverlay, List<BoundingBox>) - Method in class org.anchoranalysis.overlay.collection.ColoredOverlayCollection: Find overlays whose bounding-boxes intersect with any of the boxes in toIntersectWith.
SubstituteRegularExpression - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming: A regular expression substitution (replaceAll) is applied to the relative-path
SubstituteRegularExpression() - Constructor for class org.anchoranalysis.plugin.io.bean.file.copy.naming.SubstituteRegularExpression
subtract(int) - Method in class org.anchoranalysis.spatial.point.Tuple3i: Arithmetically subtracts a value across each dimension.
subtract(VarianceCalculatorDouble) - Method in class org.anchoranalysis.math.statistics.VarianceCalculatorDouble: Subtracts the running-sums and count from another VarianceCalculatorDouble from the current object's state.
subtract(VarianceCalculatorLong) - Method in class org.anchoranalysis.math.statistics.VarianceCalculatorLong: Subtracts the running-sums and count from another VarianceCalculatorLong from the current object's state.
subtract(ReadableTuple3i) - Method in class org.anchoranalysis.spatial.point.Tuple3i: Arithmetically subtracts a value across each dimension.
subtract(Tuple3d) - Method in class org.anchoranalysis.spatial.point.Tuple3d: Arithmetically subtract a Tuple3d's values across each dimension.
subtractFrom(int) - Method in interface org.anchoranalysis.image.voxel.arithmetic.VoxelsArithmetic: Subtracts all current voxel-values from a constant-value.
SubtractFrom<T> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic: A feature that subtracts the result of another feature from a constant value.
SubtractFrom() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.SubtractFrom
SubtractFromConstant - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic: Subtracts each voxel value in a channel from a constant value.
SubtractFromConstant() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.SubtractFromConstant
subtractFromMaxValue() - Method in class org.anchoranalysis.image.voxel.VoxelsUntyped: Subtracts all voxel-values from the maximum value associated with the data-type.
SubtractMean - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic: Subtracts the mean intensity (of the entire channel or a masked portion thereof) from every voxel.
SubtractMean() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.SubtractMean
SubtractReducedFromMerged - Class in org.anchoranalysis.plugin.image.feature.bean.list.pair: Calculates merged - reduce(first,second) for a FeatureInputPairObjects
SubtractReducedFromMerged() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.pair.SubtractReducedFromMerged
SubtractSecondFromFirst - Class in org.anchoranalysis.image.feature.bean.object.pair: Subtract second-object from first-object in a pair.
SubtractSecondFromFirst() - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.SubtractSecondFromFirst
SubtractTwoChannels - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic: Creates a new channel by subtracting corresponding voxels of the second channel from the first channel.
SubtractTwoChannels() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.SubtractTwoChannels: Constructs a new SubtractTwoChannels instance.
successiveCircles(int, Point2d, int, Point2d, double) - Static method in class org.anchoranalysis.test.image.object.CircleObjectFixture: Creates several successive circles whose center is incrementally shifted.
suffixStringForMeters(SpatialUnits.UnitSuffix) - Static method in class org.anchoranalysis.image.core.dimensions.SpatialUnits: A string that describes the suffix for meters.
suggestedSize() - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitialization: A suggested input on how to resize an image, if one is provided.
SuggestionFormatException - Exception Class in org.anchoranalysis.image.core.dimensions.size.suggestion: An exception thrown by ImageSizeSuggestionFactory to indicate a format is invalid or unknown.
SuggestionFormatException(String) - Constructor for exception class org.anchoranalysis.image.core.dimensions.size.suggestion.SuggestionFormatException: Create with a message only.
sum() - Method in interface org.anchoranalysis.image.voxel.statistics.VoxelStatistics: The sum of all voxel values.
sum() - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsCombined
sum() - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsFromHistogram
Sum<T> - Class in org.anchoranalysis.feature.bean.operator: Sums the results after calculating a list of Features.
Sum - Class in org.anchoranalysis.feature.bean.results: The sum of the results from a particular feature.
Sum - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic: Calculates the sum of all values in a Histogram.
Sum() - Constructor for class org.anchoranalysis.feature.bean.operator.Sum
Sum() - Constructor for class org.anchoranalysis.feature.bean.results.Sum
Sum() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Sum
Sum(FeatureList<T>) - Constructor for class org.anchoranalysis.feature.bean.operator.Sum: Create with a list of Features which become summed.
sumExecutionTimeSeconds() - Method in class org.anchoranalysis.core.time.RecordedExecutionTimes.RecordedOperation: The total summed execution time in seconds for the operation.
summarize() - Method in exception class org.anchoranalysis.bean.xml.exception.BeanMisconfiguredXMLException: This summarize() option just looks for the most deep exception that can be 'combined' and takes its message
summarize() - Method in exception class org.anchoranalysis.bean.xml.exception.LocalisedBeanException
summarize() - Method in exception class org.anchoranalysis.core.exception.combinable.AnchorCombinableException: Creates a new {link Throwable} that summarizes this exception and any nested causes of the exception.
summarize() - Method in exception class org.anchoranalysis.core.identifier.provider.NamedProviderGetException
SummarizeBase<T,S> - Class in org.anchoranalysis.plugin.io.bean.task
SummarizeBase() - Constructor for class org.anchoranalysis.plugin.io.bean.task.SummarizeBase
summarizeDisabled() - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputs: A comma-separated string of all output-names that were not enabled.
summarizeEnabled() - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputs: A comma-separated string of all output-names that were enabled.
summarizeIgnoreIdenticalFilePath(Path) - Method in exception class org.anchoranalysis.bean.xml.exception.LocalisedBeanException: If there is no nested-set of combinable exceptions, and the message related to this current exception is identical as the passed parameter, then we simply ignore the current exception and promote its Throwable.getCause().
SummarizeInputs<T> - Class in org.anchoranalysis.plugin.io.bean.task
SummarizeInputs() - Constructor for class org.anchoranalysis.plugin.io.bean.task.SummarizeInputs
summarizeMultiplex(boolean) - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputs: Multiplex between RecordedOutputs.summarizeEnabled() and RecordedOutputs.summarizeDisabled().
Summarizer<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer: Summarizes a set of elements by outputting a descriptive string.
Summarizer() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.Summarizer
SummarizerAggregate<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer: Collects summary data about a set of input files that will eventually be outputted to the user
SummarizerAggregate() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerAggregate
SummarizerCount<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer: A count of the number of inputs.
SummarizerCount() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerCount
SummarizerImageMetadata<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer.image: Summarizes ImageMetadataInput in different ways.
SummarizerImageMetadata() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.image.SummarizerImageMetadata
SummarizerImageMetadataSimple<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer.image: A simple summarizer, where there's one summary-item per image.
SummarizerImageMetadataSimple() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.image.SummarizerImageMetadataSimple
SummarizerInputFromManager<T,S> - Class in org.anchoranalysis.plugin.io.bean.summarizer.input: Extracts a particular item from an InputFromManager for further summarization downstream.
SummarizerInputFromManager() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.input.SummarizerInputFromManager
SummarizerListMultiline<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer: Creates a string where each line is an element.
SummarizerListMultiline() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerListMultiline
SummarizerPath - Class in org.anchoranalysis.plugin.io.bean.summarizer.path: Base class for Summarizers that operate on the Path associated with inputs.
SummarizerPath() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.path.SummarizerPath
SummarizerSplitMoreThan<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer: Multiplexes between two summarizers depending on the total number of count.
SummarizerSplitMoreThan() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerSplitMoreThan
SummaryException - Exception Class in org.anchoranalysis.core.exception.combinable: A special kind of exception that represents a summary of an existing set of exceptions.
SummaryException(String, Throwable) - Constructor for exception class org.anchoranalysis.core.exception.combinable.SummaryException: Creates with a message and a cause.
sumModulo(int, int, int) - Static method in class org.anchoranalysis.test.image.ChannelFixture: Calculates intensity as the sum of coordinates modulo 256.
sumOfSquares() - Method in interface org.anchoranalysis.image.voxel.statistics.VoxelStatistics: The sum of the square of all voxel values.
sumOfSquares() - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsCombined
sumOfSquares() - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsFromHistogram
sumOverlapFromPaired() - Method in class org.anchoranalysis.annotation.io.assignment.OverlappingObjects: Sums the overlap-ratio across all assigned pairs.
supportsMultipleChannelsPerSourceBuffer() - Method in class org.anchoranalysis.io.bioformats.copyconvert.ConvertTo: Whether the source buffer can encode more than one channel?
supportsMultipleChannelsPerSourceBuffer() - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.ToUnsignedByteWithScaling
supportsMultipleChannelsPerSourceBuffer() - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromFloat
supportsMultipleChannelsPerSourceBuffer() - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedByte
supportsMultipleChannelsPerSourceBuffer() - Method in class org.anchoranalysis.io.bioformats.copyconvert.tofloat.ToFloat
supportsMultipleChannelsPerSourceBuffer() - Method in class org.anchoranalysis.io.bioformats.copyconvert.toint.UnsignedIntFromUnsignedInt
supportsMultipleChannelsPerSourceBuffer() - Method in class org.anchoranalysis.io.bioformats.copyconvert.toshort.ToUnsignedShort
suppressedLogger() - Static method in class org.anchoranalysis.test.LoggerFixture: A Logger that doesn't output anything.
suppressedMessageLogger() - Static method in class org.anchoranalysis.test.LoggerFixture: A MessageLogger that doesn't output anything.
suppressedOperationContext() - Static method in class org.anchoranalysis.test.LoggerFixture: An OperationContext containing a logger that doesn't output anything.
SuppressNonMaximum<T> - Class in org.anchoranalysis.image.inference.bean.segment.instance: Applies a segmentation procedure followed by non-maximum suppression.
SuppressNonMaximum() - Constructor for class org.anchoranalysis.image.inference.bean.segment.instance.SuppressNonMaximum
SuppressNonMaximum(SegmentStackIntoObjectsPooled<T>) - Constructor for class org.anchoranalysis.image.inference.bean.segment.instance.SuppressNonMaximum: Creates with a particular segmentation algorithm as an input.
SuppressNonMaximum(SegmentStackIntoObjectsPooled<T>, ReduceElements<ObjectMask>, boolean) - Constructor for class org.anchoranalysis.image.inference.bean.segment.instance.SuppressNonMaximum: Creates a new SuppressNonMaximum instance.
SurfaceNumberVoxelFaces - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.surface: The number of voxel-faces along the surface (the faces of each voxel that touch outside)
SurfaceNumberVoxelFaces() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.surface.SurfaceNumberVoxelFaces
SurfaceNumberVoxels - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.surface: The number of voxels on the surface (all voxels on the exterior of the object)
SurfaceNumberVoxels() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.surface.SurfaceNumberVoxels
SurfaceNumberVoxelsBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.surface: A base class for features that calculate the number of voxels on the surface of an object.
SurfaceNumberVoxelsBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.surface.SurfaceNumberVoxelsBase
SwitchChannelTime - Class in org.anchoranalysis.io.bioformats.bean.options: Treats the channel index as if it's time, and vice versa
SwitchChannelTime() - Constructor for class org.anchoranalysis.io.bioformats.bean.options.SwitchChannelTime
SwitchDetailedLogging - Class in org.anchoranalysis.experiment.bean.log: Switches between two log-reporters depending on whether detailed logging is switched on or not
SwitchDetailedLogging() - Constructor for class org.anchoranalysis.experiment.bean.log.SwitchDetailedLogging

T

targetBox() - Method in class org.anchoranalysis.test.image.segment.InstanceSegmentationTestBase: The bounding-box we use to set an area where we expect segments to reside.
task() - Method in class org.anchoranalysis.experiment.arguments.ExecutionArguments: Arguments to help specify the outputs from the experiment.
Task<T,S> - Class in org.anchoranalysis.experiment.bean.task: Encapsulates some kind of processing to be performed on a set of inputs.
Task() - Constructor for class org.anchoranalysis.experiment.bean.task.Task
TaskArguments - Class in org.anchoranalysis.experiment.arguments: Arguments that can further specify an experiment's task in addition to its bean specification.
TaskArguments() - Constructor for class org.anchoranalysis.experiment.arguments.TaskArguments: Creates with no initial size.
TaskArguments(Optional<ImageSizeSuggestion>) - Constructor for class org.anchoranalysis.experiment.arguments.TaskArguments: Creates with a specific initial size-suggestion.
taskDirectory() - Method in class org.anchoranalysis.launcher.executor.ExperimentExecutor: Gets the path to the task directory.
TaskFactory - Class in org.anchoranalysis.launcher.executor.selectparam.path: Determines Paths related to tasks.
tasksFooter() - Method in class org.anchoranalysis.launcher.resources.Resources: Footer-message used after "show tasks".
TaskStatistics - Class in org.anchoranalysis.experiment.task: Maintains statistics on the execution of a task (considering jobs in aggregate).
TaskStatistics(long, RunningSum, RunningSum) - Constructor for class org.anchoranalysis.experiment.task.TaskStatistics: Creates a new TaskStatistics instance.
TaskWithoutSharedState<T> - Class in org.anchoranalysis.experiment.bean.task: A particular type of task that doesn't share-state between running jobs
TaskWithoutSharedState() - Constructor for class org.anchoranalysis.experiment.bean.task.TaskWithoutSharedState
test(boolean, KernelPointCursor, Supplier<UnsignedByteBuffer>, int) - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.kernel.NeighborPredicate: Tests if a neighbor satisfies a condition.
test(byte, byte) - Method in interface org.anchoranalysis.image.voxel.iterator.predicate.PredicateTwoBytes: Do the combination of two arguments fulfill the predicate?
test(double, double) - Method in interface org.anchoranalysis.math.relation.DoubleBiPredicate: Considers the relationship between valueFirst and valueSecond.
test(double, double) - Method in class org.anchoranalysis.math.relation.EqualTo
test(double, double) - Method in class org.anchoranalysis.math.relation.GreaterThan
test(double, double) - Method in class org.anchoranalysis.math.relation.GreaterThanEqualTo
test(double, double) - Method in class org.anchoranalysis.math.relation.LessThan
test(double, double) - Method in class org.anchoranalysis.math.relation.LessThanEqualTo
test(double, double) - Method in class org.anchoranalysis.math.relation.NotEqualTo
test(float, float) - Method in interface org.anchoranalysis.core.functional.unchecked.BiFloatPredicate: Tests the predicate.
test(int, int) - Method in interface org.anchoranalysis.core.functional.unchecked.BiIntPredicate: Tests the predicate.
test(int, int) - Method in interface org.anchoranalysis.core.functional.unchecked.IntBinaryPredicate: Tests the predicate on two integer values.
test(long, long) - Method in interface org.anchoranalysis.core.functional.unchecked.BiLongPredicate: Tests the predicate.
test(short, short) - Method in interface org.anchoranalysis.core.functional.unchecked.BiShortPredicate: Tests the predicate.
test(ObjectWithProperties, RGBStack, int) - Method in interface org.anchoranalysis.image.io.bean.object.draw.IfElse.Predicate: Evaluates whether the condition is true or not.
test(KernelPointCursor) - Method in interface org.anchoranalysis.image.voxel.iterator.predicate.PredicateKernelPointCursor: Whether the condition is satisfied for a particular point?
test(Point3i, T, T, int, int) - Method in interface org.anchoranalysis.image.voxel.iterator.predicate.PredicateBufferBinary: Tests a voxel location in two buffers.
test(T) - Method in interface org.anchoranalysis.core.functional.checked.CheckedPredicate: Applies a predicate like with Predicate.test(T).
TestDataInitializeException - Exception Class in org.anchoranalysis.test: An exception thrown when test-data cannot be loaded.
TestDataInitializeException(String) - Constructor for exception class org.anchoranalysis.test.TestDataInitializeException: Creates with a message only.
TestDataInitializeException(Throwable) - Constructor for exception class org.anchoranalysis.test.TestDataInitializeException: Creates with a cause only.
TestDataLoadException - Exception Class in org.anchoranalysis.test: An exception thrown when test-data cannot be loaded.
TestDataLoadException(String) - Constructor for exception class org.anchoranalysis.test.TestDataLoadException: Creates with a message only.
TestDataLoadException(Throwable) - Constructor for exception class org.anchoranalysis.test.TestDataLoadException: Creates with a cause only.
tester - Variable in class org.anchoranalysis.test.image.stackwriter.StackWriterTestBase: Performs the tests.
testFourChannels() - Method in class org.anchoranalysis.test.image.stackwriter.FourChannelStackTester: Tests a stack with four-channels of unsigned 8-bit data type.
testFourChannels(VoxelDataType[]) - Method in class org.anchoranalysis.test.image.stackwriter.FourChannelStackTester: Tests a stack with four-channels of specified types
testGrayscale8Bit() - Method in class org.anchoranalysis.test.image.segment.InstanceSegmentationTestBase: Tests the segmentation on a grayscale 8-bit image.
TestLoader - Class in org.anchoranalysis.test: Loads test data, which is found at some location on the filesystem.
TestLoaderImage - Class in org.anchoranalysis.test.image.io: A test loader for image-related operations, providing methods to open and compare images and object collections.
TestLoaderImage(TestLoader) - Constructor for class org.anchoranalysis.test.image.io.TestLoaderImage: Constructs a TestLoaderImage with a given TestLoader.
TestLoaderImage(TestLoader, StackReader) - Constructor for class org.anchoranalysis.test.image.io.TestLoaderImage: Creates a new TestLoaderImage instance.
TestLoaderObjects - Class in org.anchoranalysis.test.image.object: A utility class for loading and processing object masks in test scenarios.
TestLoaderObjects(TestLoaderImage) - Constructor for class org.anchoranalysis.test.image.object.TestLoaderObjects
TestLoaderObjects(TestLoader) - Constructor for class org.anchoranalysis.test.image.object.TestLoaderObjects: Constructs a TestLoaderObjects with a given TestLoader.
testRGB() - Method in class org.anchoranalysis.test.image.segment.InstanceSegmentationTestBase: Tests the segmentation on an RGB image.
testSingleChannel() - Method in class org.anchoranalysis.test.image.stackwriter.FourChannelStackTester: Tests the creation of a single-channel stack of unsigned 8-bit data type with the RGB flag off.
testSingleChannel(VoxelDataType) - Method in class org.anchoranalysis.test.image.stackwriter.FourChannelStackTester: Tests the creation of a single-channel stack of specified data type with the RGB flag off.
testSingleChannel(VoxelDataType[]) - Method in class org.anchoranalysis.test.image.stackwriter.FourChannelStackTester: Tests the creation of a single-channel stack of specified data types with the RGB flag off.
testSingleChannelRGB() - Method in class org.anchoranalysis.test.image.stackwriter.FourChannelStackTester: Tests the creation of a single-channel stack of unsigned 8-bit data type with the RGB flag on, which should typically produce an exception.
testThreeChannelsHeterogeneous() - Method in class org.anchoranalysis.test.image.stackwriter.FourChannelStackTester: Tests the creation of a three-channel stack of heterogeneous channel types.
testThreeChannelsRGB() - Method in class org.anchoranalysis.test.image.stackwriter.FourChannelStackTester: Tests the creation of a three-channel stack of unsigned 8-bit data type with the rgb-flag set to true.
testThreeChannelsRGB(VoxelDataType) - Method in class org.anchoranalysis.test.image.stackwriter.FourChannelStackTester: Tests the creation of a three-channel stack of specified data type with the rgb-flag set to true.
testThreeChannelsRGB(VoxelDataType[]) - Method in class org.anchoranalysis.test.image.stackwriter.FourChannelStackTester: Tests the creation of a three-channel stack of specified data types with the rgb-flag set to true.
testThreeChannelsSeparate() - Method in class org.anchoranalysis.test.image.stackwriter.FourChannelStackTester: Tests the creation of a three-channel stack of unsigned 8-bit data type with the rgb-flag set to false.
testThreeChannelsSeparate(VoxelDataType[]) - Method in class org.anchoranalysis.test.image.stackwriter.FourChannelStackTester: Tests the creation of a three-channel stack of specified data types with the rgb-flag set to false.
testTwoChannels() - Method in class org.anchoranalysis.test.image.stackwriter.FourChannelStackTester: Tests the creation of a two-channel stack of unsigned 8-bit data type.
testTwoChannels(VoxelDataType[]) - Method in class org.anchoranalysis.test.image.stackwriter.FourChannelStackTester: Tests the creation of a two-channel stack of specified data types.
TEXT - Enum constant in enum class org.anchoranalysis.core.format.NonImageFileFormat: Text files.
TextFileMessageLogger - Class in org.anchoranalysis.experiment.log: Logs messages to a text-file.
TextFileMessageLogger(String, ErrorReporter) - Constructor for class org.anchoranalysis.experiment.log.TextFileMessageLogger: Constructs a logger that (always) writes messages to a text-file with a specific path.
TextFileMessageLogger(String, OutputterChecked, ErrorReporter) - Constructor for class org.anchoranalysis.experiment.log.TextFileMessageLogger: Constructs a logger that (maybe) writes messages to a text-file, with a path based upon an output name applied to a OutputterChecked.
TextFileOutput - Class in org.anchoranalysis.io.generator.text: Utility for writing to a text-file at a particular path, but only if it is enabled.
TextFileOutput(String) - Constructor for class org.anchoranalysis.io.generator.text.TextFileOutput: Creates a new TextFileOutput instance.
TextFileOutputter - Class in org.anchoranalysis.io.generator.text: Maybe creates a TextFileOutput based upon settings in a OutputterChecked.
TextStyle - Class in org.anchoranalysis.image.io.bean.stack.combine: The size and style of text as it should appear in an image.
TextStyle() - Constructor for class org.anchoranalysis.image.io.bean.stack.combine.TextStyle
TextureScore - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity: From Page 727 from Lin et al (A Multi-Model Approach to Simultaneous Segmentation and Classification of Heterogeneous Populations of Cell Nuclei
TextureScore() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.TextureScore
ThreeChannels - Class in org.anchoranalysis.plugin.image.bean.stack.provider.color: Provides a Stack by combining up to three channels (red, green, blue) into an RGB image.
ThreeChannels() - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeChannels
ThreeColoredObjects - Class in org.anchoranalysis.plugin.image.bean.stack.provider.color: Colors three collections of objects in RED, GREEN, BLUE channels on top of a background.
ThreeColoredObjects() - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeColoredObjects
threshold() - Method in class org.anchoranalysis.bean.shared.relation.threshold.RelationToConstant
threshold() - Method in class org.anchoranalysis.bean.shared.relation.threshold.RelationToThreshold: The threshold-value.
threshold() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryNotOffVoxels
threshold() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryNotOnVoxels
threshold() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryOffVoxels
threshold() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryOnVoxels
threshold(DoublePredicate) - Method in class org.anchoranalysis.math.histogram.Histogram: Generates a new histogram containing only values that match a predicate.
threshold(RelationToThreshold) - Method in interface org.anchoranalysis.image.voxel.statistics.VoxelStatistics: Derives statistics only of the voxels that satisfy a condition, relative to a threshold.
threshold(RelationToThreshold) - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsCombined
threshold(RelationToThreshold) - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsFromHistogram
threshold(VoxelsUntyped) - Method in class org.anchoranalysis.image.bean.threshold.Thresholder: Like Thresholder.threshold(VoxelsUntyped) but using default binary-values.
threshold(VoxelsUntyped, float, BinaryValuesByte, Optional<ObjectMask>, boolean) - Static method in class org.anchoranalysis.image.voxel.thresholder.VoxelsThresholder: Applies thresholding to VoxelsUntyped.
threshold(VoxelsUntyped, BinaryValuesByte) - Method in class org.anchoranalysis.image.bean.threshold.Thresholder: Like Thresholder.threshold(VoxelsUntyped, BinaryValuesByte, Optional, Optional) applying the thresholding to the entire set of voxels.
threshold(VoxelsUntyped, BinaryValuesByte, Optional<Histogram>, Optional<ObjectMask>) - Method in class org.anchoranalysis.image.bean.threshold.Thresholder: Thresholds voxels (across a range of values) so that they have only binary range (i.e. two voxel values representing on and off).
threshold(VoxelsUntyped, BinaryValuesByte, Optional<Histogram>, Optional<ObjectMask>) - Method in class org.anchoranalysis.image.bean.threshold.ThresholderGlobal
threshold(VoxelsUntyped, BinaryValuesByte, Optional<Histogram>, Optional<ObjectMask>) - Method in class org.anchoranalysis.plugin.fiji.bean.threshold.ThresholderAutoIJ
threshold(VoxelsUntyped, BinaryValuesByte, Optional<Histogram>, Optional<ObjectMask>) - Method in class org.anchoranalysis.plugin.imagej.bean.threshold.ThresholderSimpleFillHoles2D
Threshold - Class in org.anchoranalysis.plugin.image.bean.mask.provider.segment: Thresholds a channel to produce a mask, reusing (and modifying) the input-buffers of the channel if possible.
Threshold() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.segment.Threshold
ThresholdAgainstChannel - Class in org.anchoranalysis.plugin.image.bean.segment.binary: Thresholds each voxels by comparing against another channel that has per-voxel thresholds
ThresholdAgainstChannel() - Constructor for class org.anchoranalysis.plugin.image.bean.segment.binary.ThresholdAgainstChannel
thresholdByte(Voxels<UnsignedByteBuffer>, int, BinaryValuesByte) - Static method in class org.anchoranalysis.image.voxel.thresholder.VoxelsThresholder: Applies thresholding to Voxels of unsigned byte data type.
ThresholdConfidence - Class in org.anchoranalysis.plugin.image.bean.object.segment.reduce: Combines object-masks by projecting the maximum confidence-level for each voxel and thresholding.
ThresholdConfidence() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ThresholdConfidence
ThresholdConfidence(double) - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ThresholdConfidence: Creates with a minimum-confidence level.
ThresholdedFeature - Class in org.anchoranalysis.plugin.image.bean.object.filter.independent: Only keeps objects whose feature-value satisfies a condition relative to a threshold.
ThresholdedFeature() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedFeature
ThresholdedVolume - Class in org.anchoranalysis.plugin.image.bean.object.filter.independent: Only keeps objects whose feature-value satisfies a condition relative to a threshold.
ThresholdedVolume() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedVolume
Thresholder - Class in org.anchoranalysis.image.bean.threshold: Thresholds voxels to create a binary-voxels using global thresholding.
Thresholder() - Constructor for class org.anchoranalysis.image.bean.threshold.Thresholder
ThresholderAutoIJ - Class in org.anchoranalysis.plugin.fiji.bean.threshold: Applies automatic thresholding using ImageJ's Auto_Threshold plugin.
ThresholderAutoIJ() - Constructor for class org.anchoranalysis.plugin.fiji.bean.threshold.ThresholderAutoIJ
ThresholderGlobal - Class in org.anchoranalysis.image.bean.threshold: Performs global thresholding.
ThresholderGlobal() - Constructor for class org.anchoranalysis.image.bean.threshold.ThresholderGlobal
ThresholderGlobal(CalculateLevel) - Constructor for class org.anchoranalysis.image.bean.threshold.ThresholderGlobal
ThresholderSimpleFillHoles2D - Class in org.anchoranalysis.plugin.imagej.bean.threshold: A thresholder that applies a simple intensity threshold and then fills holes in 2D.
ThresholderSimpleFillHoles2D() - Constructor for class org.anchoranalysis.plugin.imagej.bean.threshold.ThresholderSimpleFillHoles2D
ThresholderSimpleFillHoles2D(int) - Constructor for class org.anchoranalysis.plugin.imagej.bean.threshold.ThresholderSimpleFillHoles2D: Creates a new ThresholderSimpleFillHoles2D instance.
thresholdFloat(Voxels<FloatBuffer>, float, BinaryValuesByte) - Static method in class org.anchoranalysis.image.voxel.thresholder.VoxelsThresholder: Applies thresholding to Voxels of float data type.
ThresholdHistogram - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.threshold: Thresholds the histogram (using a weightedOtsu) and then applies a feature to the thresholded version.
ThresholdHistogram() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.ThresholdHistogram
ThumbnailBatch<T> - Interface in org.anchoranalysis.plugin.image.thumbnail: Creates thumbnails for a particular batch of objects that can be calibrated to have similar properties (identical scale etc.)
thumbnailFor(Stack) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.stack.ScaleToSize
thumbnailFor(Stack) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.stack.ThumbnailFromStack: Creates a thumbnail for a stack.
thumbnailFor(T) - Method in interface org.anchoranalysis.plugin.image.thumbnail.ThumbnailBatch: Creates a thumbnail for an element in the batch.
ThumbnailFromObjects - Class in org.anchoranalysis.plugin.image.bean.thumbnail.object: Creates a thumbnail of one or more objects on a stack by drawing the outline of the objects.
ThumbnailFromObjects() - Constructor for class org.anchoranalysis.plugin.image.bean.thumbnail.object.ThumbnailFromObjects
ThumbnailFromStack - Class in org.anchoranalysis.plugin.image.bean.thumbnail.stack: Creates a thumbnail from a stack.
ThumbnailFromStack() - Constructor for class org.anchoranalysis.plugin.image.bean.thumbnail.stack.ThumbnailFromStack
Tiff - Class in org.anchoranalysis.io.bioformats.bean.writer: Writes a stack to the filesystem as a TIFF using the Bioformats library.
Tiff - Class in org.anchoranalysis.io.imagej.bean.stack.writer: Writes a TIFF image using ImageJ.
Tiff() - Constructor for class org.anchoranalysis.io.bioformats.bean.writer.Tiff: Default constructor.
Tiff() - Constructor for class org.anchoranalysis.io.imagej.bean.stack.writer.Tiff
TIFF - Enum constant in enum class org.anchoranalysis.core.format.ImageFileFormat: TIFF
TiffTestBase - Class in org.anchoranalysis.test.image.stackwriter: For testing all StackWriters that create TIFFs.
TiffTestBase() - Constructor for class org.anchoranalysis.test.image.stackwriter.TiffTestBase
tile(List<StackProviderWithLabel>, int, boolean, boolean) - Static method in class org.anchoranalysis.image.io.stack.input.TileStackProviders: Creates a StackProvider that provides a tiled-representation of providers.
Tile - Class in org.anchoranalysis.image.bean.spatial.arrange.tile: A higher-level aggregate structure that arranges other StackArrangers in a tabular pattern.
Tile() - Constructor for class org.anchoranalysis.image.bean.spatial.arrange.tile.Tile
Tile(int, int) - Constructor for class org.anchoranalysis.image.bean.spatial.arrange.tile.Tile: Creates for a particular number of columns and rows.
TileStackProviders - Class in org.anchoranalysis.image.io.stack.input: Tile multiple StackProviders into a single StackProvider.
TileWithLabels - Class in org.anchoranalysis.image.io.bean.stack.combine: Tiles a number of StackProviderWithLabels as a single StackProvider.
TileWithLabels() - Constructor for class org.anchoranalysis.image.io.bean.stack.combine.TileWithLabels
TimeIntervalNamer - Class in org.anchoranalysis.plugin.io.naming.interval: Derives a human-friendly name for a time-interval.
TimeIntervalNamer(ZoneOffset) - Constructor for class org.anchoranalysis.plugin.io.naming.interval.TimeIntervalNamer: Creates a new TimeIntervalNamer instance.
TimeSeries - Class in org.anchoranalysis.image.io.stack.time: An ordered collection of Stacks, each representing a frame in a time-series.
TimeSeries(Stream<Stack>) - Constructor for class org.anchoranalysis.image.io.stack.time.TimeSeries: Creates a TimeSeries from a stream of frames.
TimeSeries(Stack) - Constructor for class org.anchoranalysis.image.io.stack.time.TimeSeries: Creates a TimeSeries containing a single frame only.
TimestampPattern - Class in org.anchoranalysis.plugin.io.bean.file.pattern: Extracts a timestamp from a file-name if it exists.
TimestampPattern() - Constructor for class org.anchoranalysis.plugin.io.bean.file.pattern.TimestampPattern
TimestampPattern(String) - Constructor for class org.anchoranalysis.plugin.io.bean.file.pattern.TimestampPattern
timestamps() - Method in interface org.anchoranalysis.image.io.stack.input.OpenedImageFile: The timestamps and file-attributes associated with the image.
timestamps() - Method in class org.anchoranalysis.plugin.io.multifile.OpenedMultiFile
TimeStyle - Enum Class in org.anchoranalysis.plugin.io.naming.interval: How to style a time in a file-name.
toAll() - Method in interface org.anchoranalysis.image.voxel.assigner.VoxelsAssigner: Assigns to all the voxels
toArray() - Method in class org.anchoranalysis.spatial.box.Extent: Derives an three-element array with each dimension in the extent.
toArray() - Method in class org.anchoranalysis.spatial.point.Point2i: Converts the point to an array.
toArray() - Method in class org.anchoranalysis.spatial.point.Point3d: Converts the point to an array.
toArrayXY() - Method in class org.anchoranalysis.spatial.point.Point3d: Converts the X and Y dimensions of the point to an array.
toAWTColor() - Method in class org.anchoranalysis.bean.shared.color.RGBColorBean: Converts to a Color representation.
toAWTColor() - Method in class org.anchoranalysis.core.color.RGBColor: Converts to a Color representation.
toBoundingBox() - Method in class org.anchoranalysis.spatial.box.PointRange: Creates a BoundingBox to just cover the range of points that have been added.
toBoundingBoxNoCheck() - Method in class org.anchoranalysis.spatial.box.PointRange: Like PointRange.toBoundingBox() but if no points exist, an exception is not thrown.
toBox(BoundingBox) - Method in interface org.anchoranalysis.image.voxel.assigner.VoxelsAssigner: Assigns to only voxels inside a bounding-box
ToByte - Class in org.anchoranalysis.plugin.image.bean.channel.convert: Converts a channel to unsigned byte format without any scaling.
ToByte() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.convert.ToByte
ToByteUpperLowerQuantileIntensity - Class in org.anchoranalysis.plugin.image.bean.channel.convert: Converts a channel to unsigned byte format using upper and lower quantile intensities from a histogram.
ToByteUpperLowerQuantileIntensity() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.convert.ToByteUpperLowerQuantileIntensity
toChannel(ImagePlus, Optional<Resolution>) - Static method in class org.anchoranalysis.io.imagej.convert.ConvertFromImagePlus: Converts an ImagePlus to a Channel.
toCommandLineException() - Method in exception class org.anchoranalysis.launcher.executor.selectparam.path.convert.InvalidPathArgumentException: Converts this exception to a CommandLineException.
ToConsole - Class in org.anchoranalysis.experiment.bean.log: Logs messages to the console.
ToConsole() - Constructor for class org.anchoranalysis.experiment.bean.log.ToConsole
ToDimensions - Class in org.anchoranalysis.plugin.image.bean.scale: Calculates a scaling-factor to make the source image have identical dimensions as dimensionsTarget.
ToDimensions() - Constructor for class org.anchoranalysis.plugin.image.bean.scale.ToDimensions
ToDimensions(int, int) - Constructor for class org.anchoranalysis.plugin.image.bean.scale.ToDimensions: Create with specific lengths for X and Y dimensions.
ToDimensions(int, int, boolean) - Constructor for class org.anchoranalysis.plugin.image.bean.scale.ToDimensions: Create with specific lengths for X and Y dimensions and preserveAspectRatio.
ToDimensions(DimensionsProvider) - Constructor for class org.anchoranalysis.plugin.image.bean.scale.ToDimensions: Create with specific dimensions.
ToDimensions(DimensionsProvider, boolean) - Constructor for class org.anchoranalysis.plugin.image.bean.scale.ToDimensions: Create with specific dimensions and preserveAspectRatio.
toEitherTwoObjects(ObjectMask, ObjectMask, BoundingBox) - Method in interface org.anchoranalysis.image.voxel.assigner.VoxelsAssigner: Sets voxels to a value if the position is on in either of two masks
toExtent() - Method in class org.anchoranalysis.plugin.io.multifile.SizeExtents
ToFloat - Class in org.anchoranalysis.image.core.channel.convert: Converts a Channel to have a voxel data type of FloatBuffer without scaling.
ToFloat - Class in org.anchoranalysis.io.bioformats.copyconvert.tofloat: Base class for implementations of ConvertTo that convert to float buffers.
ToFloat() - Constructor for class org.anchoranalysis.image.core.channel.convert.ToFloat: Creates without scaling.
ToFloat() - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.tofloat.ToFloat: Constructor populating super-class with necessary values.
ToFloatNoScaling - Class in org.anchoranalysis.image.voxel.convert: Converts voxel buffers to a FloatBuffer without scaling any values.
ToFloatNoScaling() - Constructor for class org.anchoranalysis.image.voxel.convert.ToFloatNoScaling
ToMultiple - Class in org.anchoranalysis.experiment.bean.log: Rather than logging to one location, logs to multiple locations (from a list).
ToMultiple() - Constructor for class org.anchoranalysis.experiment.bean.log.ToMultiple
ToMultiple(LoggingDestination, LoggingDestination) - Constructor for class org.anchoranalysis.experiment.bean.log.ToMultiple: Constructs a logger to two locations
toObject(ObjectMask) - Method in interface org.anchoranalysis.image.voxel.assigner.VoxelsAssigner: Sets voxels in a box to a particular value if they match an object-mask
toObject(ObjectMask, BoundingBox) - Method in interface org.anchoranalysis.image.voxel.assigner.VoxelsAssigner: Sets voxels in a box to a particular value if they match a object-mask (but only a part of the object-mask)
toObjectIf(ObjectMask, IntPredicate) - Method in interface org.anchoranalysis.image.voxel.assigner.VoxelsAssigner: Sets voxels in a box to a particular value if they match an object-mask and a voxel matches a predicate
toObjectWhile(ObjectMask, IntPredicate) - Method in interface org.anchoranalysis.image.voxel.assigner.VoxelsAssigner: Sets voxels in a box to a particular value if they match an object-mask and each voxel matches a predicate
TOP - Static variable in class org.anchoranalysis.image.bean.nonbean.spatial.align.PositionChoicesConstants: Align to the top in the Y-dimension.
toPath() - Method in class org.anchoranalysis.io.input.file.NamedFile: Like File.toPath().
toPhysicalArea(double) - Method in class org.anchoranalysis.image.core.dimensions.UnitConverter: Converts an area from square voxels to square meters.
toPhysicalArea(double, String) - Method in class org.anchoranalysis.image.core.dimensions.UnitConverter: Converts an area from square voxels to physical units.
toPhysicalDistance(double, DirectionVector) - Method in class org.anchoranalysis.image.core.dimensions.UnitConverter: Converts a distance from voxels to meters.
toPhysicalDistance(double, DirectionVector, String) - Method in class org.anchoranalysis.image.core.dimensions.UnitConverter: Converts a distance from voxels to physical units.
toPhysicalVolume(double) - Method in class org.anchoranalysis.image.core.dimensions.UnitConverter: Converts a volume from cubic voxels to cubic meters.
toPhysicalVolume(double, String) - Method in class org.anchoranalysis.image.core.dimensions.UnitConverter: Converts a volume from cubic voxels to physical units.
toRGBColor() - Method in class org.anchoranalysis.bean.shared.color.RGBColorBean: The RGBColor associated with the bean.
toSet() - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream: Converts to a HashSet.
toStack(Mat) - Static method in class org.anchoranalysis.plugin.opencv.convert.ConvertFromMat: Convert from an OpenCV Mat to a Stack.
toString() - Method in class org.anchoranalysis.annotation.image.ImageLabelAnnotation
toString() - Method in class org.anchoranalysis.annotation.io.assignment.CostMatrix
toString() - Method in class org.anchoranalysis.annotation.io.image.findable.Found
toString() - Method in class org.anchoranalysis.annotation.io.image.findable.NotFound
toString() - Method in class org.anchoranalysis.bean.AnchorBean: By default, we use AnchorBean.describeBean() as the string representation of the bean.
toString() - Method in class org.anchoranalysis.bean.initializable.property.AssignerMatchClass
toString() - Method in class org.anchoranalysis.bean.NamedBean
toString() - Method in class org.anchoranalysis.bean.shared.regex.RegExList
toString() - Method in class org.anchoranalysis.bean.shared.regex.RegExSimple
toString() - Method in class org.anchoranalysis.bean.shared.relation.EqualToBean
toString() - Method in class org.anchoranalysis.bean.shared.relation.GreaterThanBean
toString() - Method in class org.anchoranalysis.bean.shared.relation.GreaterThanEqualToBean
toString() - Method in class org.anchoranalysis.bean.shared.relation.LessThanBean
toString() - Method in class org.anchoranalysis.bean.shared.relation.LessThanEqualToBean
toString() - Method in class org.anchoranalysis.bean.shared.relation.RelationBean
toString() - Method in class org.anchoranalysis.bean.shared.relation.threshold.RelationToConstant
toString() - Method in class org.anchoranalysis.core.color.RGBColor
toString() - Method in exception class org.anchoranalysis.core.exception.AnchorRuntimeException
toString() - Method in class org.anchoranalysis.core.graph.GraphWithoutPayload
toString() - Method in class org.anchoranalysis.core.graph.GraphWithPayload
toString() - Method in class org.anchoranalysis.core.graph.TypedEdge
toString() - Method in class org.anchoranalysis.core.index.range.IndexRangeNegative
toString() - Method in class org.anchoranalysis.core.log.CommonContext
toString() - Method in class org.anchoranalysis.core.system.path.FilenameSplitExtension
toString() - Method in class org.anchoranalysis.core.system.path.PathDifference
toString() - Method in class org.anchoranalysis.core.system.path.SplitPath
toString() - Method in class org.anchoranalysis.core.time.OperationContext
toString() - Method in class org.anchoranalysis.core.value.TypedValue
toString() - Method in class org.anchoranalysis.experiment.task.InputTypesExpected
toString() - Method in class org.anchoranalysis.experiment.task.ParametersUnbound
toString() - Method in class org.anchoranalysis.experiment.task.processor.JobDescription
toString() - Method in class org.anchoranalysis.experiment.task.processor.SubmittedJob
toString() - Method in class org.anchoranalysis.feature.bean.Feature
toString() - Method in class org.anchoranalysis.feature.calculate.cache.ChildCacheName
toString() - Method in class org.anchoranalysis.feature.initialization.FeatureInitialization
toString() - Method in class org.anchoranalysis.feature.input.FeatureInputResults
toString() - Method in class org.anchoranalysis.feature.io.csv.metadata.FeatureCSVMetadata
toString() - Method in class org.anchoranalysis.feature.io.name.CombinedName
toString() - Method in interface org.anchoranalysis.feature.io.name.MultiName: The full name, including both directory and file part, as a string.
toString() - Method in class org.anchoranalysis.feature.io.name.SimpleName
toString() - Method in class org.anchoranalysis.feature.io.results.LabelledResultsVector
toString() - Method in class org.anchoranalysis.feature.name.FeatureNameList
toString() - Method in class org.anchoranalysis.feature.results.ResultsVector
toString() - Method in class org.anchoranalysis.feature.shared.SharedFeatures
toString() - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.StackArrangement
toString() - Method in class org.anchoranalysis.image.bean.spatial.arrange.fill.ExtentToArrange
toString() - Method in class org.anchoranalysis.image.bean.spatial.SizeXY
toString() - Method in class org.anchoranalysis.image.bean.unitvalue.extent.area.AreaPhysical
toString() - Method in class org.anchoranalysis.image.bean.unitvalue.extent.area.AreaPixels
toString() - Method in class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumePhysical
toString() - Method in class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumeVoxels
toString() - Method in class org.anchoranalysis.image.core.channel.Channel: A string representation of a histogram of voxel-intensities in the channel.
toString() - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
toString() - Method in class org.anchoranalysis.image.core.dimensions.Resolution
toString() - Method in class org.anchoranalysis.image.core.object.label.OverlappingObject
toString() - Method in class org.anchoranalysis.image.core.object.MatchedObject
toString() - Method in class org.anchoranalysis.image.core.object.properties.ObjectCollectionWithProperties
toString() - Method in class org.anchoranalysis.image.core.object.properties.ObjectWithProperties
toString() - Method in class org.anchoranalysis.image.core.stack.ImagePyramidMetadata
toString() - Method in class org.anchoranalysis.image.feature.calculator.NamedFeatureCalculatorMulti
toString() - Method in class org.anchoranalysis.image.feature.input.FeatureInputPairObjects: Returns a string representation of the object.
toString() - Method in class org.anchoranalysis.image.feature.input.FeatureInputSingleObject: Returns a string representation of the object.
toString() - Method in class org.anchoranalysis.image.inference.bean.reduce.ObjectForReduction
toString() - Method in class org.anchoranalysis.image.inference.ImageInferenceContext
toString() - Method in class org.anchoranalysis.image.inference.segment.LabelledWithConfidence
toString() - Method in class org.anchoranalysis.image.inference.segment.WithConfidence
toString() - Method in class org.anchoranalysis.image.io.stack.input.ImageTimestampsAttributes
toString() - Method in class org.anchoranalysis.image.io.stack.output.StackWriteAttributes: A user-friendly description of the stack-type to include in error and warning messages.
toString() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels
toString() - Method in class org.anchoranalysis.image.voxel.BoundedVoxels
toString() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBufferAsInt: Print a description and the the first {link #MAX_NUMBER_ROWS_COLUMNS_IN_TO_STRING} rows and columns as values.
toString() - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer
toString() - Method in class org.anchoranalysis.image.voxel.datatype.VoxelDataType
toString() - Method in class org.anchoranalysis.image.voxel.iterator.MinMaxRange
toString() - Method in class org.anchoranalysis.image.voxel.kernel.KernelApplicationParameters
toString() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection: Default string representation of the collection, one line with each object described by its center-of-gravity.
toString() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: A string representation of the object-mask showing: the center-of-gravity.
toString() - Method in class org.anchoranalysis.image.voxel.Voxels: Print a description and the the first Voxels.MAX_IN_TO_STRING (if they exist) rows and columns as values.
toString() - Method in class org.anchoranalysis.inference.concurrency.ConcurrentModel
toString() - Method in class org.anchoranalysis.io.bioformats.copyconvert.ImageFileEncoding
toString() - Method in class org.anchoranalysis.io.bioformats.copyconvert.ImageFileShape
toString() - Method in class org.anchoranalysis.io.generator.combined.OptionalNameValue
toString() - Method in class org.anchoranalysis.io.generator.sequence.BoundOutputter
toString() - Method in class org.anchoranalysis.io.input.file.FileNamerContext
toString() - Method in class org.anchoranalysis.io.input.file.NamedFile
toString() - Method in class org.anchoranalysis.io.input.file.SingleFileInputBase
toString() - Method in class org.anchoranalysis.io.input.InputFromManagerDelegate
toString() - Method in class org.anchoranalysis.io.input.InputsWithDirectory
toString() - Method in class org.anchoranalysis.io.input.path.GlobExtractor.GlobWithDirectory
toString() - Method in class org.anchoranalysis.io.output.outputter.directory.OutputterTarget
toString() - Method in class org.anchoranalysis.io.output.outputter.DirectoryCreationParameters
toString() - Method in class org.anchoranalysis.io.output.outputter.Outputter
toString() - Method in class org.anchoranalysis.io.output.path.prefixer.NamedPath
toString() - Method in class org.anchoranalysis.launcher.config.HelpConfig
toString() - Method in class org.anchoranalysis.math.equation.QuadraticEquationSolver.QuadraticRoots
toString() - Method in class org.anchoranalysis.math.histogram.Histogram: A string representation of what's in the histogram.
toString() - Method in class org.anchoranalysis.math.statistics.MeanScale
toString() - Method in class org.anchoranalysis.math.statistics.moment.EigenvalueAndVector
toString() - Method in class org.anchoranalysis.mpp.bean.bound.ResolvedBound
toString() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
toString() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipWithFlags
toString() - Method in class org.anchoranalysis.mpp.feature.energy.EnergyPair
toString() - Method in class org.anchoranalysis.mpp.feature.energy.EnergyTotal
toString() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown: Returns a string representation of the object.
toString() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedPairs
toString() - Method in class org.anchoranalysis.mpp.feature.input.FeatureInputPairMemo
toString() - Method in class org.anchoranalysis.mpp.mark.conic.Circle
toString() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
toString() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
toString() - Method in class org.anchoranalysis.mpp.mark.conic.Sphere
toString() - Method in class org.anchoranalysis.mpp.mark.MarkCollection
toString() - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
toString() - Method in class org.anchoranalysis.mpp.mark.points.PointList
toString() - Method in class org.anchoranalysis.mpp.mark.points.Polygon
toString() - Method in class org.anchoranalysis.mpp.mark.points.PolygonCurve
toString() - Method in class org.anchoranalysis.mpp.mark.points.RotatableBoundingBox
toString() - Method in class org.anchoranalysis.mpp.pair.MarkPair
toString() - Method in class org.anchoranalysis.mpp.pair.PairVoxelizedMarkMemo
toString() - Method in class org.anchoranalysis.mpp.proposer.ProposerContext
toString() - Method in class org.anchoranalysis.overlay.collection.ColoredOverlayCollection
toString() - Method in class org.anchoranalysis.overlay.writer.ObjectDrawAttributes
toString() - Method in class org.anchoranalysis.plugin.annotation.comparison.ObjectsToCompare
toString() - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateObjectMask
toString() - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateShellObjectMask
toString() - Method in class org.anchoranalysis.plugin.image.object.ColoredObject
toString() - Method in class org.anchoranalysis.plugin.image.object.merge.ObjectVertex
toString() - Method in class org.anchoranalysis.plugin.image.task.bean.format.ChangeableOutputSequence
toString() - Method in class org.anchoranalysis.plugin.image.task.feature.FeatureExporterContext
toString() - Method in class org.anchoranalysis.plugin.image.task.feature.InitializationWithEnergyStack
toString() - Method in class org.anchoranalysis.plugin.image.task.feature.LabelledResultsVectorWithThumbnail
toString() - Method in class org.anchoranalysis.plugin.image.task.feature.ResultsVectorWithThumbnail
toString() - Method in class org.anchoranalysis.plugin.image.task.grouped.NamedChannel
toString() - Method in class org.anchoranalysis.plugin.image.task.labeller.ImageCSVLabellerInitialization
toString() - Method in class org.anchoranalysis.plugin.image.task.labeller.ImageLabellerStringMapInitialization
toString() - Method in class org.anchoranalysis.plugin.io.input.path.CopyContext
toString() - Method in class org.anchoranalysis.plugin.io.multifile.FileDetails
toString() - Method in class org.anchoranalysis.plugin.io.shared.AnonymizeSharedState
toString() - Method in class org.anchoranalysis.plugin.mpp.shared.ConvertedInput
toString() - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult
toString() - Method in class org.anchoranalysis.plugin.points.calculate.ellipse.ObjectWithEllipse
toString() - Method in class org.anchoranalysis.spatial.box.BoundingBox
toString() - Method in class org.anchoranalysis.spatial.box.Extent
toString() - Method in class org.anchoranalysis.spatial.orientation.Orientation2D
toString() - Method in class org.anchoranalysis.spatial.orientation.Orientation3DEulerAngles
toString() - Method in class org.anchoranalysis.spatial.orientation.OrientationAxisAngle
toString() - Method in class org.anchoranalysis.spatial.orientation.RotationMatrix
toString() - Method in class org.anchoranalysis.spatial.point.Point2d
toString() - Method in class org.anchoranalysis.spatial.point.Point2f
toString() - Method in class org.anchoranalysis.spatial.point.Point2i
toString() - Method in class org.anchoranalysis.spatial.point.Tuple3d
toString() - Method in class org.anchoranalysis.spatial.point.Tuple3f
toString() - Method in class org.anchoranalysis.spatial.point.Tuple3i
toString() - Method in class org.anchoranalysis.spatial.scale.ScaleFactor
toString() - Method in class org.anchoranalysis.test.image.rasterwriter.comparison.ComparisonPlan
toString() - Method in class org.anchoranalysis.test.image.stackwriter.ChannelSpecification
toString(boolean, boolean) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection: A string representation of all objects in the collection using their center of gravities (and optionally indices).
toStringUnixStyle(String) - Static method in class org.anchoranalysis.core.system.path.FilePathToUnixStyleConverter: Converts a path to a string using Unix-style separators (forward-slashes).
toStringUnixStyle(Path) - Static method in class org.anchoranalysis.core.system.path.FilePathToUnixStyleConverter: Converts a path to a string using Unix-style separators (forward-slashes).
ToSuggested - Class in org.anchoranalysis.plugin.image.bean.scale: Scales to the suggested-size if one is provided, otherwise calls fallback.
ToSuggested() - Constructor for class org.anchoranalysis.plugin.image.bean.scale.ToSuggested
ToSuggested(ScaleCalculator) - Constructor for class org.anchoranalysis.plugin.image.bean.scale.ToSuggested: Creates a new ToSuggested instance.
total() - Method in class org.anchoranalysis.feature.results.ResultsVector: The total value of all results.
totalAll(EnergyMemoList, EnergyStackWithoutParameters) - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergySchemeWithSharedFeatures: Calculates the total energy for all marks in the list.
TotalCount - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic: Calculates the total count of all entries in a Histogram.
TotalCount() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.TotalCount
totalIndividual(VoxelizedMarkMemo, EnergyStackWithoutParameters) - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergySchemeWithSharedFeatures: Calculates the total energy for an individual mark.
totalNumberSlices() - Method in class org.anchoranalysis.io.bioformats.copyconvert.ImageFileShape: The total number of z-slices across all frames, channels.
ToTextFile - Class in org.anchoranalysis.experiment.bean.log: Logs to a text-file created in the output-directory under a particular name.
ToTextFile() - Constructor for class org.anchoranalysis.experiment.bean.log.ToTextFile
ToTextFileBase - Class in org.anchoranalysis.experiment.bean.log: Logs messages to a text-file create in the output-directory.
ToTextFileBase() - Constructor for class org.anchoranalysis.experiment.bean.log.ToTextFileBase
ToTextFileOnlyIfFailure - Class in org.anchoranalysis.experiment.bean.log: Logs to a text file like with ToTextFile but the log is ONLY written if a failure occurs in the experiment.
ToTextFileOnlyIfFailure() - Constructor for class org.anchoranalysis.experiment.bean.log.ToTextFileOnlyIfFailure
ToThePowerOfConstant<T> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic: A feature that raises the result of another feature to the power of a constant value.
ToThePowerOfConstant() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.ToThePowerOfConstant
TouchingVoxels - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.touching: Base class for features that calculate touching with a dilated bounding box intersection.
TouchingVoxels() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.TouchingVoxels
ToUnsignedByte - Class in org.anchoranalysis.image.core.channel.convert: Converts a Channel to have a voxel data type of UnsignedByteBuffer (unsigned 8-bit) without scaling.
ToUnsignedByte - Class in org.anchoranalysis.image.voxel.convert: Base class for conversion to unsigned 8-bit.
ToUnsignedByte - Class in org.anchoranalysis.io.bioformats.copyconvert.tobyte: Base class for implementations of ConvertTo that convert to unsigned byte buffers.
ToUnsignedByte() - Constructor for class org.anchoranalysis.image.core.channel.convert.ToUnsignedByte: Converting without scaling any values.
ToUnsignedByte() - Constructor for class org.anchoranalysis.image.voxel.convert.ToUnsignedByte
ToUnsignedByte() - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.tobyte.ToUnsignedByte: Constructor populating super-class with necessary values.
ToUnsignedByte(VoxelsConverter<UnsignedByteBuffer>) - Constructor for class org.anchoranalysis.image.core.channel.convert.ToUnsignedByte: Convert with a particular VoxelsConverter.
ToUnsignedByteNoScaling - Class in org.anchoranalysis.image.voxel.convert: Converts voxel buffers to an unsigned 8-bit buffer without scaling any values.
ToUnsignedByteNoScaling() - Constructor for class org.anchoranalysis.image.voxel.convert.ToUnsignedByteNoScaling
ToUnsignedByteScaleByMaxValue - Class in org.anchoranalysis.image.voxel.convert: Converts voxel buffers to an unsigned 8-bit buffer linearly scaling against the maximum constant value.
ToUnsignedByteScaleByMaxValue(int) - Constructor for class org.anchoranalysis.image.voxel.convert.ToUnsignedByteScaleByMaxValue: Creates with the maximum-value which existing values are scaled against.
ToUnsignedByteScaleByMinMaxValue - Class in org.anchoranalysis.image.core.channel.convert: Converts a Channel to have a voxel data type of UnsignedByteBuffer (unsigned 8-bit) scaling from the range of the source data-type.
ToUnsignedByteScaleByMinMaxValue - Class in org.anchoranalysis.image.voxel.convert: Converts voxel buffers to an unsigned 8-bit buffer scaling against a the minimum and maximum constant.
ToUnsignedByteScaleByMinMaxValue(int, int) - Constructor for class org.anchoranalysis.image.core.channel.convert.ToUnsignedByteScaleByMinMaxValue: Creates with the minimum- and maximum-values which existing values are scaled against.
ToUnsignedByteScaleByMinMaxValue(long, long) - Constructor for class org.anchoranalysis.image.voxel.convert.ToUnsignedByteScaleByMinMaxValue: Creates with the minimum- and maximum-values which existing values are scaled against.
ToUnsignedByteScaleByType - Class in org.anchoranalysis.image.voxel.convert: Converts voxel buffers to a UnsignedByteBuffer scaling against the maximum value in each buffer.
ToUnsignedByteScaleByType() - Constructor for class org.anchoranalysis.image.voxel.convert.ToUnsignedByteScaleByType
ToUnsignedByteWithScaling - Class in org.anchoranalysis.io.bioformats.copyconvert.tobyte: Like ToUnsignedByte but applies scaling, if necessary, to map the original value to 8-bits.
ToUnsignedByteWithScaling(int) - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.tobyte.ToUnsignedByteWithScaling: Create with the number of bits that are used in the input-type.
ToUnsignedInt - Class in org.anchoranalysis.image.voxel.convert: Base class for conversion to unsigned 32-bit.
ToUnsignedInt - Class in org.anchoranalysis.io.bioformats.copyconvert.toint: Base class for implementations of ConvertTo that convert to unsigned int buffers.
ToUnsignedInt() - Constructor for class org.anchoranalysis.image.voxel.convert.ToUnsignedInt
ToUnsignedInt() - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.toint.ToUnsignedInt: Constructor populating super-class with necessary values.
ToUnsignedShort - Class in org.anchoranalysis.image.core.channel.convert: Converts a Channel to have a voxel data type of UnsignedShortBuffer.
ToUnsignedShort - Class in org.anchoranalysis.io.bioformats.copyconvert.toshort: Base class for implementations of ConvertTo that convert to unsigned short buffers.
ToUnsignedShort() - Constructor for class org.anchoranalysis.image.core.channel.convert.ToUnsignedShort: Converting without scaling any values.
ToUnsignedShort() - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.toshort.ToUnsignedShort: Constructor populating super-class with necessary values.
ToUnsignedShort(VoxelsConverter<UnsignedShortBuffer>) - Constructor for class org.anchoranalysis.image.core.channel.convert.ToUnsignedShort: Convert with a particular VoxelsConverter.
ToUnsignedShortNoScaling - Class in org.anchoranalysis.image.voxel.convert: Converts voxel buffers to an unsigned 16-bit buffer without scaling any values.
ToUnsignedShortNoScaling() - Constructor for class org.anchoranalysis.image.voxel.convert.ToUnsignedShortNoScaling
ToUnsignedShortScaleByType - Class in org.anchoranalysis.image.voxel.convert: Converts voxel buffers to an unsigned 16-bit buffer, scaling against the maximum value in each data-type.
ToUnsignedShortScaleByType() - Constructor for class org.anchoranalysis.image.voxel.convert.ToUnsignedShortScaleByType
toVoxel(int, int, int) - Method in interface org.anchoranalysis.image.voxel.assigner.VoxelsAssigner: Assigns one particular voxel
toVoxel(Point3i) - Method in interface org.anchoranalysis.image.voxel.assigner.VoxelsAssigner: Assigns one particular voxel
toVoxelBuffer(Mat, Extent) - Static method in class org.anchoranalysis.plugin.opencv.convert.VoxelBufferFromMat: Converts a Mat to a VoxelBuffer.
toVoxels(ImagePlus) - Static method in class org.anchoranalysis.io.imagej.convert.ConvertFromImagePlus: Converts an ImagePlus to a VoxelsUntyped.
transferCount(int, int) - Method in class org.anchoranalysis.math.histogram.Histogram: Moves all count for a particular value and adds it to the count for another.
transform(List<File>) - Method in class org.anchoranalysis.io.input.bean.files.FilesProviderWithDirectoryUnary: Transform an existing collection of files.
transform(List<File>) - Method in class org.anchoranalysis.plugin.io.bean.file.provider.LimitWithDirectory
transform(List<File>) - Method in class org.anchoranalysis.plugin.io.bean.file.provider.SampleWithDirectory
transform(List<File>) - Method in class org.anchoranalysis.plugin.io.bean.file.provider.SortAlphabeticallyWithDirectory
transform(List<File>, boolean) - Method in class org.anchoranalysis.io.input.bean.files.FilesProviderUnary: Transform an existing collection of files.
transform(List<File>, boolean) - Method in class org.anchoranalysis.plugin.io.bean.file.provider.Limit
transform(List<File>, boolean) - Method in class org.anchoranalysis.plugin.io.bean.file.provider.RandomOrder
transform(List<File>, boolean) - Method in class org.anchoranalysis.plugin.io.bean.file.provider.RemoveMatching
transform(List<File>, boolean) - Method in class org.anchoranalysis.plugin.io.bean.file.provider.SortAlphabetically
transform(List<File>, boolean) - Method in class org.anchoranalysis.plugin.io.bean.input.files.provider.FilterForExistingFiles
transform(Assignment<ObjectMask>) - Method in class org.anchoranalysis.annotation.io.assignment.generator.AssignmentGenerator
transform(ColorList) - Method in class org.anchoranalysis.bean.shared.color.scheme.ColorSchemeUnary: Transform an existing ColorList.
transform(ColorList) - Method in class org.anchoranalysis.bean.shared.color.scheme.Prepend
transform(ColorList) - Method in class org.anchoranalysis.bean.shared.color.scheme.Repeat
transform(ColorList) - Method in class org.anchoranalysis.bean.shared.color.scheme.Shuffle
transform(Channel) - Method in class org.anchoranalysis.image.io.channel.output.ChannelGenerator
transform(ObjectCollectionWithProperties) - Method in class org.anchoranalysis.image.io.object.output.rgb.ObjectsAsRGBGenerator
transform(Stack) - Method in class org.anchoranalysis.image.io.stack.output.generator.StackGenerator
transform(ObjectCollection) - Method in class org.anchoranalysis.image.io.object.output.grayscale.ObjectsAsUniqueValueGenerator
transform(ObjectCollection) - Method in class org.anchoranalysis.image.io.object.output.grayscale.ObjectsMergedAsMaskGenerator
transform(ObjectMask) - Method in class org.anchoranalysis.image.io.object.output.mask.ObjectAsMaskGenerator
transform(BoundedList<ObjectMask>) - Method in class org.anchoranalysis.image.io.stack.output.box.DrawObjectOnStackGenerator
transform(BoundingBox) - Method in class org.anchoranalysis.image.io.stack.output.box.ExtractBoundingBoxAreaFromStackGenerator
transform(T) - Method in class org.anchoranalysis.image.io.stack.output.generator.RasterGeneratorBridge
transform(T) - Method in class org.anchoranalysis.image.io.stack.output.generator.RasterGeneratorDelegateToDisplayStack
transform(T) - Method in class org.anchoranalysis.image.io.stack.output.generator.RasterGeneratorDelegateToRaster
transform(T) - Method in class org.anchoranalysis.io.generator.OneStageGenerator
transform(T) - Method in class org.anchoranalysis.io.generator.SingleFileTypeGeneratorBridge
transform(T) - Method in interface org.anchoranalysis.io.generator.TransformingGenerator: Applies any necessary preprocessing to create an element suitable for writing to the filesystem.
transform(T) - Method in class org.anchoranalysis.io.generator.TransformingGeneratorBridge
TransformingGenerator<T,S> - Interface in org.anchoranalysis.io.generator: Performs preprocessing to transform the element into another type before being written to the filesystem.
TransformingGeneratorBridge<S,T,V> - Class in org.anchoranalysis.io.generator: Allows us to call an SingleFileTypeGenerator<V,S> as if it was an SingleFileTypeGenerator<T,S> using an function to connect the two.
TransformingGeneratorBridge(TransformingGenerator<V, S>, CheckedFunction<T, V, ? extends Throwable>) - Constructor for class org.anchoranalysis.io.generator.TransformingGeneratorBridge
transpose() - Method in class org.anchoranalysis.spatial.orientation.RotationMatrix: Transposes the matrix immutably.
Tuple3d - Class in org.anchoranalysis.spatial.point: A three-dimensional tuple of double values.
Tuple3d() - Constructor for class org.anchoranalysis.spatial.point.Tuple3d
Tuple3f - Class in org.anchoranalysis.spatial.point: A three-dimensional tuple of float values.
Tuple3f() - Constructor for class org.anchoranalysis.spatial.point.Tuple3f
Tuple3i - Class in org.anchoranalysis.spatial.point: A three-dimensional tuple of int values.
Tuple3i() - Constructor for class org.anchoranalysis.spatial.point.Tuple3i
twoNonOverlappingCircles(boolean) - Static method in class org.anchoranalysis.test.feature.plugins.objects.FeatureInputOverlappingCircleFixture: Creates two object-masks of circles in different locations WITHOUT any overlap.
twoOverlappingCircles(boolean) - Static method in class org.anchoranalysis.test.feature.plugins.objects.FeatureInputOverlappingCircleFixture: Creates two object-masks of circles in different locations WITH some overlap.
TwoVoxelMappingBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider: Takes the two channels and creates a NEW third channel whose pixels are a function of the two channels
TwoVoxelMappingBase(IntBinaryOperator) - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.TwoVoxelMappingBase: Creates a new TwoVoxelMappingBase instance.
TypedEdge<V,P> - Class in org.anchoranalysis.core.graph: An edge that exists in a graph, together with the two vertices that it connects.
TypedEdge(P, V, V) - Constructor for class org.anchoranalysis.core.graph.TypedEdge: Creates a new TypedEdge instance.
TypedValue - Class in org.anchoranalysis.core.value: A union of two types, either String or a numeric-value.
TypedValue(double) - Constructor for class org.anchoranalysis.core.value.TypedValue: Creates for an double value.
TypedValue(double, int) - Constructor for class org.anchoranalysis.core.value.TypedValue: Creates for an double value.
TypedValue(int) - Constructor for class org.anchoranalysis.core.value.TypedValue: Creates for an int value.
TypedValue(String) - Constructor for class org.anchoranalysis.core.value.TypedValue: Creates for a String value.
TypedValue(String, boolean) - Constructor for class org.anchoranalysis.core.value.TypedValue: Creates a new TypedValue instance.

U

UnaryIntOperator - Interface in org.anchoranalysis.core.functional.unchecked: Like a UnaryOperator but uses the primitive type int.
UnaryWithChannelBase - Class in org.anchoranalysis.plugin.image.bean.object.provider: Base class for ObjectCollectionProviderUnary that also requires a Channel.
UnaryWithChannelBase() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.UnaryWithChannelBase
UnaryWithMaskBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider.mask: A base class for a ChannelProviderUnary which also uses a binary mask.
UnaryWithMaskBase() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.mask.UnaryWithMaskBase
UnaryWithObjectsBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider: An abstract base class for creating a channel from an existing channel and a collection of objects.
UnaryWithObjectsBase() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.UnaryWithObjectsBase
UnaryWithValueBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider: A ChannelProviderUnary which has a scalar value field.
UnaryWithValueBase() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.UnaryWithValueBase
unassigned(boolean) - Method in interface org.anchoranalysis.annotation.io.assignment.Assignment: The items that are not paired for a particular set.
unassigned(boolean) - Method in class org.anchoranalysis.annotation.io.assignment.ObjectVoxelIntersection
unassigned(boolean) - Method in class org.anchoranalysis.annotation.io.assignment.OverlappingObjects
unconvertedDataType() - Method in class org.anchoranalysis.image.core.stack.DisplayStack: The data-type of the underlying voxels before they are converted to 8-bit.
underlyingBytes() - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer: THe underlying bytes that describe the voxels.
uniform3D(int, int) - Static method in class org.anchoranalysis.spatial.box.BoundingBoxFactory: Short-hand factory method for creating a 3D bounding-box, where a coordinate is identical in each dimension.
uniformHeight() - Method in interface org.anchoranalysis.image.core.dimensions.size.suggestion.ImageSizeSuggestion: A specific height, if one exists, to which each image should be resized.
uniformScaleFactor() - Method in interface org.anchoranalysis.image.core.dimensions.size.suggestion.ImageSizeSuggestion: A ScaleFactor, if one exists, that is applied uniformally, independent of the Extent to be scaled.
uniformWidth() - Method in interface org.anchoranalysis.image.core.dimensions.size.suggestion.ImageSizeSuggestion: A specific width, if one exists, to which each image should be resized.
union() - Method in class org.anchoranalysis.spatial.box.BoundingBox: For performing a union between this bounding-box and another.
uniqueIdentifierFor(FeatureInputPairObjects) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
uniqueIdentifierFor(FeatureInputSingleObject) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.EachObjectIndependently
uniqueIdentifierFor(T) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.CombineObjectsForFeatures: Generates a unique identifier for a particular input.
uniquelyIdentifyAllProperties() - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations: Creates a string that uniquely identifies all properties in the bean, in a compact format.
uniqueName() - Method in interface org.anchoranalysis.bean.GenerateUniqueParameterization: A string describing this class and all its parameterization.
uniqueName() - Method in class org.anchoranalysis.bean.shared.relation.RelationBean
uniqueName() - Method in class org.anchoranalysis.bean.shared.relation.threshold.RelationToConstant
uniqueName() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryVoxelsBase
unitArea() - Method in class org.anchoranalysis.image.core.dimensions.Resolution: Multiplying the X- and Y- resolution values together.
unitConvert() - Method in class org.anchoranalysis.image.core.dimensions.Dimensions: Converts voxel-scaled measurements to/from physical units.
unitConvert() - Method in class org.anchoranalysis.image.core.dimensions.Resolution: Converts voxelized measurements to/from physical units.
UnitConverter - Class in org.anchoranalysis.image.core.dimensions: Converts from voxelized units to different physical measurements of area / volume / distance.
UnitConverter(Resolution) - Constructor for class org.anchoranalysis.image.core.dimensions.UnitConverter: Creates a new UnitConverter instance.
unitConvertOptional() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeBase: Gets an optional UnitConverter based on the image resolution.
UnitsWithinRange<T> - Class in org.anchoranalysis.plugin.image.feature.bean.physical: Checks if a value lies within a range defined by units (a minimum and maximum boundary)
UnitsWithinRange() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.physical.UnitsWithinRange
UnitValueArea - Class in org.anchoranalysis.image.bean.unitvalue.extent.area: A base class for a value that describes an area measurement on the image.
UnitValueArea() - Constructor for class org.anchoranalysis.image.bean.unitvalue.extent.area.UnitValueArea
UnitValueDistance - Class in org.anchoranalysis.image.bean.unitvalue.distance: Base class for methods to specify a distance along a vector in an image.
UnitValueDistance() - Constructor for class org.anchoranalysis.image.bean.unitvalue.distance.UnitValueDistance
UnitValueException - Exception Class in org.anchoranalysis.image.bean.nonbean: When a failure occurs converting from one type of units to another.
UnitValueException(Exception) - Constructor for exception class org.anchoranalysis.image.bean.nonbean.UnitValueException: Create with a cause.
UnitValueException(String) - Constructor for exception class org.anchoranalysis.image.bean.nonbean.UnitValueException: Create with a message.
UnitValueExtent - Class in org.anchoranalysis.image.bean.unitvalue.extent: A base class for a value that describes an area or volume measurement, which can then be resolved to a number of voxels.
UnitValueExtent() - Constructor for class org.anchoranalysis.image.bean.unitvalue.extent.UnitValueExtent
UnitValueVolume - Class in org.anchoranalysis.image.bean.unitvalue.extent.volume: A base class for a value that describes a volume measurement on the image.
UnitValueVolume() - Constructor for class org.anchoranalysis.image.bean.unitvalue.extent.volume.UnitValueVolume
unitVolume() - Method in class org.anchoranalysis.image.core.dimensions.Resolution: Multiplying the X- and Y- and Z- resolution values together.
UnsignedBuffer - Class in org.anchoranalysis.image.voxel.buffer.primitive: Base class for buffers that represent an unsigned-type in the signed-equivalent-type NIO Buffer.
UnsignedBuffer(Buffer) - Constructor for class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer: Creates a new UnsignedBuffer instance.
UnsignedBufferAsInt - Class in org.anchoranalysis.image.voxel.buffer.primitive: A UnsignedBuffer that exposes its internal types as int.
UnsignedBufferAsInt(Buffer) - Constructor for class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBufferAsInt: Construct with a delegate buffer.
unsignedByteArray(byte[]) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferWrap: Wraps an existing array (encoding unsigned bytes as a signed array) as a voxel-buffer.
unsignedByteBuffer(UnsignedByteBuffer) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferWrap: Wraps an unsigned-byte buffer into a voxel-buffer.
UnsignedByteBuffer - Class in org.anchoranalysis.image.voxel.buffer.primitive: Wraps a ByteBuffer but automatically performs conversion to int.
UnsignedByteFromFloat - Class in org.anchoranalysis.io.bioformats.copyconvert.tobyte: Converts a ByteBuffer encoding a float type to unsigned byte type, as expected in an Anchor VoxelBuffer.
UnsignedByteFromFloat() - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromFloat
unsignedByteFromMat(Mat, Extent) - Static method in class org.anchoranalysis.plugin.opencv.convert.VoxelBufferFromMat: Converts a Mat to a VoxelBuffer with voxel data-type UnsignedByteBuffer.
UnsignedByteFromUnsignedByte - Class in org.anchoranalysis.io.bioformats.copyconvert.tobyte: Like ToUnsignedByte and provides common functionality when converting to an unsigned byte.
UnsignedByteFromUnsignedByte() - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedByte
UnsignedByteFromUnsignedByteInterleaving - Class in org.anchoranalysis.io.bioformats.copyconvert.tobyte: Converts a ByteBuffer encoding unsigned bytes (with interleaving) to unsigned byte type, as expected in an Anchor VoxelBuffer.
UnsignedByteFromUnsignedByteInterleaving() - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedByteInterleaving
UnsignedByteFromUnsignedByteNoInterleaving - Class in org.anchoranalysis.io.bioformats.copyconvert.tobyte: Converts a ByteBuffer encoding unsigned bytes (no interleaving) to unsigned byte type, as expected in an Anchor VoxelBuffer.
UnsignedByteFromUnsignedByteNoInterleaving() - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedByteNoInterleaving
UnsignedByteFromUnsignedByteNoInterleavingScale - Class in org.anchoranalysis.io.bioformats.copyconvert.tobyte: Converts data of type unsigned byte to unsigned byte.
UnsignedByteFromUnsignedByteNoInterleavingScale(int) - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedByteNoInterleavingScale: Create with a number of effective-bits.
UnsignedByteFromUnsignedInt - Class in org.anchoranalysis.io.bioformats.copyconvert.tobyte: Converts data of type unsigned int to unsigned byte.
UnsignedByteFromUnsignedInt(int) - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedInt: Create with a number of effective-bits.
UnsignedByteFromUnsignedShort - Class in org.anchoranalysis.io.bioformats.copyconvert.tobyte: Converts data of type unsigned short to unsigned byte.
UnsignedByteFromUnsignedShort(int) - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedShort: Create with a number of effective-bits.
unsignedByteRaw(ByteBuffer) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferWrap: Wraps an unsigned-byte buffer (represented by a NIO signed-buffer) into a voxel-buffer.
unsignedByteToInt(byte) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.PrimitiveConverter: Converts an unsigned-byte value to a signed int.
unsignedByteToShort(byte) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.PrimitiveConverter: Converts an unsigned-byte value to a signed short.
UnsignedByteVoxelType - Class in org.anchoranalysis.image.voxel.datatype: A 8-bit voxel data-type representing unsigned-byte numbers.
unsignedIntArray(int[]) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferWrap: Wraps an unsigned-int buffer into a voxel-buffer.
unsignedIntBuffer(UnsignedIntBuffer) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferWrap: Wraps an unsigned-int buffer (represented by a NIO signed-buffer) into a voxel-buffer.
UnsignedIntBuffer - Class in org.anchoranalysis.image.voxel.buffer.primitive: Wraps an IntBuffer but automatically performs conversion to long.
UnsignedIntFromUnsignedInt - Class in org.anchoranalysis.io.bioformats.copyconvert.toint: Convert to an unsigned int buffer, given an unsigned int source buffer.
UnsignedIntFromUnsignedInt() - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.toint.UnsignedIntFromUnsignedInt
unsignedIntToInt(int) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.PrimitiveConverter: Converts an unsigned-int value to a signed int.
unsignedIntToLong(int) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.PrimitiveConverter: Converts an unsigned-int value to a signed long.
unsignedIntToShort(int) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.PrimitiveConverter: Converts an unsigned-int value to a signed int.
UnsignedIntVoxelType - Class in org.anchoranalysis.image.voxel.datatype: A 32-bit voxel data-type representing unsigned-int numbers.
unsignedShortArray(short[]) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferWrap: Wraps an existing array (encoding unsigned shorts as a signed array) as a voxel-buffer.
unsignedShortBuffer(UnsignedShortBuffer) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferWrap: Wraps an unsigned-short buffer into a voxel-buffer.
UnsignedShortBuffer - Class in org.anchoranalysis.image.voxel.buffer.primitive: Wraps a ShortBuffer but automatically performs conversion to int.
unsignedShortFromMat(Mat, Extent) - Static method in class org.anchoranalysis.plugin.opencv.convert.VoxelBufferFromMat: Converts a Mat to a VoxelBuffer with voxel data-type UnsignedShortBuffer.
UnsignedShortFromSignedShort - Class in org.anchoranalysis.io.bioformats.copyconvert.toshort: Convert to an unsigned short buffer, given an signed short source buffer.
UnsignedShortFromSignedShort() - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.toshort.UnsignedShortFromSignedShort
UnsignedShortFromUnsignedShort - Class in org.anchoranalysis.io.bioformats.copyconvert.toshort: Convert to an unsigned short buffer, given an unsigned short source buffer.
UnsignedShortFromUnsignedShort() - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.toshort.UnsignedShortFromUnsignedShort
unsignedShortRaw(ShortBuffer) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferWrap: Wraps an unsigned-short buffer (represented by a NIO signed-buffer) into a voxel-buffer.
unsignedShortToInt(short) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.PrimitiveConverter: Converts an unsigned-short value to a signed int.
UnsignedShortVoxelType - Class in org.anchoranalysis.image.voxel.datatype: A 16-bit voxel data-type representing unsigned-short numbers.
UnsignedVoxelType - Class in org.anchoranalysis.image.voxel.datatype: Base class for voxel-data-types that are unsigned and integral.
UnsignedVoxelType(int, String, long) - Constructor for class org.anchoranalysis.image.voxel.datatype.UnsignedVoxelType: Construct for a particular number of bits, with a unique identifier, and with bounds on the values.
UnsupportedMarkTypeException - Exception Class in org.anchoranalysis.mpp.mark: Exception thrown when an unsupported mark type is encountered.
UnsupportedMarkTypeException(Exception) - Constructor for exception class org.anchoranalysis.mpp.mark.UnsupportedMarkTypeException: Constructs a new UnsupportedMarkTypeException with the specified cause.
UnsupportedMarkTypeException(String) - Constructor for exception class org.anchoranalysis.mpp.mark.UnsupportedMarkTypeException: Constructs a new UnsupportedMarkTypeException with the specified detail message.
untilFirstIntensityEqualTo(BoundedVoxels<UnsignedByteBuffer>, byte) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsEqualTo: Iterates each voxel until a specific intensity value is found.
UpdatableBeforeCondition - Interface in org.anchoranalysis.plugin.image.object.merge.condition: A two-stage process for checking if two ObjectMasks should be merged.
UpdatableMarks - Interface in org.anchoranalysis.mpp.mark: An interface for managing a set of marks that can be updated.
update(Point2d, Point2d, Orientation) - Method in class org.anchoranalysis.mpp.mark.points.RotatableBoundingBox: Updates the bounding box with new dimensions and orientation.
updateAfterMarkChange() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid: Updates internal calculations after a change in the mark's properties.
updateAfterPointsChange() - Method in class org.anchoranalysis.mpp.mark.points.PointList
updateAfterPointsChange() - Method in class org.anchoranalysis.mpp.mark.points.PointListBase: Updates the min and max points after the list of points has changed.
updateAfterPointsChange() - Method in class org.anchoranalysis.mpp.mark.points.Polygon
updateLabeling(double) - Method in class org.anchoranalysis.math.optimization.HungarianAlgorithm: Update labels with the specified slack by adding the slack value for committed workers and by subtracting the slack value for committed jobs.
UpdateMarkSetException - Exception Class in org.anchoranalysis.mpp.mark: Exception thrown when an error occurs while updating a mark set.
UpdateMarkSetException(Exception) - Constructor for exception class org.anchoranalysis.mpp.mark.UpdateMarkSetException: Constructs a new UpdateMarkSetException with the specified cause.
UpdateMarkSetException(String) - Constructor for exception class org.anchoranalysis.mpp.mark.UpdateMarkSetException: Constructs a new UpdateMarkSetException with the specified detail message.
updateshell(double) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse: Updates the shell size and recalculates internal values.
updateSourceObject(ObjectMask, Optional<UnitConverter>) - Method in class org.anchoranalysis.plugin.image.object.merge.condition.AndCondition
updateSourceObject(ObjectMask, Optional<UnitConverter>) - Method in class org.anchoranalysis.plugin.image.object.merge.condition.NeighborhoodCondition
updateSourceObject(ObjectMask, Optional<UnitConverter>) - Method in interface org.anchoranalysis.plugin.image.object.merge.condition.UpdatableBeforeCondition: Updates the source object and performs any necessary pre-computations.
updateSourceObject(ObjectMask, Optional<UnitConverter>) - Method in class org.anchoranalysis.plugin.image.object.merge.condition.WrapAsUpdatable
updateTotal(EnergyMemoList, EnergyStackWithoutParameters) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown: Updates the total energy based on the current state.
UpperLowerQuantileIntensity - Class in org.anchoranalysis.image.core.channel.convert.attached.channel: Converts a Channel to UnsignedByteBuffer by scaling against lower and upper quantiles of the intensity values that appear in it.
UpperLowerQuantileIntensity(double, double) - Constructor for class org.anchoranalysis.image.core.channel.convert.attached.channel.UpperLowerQuantileIntensity: Scale with quantile values for the lower and upper boundaries.
UpperLowerQuantileIntensityFromHistogram - Class in org.anchoranalysis.image.core.channel.convert.attached.histogram: Converts a Channel to UnsignedByteBuffer by scaling against lower and upper quantiles of the intensity values from a corresponding histogram.
UpperLowerQuantileIntensityFromHistogram(double, double) - Constructor for class org.anchoranalysis.image.core.channel.convert.attached.histogram.UpperLowerQuantileIntensityFromHistogram: Scale with quantile values for the lower and upper boundaries - without any scaling factors.
UpperLowerQuantileIntensityFromHistogram(double, double, double, double) - Constructor for class org.anchoranalysis.image.core.channel.convert.attached.histogram.UpperLowerQuantileIntensityFromHistogram: Scale with quantile values for the lower and upper boundaries - with explicit scaling factors.
URL_OUTPUT_OPTIONS - Static variable in class org.anchoranalysis.launcher.AnchorWebsiteLinks: A URL for showing command-line options relating to outputting.
URL_PREDEFIEND_TASKS - Static variable in class org.anchoranalysis.launcher.AnchorWebsiteLinks: A URL for showing predefined tasks that can be used.
usageFooter() - Method in class org.anchoranalysis.launcher.resources.Resources: Footer-message that describes usage.
usageHeader() - Method in class org.anchoranalysis.launcher.resources.Resources: Header-message that describes usage.
useDefault() - Static method in class org.anchoranalysis.launcher.executor.selectparam.SelectParamFactory: Creates a SelectParam that uses the default manager.
UseDefaultManager - Class in org.anchoranalysis.launcher.executor.selectparam: Uses whatever default-manager exists
UseDefaultManager() - Constructor for class org.anchoranalysis.launcher.executor.selectparam.UseDefaultManager
useDetailedLogging() - Method in class org.anchoranalysis.experiment.bean.Experiment: Whether to log in more or less detail.
useDetailedLogging() - Method in class org.anchoranalysis.experiment.bean.io.InputOutputExperiment
useDetailedLogging() - Method in class org.anchoranalysis.experiment.bean.io.OutputExperiment
useElseInstead(int, int) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelRelativeToThreshold: Determines whether to use the alternative calculation method.
useElseInstead(int, int) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.IfGreaterThan
useElseInstead(int, int) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.IfLessThan

V

VALUE_NOT_COMPATIBLE - Static variable in class org.anchoranalysis.image.voxel.datatype.VoxelDataType: A placeholder value for maxValue or minValue if the true maximum or minimum value cannot be expressed as a long.
valueByDimension(int) - Method in class org.anchoranalysis.image.core.dimensions.Resolution: A component of a resolution corresponding to a particular dimension by index.
valueByDimension(int) - Method in class org.anchoranalysis.spatial.box.Extent: The size in the dimension identified by dimensionIndex.
valueByDimension(int) - Method in interface org.anchoranalysis.spatial.point.ReadableTuple3i: A component of a tuple corresponding to a particular dimension by index.
valueByDimension(int) - Method in class org.anchoranalysis.spatial.point.Tuple3d: A component of the tuple corresponding to a particular dimension by index.
valueByDimension(int) - Method in class org.anchoranalysis.spatial.point.Tuple3f: A component of a tuple corresponding to a particular dimension by index.
valueByDimension(int) - Method in class org.anchoranalysis.spatial.point.Tuple3i: A component of a tuple corresponding to a particular dimension by index.
valueByDimension(Axis) - Method in class org.anchoranalysis.image.core.dimensions.Resolution: A component of the tuple corresponding to a particular axis.
valueByDimension(Axis) - Method in class org.anchoranalysis.spatial.box.Extent: The size in the dimension identified by axis.
valueByDimension(Axis) - Method in interface org.anchoranalysis.spatial.point.ReadableTuple3i: A component of a tuple corresponding to a particular axis.
valueByDimension(Axis) - Method in class org.anchoranalysis.spatial.point.Tuple3d: A component of the tuple corresponding to a particular axis.
valueByDimension(Axis) - Method in class org.anchoranalysis.spatial.point.Tuple3f: A component of a tuple corresponding to a particular axis.
valueByDimension(Axis) - Method in class org.anchoranalysis.spatial.point.Tuple3i
valueFor(int, int, int) - Method in interface org.anchoranalysis.test.image.ChannelFixture.IntensityFunction: Calculates the intensity value for given coordinates.
valueFor(FeatureCalculationInput<FeatureInputSingleObject>, ResolvedPart<ObjectCollection, FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjects: Calculates a value based on the input and the intersecting objects.
valueFor(FeatureCalculationInput<FeatureInputSingleObject>, ResolvedPart<ObjectCollection, FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjectsSingleElement
valueFor(FeatureCalculationInput<FeatureInputSingleObject>, ResolvedPart<ObjectCollection, FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.NumberIntersectingObjects
valueFor(Axis, int, int, int) - Static method in class org.anchoranalysis.spatial.axis.AxisConverter: Multiplexes the a value corresponding to a particular axis.
valueFor(Point3i) - Method in interface org.anchoranalysis.test.image.ChannelFixture.IntensityFunction: Calculates the intensity value for a given point.
valueFromFirst(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.image.feature.bean.object.pair.FeatureDeriveFromPair: Calculates the feature value for the first object in the pair.
valueFromMerged(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.image.feature.bean.object.pair.FeatureDeriveFromPair: Calculates the feature value for the merged object from the pair.
valueFromSecond(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.image.feature.bean.object.pair.FeatureDeriveFromPair: Calculates the feature value for the second object in the pair.
valueOf(String) - Static method in enum class org.anchoranalysis.core.format.ImageFileFormat: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.anchoranalysis.core.format.NonImageFileFormat: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.anchoranalysis.image.bean.nonbean.spatial.align.AlignmentOnDimension: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.anchoranalysis.image.core.channel.convert.ConversionPolicy: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.anchoranalysis.image.core.dimensions.OrientationChange: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.anchoranalysis.image.core.dimensions.SpatialUnits.UnitSuffix: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.anchoranalysis.image.feature.calculation.CalculateInputFromPair.Extract: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.anchoranalysis.image.io.stack.output.StackRGBState: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.anchoranalysis.image.voxel.kernel.OutsideKernelPolicy: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.anchoranalysis.plugin.io.naming.interval.DateStyle: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.anchoranalysis.plugin.io.naming.interval.TimeStyle: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.anchoranalysis.spatial.axis.Axis: Returns the enum constant of this class with the specified name.
values() - Method in class org.anchoranalysis.core.collection.StringSetTrie: A view over the values in the set.
values() - Static method in enum class org.anchoranalysis.core.format.ImageFileFormat: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.anchoranalysis.core.format.NonImageFileFormat: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.anchoranalysis.image.bean.nonbean.spatial.align.AlignmentOnDimension: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.anchoranalysis.image.core.channel.convert.ConversionPolicy: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.anchoranalysis.image.core.dimensions.OrientationChange: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.anchoranalysis.image.core.dimensions.SpatialUnits.UnitSuffix: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.anchoranalysis.image.feature.calculation.CalculateInputFromPair.Extract: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Method in class org.anchoranalysis.image.io.channel.input.ChannelMap: All IndexedChannels that exist in the map.
values() - Static method in enum class org.anchoranalysis.image.io.stack.output.StackRGBState: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.anchoranalysis.image.voxel.kernel.OutsideKernelPolicy: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.anchoranalysis.plugin.io.naming.interval.DateStyle: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.anchoranalysis.plugin.io.naming.interval.TimeStyle: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.anchoranalysis.spatial.axis.Axis: Returns an array containing the constants of this enum class, in the order they are declared.
variance() - Method in interface org.anchoranalysis.image.voxel.statistics.VoxelStatistics: The variance of all voxel values.
variance() - Method in class org.anchoranalysis.math.histogram.Histogram: Calculates the variance of the distribution represented by the histogram.
variance() - Method in class org.anchoranalysis.math.statistics.VarianceCalculatorDouble: Calculate the variance, based on the current state of running-sums.
variance() - Method in class org.anchoranalysis.math.statistics.VarianceCalculatorLong: Calculate the variance, based on the current state of running-sums.
Variance - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic: Calculates the variance of all the values in the histogram.
Variance() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Variance
VarianceCalculatorDouble - Class in org.anchoranalysis.math.statistics: Calculates variance efficiently, as successive values are added, using double to store sums internally.
VarianceCalculatorDouble() - Constructor for class org.anchoranalysis.math.statistics.VarianceCalculatorDouble
VarianceCalculatorDouble(double, double, long) - Constructor for class org.anchoranalysis.math.statistics.VarianceCalculatorDouble: Creates a new VarianceCalculatorDouble instance.
VarianceCalculatorLong - Class in org.anchoranalysis.math.statistics: Calculates variance efficiently, as successive values are added, using long to store sums internally.
VarianceCalculatorLong() - Constructor for class org.anchoranalysis.math.statistics.VarianceCalculatorLong
VarianceCalculatorLong(long, long, long) - Constructor for class org.anchoranalysis.math.statistics.VarianceCalculatorLong: Creates a new VarianceCalculatorLong instance.
VarianceFilter2D - Class in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.moments: Applies a 2D variance filter to a channel using ImageJ's RankFilters.
VarianceFilter2D() - Constructor for class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.moments.VarianceFilter2D: Creates a new VarianceFilter2D instance.
Vector3d - Class in org.anchoranalysis.spatial.point: A three-dimensional vector of double values.
Vector3d() - Constructor for class org.anchoranalysis.spatial.point.Vector3d
Vector3d(double, double, double) - Constructor for class org.anchoranalysis.spatial.point.Vector3d: Create with values for each dimension.
Vector3d(Tuple3d) - Constructor for class org.anchoranalysis.spatial.point.Vector3d: Creates with the same values as an existing Tuple3d.
versionFooter() - Method in class org.anchoranalysis.launcher.resources.Resources: Footer-message that accompanies a version message, if it exists.
versionFromMavenProperties() - Method in class org.anchoranalysis.launcher.resources.Resources: Gets the current version of the software by reading a properties-file provided by the Maven build
vertices() - Method in class org.anchoranalysis.core.graph.GraphWithoutPayload: The set of all vertices in the graph.
vertices() - Method in class org.anchoranalysis.core.graph.GraphWithPayload: The set of all vertices in the graph.
verticesAsObjects() - Method in class org.anchoranalysis.plugin.image.object.merge.MergeGraph: Retrieves all vertices in the graph as an ObjectCollection.
VeryBright - Class in org.anchoranalysis.bean.shared.color.scheme: Creates a list by repeating a defined constant list of very bright colors.
VeryBright() - Constructor for class org.anchoranalysis.bean.shared.color.scheme.VeryBright
VisualizeOnBackground - Class in org.anchoranalysis.plugin.mpp.bean.define: Adds a visualization for all binary-masks and object-collections that are added using a particular background
VisualizeOnBackground() - Constructor for class org.anchoranalysis.plugin.mpp.bean.define.VisualizeOnBackground
volume(int) - Method in class org.anchoranalysis.mpp.mark.conic.Circle
volume(int) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
volume(int) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
volume(int) - Method in class org.anchoranalysis.mpp.mark.conic.Sphere
volume(int) - Method in class org.anchoranalysis.mpp.mark.Mark: Calculates the volume of a specific region of the mark.
volume(int) - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
volume(int) - Method in class org.anchoranalysis.mpp.mark.points.PointList
volume(int) - Method in class org.anchoranalysis.mpp.mark.points.Polygon
volume(int) - Method in class org.anchoranalysis.mpp.mark.points.PolygonCurve
volume(int) - Method in class org.anchoranalysis.mpp.mark.points.RotatableBoundingBox
Volume<T> - Class in org.anchoranalysis.plugin.image.feature.bean.dimensions: Calculates the volume (x, y and z dimensions) of the scene from the dimensions
Volume() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.dimensions.Volume
VolumePhysical - Class in org.anchoranalysis.image.bean.unitvalue.extent.volume: Volume expressed in cubic meters, or units thereof.
VolumePhysical() - Constructor for class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumePhysical
VolumeVoxels - Class in org.anchoranalysis.image.bean.unitvalue.extent.volume: Volume expressed in voxels.
VolumeVoxels() - Constructor for class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumeVoxels
VolumeVoxels(double) - Constructor for class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumeVoxels: Creates a new VolumeVoxels instance.
voxel(int, int) - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter: Gets the value of one particular voxel.
voxel(int, int, int) - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter: Gets the value of one particular voxel.
voxel(ReadableTuple3i) - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter: Gets the value of one particular voxel.
VoxelBuffer<T> - Class in org.anchoranalysis.image.voxel.buffer: A buffer of voxel-values, usually corresponding to a single z-slice in Voxels.
VoxelBuffer() - Constructor for class org.anchoranalysis.image.voxel.buffer.VoxelBuffer
VoxelBufferFactory - Class in org.anchoranalysis.image.voxel.buffer: Creating voxel-buffers and arrays of voxel-buffers of various types.
VoxelBufferFromMat - Class in org.anchoranalysis.plugin.opencv.convert: Converts a Mat to a VoxelBuffer.
VoxelBufferUnsigned<T> - Class in org.anchoranalysis.image.voxel.buffer: A parent class for VoxelBuffer that accepts unsigned-buffers and implements some common operations.
VoxelBufferUnsigned(T) - Constructor for class org.anchoranalysis.image.voxel.buffer.VoxelBufferUnsigned: Creates a new VoxelBufferUnsigned instance.
VoxelBufferWrap - Class in org.anchoranalysis.image.voxel.buffer: Wraps arrays and buffers of primitive-types into VoxelBuffer.
VoxelDataType - Class in org.anchoranalysis.image.voxel.datatype: The type of data that a single voxel represents in an image or related buffer.
VoxelDataType(int, String, long, long) - Constructor for class org.anchoranalysis.image.voxel.datatype.VoxelDataType: Creates a new VoxelDataType instance.
VoxelDataTypeFactoryMultiplexer<T> - Class in org.anchoranalysis.image.voxel.datatype: Multiplexes between factories for the various VoxelDataTypes.
VoxelDataTypeFactoryMultiplexer(T, T, T, T) - Constructor for class org.anchoranalysis.image.voxel.datatype.VoxelDataTypeFactoryMultiplexer
voxelized() - Method in class org.anchoranalysis.mpp.mark.voxelized.memo.VoxelizedMarkMemo: Gets the voxelized representation of the mark.
VoxelizedMark - Interface in org.anchoranalysis.mpp.mark.voxelized: A voxelized representation of a Mark i.e. a mark turned into voxels.
VoxelizedMarkFactory - Class in org.anchoranalysis.mpp.mark.voxelized: Factory class for creating VoxelizedMarkHistogram instances.
VoxelizedMarkMemo - Class in org.anchoranalysis.mpp.mark.voxelized.memo: Memoization of retrieving a VoxelizedMark from a mark.
VoxelizedMarkMemo(Mark, EnergyStackWithoutParameters, RegionMap) - Constructor for class org.anchoranalysis.mpp.mark.voxelized.memo.VoxelizedMarkMemo: Creates a new VoxelizedMarkMemo.
VoxelizedMarkMemoFactory - Class in org.anchoranalysis.mpp.mark.voxelized.memo: Factory class for creating VoxelizedMarkMemo instances.
VoxelPartition<T> - Interface in org.anchoranalysis.mpp.index: A partition of voxel values by slice.
VoxelPartitionFactory<T> - Interface in org.anchoranalysis.mpp.index.factory: A factory for creating VoxelPartition instances.
VoxelPartitionHistogram - Class in org.anchoranalysis.mpp.index: A voxel partition implementation using histograms to represent voxel value distributions.
VoxelPartitionHistogram(int, Supplier<Histogram>) - Constructor for class org.anchoranalysis.mpp.index.VoxelPartitionHistogram: Constructs a VoxelPartitionHistogram with a specified number of slices.
VoxelPartitonFactoryHistogram - Class in org.anchoranalysis.mpp.index.factory: A factory for creating VoxelPartition instances that use Histograms as parts.
VoxelPartitonFactoryHistogram() - Constructor for class org.anchoranalysis.mpp.index.factory.VoxelPartitonFactoryHistogram
VoxelPattern - Interface in org.anchoranalysis.test.image.object: Defines a pattern of voxels in a 3D space.
VoxelPhysicalSize<T> - Class in org.anchoranalysis.plugin.image.feature.bean.dimensions: The physical size of a pixel in a specific dimension.
VoxelPhysicalSize() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.dimensions.VoxelPhysicalSize
voxels() - Method in class org.anchoranalysis.image.core.channel.Channel: The underlying voxels in the channel.
voxels() - Method in class org.anchoranalysis.image.core.mask.Mask: The underlying voxels in the mask.
voxels() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels: Voxels that should only have two intensity-values (representing on and off states).
voxels() - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: Voxel-data that fits inside the bounding-box (its extent is invariant with the extent of the bounding-box).
voxels() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: The underlying voxel memory buffers for the object-mask, exposed via Voxels.
voxels() - Method in interface org.anchoranalysis.mpp.mark.voxelized.VoxelizedMark: Gets the voxel representation of the mark.
voxels() - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels: The voxels containing encoded information.
Voxels<T> - Class in org.anchoranalysis.image.voxel: A box (3-dimensions) with voxel-data.
Voxels(SliceBufferIndex<T>, VoxelsFactoryTypeBound<T>, VoxelsArithmetic) - Constructor for class org.anchoranalysis.image.voxel.Voxels: Creates a new Voxels instance.
VoxelsArithmetic - Interface in org.anchoranalysis.image.voxel.arithmetic: Allows manipulation of voxel intensities via arithmetic operations.
VoxelsArithmeticFactory - Class in org.anchoranalysis.image.voxel.arithmetic: Creates VoxelsArithmetic for buffers of different types.
VoxelsAssigner - Interface in org.anchoranalysis.image.voxel.assigner: Assigns values to some or all voxels.
VoxelsAssignerFactory - Class in org.anchoranalysis.image.voxel.assigner: Creates VoxelsAssigner for buffers of different types.
VoxelsConverter<T> - Class in org.anchoranalysis.image.voxel.convert: Converts voxels from one data-type to another.
VoxelsConverter() - Constructor for class org.anchoranalysis.image.voxel.convert.VoxelsConverter
VoxelsConverterMulti - Class in org.anchoranalysis.image.voxel.convert: Converts a channel from one voxel data-type to one of multiple other types.
VoxelsConverterMulti() - Constructor for class org.anchoranalysis.image.voxel.convert.VoxelsConverterMulti
VoxelScore - Class in org.anchoranalysis.image.feature.bean: Calculates a per-voxel score.
VoxelScore() - Constructor for class org.anchoranalysis.image.feature.bean.VoxelScore
voxelsEqualTo(int) - Method in class org.anchoranalysis.image.core.channel.Channel: Operations on whether particular voxels are equal to a particular value.
voxelsEqualTo(int) - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter: Operations on whether particular voxels are equal to a particular value.
VoxelsExtracter<T> - Interface in org.anchoranalysis.image.voxel.extracter: Provides methods to read/copy/duplicate regions of voxels.
VoxelsExtracterFactory - Class in org.anchoranalysis.image.voxel.extracter: Creates VoxelsExtracter corresponding to Voxels of differing data-type.
VoxelsFactory - Class in org.anchoranalysis.image.voxel.factory: Creates VoxelsUntyped and provides a singleton location for implementations of VoxelsFactoryTypeBound for different types.
VoxelsFactoryTypeBound<T> - Interface in org.anchoranalysis.image.voxel.factory: A factory for creating voxels with a particular buffer-type.
VoxelsFloat - Class in org.anchoranalysis.image.voxel: Implementation of Voxels whose voxels are of type float.
VoxelsFloat(SliceBufferIndex<FloatBuffer>) - Constructor for class org.anchoranalysis.image.voxel.VoxelsFloat: Create from a buffer, indexed by slice.
voxelsGreaterThan(int) - Method in class org.anchoranalysis.image.core.channel.Channel: Operations on whether particular voxels are greater than a threshold (but not equal to).
voxelsGreaterThan(int) - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter: Operations on whether particular voxels are greater than a threshold (but not equal to).
voxelsMaximumIntensityProjection() - Method in interface org.anchoranalysis.mpp.mark.voxelized.VoxelizedMark: Gets the maximum intensity projection of the voxelized mark.
voxelsOff() - Method in class org.anchoranalysis.image.core.mask.Mask: Operations on whether particular voxels are off.
voxelsOff() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Provides a VoxelsPredicate that finds or counts all off voxels in the object-mask.
voxelsOn() - Method in class org.anchoranalysis.image.core.mask.Mask: Operations on whether particular voxels are on.
voxelsOn() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Provides a VoxelsPredicate that finds or counts all on voxels in the object-mask.
VoxelsPredicate - Interface in org.anchoranalysis.image.voxel.extracter.predicate: Methods to find or count voxels that satisfy a predicate.
voxelsResizer() - Method in class org.anchoranalysis.image.bean.interpolator.Interpolator: Memoizes a call to Interpolator.createVoxelsResizer().
VoxelsResizer - Class in org.anchoranalysis.image.voxel.resizer: Copies voxels while performing interpolation.
VoxelsResizer() - Constructor for class org.anchoranalysis.image.voxel.resizer.VoxelsResizer
VoxelsResizerExecutionTime - Class in org.anchoranalysis.image.voxel.resizer: Calls another VoxelsResizer recording each resize call via a ExecutionTimeRecorder.
VoxelsResizerExecutionTime(VoxelsResizer, ExecutionTimeRecorder, String) - Constructor for class org.anchoranalysis.image.voxel.resizer.VoxelsResizerExecutionTime: Creates with an VoxelsResizer and ExecutionTimeRecorder.
VoxelsResizerFactory - Class in org.anchoranalysis.image.voxel.resizer: Creates instances of VoxelsResizer to match particular circumstances.
VoxelsResizerImageJ - Class in org.anchoranalysis.io.imagej.resizer: Resizes with linear interpolation as implemented in ImageJ.
VoxelsResizerImageJ() - Constructor for class org.anchoranalysis.io.imagej.resizer.VoxelsResizerImageJ
VoxelsResizerImgLib2 - Class in org.anchoranalysis.image.voxel.resizer: Performs resizing of VoxelBuffers using ImgLib2's interpolation.
VoxelsResizerImgLib2(InterpolatorFactory<UnsignedByteType, RandomAccessible<UnsignedByteType>>, InterpolatorFactory<UnsignedShortType, RandomAccessible<UnsignedShortType>>, InterpolatorFactory<FloatType, RandomAccessible<FloatType>>) - Constructor for class org.anchoranalysis.image.voxel.resizer.VoxelsResizerImgLib2
VoxelsResizerNone - Class in org.anchoranalysis.image.voxel.resizer: Doesn't do any interpolation, just copies a single value for each voxel.
VoxelsResizerNone() - Constructor for class org.anchoranalysis.image.voxel.resizer.VoxelsResizerNone
VoxelsResizerOpenCV - Class in org.anchoranalysis.plugin.opencv.resizer: Resizes VoxelBuffers using OpenCV's cv2.resize function.
VoxelsResizerOpenCV() - Constructor for class org.anchoranalysis.plugin.opencv.resizer.VoxelsResizerOpenCV
voxelsSum - Variable in class org.anchoranalysis.image.voxel.projection.CountedProjectableBuffer: Accumulates the sum of voxel values.
VoxelStatistics - Interface in org.anchoranalysis.image.voxel.statistics: Allows retrieval of statistics about voxel values.
VoxelStatisticsCombined - Class in org.anchoranalysis.image.voxel.statistics: Aggregates statistics of a list of VoxelStatistics as if they were one.
VoxelStatisticsCombined() - Constructor for class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsCombined
VoxelStatisticsFromHistogram - Class in org.anchoranalysis.image.voxel.statistics: Calculates statistics from a Histogram of voxel intensities.
VoxelStatisticsFromHistogram(Histogram) - Constructor for class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsFromHistogram: Creates a new VoxelStatisticsFromHistogram instance.
VoxelsThresholder - Class in org.anchoranalysis.image.voxel.thresholder: Performs a thresholding operation on voxels.
VoxelsUnsignedByte - Class in org.anchoranalysis.image.voxel: Implementation of Voxels whose voxels are of type unsigned byte (8-bit).
VoxelsUnsignedByte(SliceBufferIndex<UnsignedByteBuffer>) - Constructor for class org.anchoranalysis.image.voxel.VoxelsUnsignedByte: Create from a buffer, indexed by slice.
VoxelsUnsignedInt - Class in org.anchoranalysis.image.voxel: Implementation of Voxels whose voxels are of type unsigned int (32-bit).
VoxelsUnsignedInt(SliceBufferIndex<UnsignedIntBuffer>) - Constructor for class org.anchoranalysis.image.voxel.VoxelsUnsignedInt: Create from a buffer, indexed by slice.
VoxelsUnsignedShort - Class in org.anchoranalysis.image.voxel: Implementation of Voxels whose voxels are of type unsigned short (16-bit).
VoxelsUnsignedShort(SliceBufferIndex<UnsignedShortBuffer>) - Constructor for class org.anchoranalysis.image.voxel.VoxelsUnsignedShort: Create from a buffer, indexed by slice.
VoxelsUntyped - Class in org.anchoranalysis.image.voxel: Stores memory buffers representing image voxels, without explicit typing of buffers.
VoxelsUntyped(Voxels<?>) - Constructor for class org.anchoranalysis.image.voxel.VoxelsUntyped: Creates to wrap a Voxels of unspecified type.
voxelsWithMinMaxIntensity() - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter: Finds the minimum-value and maximum of any voxel.
voxelWithMaxIntensity() - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter: Finds the maximum-value of any voxel and rounding up (ceiling) to the nearest long.
voxelWithMinIntensity() - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter: Finds the minimum-value of any voxel and rounding down (floor) to the nearest long.

W

walk(UnsignedByteBuffer, BufferRetriever) - Method in class org.anchoranalysis.image.voxel.iterator.neighbor.kernel.WalkPredicate: Do any neighboring voxels in any direction satisfy the predicate?
walk(UnsignedByteBuffer, BufferRetriever) - Method in class org.anchoranalysis.image.voxel.iterator.neighbor.kernel.WalkRunnable: Walks in X and Y direction, and Z direction if enabled.
WalkPredicate - Class in org.anchoranalysis.image.voxel.iterator.neighbor.kernel: Walks in X, Y and Z directions from a point, test a NeighborPredicate to determine if a neighbor satisfies conditions.
WalkPredicate(KernelPointCursor, NeighborPredicate, boolean) - Constructor for class org.anchoranalysis.image.voxel.iterator.neighbor.kernel.WalkPredicate: Creates a new WalkPredicate instance.
WalkRunnable - Class in org.anchoranalysis.image.voxel.iterator.neighbor.kernel: Walks in X, Y and Z directions from a point, executing a Runnable if the neighbor satisfies conditions.
WalkRunnable(KernelPointCursor, Predicate<Point3i>, Runnable) - Constructor for class org.anchoranalysis.image.voxel.iterator.neighbor.kernel.WalkRunnable: Creates a new WalkRunnable instance.
WatershedEncoding - Class in org.anchoranalysis.plugin.image.segment.watershed.encoding: Encodes watershed-related information in an integer range.
WatershedEncoding() - Constructor for class org.anchoranalysis.plugin.image.segment.watershed.encoding.WatershedEncoding
WatershedYeong - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong: A 'rainfall' watershed algorithm
WatershedYeong() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong.WatershedYeong
weightWidthDescription() - Method in class org.anchoranalysis.annotation.io.bean.AnnotatorStrategy: The degree as to how lengthy the labels from AnnotatorStrategy.annotationLabelFor(ProvidesStackInput, OperationContext) can be.
weightWidthDescription() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.ImageLabelStrategy
weightWidthDescription() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy
width() - Method in class org.anchoranalysis.image.bean.spatial.arrange.fill.ExtentToArrange: The size in the X-dimension.
width() - Static method in class org.anchoranalysis.test.image.MaskFixture: The **width** of the mask that will be created.
with(Feature<T>, Logger) - Static method in class org.anchoranalysis.feature.session.FeatureSession: Starts a feature-session for a single feature.
with(Feature<T>, FeatureInitialization, SharedFeatures, Logger) - Static method in class org.anchoranalysis.feature.session.FeatureSession: Starts a feature-session for a single feature, with specific initialization.
with(Feature<T>, SharedFeatures, Logger) - Static method in class org.anchoranalysis.feature.session.FeatureSession: Starts a feature-session for a single feature, with default initialization.
with(FeatureList<T>, Logger) - Static method in class org.anchoranalysis.feature.session.FeatureSession: Starts a feature-session for a list of features, with default initialization.
with(FeatureList<T>, FeatureInitialization, Optional<SharedFeatures>, Logger, BoundReplaceStrategy<T, ? extends ReplaceStrategy<T>>) - Static method in class org.anchoranalysis.feature.session.FeatureSession: Starts a feature-session for a list of features, with particular initialization, and a replaceStrategy.
with(FeatureList<T>, FeatureInitialization, SharedFeatures, Logger) - Static method in class org.anchoranalysis.feature.session.FeatureSession: Starts a feature-session for a list of features, with particular initialization.
with(BoundingBox) - Method in class org.anchoranalysis.spatial.box.BoundingBoxIntersection: Finds the intersection with another bounding-box, if it exists.
with(BoundingBox) - Method in class org.anchoranalysis.spatial.box.BoundingBoxUnion: Performs a union with another box (immutably).
withBackgroundAndColors(DrawObject, DisplayStack, ColorIndex) - Static method in class org.anchoranalysis.image.io.object.output.rgb.DrawObjectsGenerator: Creates a generator that draws an object in a particular way with particular colors and background.
withBuffer(Optional<ObjectMask>, Voxels<T>, ProcessBufferUnary<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsObjectMaskOptional: Iterate over each voxel (or optionally only on object-mask) with one associated buffer.
withBuffer(Mask, Voxels<T>, ProcessBufferUnary<T>) - Static method in class org.anchoranalysis.image.core.mask.IterateVoxelsMask: Iterate over each voxel in a mask - with an associated buffer for each slice from a voxel-bo
withBuffer(ObjectMask, Voxels<T>, ProcessBufferUnary<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsObjectMask: Iterate over each voxel in an object-mask - with one associated buffer for each slice from Voxels.
withBuffer(Voxels<T>, ProcessBufferUnary<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll: Iterate over each voxel - with one associated buffer for each slice.
withBuffer(BoundingBox, Voxels<T>, ProcessBufferUnary<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsBoundingBox: Iterate over each voxel in a bounding-box - with one associated buffer for each slice
withCalculateLevel(Histogram, CalculateLevel) - Static method in class org.anchoranalysis.plugin.image.intensity.HistogramThresholder: Retains the portion of the histogram greater or equal to the calculated-level.
WithChannelBase - Class in org.anchoranalysis.plugin.image.bean.object.provider: Base class for ObjectCollectionProviders that create objects from a Channel.
WithChannelBase() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.WithChannelBase
WithConfidence<T> - Class in org.anchoranalysis.image.inference.segment: Wraps an element with a confidence-score.
WithConfidence(T, double) - Constructor for class org.anchoranalysis.image.inference.segment.WithConfidence: Creates a new WithConfidence instance.
WithContainerBase - Class in org.anchoranalysis.plugin.image.bean.object.provider: Base class for ObjectCollectionProviderUnary that take an optional objectsContainer bean-field.
WithContainerBase() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.WithContainerBase
withCursor(BinaryVoxels<UnsignedByteBuffer>, KernelApplicationParameters, ProcessKernelPointCursor) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll: Iterate over each voxel using a KernelPointCursor.
withCursor(BinaryVoxels<UnsignedByteBuffer>, BoundingBox, KernelApplicationParameters, ProcessKernelPointCursor) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsBoundingBox: Iterate over each voxel in a bounding-box using a KernelPointCursor.
withCursorUntil(BinaryVoxels<UnsignedByteBuffer>, BoundingBox, KernelApplicationParameters, PredicateKernelPointCursor) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsBoundingBox: Iterate over each voxel in a bounding-box using a KernelPointCursor until a predicate returns true..
WithDimensionsBase - Class in org.anchoranalysis.plugin.image.bean.object.provider: Base class for ObjectCollectionProviderUnary classes that require dimensions to be specified.
WithDimensionsBase() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.WithDimensionsBase
WithFilterBase - Class in org.anchoranalysis.plugin.imagej.bean.channel.provider: A base class for applying ImageJ rank filters to channels.
WithFilterBase(int) - Constructor for class org.anchoranalysis.plugin.imagej.bean.channel.provider.WithFilterBase: Creates a new WithFilterBase instance.
within(Optional<ObjectMask>, Extent, ProcessVoxelNeighborAbsolute<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborFactory: Creates to process neighbors that must lie within either an object-mask or an extent (as a fallback).
withinExtent(ProcessVoxelNeighborAbsoluteWithSlidingBuffer<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborFactory: Creates to process neighbors that must lie within an extent.
withinMask(ObjectMask, ProcessChangedPointAbsoluteMasked<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborFactory: Creates to process neighbors that must lie within an ObjectMask.
withinMask(ObjectMask, ProcessVoxelNeighborAbsolute<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborFactory: Creates to process neighbors that must lie within an ObjectMask.
withInputs(List<S>) - Method in class org.anchoranalysis.io.input.InputsWithDirectory: Changes the inputs, but preserves the directory.
withinRangeValue(double, FeatureCalculationInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.CompareWithRange
withinRangeValue(double, FeatureCalculationInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.CompareWithRangeFeature
withinRangeValue(double, FeatureCalculationInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.IfConditionWithinRange
withinRangeValue(double, FeatureCalculationInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.IfOutsideRange
withinRangeValue(double, FeatureCalculationInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareBase: Calculates the value to return if the input is within the range.
withInside(BoundingBox, Extent) - Method in class org.anchoranalysis.spatial.box.BoundingBoxIntersection: Finds the intersection and clamp to a containing extent.
withLabel(String) - Method in class org.anchoranalysis.core.log.Divider: Creates a line of repeated dashes with a centered label of text.
withLogger(Logger) - Static method in class org.anchoranalysis.test.image.InputOutputContextFixture: Creates an InputOutputContext with a specified logger.
withMatchingPoints(BoundingBox, Predicate<Point3i>, ProcessPoint) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsBoundingBox: Iterate over each voxel in a bounding-box that matches a predicate.
WithOptionalDimensionsBase - Class in org.anchoranalysis.plugin.image.bean.object.provider: Base class for ObjectCollectionProviderUnary classes that offer an optional means to specify dimensions.
WithOptionalDimensionsBase() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.WithOptionalDimensionsBase
WithoutGrouping - Class in org.anchoranalysis.io.input.bean.grouper: Avoids grouping of inputs, effectively processing all inputs as one large group.
WithoutGrouping() - Constructor for class org.anchoranalysis.io.input.bean.grouper.WithoutGrouping
withoutLabel() - Method in class org.anchoranalysis.core.log.Divider: Creates a line of repeated dashes.
withoutOrder(OutputPatternStringSuffix) - Method in class org.anchoranalysis.io.generator.sequence.OutputSequenceFactory: Writes elements (indexed by strings) to directory, without any order in the sequence.
withoutOrderCurrentDirectory(String) - Method in class org.anchoranalysis.io.generator.sequence.OutputSequenceFactory: Writes elements (indexed by strings) to the current directory, without any order in the sequence.
withoutOrderCurrentDirectory(String, OutputterChecked) - Method in class org.anchoranalysis.image.io.stack.output.OutputSequenceStackFactory: Creates a sequence of stacks in the current context's directory that has no pattern.
withoutOrderSubset(NamedProvider<Stack>, String, boolean, OutputterChecked) - Method in class org.anchoranalysis.image.io.stack.output.OutputSequenceStackFactory: Writes all or a subset from a set of named-stacks to a directory.
WithoutOutputNameStyle - Class in org.anchoranalysis.io.output.namestyle: Avoids including an output-name in the filename.
WithoutOutputNameStyle(String) - Constructor for class org.anchoranalysis.io.output.namestyle.WithoutOutputNameStyle: Creates with an output-name.
withoutParameters() - Method in class org.anchoranalysis.feature.energy.EnergyStack: The energy-stack without associated parameters.
withoutProperties() - Method in class org.anchoranalysis.image.core.object.properties.ObjectCollectionWithProperties: Returns the contained-objects without the corresponding properties.
withoutThumbnail() - Method in class org.anchoranalysis.plugin.image.task.feature.LabelledResultsVectorWithThumbnail: Exposes as a LabelledResultsVector without a thumbnail.
withPoint(Optional<ObjectMask>, Extent, ProcessPoint) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsObjectMaskOptional: Iterate over all points that are located on a object-mask or else all points in an extent.
withPoint(ObjectMask, Optional<ObjectMask>, ProcessPoint) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsObjectMask: Iterate over each point that is located on an object-mask AND optionally a second-mask
withPoint(ObjectMask, ProcessPoint) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsObjectMask: Iterate over each voxel that is located on an object-mask
withPoint(BoundingBox, ProcessPoint) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsBoundingBox: Iterate over each voxel in a bounding-box
withPoint(Extent, ProcessPoint) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll: Iterate over each voxel in an Extent
withPointAndIndex(BoundingBox, ProcessPointAndIndex) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsBoundingBox: Iterate over each voxel in a bounding-box
withPointAndIndex(Extent, ProcessPointAndIndex) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll: Iterate over each voxel in an Extent.
WithPriority<T> - Class in org.anchoranalysis.inference.concurrency: Wraps an element of type T to ensure priority is given when the flag gpu==true.
WithPriority(T, boolean) - Constructor for class org.anchoranalysis.inference.concurrency.WithPriority: Creates a new WithPriority instance.
WithRadiusBase - Class in org.anchoranalysis.plugin.imagej.bean.channel.provider: A ChannelProviderUnary with a 'radius' parameter.
WithRadiusBase() - Constructor for class org.anchoranalysis.plugin.imagej.bean.channel.provider.WithRadiusBase
WithResolutionBase<T> - Class in org.anchoranalysis.image.feature.bean.physical: Base class for a feature that requires input resolution to be calculated.
WithResolutionBase() - Constructor for class org.anchoranalysis.image.feature.bean.physical.WithResolutionBase
WithResolutionBase(Feature<T>) - Constructor for class org.anchoranalysis.image.feature.bean.physical.WithResolutionBase: Creates a new instance with a specified feature.
withSlidingBuffer(Optional<ObjectMask>, SlidingBuffer<?>, ProcessPoint) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsObjectMaskOptional: Iterate over each voxel in a sliding-buffer, optionally restricting it to be only voxels in a certain object
withSuppressedLogger() - Static method in class org.anchoranalysis.test.image.InputOutputContextFixture: Creates an InputOutputContext with a suppressed logger.
withSuppressedLogger(Path) - Static method in class org.anchoranalysis.test.image.InputOutputContextFixture: Creates an InputOutputContext with a suppressed logger and a specified model directory.
withThreeBuffers(Voxels<T>, Voxels<T>, Voxels<T>, ProcessBufferTernary<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll: Iterate over each voxel - with three associated buffers for each slice.
withThreeBuffers(BoundingBox, ReadableTuple3i, ReadableTuple3i, Voxels<T>, Voxels<T>, Voxels<T>, ProcessBufferTernary<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsBoundingBox: Iterate over each voxel in a bounding-box - with three associated buffers for each slice.
withTwoBuffers(Optional<ObjectMask>, Voxels<S>, Voxels<T>, ProcessBufferBinary<S, T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsObjectMaskOptional: Iterate over each voxel (or optionally only on object-mask) with two associated buffers.
withTwoBuffers(BoundedVoxels<T>, BoundedVoxels<T>, ProcessBufferBinary<T, T>) - Static method in class org.anchoranalysis.image.voxel.iterator.intersecting.IterateVoxelsIntersectingBounded: Iterates over the intersection of two bounded-voxels of type BoundedVoxels.
withTwoBuffers(ObjectMask, Voxels<S>, Voxels<T>, ProcessBufferBinary<S, T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsObjectMask: Iterate over each voxel with a corresponding on value in an object-mask - and with two associated buffers for each slice covering the all the global space i.e. the entire image.
withTwoBuffers(Voxels<UnsignedByteBuffer>, byte, BoundedVoxels<UnsignedByteBuffer>, BoundedVoxels<UnsignedByteBuffer>, ProcessBufferBinary<UnsignedByteBuffer, UnsignedByteBuffer>) - Static method in class org.anchoranalysis.image.voxel.iterator.intersecting.IterateVoxelsIntersectingBounded: Iterates over the intersection of two bounded-voxels of type BoundedVoxels but only voxels that lie on an object-mask.
withTwoBuffers(BoundingBox, ReadableTuple3i, Voxels<T>, Voxels<T>, ProcessBufferBinary<T, T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsBoundingBox: Iterate over each voxel in a bounding-box - with two associated buffers for each slice, one VoxelBuffer and one Buffer
withTwoBuffersAndPoint(Voxels<S>, Voxels<T>, ProcessBufferBinary<S, T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll: Iterate over each voxel - with two associated buffers for each slice
withTwoBuffersUntil(BoundedVoxels<T>, BoundedVoxels<T>, PredicateBufferBinary<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.intersecting.IterateVoxelsIntersectingBounded: Iterates over the intersection of two bounded-voxels of type BoundedVoxels until a predicate is satisfied.
withTwoBuffersUntil(BoundingBox, ReadableTuple3i, Voxels<T>, Voxels<T>, PredicateBufferBinary<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsBoundingBox: Iterate over each voxel in a bounding-box - with two associated buffers for each slice - until a predicate evaluates to true.
withTwoBuffersWithoutOffset(VoxelBuffer<S>, VoxelBuffer<T>, ProcessBufferBinaryWithoutOffset<S, T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsRemaining: Iterate over remaining voxels each voxel - with two associated buffers for each slice.
withTwoMixedBuffers(ObjectMask, Voxels<S>, Voxels<T>, ProcessVoxelBufferBinaryMixed<S, T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsObjectMask: Iterate over each voxel in an object-mask - with one associated voxel-buffer and one associated buffer for each slice.
withTwoMixedBuffers(Voxels<S>, Voxels<T>, ProcessVoxelBufferBinaryMixed<S, T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll: Iterate over each voxel in a bounding-box - with one associated voxel-buffer and one associated buffer for each slice.
withTwoMixedBuffers(BoundingBox, ReadableTuple3i, Voxels<S>, Voxels<T>, ProcessBufferBinaryMixed<S, T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsBoundingBox: Iterate over each voxel in a bounding-box - with two associated buffers for each slice.
withTwoVoxelBuffers(ObjectMask, Voxels<S>, Voxels<T>, ProcessVoxelBufferBinary<S, T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsObjectMask: Iterate over each voxel in an object-mask - with two associated voxel-buffers and for each slice.
withTwoVoxelBuffers(Voxels<S>, Voxels<T>, ProcessVoxelBufferBinary<S, T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll: Iterate over each voxel in a bounding-box - with two associated voxel-buffers for each slice
WithValueBase<T> - Class in org.anchoranalysis.plugin.operator.feature.bean: A base class for operations that use a specified constant value in combination with a feature.
WithValueBase() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.WithValueBase
withVoxelBuffer(ObjectMask, Voxels<T>, Optional<BoundingBox>, ProcessVoxelBufferUnary<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsObjectMask: Iterate over each voxel on an object-mask with one associated VoxelBuffer.
withVoxelBuffer(ObjectMask, Voxels<T>, ProcessVoxelBufferUnary<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsObjectMask: Iterate over each voxel on an object-mask with one associated VoxelBuffer.
withVoxelBuffer(Voxels<T>, ProcessVoxelBufferUnary<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll: Iterate over each voxel - with one associated voxel-buffer for each slice.
withVoxelBuffer(Voxels<T>, ProcessVoxelBufferUnaryWithPoint<T, E>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll: Iterate over each voxel - with one associated voxel-buffer for each slice.
WrapAsUpdatable - Class in org.anchoranalysis.plugin.image.object.merge.condition: Wraps a BeforeCondition as an UpdatableBefoerCondition
WrapAsUpdatable(BeforeCondition) - Constructor for class org.anchoranalysis.plugin.image.object.merge.condition.WrapAsUpdatable
wrapDuplicate(List<Feature<T>>) - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory: Wraps an existing list, WITHOUT reusing the list in the internals of the FeatureList i.e. create a new list internally
wrapRaw(byte[]) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer: Exposes a raw byte-array as a buffer with unsigned-bytes.
wrapRaw(int[]) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer: Exposes a raw int-array as a buffer with unsigned-ints.
wrapRaw(short[]) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer: Exposes a raw short-array as a buffer with unsigned-shorts.
wrapRaw(ByteBuffer) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer: Exposes a raw ByteBuffer as a buffer with unsigned-bytes.
wrapRaw(IntBuffer) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer: Exposes a raw UnsignedIntBuffer as a buffer with unsigned-ints.
wrapRaw(ShortBuffer) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer: Exposes a raw UnsignedShortBuffer as a buffer with unsigned-shorts.
wrapReuse(List<Feature<T>>) - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory: Wraps an existing list, reusing the list in the internals of the FeatureList
write(String, ElementWriterSupplier<T>, ElementSupplier<T>) - Method in class org.anchoranalysis.io.output.writer.AlwaysAllowed
write(String, ElementWriterSupplier<T>, ElementSupplier<T>) - Method in class org.anchoranalysis.io.output.writer.CheckIfAllowed
write(String, ElementWriterSupplier<T>, ElementSupplier<T>) - Method in interface org.anchoranalysis.io.output.writer.Writer: Writes an element using an ElementWriter to the current directory.
write(String, ElementWriterSupplier<T>, ElementSupplier<T>) - Method in class org.anchoranalysis.io.output.writer.WriterRouterErrors: Writes an element using an ElementWriter to the current directory.
write(Collection<T>, OutputNameStyle, ElementOutputter) - Method in class org.anchoranalysis.io.generator.collection.CollectionGenerator
write(ImageLabelAnnotation, Path) - Method in class org.anchoranalysis.annotation.io.image.ImageLabelAnnotationWriter
write(DualMarksAnnotation<T>, Path) - Method in class org.anchoranalysis.annotation.io.mark.DualMarksAnnotationWriter
write(S, OutputNameStyle, ElementOutputter) - Method in class org.anchoranalysis.io.generator.GeneratorBridge
write(T, Path) - Method in interface org.anchoranalysis.annotation.io.AnnotationWriter: Saves the annotation to the filesystem.
write(T, OutputNameStyle, ElementOutputter) - Method in class org.anchoranalysis.image.io.stack.output.generator.RasterGenerator
write(T, OutputNameStyle, ElementOutputter) - Method in class org.anchoranalysis.io.generator.combined.CombinedListGenerator
write(T, OutputNameStyle, ElementOutputter) - Method in class org.anchoranalysis.io.generator.SingleFileTypeGenerator
write(T, OutputNameStyle, ElementOutputter) - Method in class org.anchoranalysis.io.generator.TransformingGeneratorBridge
write(T, OutputNameStyle, ElementOutputter) - Method in interface org.anchoranalysis.io.output.writer.ElementWriter: Writes a non-indexable output (an output that isn't part of a collection of other similar items).
writeAsRGB(Stack) - Method in class org.anchoranalysis.image.io.stack.output.StackWriteAttributes: Whether to write a stack in RGB mode?
writeChannel(String, Channel) - Method in class org.anchoranalysis.test.image.WriteIntoDirectory: Writes a Channel to the output directory.
writeEnergyStack() - Method in class org.anchoranalysis.mpp.io.output.EnergyStackWriter: Writes the energy stack to output.
writeFeaturesToCSV(CSVWriter, List<ImageAnnotation>, List<String>) - Method in class org.anchoranalysis.plugin.annotation.bean.aggregate.AnnotationAggregateCSVGenerator
writeFeaturesToCSV(CSVWriter, T, List<String>) - Method in class org.anchoranalysis.feature.io.csv.table.FeatureTableCSVGenerator: Writes the features to the CSV-file.
writeGroupedResults(Optional<NamedFeatureStore<FeatureInputResults>>, boolean, Function<InputOutputContext, FeatureCSVWriterFactory>, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.feature.FeatureResultsAndThumbnails: Writes all the results that have been collected as a CSV file.
writeGroupResults(Optional<NamedFeatureStore<FeatureInputResults>>, boolean, FeatureOutputMetadata, FeatureCSVWriterFactory, InputOutputContextSubdirectoryCache) - Method in class org.anchoranalysis.feature.io.results.group.GroupedResults: Writes outputs for groups that have been previously added with GroupedResults.addResultsFor(org.anchoranalysis.feature.io.results.LabelledResultsVector).
writeHeaders(List<String>) - Method in class org.anchoranalysis.io.generator.tabular.CSVWriter: Writes a line with the header-names of the columns.
WriteIntoDirectory - Class in org.anchoranalysis.test.image: Writes one or more stacks/objects/channels into a directory during testing.
WriteIntoDirectory(Path) - Constructor for class org.anchoranalysis.test.image.WriteIntoDirectory: Creates a new WriteIntoDirectory instance with directory printing enabled.
WriteIntoDirectory(Path, boolean) - Constructor for class org.anchoranalysis.test.image.WriteIntoDirectory: Creates a new WriteIntoDirectory instance.
writeLevelsForObjects(Channel, ObjectCollection, Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectBase: Creates a channel with the levels for a set of objects.
writeLevelsForObjects(Channel, ObjectCollection, Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectIndependently
writeLevelsForObjects(Channel, ObjectCollection, Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectNeighbors
writeList(String, List<DisplayStack>, boolean) - Method in class org.anchoranalysis.test.image.WriteIntoDirectory: Writes a list of display-stacks.
writeObject(String, ObjectMask) - Method in class org.anchoranalysis.test.image.WriteIntoDirectory: Writes an ObjectMask to the output directory.
writeObjects(String, ObjectCollection) - Method in class org.anchoranalysis.test.image.WriteIntoDirectory: Writes the outline of objects on a blank RGB image, inferring dimensions of the image to center the object.
writeObjects(String, ObjectCollection, Stack) - Method in class org.anchoranalysis.test.image.WriteIntoDirectory: Writes the outline of objects on a background.
writeOffByte(int, UnsignedByteBuffer) - Method in class org.anchoranalysis.plugin.image.segment.thresholder.slice.SliceThresholder: Writes the 'off' binary value to the output buffer at the specified offset.
writer(OutputWriteSettings) - Static method in class org.anchoranalysis.image.io.stack.output.generator.GeneratorOutputter: Gets the default StackWriter.
Writer - Interface in org.anchoranalysis.io.output.writer: Write data via ElementWriters to the file system, or creates new sub-directories for writing data to.
writeRaster(FileSaver, String, boolean) - Method in class org.anchoranalysis.io.imagej.bean.stack.writer.ImageJRasterWriter: Writes an annotation to the filesystem at outPath.
writeRaster(FileSaver, String, boolean) - Method in class org.anchoranalysis.io.imagej.bean.stack.writer.PNG
writeRaster(FileSaver, String, boolean) - Method in class org.anchoranalysis.io.imagej.bean.stack.writer.Tiff
WriterErrorMessageHelper - Class in org.anchoranalysis.image.io.bean.stack.writer: Helps create similar error messages among StackWriters.
writeResolutionXML(Resolution, Path) - Static method in class org.anchoranalysis.plugin.io.xml.ResolutionAsXML: Writes a XML metadata file describing the image-resolution.
WriteResolutionXml - Class in org.anchoranalysis.plugin.io.bean.stack.writer: When writing a stack, an additional file is written to indicate the physical voxel sizes, if this information is known.
WriteResolutionXml() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.writer.WriteResolutionXml
WriterExecuteBeforeEveryOperation - Interface in org.anchoranalysis.io.output.writer: Interface for classes with a method that should be called before every outputting write operation.
writerMultiplex(boolean) - Method in class org.anchoranalysis.io.output.outputter.Outputter: Multiplexes between the selective and permissive writers based on a flag.
writeRow(String, int, double) - Method in class org.anchoranalysis.plugin.image.task.stack.SharedStateSelectedSlice: Writes a row of selected slice information to the CSV file.
writeRow(String, String) - Method in class org.anchoranalysis.plugin.image.task.labeller.SharedStateFilteredImageOutput: Writes a row to the CSV file with image name and group identifier.
writeRow(List<TypedValue>) - Method in class org.anchoranalysis.io.generator.tabular.CSVWriter: Writes a line with values of a particular row
writerPermissive() - Method in class org.anchoranalysis.io.output.outputter.Outputter: The writer that allows all outputs.
WriterRouterErrors - Class in org.anchoranalysis.io.output.writer: Write data via ElementWriters to the file system.
WriterRouterErrors(Writer, ErrorReporter) - Constructor for class org.anchoranalysis.io.output.writer.WriterRouterErrors
writerSecondLevel(String) - Method in class org.anchoranalysis.io.output.outputter.Outputter: A writer that performs a second-level check on which outputs occur, but writes to the top-level directory.
writerSelective() - Method in class org.anchoranalysis.io.output.outputter.Outputter: The writer that allows only certain selected outputs.
writeStack(String, DisplayStack) - Method in class org.anchoranalysis.test.image.WriteIntoDirectory: Writes a DisplayStack to the output directory.
writeStack(Stack, Path, StackWriteOptions) - Method in class org.anchoranalysis.image.io.bean.stack.writer.OneOrThreeChannelsWriter
writeStack(Stack, Path, StackWriteOptions) - Method in class org.anchoranalysis.image.io.bean.stack.writer.StackWriter: Writes a stack to the filesystem at a particular path.
writeStack(Stack, Path, StackWriteOptions) - Method in class org.anchoranalysis.io.bioformats.bean.writer.BioformatsWriter
writeStack(Stack, Path, StackWriteOptions) - Method in class org.anchoranalysis.io.bioformats.bean.writer.Tiff
writeStack(Stack, Path, StackWriteOptions) - Method in class org.anchoranalysis.io.imagej.bean.stack.writer.ImageJRasterWriter
writeStack(Stack, Path, StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.StackWriterDelegateBase
writeStack(Stack, Path, StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.WriteResolutionXml
writeStackAfterCheck(Stack, Path) - Method in class org.anchoranalysis.image.io.bean.stack.writer.OneOrThreeChannelsWriter: Writes the Stack to the file-system, after a check has already occurred that the correct number of channels exist.
writeStackAfterCheck(Stack, Path) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.ImageIOWriter
writeStackAfterCheck(Stack, Path) - Method in class org.anchoranalysis.plugin.opencv.bean.stack.OpenCVWriter
writeStackTime(Stack, Path, boolean) - Method in class org.anchoranalysis.io.imagej.bean.stack.writer.ImageJRasterWriter: Writes a stack as a time-sequence (many images together in a single file.).
writeStackWithExtension(Stack, Path, StackWriteOptions) - Method in class org.anchoranalysis.image.io.bean.stack.writer.StackWriter: Writes a stack to the filesystem at a particular path with an extension appended to the path.
WriteStringToFile - Class in org.anchoranalysis.io.generator.text: Writes a string to a text file.
WriteText - Class in org.anchoranalysis.image.io.bean.stack.combine: Creates an image that contains text only.
WriteText() - Constructor for class org.anchoranalysis.image.io.bean.stack.combine.WriteText
WriteText(String) - Constructor for class org.anchoranalysis.image.io.bean.stack.combine.WriteText: Creates the bean to write particular text, otherwise using default settings.
writeTextFile(String, Path) - Static method in class org.anchoranalysis.io.generator.text.WriteStringToFile: Creates a new text-file at filePath whose contents are contents.
writeThresholdedByte(int, UnsignedByteBuffer, VoxelBuffer<?>, VoxelBuffer<?>) - Method in class org.anchoranalysis.plugin.image.segment.thresholder.slice.SliceThresholder: Writes a thresholded value to the output buffer based on the input and threshold buffers.
writeToFile(String, OutputWriteSettings, Path) - Method in class org.anchoranalysis.io.generator.text.StringGenerator
writeToFile(Path) - Method in class org.anchoranalysis.core.value.Dictionary: Serializes the key-value parameters to a file.
writeToFile(Dictionary, OutputWriteSettings, Path) - Method in class org.anchoranalysis.io.generator.serialized.DictionaryGenerator
writeToFile(ObjectCollection, OutputWriteSettings, Path) - Method in class org.anchoranalysis.image.io.object.output.hdf5.HDF5ObjectsGenerator
writeToFile(Histogram, OutputWriteSettings, Path) - Method in class org.anchoranalysis.image.io.histogram.output.HistogramCSVGenerator
writeToFile(T, Stack, StackWriteOptions, OutputWriteSettings, Path) - Method in class org.anchoranalysis.image.io.stack.output.generator.RasterGenerator: Writes a stack to the file-system.
writeToFile(T, Stack, StackWriteOptions, OutputWriteSettings, Path) - Method in class org.anchoranalysis.image.io.stack.output.generator.RasterGeneratorSelectFormat
writeToFile(T, OutputWriteSettings, Path) - Method in class org.anchoranalysis.feature.io.csv.table.FeatureTableCSVGenerator
writeToFile(T, OutputWriteSettings, Path) - Method in class org.anchoranalysis.io.generator.serialized.ObjectOutputStreamGenerator
writeToFile(T, OutputWriteSettings, Path) - Method in class org.anchoranalysis.io.generator.serialized.XStreamGenerator
writeToFile(T, OutputWriteSettings, Path) - Method in class org.anchoranalysis.io.generator.SingleFileTypeGenerator: Write generated content for {code element} to the file filePath.
writeToFile(T, OutputWriteSettings, Path) - Method in class org.anchoranalysis.io.generator.SingleFileTypeGeneratorBridge
writeVoxels(String, Voxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.test.image.WriteIntoDirectory: Writes Voxels to the output directory.
writeWithIndex(Collection<T>, String, IndexableOutputNameStyle, ElementOutputter) - Method in class org.anchoranalysis.io.generator.collection.CollectionGenerator
writeWithIndex(IndexableOutputNameStyle, ElementWriterSupplier<T>, ElementSupplier<T>, String) - Method in class org.anchoranalysis.io.output.writer.AlwaysAllowed
writeWithIndex(IndexableOutputNameStyle, ElementWriterSupplier<T>, ElementSupplier<T>, String) - Method in class org.anchoranalysis.io.output.writer.CheckIfAllowed
writeWithIndex(IndexableOutputNameStyle, ElementWriterSupplier<T>, ElementSupplier<T>, String) - Method in interface org.anchoranalysis.io.output.writer.Writer: Writes an indexed-element using an ElementWriter in the current directory.
writeWithIndex(IndexableOutputNameStyle, ElementWriterSupplier<T>, ElementSupplier<T>, String) - Method in class org.anchoranalysis.io.output.writer.WriterRouterErrors: Writes an indexed-element using an ElementWriter in the current directory.
writeWithIndex(S, String, IndexableOutputNameStyle, ElementOutputter) - Method in class org.anchoranalysis.io.generator.GeneratorBridge
writeWithIndex(T, String, IndexableOutputNameStyle, ElementOutputter) - Method in class org.anchoranalysis.image.io.stack.output.generator.RasterGenerator: As only a single-file is involved, this methods delegates to a simpler virtual method.
writeWithIndex(T, String, IndexableOutputNameStyle, ElementOutputter) - Method in class org.anchoranalysis.io.generator.combined.CombinedListGenerator
writeWithIndex(T, String, IndexableOutputNameStyle, ElementOutputter) - Method in class org.anchoranalysis.io.generator.SingleFileTypeGenerator
writeWithIndex(T, String, IndexableOutputNameStyle, ElementOutputter) - Method in class org.anchoranalysis.io.generator.TransformingGeneratorBridge
writeWithIndex(T, String, IndexableOutputNameStyle, ElementOutputter) - Method in interface org.anchoranalysis.io.output.writer.ElementWriter: Writes an indexable output (many outputs of the same type, uniquely identified by an index).
writeWithoutName(String, ElementWriterSupplier<T>, ElementSupplier<T>) - Method in class org.anchoranalysis.io.output.writer.AlwaysAllowed
writeWithoutName(String, ElementWriterSupplier<T>, ElementSupplier<T>) - Method in class org.anchoranalysis.io.output.writer.CheckIfAllowed
writeWithoutName(String, ElementWriterSupplier<T>, ElementSupplier<T>) - Method in interface org.anchoranalysis.io.output.writer.Writer: Writes an element using an ElementWriter to the current directory, without including an output name in the path.
writeXMLToFile(Document, Path) - Static method in class org.anchoranalysis.io.output.xml.XMLWriter: Writes a XML-document to the file-system.

X

x - Variable in class org.anchoranalysis.spatial.point.Tuple3d: X-axis component of the tuple.
x - Variable in class org.anchoranalysis.spatial.point.Tuple3f: X-axis component of the tuple.
x - Variable in class org.anchoranalysis.spatial.point.Tuple3i: X-axis component of the tuple.
x() - Method in class org.anchoranalysis.image.core.dimensions.Dimensions: The size in the X dimension.
x() - Method in class org.anchoranalysis.image.core.dimensions.Resolution: The resolution in the X-dimension in meters.
x() - Method in class org.anchoranalysis.spatial.box.Extent: The size in the X dimension.
x() - Method in class org.anchoranalysis.spatial.orientation.DirectionVector: The x-component of the vector.
x() - Method in class org.anchoranalysis.spatial.point.Point2d: X-axis component of point.
x() - Method in class org.anchoranalysis.spatial.point.Point2f: X-axis component of point.
x() - Method in class org.anchoranalysis.spatial.point.Point2i: X-axis component of point.
x() - Method in interface org.anchoranalysis.spatial.point.ReadableTuple3i: X-axis component of the tuple.
x() - Method in class org.anchoranalysis.spatial.point.Tuple3d: X-axis component of the tuple.
x() - Method in class org.anchoranalysis.spatial.point.Tuple3f: X-axis component of the tuple.
x() - Method in class org.anchoranalysis.spatial.point.Tuple3i
x() - Method in class org.anchoranalysis.spatial.scale.ScaleFactor: How much to multiply the existing x-dimension by to create a scaled X-dimension.
x(float) - Method in class org.anchoranalysis.spatial.point.Tuple3f: X-axis component of the tuple.
x(int) - Method in class org.anchoranalysis.spatial.box.BoundingBoxContains: Is this value in the X-dimension within the bounding box range?
X - Enum constant in enum class org.anchoranalysis.spatial.axis.Axis: X-axis.
xFromChainCode(int) - Static method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.ChainCodesDirection: Extracts the x-component from a chain code.
XML - Enum constant in enum class org.anchoranalysis.core.format.NonImageFileFormat: XML
XMLGenerator<T> - Class in org.anchoranalysis.io.generator.xml: A generator that writes the contents of a XML file to the file-system.
XMLGenerator() - Constructor for class org.anchoranalysis.io.generator.xml.XMLGenerator
XMLParser - Class in org.anchoranalysis.core.serialize: Utility functions for parsing XML files using standard Java APIs.
XMLWriter - Class in org.anchoranalysis.io.output.xml: Writes XML in the form of a Document to the file-system.
Xor - Class in org.anchoranalysis.plugin.image.bean.mask.provider.combine: Outputs the logical operation xor (exclusive or) voxelwise on both masks, modifying {mask} with the result.
Xor() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.combine.Xor
XStreamDeserializer<T> - Class in org.anchoranalysis.core.serialize: Deserializes an object using the XStream library.
XStreamDeserializer() - Constructor for class org.anchoranalysis.core.serialize.XStreamDeserializer
XStreamGenerator<T> - Class in org.anchoranalysis.io.generator.serialized: A generator that serialized using the XStream library and format.
XStreamGenerator() - Constructor for class org.anchoranalysis.io.generator.serialized.XStreamGenerator
XStreamSerializer - Class in org.anchoranalysis.core.serialize: Serializes an object using the XStream library.

Y

y - Variable in class org.anchoranalysis.spatial.point.Tuple3d: Y-axis component of the tuple.
y - Variable in class org.anchoranalysis.spatial.point.Tuple3f: Y-axis component of the tuple.
y - Variable in class org.anchoranalysis.spatial.point.Tuple3i: Y-axis component of the tuple.
y() - Method in class org.anchoranalysis.image.core.dimensions.Dimensions: The size in the Y dimension.
y() - Method in class org.anchoranalysis.image.core.dimensions.Resolution: The resolution in the Y-dimension in meters.
y() - Method in class org.anchoranalysis.spatial.box.Extent: The size in the Y dimension.
y() - Method in class org.anchoranalysis.spatial.orientation.DirectionVector: The y-component of the vector.
y() - Method in class org.anchoranalysis.spatial.point.Point2d: Y-axis component of point.
y() - Method in class org.anchoranalysis.spatial.point.Point2f: Y-axis component of point.
y() - Method in class org.anchoranalysis.spatial.point.Point2i: Y-axis component of point.
y() - Method in interface org.anchoranalysis.spatial.point.ReadableTuple3i: Y-axis component of the tuple.
y() - Method in class org.anchoranalysis.spatial.point.Tuple3d: Y-axis component of the tuple.
y() - Method in class org.anchoranalysis.spatial.point.Tuple3f: Y-axis component of the tuple.
y() - Method in class org.anchoranalysis.spatial.point.Tuple3i
y() - Method in class org.anchoranalysis.spatial.scale.ScaleFactor: How much to multiply the existing y-dimension by to create a scaled Y-dimension.
y(float) - Method in class org.anchoranalysis.spatial.point.Tuple3f: Y-axis component of the tuple.
y(int) - Method in class org.anchoranalysis.spatial.box.BoundingBoxContains: Is this value in the Y-dimension within the bounding box range?
Y - Enum constant in enum class org.anchoranalysis.spatial.axis.Axis: Y-axis.
yFromChainCode(int) - Static method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.ChainCodesDirection: Extracts the y-component from a chain code.

Z

z - Variable in class org.anchoranalysis.spatial.point.Tuple3d: Z-axis component of the tuple.
z - Variable in class org.anchoranalysis.spatial.point.Tuple3f: Z-axis component of the tuple.
z - Variable in class org.anchoranalysis.spatial.point.Tuple3i: Z-axis component of the tuple.
z() - Method in class org.anchoranalysis.image.core.dimensions.Dimensions: The size in the Z dimension.
z() - Method in class org.anchoranalysis.image.core.dimensions.Resolution: The resolution in the Z-dimension in meters.
z() - Method in class org.anchoranalysis.spatial.box.Extent: The size in the Z dimension.
z() - Method in class org.anchoranalysis.spatial.orientation.DirectionVector: The z-component of the vector.
z() - Method in interface org.anchoranalysis.spatial.point.ReadableTuple3i: Z-axis component of the tuple.
z() - Method in class org.anchoranalysis.spatial.point.Tuple3d: Z-axis component of the tuple.
z() - Method in class org.anchoranalysis.spatial.point.Tuple3f: Z-axis component of the tuple.
z() - Method in class org.anchoranalysis.spatial.point.Tuple3i
z(float) - Method in class org.anchoranalysis.spatial.point.Tuple3f: Z-axis component of the tuple.
z(int) - Method in class org.anchoranalysis.spatial.box.BoundingBoxContains: Is this value in the Z-dimension within the bounding box range?
Z - Enum constant in enum class org.anchoranalysis.spatial.axis.Axis: Z-axis (existing only in 3D images, often known as z-stacks).
zChange - Variable in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsoluteWithSlidingBuffer: The change in the Z-dimension to reach this neighbor relative to the source coordinate.
ZeroOutsideMask - Class in org.anchoranalysis.plugin.image.bean.channel.provider.mask: Set pixels NOT IN the mask to 0, but keep pixels IN the mask identical.
ZeroOutsideMask() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.mask.ZeroOutsideMask
zeroValue(int) - Method in class org.anchoranalysis.math.histogram.Histogram: Sets the count for a particular value to 0.
zFromChainCode(int) - Static method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.ChainCodesDirection: Extracts the z-component from a chain code.
zIfDefined(double) - Method in class org.anchoranalysis.image.core.dimensions.Resolution: Returns the z-resolution like Resolution.z() if the z-resolution is not Double.NaN.
zip(Collection<S>, Collection<T>) - Static method in class org.anchoranalysis.core.functional.FunctionalList: Create a list of pairs of elements from two separate collections.
zip(Collection<S>, Collection<T>, BiFunction<S, T, V>) - Static method in class org.anchoranalysis.core.functional.FunctionalList: Create a list of elements from two separate collections.
zRelative() - Method in class org.anchoranalysis.image.core.dimensions.Resolution: Gives the relative resolution of the z-component to the x-component.
zScore(double) - Method in class org.anchoranalysis.math.statistics.MeanScale: Converts a value to a z-score given the parameterization in this object.
ZScore<T> - Class in org.anchoranalysis.plugin.operator.feature.bean.statistics: Calculates the Z-score of a value based on the mean and standard deviation.
ZScore() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.statistics.ZScore
ZScoreCalculator - Class in org.anchoranalysis.math.statistics: Calculates a Z-Score.

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