Index (Anchor - merged Javadoc across key repositories. This documentation is a work-in-progress. 0.0.1-SNAPSHOT API)

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absolute() - Method in class Tuple3d: Convert each dimension's component into its absolute value.
AbsoluteValue<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic
AbsoluteValue() - Constructor for class AbsoluteValue
accept(S, T) - Method in interface CheckedBiConsumer: Calls the function.
accept(S) - Method in interface CheckedConsumer: Like Consumer.accept(T) but throws an exception.
accept(int) - Method in interface CheckedIntConsumer: Like IntConsumer.accept(int) but throws an exception.
accept(BinaryVoxels<UnsignedByteBuffer>) - Method in class AcceptIterationList
accept(BinaryVoxels<UnsignedByteBuffer>) - Method in interface AcceptIterationPredicate: Whether a particular voxels fulfills the condition or not.
accept(int, int) - Method in interface Histogram.BinConsumer: Accepts a particular bin and corresponding count.
accept(ObjectMask, ObjectMask, ObjectMask) - Method in interface AfterCondition
accept(ObjectMask) - Method in class AndCondition
accept(ObjectMask, ObjectMask, Optional<UnitConverter>) - Method in interface BeforeCondition
accept(ObjectMask, ObjectMask, Optional<UnitConverter>) - Method in class DistanceCondition
accept(ObjectMask, ObjectMask, ObjectMask) - Method in class IncreaseFeatureCondition
accept(ObjectMask) - Method in class NeighborhoodCondition
accept(ObjectMask) - Method in interface UpdatableBeforeCondition
accept(ObjectMask) - Method in class WrapAsUpdatable
accept(ParsedFilePathBag) - Method in class AtLeastZSlices
accept(ParsedFilePathBag) - Method in class CheckParsedFilePathBag
accept(Point2i, int) - Method in interface OffsettedPointTwoDimensionalConsumer: Accepts a point like with a Consumer in general.
accept(int, int, int) - Method in interface OffsettedScalarTwoDimensionalConsumer: Accepts a point
accept(Point2i) - Method in interface PointTwoDimensionalConsumer: Accepts a point like with a Consumer in general.
accept(int, int, int) - Method in interface ScalarThreeDimensionalConsumer: Accepts a point like with a Consumer in general.
accept(int, int) - Method in interface ScalarTwoDimensionalConsumer: Accepts a point like with a Consumer in general.
acceptableProbability(AnnealScheme) - Method in class AssignMode
acceptableProbability(AnnealScheme) - Method in class DirectAssignMode
acceptableProbability(AnnealScheme) - Method in class TransformationAssignMode
AcceptanceProbabilityCalculator<T> - Class in org.anchoranalysis.plugin.mpp.segment.optimization
AcceptanceProbabilityCalculator(AnnealScheme, ExtractScoreSize<T>) - Constructor for class AcceptanceProbabilityCalculator
accepted() - Method in interface 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 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.
acceptPathViaRegEx(Path, Pattern) - Static method in class MatchRegularExpression
acceptProposal(ToDoubleFunction<T>) - Method in class OptimizationStep
accepts(Class<?>) - Method in class AssignerMatchClass
accepts(Class<?>) - Method in interface 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 AccessObjectMaskSimple
AcquisitionDateReader - Class in org.anchoranalysis.io.bioformats.metadata: Reads the image acquisition-date.
activateDebugMode(String) - Method in class ExecutionArguments: Activates debug-mode.
add(NamedBean<?>) - Method in class Define: Adds a named-bean to our definitions, using the {#link GroupingRoot} annotation to determine a group where definitions are stored.
add(Double) - Method in class DoubleList
add(Double) - Method in class DoubleSet
add(Integer) - Method in class IntegerList
add(Integer) - Method in class IntegerSet
add(T) - Method in interface PrimitiveBeanCollection: Add an element to the collection.
add(String) - Method in class StringList
add(String) - Method in class StringSet
add(Color) - Method in class ColorList: Appends a Color to the list.
add(RGBColor) - Method in class ColorList: Like ColorList.add(Color) but adds a RGBColor.
add(int, RGBColor) - Method in class ColorList: Inserts a Color into the list, at a particular index.
add(String, T) - Method in class NameValueMap: Adds an element.
add(NameValue<T>) - Method in class NameValueMap: Adds an element.
add(String, StoreSupplier<T>) - Method in class EagerEvaluationStore
add(String, StoreSupplier<T>) - Method in class LazyEvaluationStore
add(String, StoreSupplier<T>) - Method in interface NamedProviderStore: Adds an element to the store.
add(StatefulMessageLogger) - Method in class MessageLoggerList
add(Class<? extends InputFromManager>) - Method in class InputTypesExpected
add(SubmittedJob) - Method in class ConcurrentJobMonitor
add(Feature<? extends T>) - Method in class FeatureList: Adds a feature to the current list.
add(LabelledResultsVector) - Method in interface FeatureCalculationResults: Adds a results-element to be written.
add(String) - Method in class FeatureNameList: Adds a feature-name.
add(String, int) - Method in class FeatureNameMapToIndex: Adds a new featureName and index
add(ResultsVector) - Method in class ResultsVectorList: Add a ResultsVector to the list in the final position.
add(CacheTransferSource<? extends FeatureInput>) - Method in class CacheTransferSourceCollection
add(String, Feature<T>) - Method in class NamedFeatureStore: Adds a named-feature to the store.
add(BoundingBox) - Method in class BoundingBoxesOnPlane
add(ObjectMask) - Method in class ObjectCollectionWithProperties: Add an ObjectMask to the collection, assigning empty properties to it.
add(ObjectWithProperties) - Method in class ObjectCollectionWithProperties: Add an ObjectWithProperties to the collection.
add(String, Stack) - Method in class NamedStacks: Add a stack.
add(String, StoreSupplier<Stack>) - Method in class NamedStacks
add(String, Stack) - Method in class NamedStacksUniformSize: Adds an element to the store.
add(RasterGenerator<T>) - Method in class CombineRasterGenerator
add(ChannelEntry) - Method in class NamedEntries
add(NamedChannelsForSeries) - Method in class NamedChannelsForSeriesConcatenate
add(Stack) - Method in class StackSeries
add(Stack) - Method in class TimeSequence
add(String, StoreSupplier<TimeSequence>) - Method in class WrapStackAsTimeSequenceStore
add(AcceptIterationPredicate) - Method in class AcceptIterationList: Adds an item to the list of predicates.
add(ObjectMask) - Method in class ObjectCollection: Adds an object to the collection.
add(VoxelStatistics) - Method in class VoxelStatisticsCombined: Adds an element.
add(String, Generator<T>) - Method in class CombinedListGenerator
add(FileType[]) - Method in class ConcatenateFileTypes
add(T) - Method in class OutputSequenceIncrementing: Outputs an additional element in the sequence.
add(T, S) - Method in class OutputSequenceIndexed: Outputs an additional element in the sequence.
add(T, Optional<S>) - Method in class OutputSequenceIndexed: Outputs an additional element in the sequence.
add(OutputtedFile) - Method in class RootDirectory
add(MutableDirectory) - Method in class RootDirectory
add(OutputtedFile) - Method in class Subdirectory
add(String, boolean) - Method in class RecordedOutputs: Adds a new output-name to the set of recorded names.
add(RunningSum) - Method in class RunningSum: Adds the values of another RunningSum to the current values.
add(double) - Method in class 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 VarianceCalculatorDouble: Adds a value to the running sum.
add(int) - Method in class VarianceCalculatorLong: Adds a value to the running sum.
add(int, int) - Method in class VarianceCalculatorLong: Adds a multiple instances of a value to the running sum.
add(MemoForIndex, VoxelizedMarkMemo) - Method in class RandomCollectionWithAddCriteria
add(double) - Method in class EnergyTotal
add(EnergyMemoList, VoxelizedMarkMemo, EnergyStackWithoutParameters) - Method in class MarksWithEnergyBreakdown
add(VoxelizedMarkMemo) - Method in class MarksWithTotalEnergy
add(VoxelizedMarkMemo, EnergyStackWithoutParameters) - Method in class VoxelizedMarksWithEnergy
add(EnergyTotal) - Method in class EnergySavedInd
add(MemoForIndex, VoxelizedMarkMemo) - Method in class EnergySavedPairs
add(String, EnergyScheme) - Method in class EnergySchemeSet
add(EnergySavedInd, VoxelizedMarkMemo, EnergyStackWithoutParameters, EnergySchemeWithSharedFeatures) - Method in class EnergyMemoList
add(VoxelizedMarkMemo) - Method in class MemoList
add(UpdatableMarks) - Method in class UpdatableMarksList
add(MemoForIndex, VoxelizedMarkMemo) - Method in class UpdatableMarksList
add(MemoForIndex) - Method in class UpdatableMarksList
add(int, UpdatableMarks) - Method in class UpdatableMarksList
add(IndexByRegion<T>) - Method in class IndexByChannel
add(String, StoreSupplier<T>) - Method in interface MultiInputSubMap: Adds an entry to the map
add(String, StoreSupplier<T>) - Method in class OperationMap
add(String, StoreSupplier<TimeSequence>) - Method in class StackWithMap
add(Mark, Color) - Method in class ColoredMarks
add(Mark, RGBColor) - Method in class ColoredMarks
add(Mark) - Method in class MarkCollection
add(MemoForIndex, VoxelizedMarkMemo) - Method in interface UpdatableMarks
add(String) - Method in class ErrorNode
add(Exception) - Method in class ErrorNode
add(String) - Method in class ErrorNodeImpl
add(Exception) - Method in class ErrorNodeImpl
add(String) - Method in class ErrorNodeNull
add(Exception) - Method in class ErrorNodeNull
add(FeedbackReceiver<T>) - Method in class FeedbackReceiverList
add(TerminationCondition) - Method in class TerminationConditionListOr
add(AggregateReceiver<T>) - Method in class AggregateReceiverList
add(PeriodReceiver<T>) - Method in class PeriodReceiverList
add(WeightedKernel<T, S>) - Method in class WeightedKernelList
add(Overlay, RGBColor) - Method in class ColoredOverlayCollection
add(Overlay) - Method in class OverlayCollection
add(String, String) - Method in class OverlayProperties
add(String, int) - Method in class OverlayProperties
add(double) - Method in class AxisLimits
add(ImageCounter<T>) - Method in class ImageCounterList
add(LevelResult) - Method in class LevelResultCollection
add(S, T) - Method in interface AddToAggregateItem
add(Optional<String>, String, S) - Method in class GroupMapByName: Adds an item with an identifier
add(T, String) - Method in class FileLabelMap
add(ImageMetadataInput) - Method in class ImageSize
add(ImageMetadataInput) - Method in class SummarizerImageMetadataSimple
add(T) - Method in class SummarizerInputFromManager
add(Path) - Method in class ExtensionCount
add(Path) - Method in class FilePathPattern
add(Path) - Method in class FileSizeStatistics
add(T) - Method in class Summarizer: Adds a element to the summary.
add(T) - Method in class SummarizerAggregate
add(T) - Method in class SummarizerCount
add(T) - Method in class SummarizerListMultiline
add(T) - Method in class SummarizerSplitMoreThan
add(FileDetails) - Method in class ParsedFilePathBag
add(int, String) - Method in class SortedSetChannel
add(Point3i) - Method in class PointRange: Adds a new point to be considered in the range.
add(int, int, int) - Method in class PointRange: Adds a new point to be considered in the range.
add(Point2i) - Method in class Point2d: Arithmetically adds a Point2i's values across each dimension.
add(Point2d) - Method in class Point2d: Arithmetically adds a Point2d's values across each dimension.
add(Point2i) - Method in class Point2i: Adds values from a Point2i across each corresponding dimension.
add(double, double, double) - Method in class Tuple3d: Arithmetically adds values to each dimension's component.
add(Tuple3d) - Method in class Tuple3d: Arithmetically adds a Tuple3d's values across each dimension.
add(ReadableTuple3i) - Method in class Tuple3d: Arithmetically adds a ReadableTuple3i's values across each dimension.
add(ReadableTuple3i) - Method in class Tuple3i: Arithmetically adds a ReadableTuple3i's values across each dimension.
add(BoundingBox, T) - Method in class BoundingBoxRTree: Adds a bounding-box with a corresponding payload.
add(double, double, T) - Method in class IntervalRTree: Adds a bounding-box with a corresponding index.
add(Rectangle, T) - Method in class RTree: Adds a Rectangle with a corresponding payload.
addAdditionalOptions(Options) - Method in class LauncherConfig
addAdditionalOptions(Options) - Static method in class CommandLineOptions
addAll(Define) - Method in class Define: Adds all the named-beans from source to the current map.
addAll(List<NamedBean<T>>) - Method in class Define: Adds all the named-beans from source to the current map.
addAll(ColorList) - Method in class ColorList: Appends Colors to the list.
addAll(FeatureList<? extends T>) - Method in class FeatureList: Add all the features in other to the current list.
addAll(ObjectCollection) - Method in class ObjectCollection: Adds all objects in objects to the collection.
addAll(Collection<? extends ObjectMask>) - Method in class ObjectCollection: Adds all objects in collection to the collection.
addAll(MemoForIndex) - Method in class MemoList
addAll(Collection<? extends UpdatableMarks>) - Method in class UpdatableMarksList
addAll(int, Collection<? extends UpdatableMarks>) - Method in class UpdatableMarksList
addAll(MarkCollection, RGBColor) - Method in class ColoredMarks
addAll(ColoredMarks) - Method in class ColoredMarks
addAll(MarkCollection) - Method in class MarkCollection
addAll(OverlayCollection) - Method in class OverlayCollection
addAll(Collection<S>) - Method in class ImageCounterList
addAll(Collection<T>) - Method in class Summarizer: Adds the elements to the summary.
addAllOutputNamesTo(OutputEnabledMutable) - Method in class DefineOutputter: Adds all possible output-names to a OutputEnabledMutable.
addAllToUpdatablePairList(UpdatableMarksList) - Method in class VoxelizedMarksWithEnergy
addAnnotatedImage(T) - Method in interface ImageCounter: Add an image that had an associated annotation.
addAnnotatedImage(T) - Method in class ImageCounterList
addAsSeparateChannels(NamedStacks, int, Progress, Logger) - Method in interface NamedChannelsForSeries
addAsSeparateChannels(NamedProviderStore<TimeSequence>, int, Logger) - Method in interface NamedChannelsForSeries
addAsSeparateChannels(NamedStacks, int, Progress, Logger) - Method in class NamedChannelsForSeriesConcatenate
addAsSeparateChannels(NamedProviderStore<TimeSequence>, int, Logger) - Method in class NamedChannelsForSeriesConcatenate
addAsSeparateChannels(NamedStacks, int, Progress, Logger) - Method in class NamedChannelsForSeriesMap
addAsSeparateChannels(NamedProviderStore<TimeSequence>, int, Logger) - Method in class NamedChannelsForSeriesMap
addAssignedPair(ObjectMask, ObjectMask, double) - Method in class OverlappingObjects: Adds an assigned pair of objects with a particular overlap-ratio.
addBasicOptions(Options) - Static method in class CommandLineOptions
addBlankChannel() - Method in class Stack: Adds a new empty Channel in the final-most position in the list.
addChangeID(Mark, Color) - Method in class ColoredMarks
addChangeID(Mark, RGBColor) - Method in class ColoredMarks
addChannel(Channel) - Method in class Stack: Appends a channel to the stack, as the new final-most channel position-wise.
addChannel(Channel) - Method in class StackNotUniformSized: Appends a channel to the stack, as the new final-most channel positionwise.
addChannelsFrom(Stack) - Method in class Stack: Add the channels from another instance into this instance.
AddConstant - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
AddConstant() - Constructor for class AddConstant
AddConstantTo<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic
AddConstantTo() - Constructor for class AddConstantTo
AddCriteria<T> - Interface in org.anchoranalysis.mpp.feature.addcriteria: Add Criteria
AddCriteriaEnergyPair - Class in org.anchoranalysis.mpp.feature.addcriteria
AddCriteriaEnergyPair(FeatureList<FeatureInputPairMemo>, AddCriteriaPair) - Constructor for class AddCriteriaEnergyPair
AddCriteriaFeatureRelationThreshold - Class in org.anchoranalysis.plugin.mpp.bean.addcriteria
AddCriteriaFeatureRelationThreshold() - Constructor for class AddCriteriaFeatureRelationThreshold
AddCriteriaNever<T> - Class in org.anchoranalysis.mpp.feature.addcriteria
AddCriteriaNever() - Constructor for class AddCriteriaNever
AddCriteriaOr - Class in org.anchoranalysis.mpp.feature.addcriteria
AddCriteriaOr() - Constructor for class AddCriteriaOr
AddCriteriaPair - Class in org.anchoranalysis.mpp.feature.addcriteria
AddCriteriaPair() - Constructor for class AddCriteriaPair
addDefaultOutputs(OutputEnabledMutable) - Method in class AnnotationComparisonAssigner: Adds any default outputs that should occur from the assigner.
addDefaultOutputs(OutputEnabledMutable) - Method in class FeatureCostAssigner
addDefaultOutputs(OutputEnabledMutable) - Method in class MaskIntersectionAssigner
addDictionary(String, Dictionary) - Method in class ImageInitialization: Adds a dictionary to named-collection of dictionaries.
AddDistanceTransform - Class in org.anchoranalysis.plugin.fiji.bean.define: Performs a Watershed on distance transform by bundling together several other beans.
AddDistanceTransform() - Constructor for class AddDistanceTransform
addDouble(String, double) - Method in class StatisticsToExport: Adds a statistic that is a double.
addDoubleAsString(String, double) - Method in class OverlayProperties
AddDualTransformer - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.dual
AddDualTransformer() - Constructor for class AddDualTransformer
addEdge(V, V) - Method in class GraphWithoutPayload: Add an edge between two vertices.
addEdge(V, V, P) - Method in class GraphWithPayload: Add an edge between two vertices.
AddEdgeFilters - Class in org.anchoranalysis.plugin.imagej.bean.define
AddEdgeFilters() - Constructor for class AddEdgeFilters
addEdges(V, Collection<V>) - Method in class GraphWithoutPayload: Adds edge(s) from the vertex from to each element in toCollection.
addEnabledOutputFirst(String...) - Method in class OutputEnabledMutable: Adds enabled first-level outputs.
addEnabledOutputs(OutputEnabledMutable) - Method in class OutputEnabledMutable: Adds enabled outputs from another OutputEnabledMutable.
addEnabledOutputSecond(String, String...) - Method in class OutputEnabledMutable: Adds enabled second-level outputs.
AddEnergy - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized
AddEnergy() - Constructor for class AddEnergy
addErrorDescription(StringBuilder) - Method in class ErrorNode
addErrorDescription(StringBuilder) - Method in class ErrorNodeImpl
addErrorDescription(StringBuilder) - Method in class ErrorNodeNull
addErrorLevel(String) - Method in class ProposerContext
addFormatted(String, Object...) - Method in class ErrorNode
addFormatted(String, Object...) - Method in class ErrorNodeImpl
addFormatted(String, Object...) - Method in class ErrorNodeNull
addForSlice(int, int) - Method in interface VoxelPartition
addForSlice(int, int) - Method in class VoxelPartitionHistogram
addFrom(BeanInstanceMap) - Method in class BeanInstanceMap: Populates the entries from another BeanInstanceMap
addFrom(List<NamedBean<?>>) - Method in class BeanInstanceMap: Populates from a list of NamedBean.
addFrom(NamedProvider<Stack>) - Method in class NamedStacks: Adds a Stack from a NamedProvider.
addFrom(CommandLineExtracter, InputArguments) - Static method in class AddInputOptions: Adds options to change the inputs from the command-line.
addFrom(CommandLineExtracter, OutputArguments) - Static method in class AddOutputOptions: Adds options to add/remove change the outputs the inputs from the command-line.
addFromList(FeatureList<FeatureInput>) - Method in class SharedFeatures: Add features from a feature-list.
addFromProviders(NamedProvider<FeatureList<FeatureInput>>) - Method in class SharedFeatures: Add features from a NamedProvider of feature-lists.
addFromWithPrefix(NamedProvider<Stack>, String) - Method in class NamedStacks: Like NamedStacks.addFrom(NamedProvider) but additionally adds a prefix to the name when adding.
addFromXmlFile(Path) - Method in class RootPathMap: Adds root-paths contained in a list of XML Beans in an xml file
addHistogram(Histogram) - Method in class Histogram: Adds the counts from another histogram to the current object.
addIgnoreInfinity(double) - Method in class AxisLimits
addInputOptions(Options) - Static method in class CommandLineOptions
AddInputOptions - Class in org.anchoranalysis.launcher.options.process: Adds options relating to inputting from the command-line.
addInt(String, int) - Method in class StatisticsToExport: Adds a statistic that is an int.
additionalLabelsFor(FileInput) - Method in class FromHistogram
additionalLabelsFor(ProvidesStackInput) - Method in class FromImage
additionalLabelsFor(ImageMetadataInput) - Method in class FromImageMetadata
additionalLabelsFor(T) - Method in class SingleRowPerInput: Additional labels for an input to include (after the identifier, and before any group labels).
addLabelToDataset(DefaultCategoryDataset, T, int, String, String) - Method in class BarPlot
addLabelToDataset(DefaultBoxAndWhiskerCategoryDataset, T, int, String, String) - Method in class BoxPlot
addLabelToDataset(S, T, int, String, String) - Method in class PlotIndexBaseCategorical
addManifestExperimentFileSet(Collection<File>, ManifestDeserializer, Logger) - Method in class ManifestCouplingDefinition
addMeanExtrema(String, double, double, double) - Method in class StatisticsToExport: Adds three statistics a mean, min and max.
addMeanExtrema(String, RunningSumExtrema) - Method in class StatisticsToExport: Like StatisticsToExport.addMeanExtrema(String, double, double, double) but determines the statistics from a RunningSumExtrema.
addMultiple(RGBColor, int) - Method in class ColorList: Append multiple entries for the same color to the end of the list.
addObjectsNoBoundingBoxChange(Collection<T>) - Method in class BoundedList: Adds elements without changing the bounding-box
addObjectsToGraph(ObjectCollection) - Method in class MergeGraph
addObjectsWithColor(ObjectCollectionProvider, RGBColor) - Method in class ColoredObjectCollection: Adds objects from a ObjectCollectionProvider all with one specific color
addOperationRecorder(WriteOperationRecorder) - Method in class Outputter
addOperationRecorder(WriteOperationRecorder) - Method in class OutputterChecked: Adds an additional operation recorder alongside any existing recorders.
addOptionsFromCommandLine() - Method in class AddInputOptions
AddOptionsFromCommandLine<T> - Class in org.anchoranalysis.launcher.options.process: Base class for adding options from command-line arguments.
AddOptionsFromCommandLine(CommandLineExtracter, T) - Constructor for class AddOptionsFromCommandLine
addOptionsFromCommandLine() - Method in class AddOptionsFromCommandLine: Maybe add options to the arguments from the command-line.
addOptionsFromCommandLine() - Method in class AddOutputOptions
AddOutputOptions - Class in org.anchoranalysis.launcher.options.process: Adds options relating to outputting from the command-line.
addResults(LabelledResultsVectorWithThumbnail) - Method in class FeatureCalculationContext
addResultsFor(LabelledResultsVector) - Method in class GroupedResults: Adds a result to the group-writer, but doesn't write yet.
addRow(LabelledResultsVector) - Method in class FeatureCSVWriter: Directly adds a row of feature-values.
addRow(List<TypedValue>) - Method in class FeatureCSVWriter: Directly adds a row in the form of typed-values.
addSharedObjectsDictionary(Optional<SharedObjects>, Optional<Dictionary>) - Method in class ImageInitialization
addShift(ReadableTuple3i) - Method in class ContiguousVoxelPath: Adds a shift to each point (modifying the existing points in memory), and returns them as a list
addSlice(VoxelBuffer<T>) - Method in interface ProjectableBuffer: Adds a slice to the buffer.
addStack(Provider<Stack>) - Method in class ArrangeRaster: Adds a stack to the existing list of stack-providers.
addString(String, String) - Method in class StatisticsToExport: Adds a statistic that is a String.
addTimestamp(long) - Method in class ClusterIdentifier: Adds a timestamp to the cluster.
addTo(Define) - Method in class Concatenate
addTo(Define) - Method in interface DefineAdder: Adds items to define.
addTo(Define) - Method in class FromXMLList
addTo(ObjectMask, int) - Method in interface VoxelsArithmetic: Adds a constant-value to each voxel but only for voxels inside an object-mask.
addTo(Define) - Method in class AddDistanceTransform
addTo(S, T) - Method in class GroupMapByName
addTo(Define) - Method in class AddEdgeFilters
addTo(Define) - Method in class VisualizeOnBackground
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 AddToDefaults
addToErrorNode(ErrorNode) - Method in exception ErrorNodeException
addToManager(MultiInputManager, String, String) - Method in class FilePathBaseAppendToManager
addToRow(List<TypedValue>) - Method in class RowLabels: Adds the identifiers to a row to be outputted in a features CSV.
addToStacks(String, Stack) - Method in class ImageInitialization
addToStacks(String, StackProvider) - Method in class ImageInitialization
addToStore(NamedProviderStore<T>, Logger) - Method in interface MultiInputSubMap: Copies all the existing entries into a NamedProviderStore.
addToStore(NamedProviderStore<T>, Logger) - Method in class OperationMap
addToStore(NamedProviderStore<TimeSequence>, Logger) - Method in class StackWithMap
addToStore(NamedProviderStore<TimeSequence>, int, Progress, Logger) - Method in class StackWithMap
addToStoreInferNames(NamedProviderStore<TimeSequence>, int, Progress, Logger) - Method in class NamedChannelsInput
addToStoreInferNames(NamedProviderStore<Stack>, Logger) - Method in interface ProvidesStackInput: Adds the current object to a named-store of stacks (using the default series).
addToStoreInferNames(NamedProviderStore<TimeSequence>, int, Progress, Logger) - Method in interface ProvidesStackInput: Adds the current object to a named-store of stacks.
addToStoreInferNames(NamedProviderStore<TimeSequence>, int, Progress, Logger) - Method in class MultiInput
addToStoreInferNames(NamedProviderStore<TimeSequence>, int, Progress, Logger) - Method in class ConvertNamedChannelsInputToStack
addToStoreWithName(String, NamedProviderStore<TimeSequence>, int, Progress, Logger) - Method in class NamedChannelsInput
addToStoreWithName(String, NamedProviderStore<TimeSequence>, int, Progress, Logger) - Method in interface ProvidesStackInput
addToStoreWithName(String, NamedProviderStore<TimeSequence>, int, Progress, Logger) - Method in class MultiInput
addToStoreWithName(String, NamedProviderStore<TimeSequence>, int, Progress, Logger) - Method in class ConvertNamedChannelsInputToStack
addToUpdatablePairList(UpdatableMarksList, VoxelizedMarkMemo) - Method in class VoxelizedMarksWithEnergy
addToVoxelList(int, int, int) - Method in class IndexByRegion
addTypedValuesTo(Collection<TypedValue>, int) - Method in class ResultsVector: Adds TypedValue representations of the results to a Collection.
addUnannotatedImage() - Method in interface ImageCounter: Add an image that did not have an associated annotation.
addUnannotatedImage() - Method in class ImageCounterList
addUnassignedLeft(ObjectMask) - Method in class OverlappingObjects: Add an unassigned object to the left set.
addUnassignedLeft(ObjectCollection) - Method in class OverlappingObjects: Add unassigned objects to the left set.
addUnassignedRight(ObjectMask) - Method in class OverlappingObjects: Add an unassigned object to the right set.
addUnassignedRight(ObjectCollection) - Method in class OverlappingObjects: Add unassigned objects to the right set.
addUncoupledJobs(Collection<File>, ManifestDeserializer, Logger) - Method in class ManifestCouplingDefinition: Adds job-manifests that don't have corresponding experiment-manifests.
addUnused(T) - Method in interface VoxelPartitionFactory
addUnused(Histogram) - Method in class VoxelPartitonFactoryHistogram
addVertex(V) - Method in class GraphWithoutPayload: Adds a vertex.
addVertex(V) - Method in class GraphWithPayload: Adds a vertex.
addWeightedKernelFactories(List<WeightedKernel<T, S>>) - Method in class KernelProposerOption
addWeightedKernelFactories(List<WeightedKernel<T, S>>) - Method in class KernelProposerOptionDual
addWeightedKernelFactories(List<WeightedKernel<T, S>>) - Method in class KernelProposerOptionSingle
addWithName(Define, String, AnchorBean<?>) - Method in class DefineAdderWithPrefixBean: Add an item to define with a name being added.
addWithUnits(String, double, DoubleUnaryOperator, SpatialUnits.UnitSuffix) - Method in class OverlayProperties
AdjacentFile - Class in org.anchoranalysis.plugin.quick.bean.input
AdjacentFile() - Constructor for class AdjacentFile
adjacentVerticesOutgoing(V) - Method in class GraphWithoutPayload: The vertices that are connected to a particular vertex by an outgoing edge.
adjacentVerticesOutgoing(V) - Method in class GraphWithPayload: The vertices that are connected to a particular vertex by an outgoing edge.
adjacentVerticesOutgoingStream(V) - Method in class GraphWithoutPayload: Like GraphWithoutPayload.adjacentVerticesOutgoing(V) but returns a Stream instead of a Set.
adjacentVerticesOutgoingStream(V) - Method in class GraphWithPayload: Like GraphWithPayload.adjacentVerticesOutgoing(V) but returns a Stream instead of a Set.
afterAllJobsAreExecuted(S, InputOutputContext) - Method in class Task: Called once after all calls to Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>).
afterAllJobsAreExecuted(NoSharedState, InputOutputContext) - Method in class TaskWithoutSharedState
afterAllJobsAreExecuted(AggregateSharedState, InputOutputContext) - Method in class AggregateAnnotations
afterAllJobsAreExecuted(ComparisonSharedState<T>, InputOutputContext) - Method in class CompareAnnotations
afterAllJobsAreExecuted(FeatureExporter<S>, InputOutputContext) - Method in class ExportFeatures
afterAllJobsAreExecuted(NoSharedState, InputOutputContext) - Method in class ConvertImageFormat
afterAllJobsAreExecuted(GroupedSharedState<S, T>, InputOutputContext) - Method in class GroupedStackBase
afterAllJobsAreExecuted(SharedStateFilteredImageOutput<T>, InputOutputContext) - Method in class ImageAssignLabel
afterAllJobsAreExecuted(NoSharedState, InputOutputContext) - Method in class ScaleImage
afterAllJobsAreExecuted(SharedStateSegmentInstance<T>, InputOutputContext) - Method in class SegmentInstanceWithModel
afterAllJobsAreExecuted(SharedStateSelectedSlice, InputOutputContext) - Method in class ExtractSlice
afterAllJobsAreExecuted(OutputSequenceIncrementing<Stack>, InputOutputContext) - Method in class MovieFromSlices
afterAllJobsAreExecuted(CSVWriter, InputOutputContext) - Method in class CombineCSV
afterAllJobsAreExecuted(RecordingCounter<T>, InputOutputContext) - Method in class CopyFiles
afterAllJobsAreExecuted(Summarizer<S>, InputOutputContext) - Method in class SummarizeBase
afterAllJobsAreExecuted(SharedStateRememberConverted<U, S>, InputOutputContext) - Method in class ConvertNamedChannels
afterAllJobsAreExecuted(NoSharedState, InputOutputContext) - Method in class ExportReportFeaturesFromManifest
afterAllJobsAreExecuted(CSVWriter, InputOutputContext) - Method in class ExportReportFeaturesFromMulti
afterAllJobsAreExecuted(NoSharedState, InputOutputContext) - Method in class ExportObjectsAsCroppedImages
afterAllJobsAreExecuted(FromCSVSharedState, InputOutputContext) - Method in class ExportObjectsFromCSV
afterAllJobsAreExecuted(ExperimentState, InputOutputContext) - Method in class SegmentMarksFromImage
AfterCondition - Interface in org.anchoranalysis.plugin.image.object.merge.condition
afterCreateObject(Point3i, Optional<Resolution>, RandomNumberGenerator) - Method in class VisitScheduler
afterCreateObject(Point3i, Optional<Resolution>, RandomNumberGenerator) - Method in class VisitSchedulerAnd
afterCreateObject(Point3i, Optional<Resolution>, RandomNumberGenerator) - Method in class VisitSchedulerConvexAboutRoot
afterCreateObject(Point3i, Optional<Resolution>, RandomNumberGenerator) - Method in class VisitSchedulerMaxDistanceAlongContour
afterCreateObject(Point3i, Optional<Resolution>, RandomNumberGenerator) - Method in class VisitSchedulerUniformSample
aggEnd(Aggregator) - Method in interface AggregateReceiver
aggEnd(Aggregator) - Method in class AggregateReceiverList
aggEnd(Aggregator) - Method in class ConsoleAggregatedReporter
aggEnd(Aggregator) - Method in class CSVReporterAggregated
aggEnd(Aggregator) - Method in class Log4JReporter
aggEnd(Aggregator) - Method in class OptimizationStepLogReporter
aggEnd(Aggregator) - Method in class TextFile
AggIDCounter - Class in org.anchoranalysis.mpp.segment.optimization.feedback.aggregate
AggIDCounter(int) - Constructor for class AggIDCounter
AggregateAnnotations<S extends AnnotatorStrategy> - Class in org.anchoranalysis.plugin.annotation.bean.aggregate: Aggregates many per-image annotations together in form of a CSV file.
AggregateAnnotations() - Constructor for class AggregateAnnotations
AggregateReceiver<T> - Interface in org.anchoranalysis.mpp.segment.optimization.feedback.aggregate
AggregateReceiverList<T> - Class in org.anchoranalysis.mpp.segment.optimization.feedback.aggregate
AggregateReceiverList() - Constructor for class AggregateReceiverList
aggregateResults(List<Double>) - Method in class FeatureIntersectingObjectsSingleElement
aggregateResults(List<Double>) - Method in class MaxFeatureIntersectingObjects
aggregateResults(List<Double>) - Method in class MinFeatureIntersectingObjectsAboveThreshold
aggregateResults(List<Double>) - Method in class NumberIntersectingObjectsAboveThreshold
AggregateTriggerBank<T> - Class in org.anchoranalysis.mpp.segment.optimization.feedback.aggregate
AggregateTriggerBank(ExtractScoreSize<T>) - Constructor for class AggregateTriggerBank
Aggregator - Class in org.anchoranalysis.mpp.segment.optimization.feedback.aggregate
Aggregator(int) - Constructor for class Aggregator
AggregatorException - Exception in org.anchoranalysis.mpp.segment.optimization.feedback.aggregate
AggregatorException() - Constructor for exception AggregatorException
AggregatorException(String) - Constructor for exception AggregatorException
AggregatorException(Exception) - Constructor for exception AggregatorException
aggReport(Reporting<T>, Aggregator) - Method in interface AggregateReceiver
aggReport(Reporting<T>, Aggregator) - Method in class AggregateReceiverList
aggReport(Reporting<VoxelizedMarksWithEnergy>, Aggregator) - Method in class ConsoleAggregatedReporter
aggReport(Reporting<VoxelizedMarksWithEnergy>, Aggregator) - Method in class CSVReporterAggregated
aggReport(Reporting<VoxelizedMarksWithEnergy>, Aggregator) - Method in class Log4JReporter
aggReport(Reporting<VoxelizedMarksWithEnergy>, Aggregator) - Method in class OptimizationStepLogReporter
aggReport(Reporting<VoxelizedMarksWithEnergy>, Aggregator) - Method in class TextFile
aggStart(FeedbackBeginParameters<T>, Aggregator) - Method in interface AggregateReceiver
aggStart(FeedbackBeginParameters<T>, Aggregator) - Method in class AggregateReceiverList
aggStart(FeedbackBeginParameters<VoxelizedMarksWithEnergy>, Aggregator) - Method in class ConsoleAggregatedReporter
aggStart(FeedbackBeginParameters<VoxelizedMarksWithEnergy>, Aggregator) - Method in class CSVReporterAggregated
aggStart(FeedbackBeginParameters<VoxelizedMarksWithEnergy>, Aggregator) - Method in class Log4JReporter
aggStart(FeedbackBeginParameters<VoxelizedMarksWithEnergy>, Aggregator) - Method in class OptimizationStepLogReporter
aggStart(FeedbackBeginParameters<VoxelizedMarksWithEnergy>, Aggregator) - Method in class TextFile
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 All
allAssociatedPaths() - Method in interface InputFromManager: A path to all files associated with the input, including InputFromManager.pathForBinding().
allChannelsAsStack(int, Logger) - Method in interface NamedChannelsForSeries
allChannelsAsStack(int, Logger) - Method in class NamedChannelsForSeriesConcatenate
allChannelsAsStack(int, Logger) - Method in class NamedChannelsForSeriesMap
allChannelsEightBit() - Method in class StackWriteAttributes: Mark the attributes to indicate that channels are no longer guaranteed to be 8-bit.
allChannelsHaveIdenticalType() - Method in class Stack: Determines if all channels have an identical voxel data-type.
allChannelsHaveType(VoxelDataType) - Method in class RGBStack: Determines if all channels have a specific data-type.
allChannelsHaveType(VoxelDataType) - Method in class Stack: Determines if all channels have a specific data-type.
allChannelsHaveType(VoxelDataType) - Method in class TimeSequence
allExtensions() - Method in enum ImageFileFormat: All extensions associated with a file-format.
allFileTypes() - Method in class ConcatenateFileTypes
allHeaders() - Method in class LabelHeaders: The non-group and group headers combined (in this order respectively)
allImageExtensions() - Static method in class FormatExtensions: The extensions of all image file formats as enumerated in ImageFileFormat.
allLabels(NoSharedState) - Method in class BinaryOutcomeImageLabeller
allLabels(ImageCSVLabellerInitialization) - Method in class ImageCSVLabeller
allLabels(T) - Method in class ImageLabeller: A set of identifiers for all groups that can be outputted by the labeller.
allLabels(ImageLabellerStringMapInitialization<T>) - Method in class ImageLabellerStringMap
allMatchIntensity(ObjectMask, Voxels<T>, IntPredicate) - Static method in class IterateVoxelsObjectMask: Do all points on an object-mask match a predicate on the point's voxel-intensity?
allocate(int) - Static method in class UnsignedByteBuffer: Allocates a new buffer of unsigned-bytes.
allocate(int) - Static method in class UnsignedIntBuffer: Allocates a new (direct) buffer of unsigned-ints.
allocate(int) - Static method in class UnsignedShortBuffer: Allocates a new (direct) buffer of unsigned-shorts.
allocateFloat(int) - Static method in class VoxelBufferFactory: Allocates a new float voxel-buffers of given size.
allocateFloatArray(int) - Static method in class VoxelBufferFactory: Creates an array of float voxel-buffers of given size.
allocateUnsignedByte(int) - Static method in class VoxelBufferFactory: Allocates a new unsigned byte voxel-buffer of given size.
allocateUnsignedByteArray(int) - Static method in class VoxelBufferFactory: Creates an array of unsigned byte voxel-buffers of given size.
allocateUnsignedInt(int) - Static method in class VoxelBufferFactory: Allocates a new unsigned int voxel-buffers of given size.
allocateUnsignedIntArray(int) - Static method in class VoxelBufferFactory: Creates an array of unsigned int voxel-buffers of given size.
allocateUnsignedShort(int) - Static method in class VoxelBufferFactory: Allocates a new unsigned short voxel-buffers of given size.
allocateUnsignedShortArray(int) - Static method in class VoxelBufferFactory: Creates an array of unsigned short voxel-buffers of given size.
AllowEmpty - Annotation Type in org.anchoranalysis.bean.annotation: Indicates that a String is allowed be empty, otherwise by default it must be non-empty.
AllSlicesMaskEverythingNonZero - Class in org.anchoranalysis.plugin.mpp.bean.region: Only considers voxels with non-zero intensity.
AllSlicesMaskEverythingNonZero() - Constructor for class AllSlicesMaskEverythingNonZero
AllSlicesMaskNonZero - Class in org.anchoranalysis.plugin.mpp.bean.region: Gets all slices where indexNonZero has at least one non-zero pixel in that slice
AllSlicesMaskNonZero() - Constructor for class AllSlicesMaskNonZero
allSuccessful() - Method in class 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 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 AllValuesOn
ALPHA - Static variable in class 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 Always
always2D(String) - Static method in class OutputSequenceStackFactory: The stacks that are outputted are guaranteed to be two-dimensional.
always2D(boolean) - Method in class 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 AlwaysAllowed
alwaysExecuteBeforeCallingLibrary() - Static method in class CVInit: This routine must always be executed at least once before calling any routines in the OpenCV library
AlwaysNew<T extends FeatureInput> - Class in org.anchoranalysis.feature.session.replace: Always create a new session-input with no reuse or caching.
AlwaysNew(CacheCreator) - Constructor for class AlwaysNew: Constructor with default means of creating a session-input
AlwaysNew(CacheCreator, ChildCacheFinder) - Constructor for class 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 AlwaysReject
AnchorBean<F> - Class in org.anchoranalysis.bean: The base class of all beans used in Anchor.
AnchorBean() - Constructor for class AnchorBean
AnchorBeanFactory - Class in org.anchoranalysis.bean.xml.factory: Base class for all Anchor-specific bean factories.
AnchorBeanFactory() - Constructor for class AnchorBeanFactory
AnchorCheckedException - Exception in org.anchoranalysis.core.exception: A base class for all checked exceptions used on the Anchor platform.
AnchorCheckedException() - Constructor for exception AnchorCheckedException: Creates without message or cause.
AnchorCheckedException(String, Throwable) - Constructor for exception AnchorCheckedException: Creates with message and cause.
AnchorCheckedException(String) - Constructor for exception AnchorCheckedException: Creates with only a message.
AnchorCheckedException(Throwable) - Constructor for exception AnchorCheckedException: Creates with only a cause.
AnchorCombinableException - Exception in org.anchoranalysis.core.exception.combinable: An exception that can be combined with similar exceptions and summarized.
AnchorCombinableException(String, Throwable) - Constructor for exception 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 AnchorDefaultBeanFactory
AnchorFriendlyCheckedException - Exception 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, Throwable) - Constructor for exception AnchorFriendlyCheckedException: A user-friendly error message and its cause.
AnchorFriendlyCheckedException(String) - Constructor for exception AnchorFriendlyCheckedException: A user-friendly error message WITHOUT a cause.
AnchorFriendlyCheckedException(Throwable) - Constructor for exception AnchorFriendlyCheckedException: A wrapped exception.
AnchorFriendlyRuntimeException - Exception 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, Throwable) - Constructor for exception AnchorFriendlyRuntimeException: A user-friendly error message and its cause.
AnchorFriendlyRuntimeException(String) - Constructor for exception AnchorFriendlyRuntimeException: A user-friendly error message without a cause.
AnchorFriendlyRuntimeException(Throwable) - Constructor for exception AnchorFriendlyRuntimeException: A wrapped exception.
AnchorImpossibleSituationException - Exception 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 AnchorImpossibleSituationException: Default constructor.
AnchorImpossibleSituationException(String) - Constructor for exception AnchorImpossibleSituationException: Creates with a specific message explaining the exception.
AnchorNeverOccursException - Exception in org.anchoranalysis.core.exception: This is an exceotion that should never be thrown, but can be used for type-safety where an exception is needed
AnchorNeverOccursException() - Constructor for exception AnchorNeverOccursException
AnchorRuntimeException - Exception in org.anchoranalysis.core.exception: A base class for all unchecked (runtime) exceptions used on the Anchor platform.
AnchorRuntimeException() - Constructor for exception AnchorRuntimeException: Creates without message or cause.
AnchorRuntimeException(String, Throwable) - Constructor for exception AnchorRuntimeException: Creates with message and cause.
AnchorRuntimeException(String) - Constructor for exception AnchorRuntimeException: Creates with only a message.
AnchorRuntimeException(Throwable) - Constructor for 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 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() - Constructor for class And
And - Class in org.anchoranalysis.plugin.image.bean.object.filter.combine: Applies multiples filter with logical AND i.e.
And() - Constructor for class And
AndCondition - Class in org.anchoranalysis.plugin.image.object.merge.condition: Combines two UpdatableBeforeConditions as LOGICAL ANDs
AndCondition(UpdatableBeforeCondition, UpdatableBeforeCondition) - Constructor for class 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 AndKernel: Create for the two kernels.
AndList - Class in org.anchoranalysis.plugin.mpp.bean.check
AndList() - Constructor for class AndList
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 AndObjectsWithMasks
AngleRotation - Class in org.anchoranalysis.plugin.mpp.bean.proposer.orientation
AngleRotation() - Constructor for class AngleRotation
AnisotropicDiffusion - Class in org.anchoranalysis.plugin.fiji.bean.channel.provider: Perona-Malik Anisotropic Diffusion
AnisotropicDiffusion() - Constructor for class AnisotropicDiffusion
AnnealScheme - Class in org.anchoranalysis.mpp.bean: Base class for approaches to simulated annealing.
AnnealScheme() - Constructor for class AnnealScheme
Annotation - Interface in org.anchoranalysis.annotation: Base class for types of image annotations.
AnnotationAggregateCSVGenerator - Class in org.anchoranalysis.plugin.annotation.bean.aggregate
AnnotationAggregateCSVGenerator() - Constructor for class AnnotationAggregateCSVGenerator
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 AnnotationBackground
AnnotationComparisonAssigner<T extends Assignment<ObjectMask>> - Class in org.anchoranalysis.plugin.annotation.bean.comparison.assigner: Compares elements in an annotation to elements from an experiment.
AnnotationComparisonAssigner() - Constructor for class AnnotationComparisonAssigner
AnnotationComparisonInput<T extends InputFromManager> - Class in org.anchoranalysis.plugin.annotation.comparison
AnnotationComparisonInput(T, Tuple2<ComparableSource, ComparableSource>, Tuple2<String, String>, StackReader) - Constructor for class AnnotationComparisonInput
AnnotationComparisonInputManager<T extends InputFromManager> - Class in org.anchoranalysis.plugin.annotation.bean.comparison
AnnotationComparisonInputManager() - Constructor for class AnnotationComparisonInputManager
AnnotationDeleter - Interface in org.anchoranalysis.annotation.io: Allows an annotation to be deleted from the file-system.
annotationExistsAt(Path) - Method in class DualMarksAnnotationReader: Whether an annotation exists at a particular path on the file-system.
AnnotationInputManager<T extends ProvidesStackInput,S extends AnnotatorStrategy> - Class in org.anchoranalysis.annotation.io.bean: An InputManager that provides annotations corresponding to images.
AnnotationInputManager() - Constructor for class AnnotationInputManager
AnnotationLabel - Class in org.anchoranalysis.plugin.annotation.bean.label
AnnotationLabel() - Constructor for class AnnotationLabel
annotationLabelFor(ProvidesStackInput, Logger) - Method in class AnnotatorStrategy: A human-friendly textual description of the annotation, or Optional.empty() if no label is available.
annotationLabelFor(ProvidesStackInput, Logger) - Method in class ImageLabelStrategy
annotationLabelFor(ProvidesStackInput, Logger) - Method in class MarkProposerStrategy
AnnotationReader<T extends Annotation> - 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 extends AnnotatorStrategy> - Class in org.anchoranalysis.annotation.io: One particular annotation, associated with its strategy.
AnnotationWithStrategy(ProvidesStackInput, T) - Constructor for class AnnotationWithStrategy: Creates for a particular input and associated annotation strategy.
AnnotationWriter<T extends Annotation> - 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 AnnotatorStrategy
Anonymize - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming: Copies files to a number 001, 002 etc.
Anonymize() - Constructor for class Anonymize
AnonymizeSharedState - Class in org.anchoranalysis.plugin.io.shared
AnonymizeSharedState(NumberToStringConverter, Map<Integer, Integer>) - Constructor for class AnonymizeSharedState
any() - Method in class VoxelsUntyped: Exposes without any specific buffer type.
anyDimensionIsLargerThan(Extent) - Method in class Extent: Returns true if any dimension in this extent is larger than the corresponding dimension in other extent.
anyExists() - Method in class PredicateAtCorner
anyExists() - Method in class PredicateImplementation
anyExists() - Method in interface VoxelsPredicate: Does at least one value satisfy the predicate - across all voxels?
anyMatch(Predicate<ObjectMask>) - Method in class ObjectMaskStream: Does the predicate evaluate to true on any object in the collection?
anyPredicateMatch(Voxels<T>, Predicate<T>) - Static method in class IterateVoxelsAll: Tries to apply a predicate to all the remaining buffer locations, returning true if the predicate matches.
AnySliceCenterOnMask - Class in org.anchoranalysis.plugin.mpp.bean.check: The center ps of at least one slice should be on the stack Tries overall center point first, and then projects it onto each slice
AnySliceCenterOnMask() - Constructor for class AnySliceCenterOnMask
append(StatisticsToExport) - Method in class StatisticsToExport: Appends the names and values from another AnnotationComparison to the existing.
append(Optional<FeatureList<T>>) - Method in class FeatureList: Appends the features one or more (optional) feature-lists to the existing list.
AppendCsv - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend: A CSV that is appended from the root of a project
AppendCsv() - Constructor for class AppendCsv
AppendDictionary - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
AppendDictionary() - Constructor for class AppendDictionary
appendExtension(String, Optional<String>) - Static method in class 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 ExtensionUtilities: Like ExtensionUtilities.appendExtension(String, Optional) but accepts and returns a Path.
AppendFilePath - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
AppendFilePath() - Constructor for class AppendFilePath
AppendHistogram - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
AppendHistogram() - Constructor for class AppendHistogram
AppendMarks - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
AppendMarks() - Constructor for class AppendMarks
AppendObjects - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
AppendObjects() - Constructor for class AppendObjects
AppendStack - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend: A stack from a stack-collection
AppendStack() - Constructor for class AppendStack
AppendStackDirect - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend: A stack from a stack-collection
AppendStackDirect() - Constructor for class AppendStackDirect
apply(Throwable, Writer, String, int, boolean) - Static method in class 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(S, T) - Method in interface CheckedBiFunction: Calls the function.
apply(S) - Method in interface CheckedFunction: Calls the function.
apply(int) - Method in interface CheckedIntFunction: Calls the function
apply(T) - Method in interface CheckedUnaryOperator: Applies the operation.
apply(int, int) - Method in interface IntBinaryOperation: Applies the operation on two integer values.
apply(ImageInitialization) - Static method in class CreateCombinedStack
apply(Mask, Mask) - Static method in class MaskAnd: Performs a logical and operation on each voxel in two masks, writing the result onto the second mask.
apply(Voxels<UnsignedByteBuffer>, Voxels<UnsignedByteBuffer>, BinaryValuesByte, BinaryValuesByte) - Static method in class MaskAnd: Performs a logical and operation on each voxel in two Voxels (considered to be masks), writing the result onto the second mask.
apply(Mask, Mask) - Static method in class 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 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 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(List<ChannelEntry>) - Method in class NamedEntriesCreator
apply(BinaryKernel, BinaryVoxels<UnsignedByteBuffer>, KernelApplicationParameters) - Static method in class ApplyKernel: Apply the kernel to BinaryVoxels<UnsignedByteBuffer> using the same binary-values as voxels to calculate a value for each voxel.
apply(IFormatReader, ReadOptions, int) - Method in class DimensionsCreator
apply(String, Path) - Static method in class WriteStringToFile
applyAsDouble(T, U) - Method in interface CheckedToDoubleBiFunction: Applies this function to the given arguments.
applyAsFloat(int) - Method in interface IntToFloatFunction: Applies this function to the given argument.
applyAsInt(S) - Method in interface CheckedToIntFunction: Calls the function
applyCoefficientsToMark(DoubleMatrix2D, Mark, Dimensions) - Method in class LinearLeastSquaresViaNormalEquationBase
applyDelta(MultiLevelOutputEnabled) - Method in class OutputEnabledDelta: Applies the changes to enable or disable additional outputs, if they are defined.
applyFitResultToMark(Ellipsoid, Dimensions, double) - Method in class FitResult
applyForCount(CountKernel, BinaryVoxels<UnsignedByteBuffer>, KernelApplicationParameters) - Static method in class ApplyKernel: Applies the kernel to voxels and sums the returned value.
applyForCount(CountKernel, BinaryVoxels<UnsignedByteBuffer>, BoundingBox, KernelApplicationParameters) - Static method in class ApplyKernel: Applies the kernel to voxels and sums the returned value.
applyForCount(BinaryKernel, BinaryVoxels<UnsignedByteBuffer>, KernelApplicationParameters) - Static method in class ApplyKernel: Applies a BinaryKernel to voxels and counts how many true values occur en aggregate.
ApplyImageJMorphologicalOperation - Class in org.anchoranalysis.plugin.imagej.mask: Applies an ImageJ (2D) morphological operation to voxels
applyInitializationIfPossibleTo(Object, Object, Logger) - Method in class 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 Dilate
applyMorphologicalOperation(Mask, boolean) - Method in class Erode
applyMorphologicalOperation(Mask, boolean) - Method in class MorphologicalOperatorBase
applyMorphologicalOperation(ObjectMask, Optional<Extent>) - Method in class Dilate
applyMorphologicalOperation(ObjectMask, Optional<Extent>) - Method in class Erode
applyMorphologicalOperation(ObjectMask, Optional<Extent>) - Method in class ObjectCollectionProviderMorphological
applyOperation(UnaryOperator<Stack>, Optional<Dimensions>) - Method in class NamedStacks: Applies an operation on each Stack in the collection and returns a new derived collection.
applyOperation(ObjectMask, Extent, boolean) - Method in class CalculateIncrementalOperationMap
applyOperation(ObjectMask, Extent, boolean) - Method in class CalculateDilationMap
applyOperation(ObjectMask, Extent, boolean) - Method in class CalculateErosionMap
applyOperation(BinaryVoxels<UnsignedByteBuffer>, String, int) - Static method in class ApplyImageJMorphologicalOperation
applyRadiiSubtractScale(double, double) - Method in class FitResult
applyRankFilter(Channel, int, int) - Static method in class FilterHelper: Applies a 2D rank-filter to each slice independently.
applyStrategy(MergeCandidate) - Method in class MergeStrategy
applyUntilPositive(CountKernel, BinaryVoxels<UnsignedByteBuffer>, BoundingBox, KernelApplicationParameters) - Static method in class ApplyKernel: Applies the kernel to voxels until a positive value is returned, then exits with true.
ArbitraryInsidePoint - Class in org.anchoranalysis.plugin.image.feature.bean.object.single: Calculates deterministicly a point that is definitely inside the object-mask.
ArbitraryInsidePoint(String) - Constructor for class ArbitraryInsidePoint
ArbitraryInsidePoint() - Constructor for class ArbitraryInsidePoint
ArbitraryPointCommon - Class in org.anchoranalysis.mpp.feature.addcriteria: If one arbitrarily point overlaps between two MarkPointList then true, otherwise false
ArbitraryPointCommon() - Constructor for class ArbitraryPointCommon
Area<T extends FeatureInputEnergy> - 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 Area
areAllPointsInBigNeighborhood(List<Point3i>) - Static method in class 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 physical coordinates
AreaPhysical() - Constructor for class AreaPhysical
AreaPixels - Class in org.anchoranalysis.image.bean.unitvalue.extent.area: Area expressed as square pixels
AreaPixels(double) - Constructor for class AreaPixels
AreaPixels() - Constructor for class AreaPixels
areaXY() - Method in class Dimensions: Size in X multiplied by size in Y.
areaXY() - Method in class Extent: Size in X multiplied by size in Y.
areDocumentsEqual(Document, Document) - Static method in class CompareXML: Are two XML-documents equal in content, ignoring whitespace and comments?
areEqual(double, double) - Static method in class DoubleUtilities: Are the two numbers equal?
areEqual(float, float) - Static method in class FloatUtilities: Are the two numbers equal?
arePointsNeighbors(Point3i, Point3i) - Static method in class 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 Channel: Interface that allows manipulation of voxel intensities via arithmetic operations.
arithmetic() - Method in class BoundedVoxels: Interface that allows manipulation of voxel intensities via arithmetic operations.
arithmetic() - Method in class Voxels: Interface that allows manipulation of voxel intensities via arithmetic operations.
arithmetic() - Method in class 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 ArithmeticWithConstantBase
ArithmeticWithConstantConditionallyWriteBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
ArithmeticWithConstantConditionallyWriteBase() - Constructor for class ArithmeticWithConstantConditionallyWriteBase
ArrangeRaster - Class in org.anchoranalysis.image.bean.provider.stack: Creates a stack that tiles (or otherwise combines) other providers
ArrangeRaster(boolean, boolean) - Constructor for class ArrangeRaster
ArrangeRaster() - Constructor for class ArrangeRaster
ArrangeStack - Interface in org.anchoranalysis.image.bean.nonbean.spatial.arrange
ArrangeStackBean - Class in org.anchoranalysis.image.bean.spatial.arrange
ArrangeStackBean() - Constructor for class ArrangeStackBean
ArrangeStackException - Exception in org.anchoranalysis.image.bean.nonbean.spatial.arrange
ArrangeStackException(String) - Constructor for exception ArrangeStackException
ArrangeStackException(Exception) - Constructor for exception ArrangeStackException
array() - Method in class UnsignedByteBuffer: The array of the buffer ala ByteBuffer.array().
array() - Method in class UnsignedIntBuffer: The array of the buffer ala IntBuffer.array().
array() - Method in class UnsignedShortBuffer: The array of the buffer ala ShortBuffer.array().
as(boolean) - Static method in enum OutsideKernelPolicy: Multiplexes between OutsideKernelPolicy.AS_ON and OutsideKernelPolicy.AS_OFF.
asArray(boolean) - Static method in class RGBChannelNames: Creates an array with all channel-names in R-G-B order.
asByte() - Method in class BinaryValuesInt: Derives a BinaryValuesByte representation from the current values.
asByte() - Method in class VoxelsUntyped: Casts to use a UnsignedByteBuffer if the voxels contain this data-type, otherwise throws a IncorrectVoxelTypeException.
asByte(ImageProcessor) - Static method in class ConvertToVoxelBuffer: Convert a ImageProcessor to VoxelBuffer<UnsignedByteBuffer>
asCollection() - Method in class StackSeries
AsCollection - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.all
AsCollection() - Constructor for class AsCollection
asCollectionOrderNotPreserved() - Method in class ScaledElements: Returns the scaled-elements as a collection but without preserving the original element order.
asExtent() - Method in class SizeXY: Creates an extent with identical width and height and depth (z-extent) of 1
asExtent(int) - Method in class SizeXY: Creates an extent with identical width and height and a specific depth (z-extent)
asFile() - Method in interface InputFromManager: Expresses the input as a file with a name (the unique identifier).
asFloat() - Method in class VoxelsUntyped: Casts to use a FloatBuffer if the voxels contain this data-type, otherwise throws a IncorrectVoxelTypeException.
asFloat(ImageProcessor) - Static method in class ConvertToVoxelBuffer: Convert a ImageProcessor to VoxelBuffer<FloatBuffer>
asGraph() - Method in class IntersectingObjects: Constructs a graph where each vertex is an element and an edge exists between any elements that intersect.
asInt() - Method in class BinaryValuesByte: Derives a BinaryValuesInt representation from the current values.
asInt() - Method in class VoxelsUntyped: Casts to use a UnsignedIntBuffer if the voxels contain this data-type, otherwise throws a IncorrectVoxelTypeException.
asList() - Method in class FeatureList: Exposes the underlying list of features in this data-structure.
asList() - Method in class FeatureNameList: Exposes the underlying list of names.
asList(boolean) - Static method in class RGBChannelNames: Creates a list with all channel-names in R-G-B order.
asList() - Method in class ObjectCollection: Exposes the underlying objects as a list.
asList() - Method in class OverlayCollection
asListChannels() - Method in class Stack: Derives a List of Channels from those in the Stack, preserving order.
asListOrderPreserved(List<T>) - Method in class ScaledElements: Returns a list of scaled-elements corresponding to a list of unscaled-elements.
asMap() - Method in class ScaledElements: The underlying map used to map an unscaled object to its scaled counterpart.
AsMark - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
AsMark() - Constructor for class AsMark
asMarks() - Method in class EnergyMemoList
asNamedStacks() - Method in class NamedStacksUniformSize: Exposes the stacks as a NamedStacks.
AsObject - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
AsObject() - Constructor for class AsObject
asObjectMask() - Method in class 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 AsObjectMask
asOperationFailedException() - Method in exception GetOperationFailedException: Converts to a OperationFailedException using an identical message.
asPath() - Method in class RootPath: Exposes the path field as a Path.
asPath(boolean) - Method in class DirectoryWithPrefix: A path that combines the directory and fileNamePrefix and delimiter.
asPoint() - Method in class Padding
asPredicateDouble() - Method in class RelationToThreshold: Expresses the relation as a predicate on values, where only values that fulfill the relation to threshold are true.
asPredicateInt() - Method in class RelationToThreshold: Like RelationToThreshold.asPredicateDouble() but expresses the relationship for an integer.
asScaleFactor() - Method in class ScaleFactorInt: Converts to a ScaleFactor that accepts floating-point values.
assertCalc(ResultsVector, Object...) - Static method in class ResultsVectorTestUtilities
assertDoubleResult(String, Feature<T>, T, double) - Static method in class FeatureTestCalculator
assertDoubleResult(String, Feature<T>, T, Optional<SharedObjects>, double) - Static method in class FeatureTestCalculator
assertDoubleResult(String, Feature<T>, T, T, double, double) - Static method in class FeatureTestCalculatorDuo
assertIntResult(String, Feature<T>, T, int) - Static method in class FeatureTestCalculator
assertIntResult(String, Feature<T>, T, Optional<SharedObjects>, int) - Static method in class FeatureTestCalculator
assertIntResult(String, Feature<T>, T, T, int, int) - Static method in class FeatureTestCalculatorDuo
assertValid() - Method in class MarksWithEnergyBreakdown
assertValid() - Method in class EnergySavedInd
assertValid() - Method in class EnergySavedPairs
asSet(boolean) - Static method in class RGBChannelNames: Creates a set of the channel names.
asSet(Progress, Logger) - Method in interface ProvidesStackInput: Exposes the input as a set of named stacks (inferring the names).
asSet() - Method in class RTree: All elements contained within the tree, as a Set.
asShort() - Method in class VoxelsUntyped: Casts to use a UnsignedShortBuffer if the voxels contain this data-type, otherwise throws a IncorrectVoxelTypeException.
asShort(ImageProcessor) - Static method in class ConvertToVoxelBuffer: Convert a ImageProcessor to VoxelBuffer<UnsignedShortBuffer>
assignAccepted(DualMarks) - Method in class DualMarksAnnotation: Assigns marks with an overall accepted state.
assignBestFromCurrent() - Method in class DualState
assignBoundingBox(BoundingBox) - Method in class BoundedList: Assigns a new containing bounding-box.
assignBoundingBoxAndMap(BoundingBox, UnaryOperator<T>) - Method in class BoundedList: Assigns a new containing bounding-box and maps each individual element.
assignColor(Point3i, RGBColor) - Method in class RGBStack: Assigns a RGBColor to the respective channels for a single voxel.
assignCopyNonInputs() - Method in class InputArguments
assignCurrent(Optional<T>) - Method in class DualState
assignDescription(ManifestDirectoryDescription) - Method in class MutableDirectory: Assigns a description, which may not already exist.
assignEachMatchingPoint(Voxels<?>, IntPredicate, int) - Static method in class IterateVoxelsAll: Assigns a value to any voxel whose intensity matches a predicate, reading and writing the buffer as an int.
AssignerMatchClass<P extends BeanInitialization> - 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 AssignerMatchClass
AssignFeatureNameUtilities - Class in org.anchoranalysis.feature.name: Utilities for assigning a name to a feature.
assignFilterExtensions(Set<String>) - Method in class InputArguments
assignFilterExtensionsIfMissing(Optional<Set<String>>) - Method in class InputArguments
assignFilterGlob(String) - Method in class InputArguments
assignFrom(Mark) - Method in class 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 AssignFromChannel
AssignFromDictionary - Class in org.anchoranalysis.plugin.image.bean.channel.provider.assign
AssignFromDictionary() - Constructor for class 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 AssignFromIntersectingObjects
assignFunction(String) - Method in class ManifestDescription: Assigns a new function.
assignIdentifierSubrange(IndexRangeNegative) - Method in class InputArguments: 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 AssignerMatchClass
assignInitializationToProperties(Object, Object, Object, Logger) - Method in interface InitializationParameterAssigner: Assigns the parameter to the bean.
assignInputDirectory(Optional<Path>) - Method in class InputArguments: Sets an input-directory.
assignLogger(Logger) - Method in class OutputterChecked: Assigns a logger to the outputter, which is used to output warnings or messages when outputting.
assignMaximumIndex(int) - Method in class IncreasingIntegers
assignMaximumIndex(int) - Method in class IncrementingIntegers
assignMaximumIndex(int) - Method in class SequenceType: If the sequence-type supports a different maximum-index to that derived from the elements SequenceType.update(T), this assigns it.
assignMaximumIndex(int) - Method in class StringsWithoutOrder
assignMaxNumberProcessors(String) - Method in class TaskArguments
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 AssignmentColorPool: Creates with a number and colors for the paired objects, and defaults colors for unpaired.
AssignmentColorPool(int, ColorScheme, ColorScheme, boolean) - Constructor for class AssignmentColorPool
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 AssignmentGenerator
AssignMode<S,T,U> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode: How assignments and other decisions are made in the SimulatedAnnealing optimizaton
AssignMode() - Constructor for class AssignMode
assignModelDirectory(Path) - Method in class InputArguments
assignName(String) - Method in class ClusterIdentifier: Assigns a name for the cluster.
assignOff() - Method in class Mask: Interface that allows assignment of an off state to all or subsets of the voxels.
assignOff() - Method in class BinaryVoxels: Creates an assigner that may set the off state in subsequently specified regions of the voxels.
assignOff() - Method in class ObjectMask: Assigns the off value to voxels, expecting global coordinates.
assignOn() - Method in class Mask: Interface that allows assignment of an on state to all or subsets of the voxels.
assignOn() - Method in class BinaryVoxels: Creates an assigner that may set the on state in subsequently specified regions of the voxels.
assignOn() - Method in class ObjectMask: Assigns the on value to voxels, expecting global coordinates.
assignOutputDirectory(Path) - Method in class OutputPrefixerSettings
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 AssignOverlappingObjects
assignParentDirectory(Optional<MutableDirectory>) - Method in class MutableDirectory
assignPath(Path) - Method in class SubdirectoryBase
assignPaths(List<Path>) - Method in class InputArguments
assignPaused(DualMarks) - Method in class DualMarksAnnotation: Assigns marks with an overall paused state.
AssignPermutationException - Exception in org.anchoranalysis.bean.permute.assign: When the assignment of a permuted value to a property cannot succeed.
AssignPermutationException(String) - Constructor for exception AssignPermutationException: Create with an error message.
assignPrevious(double, int) - Method in class UnchangedBase: Assigns the previous value to be remembered for comparison next time.
assignPrevious(double, int) - Method in class UnchangedScore
assignPrevious(double, int) - Method in class UnchangedSize
AssignPriority - Class in org.anchoranalysis.plugin.image.object.merge.priority
AssignPriority() - Constructor for class AssignPriority
assignPriority(ObjectVertex, ObjectVertex, GraphLogger) - Method in class AssignPriority: Assigns a priority to a potential merge
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 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 AssignPriorityFromPair
assignPriorityToEdge(ObjectVertex, ObjectVertex, ObjectMask, ErrorReporter) - Method in class AssignPriority
assignPriorityToEdge(ObjectVertex, ObjectVertex, ObjectMask, ErrorReporter) - Method in class AssignPriorityFromImprovement
assignPriorityToEdge(ObjectVertex, ObjectVertex, ObjectMask, ErrorReporter) - Method in class AssignPriorityFromPair
assignProposal(OptimizationStep<S, T, U>, TransformationContext, KernelWithIdentifier<S, U>) - Method in interface KernelAssigner
assignProposal(Optional<T>, KernelWithIdentifier<S, V>) - Method in class OptimizationStep
assignProposal(OptimizationStep<S, T, U>, TransformationContext, KernelWithIdentifier<S, U>) - Method in class KernelAssignerAddErrorLevel
assignProposal(OptimizationStep<S, T, V>, TransformationContext, KernelWithIdentifier<S, V>) - Method in class KernelAssignerCalculateEnergyFromKernel
assignRejected(DualMarks, T) - Method in class DualMarksAnnotation: Assigns marks with an overall rejected state.
assignRelativeForIdentifier() - Method in class InputArguments
assignResolution(Optional<Resolution>) - Method in class Channel: Assigns a new resolution.
assignResolution(Resolution) - Method in class Stack: Assigns a new resolution.
assignShuffle() - Method in class InputArguments
assignSize(String) - Method in class TaskArguments
assignSuggestedImageOutputFormat(ImageFileFormat) - Method in class OutputArguments
assignSuggestedImageOutputFormat(ImageFileFormat) - Method in class OutputPrefixerSettings
assignTaskName(Optional<String>) - Method in class TaskArguments
assignTo(Feature<FeatureInput>) - Method in class Feature: Copies fields in this (base) class to target.
assignTo(KernelPosNeg<T, S>) - Method in class KernelPosNeg: Copies fields in this (base) class to target.
assignTo(ConicFitterBase) - Method in class ConicFitterBase: Copies fields in this (base) class to target.
assignType(String) - Method in class ManifestDescription: Assigns a new type.
assignValue(AnchorBean<?>, Object) - Method in interface PermutationAssigner: Assigns value to one or more properties in bean.
assignValue(int) - Method in class Channel: Interface that allows assignment of a particular value to all or subsets of the voxels.
assignValue(int) - Method in class BoundedVoxels: Assigns a value to a bounded-voxels accepting global coordinates for objects, boxes etc.
assignValue(int) - Method in class Voxels: Interface that allows assignment of a particular value to all or subsets of the voxels.
assignValue(int) - Method in class VoxelsFloat
assignValue(int) - Method in class VoxelsUnsignedByte
assignValue(int) - Method in class VoxelsUnsignedInt
assignValue(int) - Method in class VoxelsUnsignedShort
assignValue(int) - Method in class VoxelsUntyped: Interface that allows assignment of a particular value to all or subsets of the voxels.
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 AssignValue
assignWithPrefix(Feature<? extends FeatureInput>, String, String) - Static method in class 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 AsSingle
AsSingleMark - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.all
AsSingleMark() - Constructor for class AsSingleMark
associated - Variable in class AddOptionsFromCommandLine: An associated entity which consumers accept.
associatedFile() - Method in class 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 ClusterMembership: Indicates a particular file is a member of a particular cluster.
associateXML(XMLConfiguration) - Method in interface AssociateXMLUponLoad: Associated an XML configuration with an object.
associateXML(XMLConfiguration) - Method in class Experiment
associateXML(XMLConfiguration) - Method in class QuickMultiDatasetStructuredExperiment
AssociateXMLUponLoad - Interface in org.anchoranalysis.bean.xml: For classes that wish to have a XmlConfiguration associated with them.
asStack() - Method in class EnergyStack: Derive a Stack representation containing the identical channels to the current instance.
asStack() - Method in class EnergyStackWithoutParameters: Derive a Stack representation containing the identical channels to the current instance.
asStack() - Method in class RGBStack: Exposes the underlying stack, storing the three RGB channels in respective order.
asTuple() - Method in class Extent: Exposes the extent as a tuple.
asVector3d() - Method in class DirectionVector: Converts to a Vector3d representation.
at(int, int, int, int) - Static method in class BoundingBoxFactory: Short-hand factory method for creating a 2D bounding-box.
at(int, int, int, int, int, int) - Static method in class BoundingBoxFactory: Short-hand factory method for creating a 3D bounding-box.
atanHandlingNan(double) - Static method in class EllipseStandardFormConverter
atBorder(Extent) - Method in class 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
AtBorderBase() - Constructor for class AtBorderBase
AtBorderXY - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.border
AtBorderXY() - Constructor for class AtBorderXY
atBorderXY(Extent) - Method in class BoundingBox: Like BoundingBox.atBorder(Extent) but considers only the X- and Y- dimensions.
AtBorderZ - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.border
AtBorderZ() - Constructor for class AtBorderZ
atBorderZ(Extent) - Method in class BoundingBox: Like BoundingBox.atBorder(Extent) but considers only the Z-dimension.
atCorner(ReadableTuple3i, VoxelsExtracter<T>) - Static method in class VoxelsExtracterFactory: Projects a VoxelsExtracter to a corner in a larger global space.
AtIndex - Class in org.anchoranalysis.plugin.image.bean.object.provider: Creates a new object-collection with only a single element (at a particular index) in the existing collection.
AtIndex() - Constructor for class AtIndex
AtLeastZSlices - Class in org.anchoranalysis.plugin.io.bean.file.group.check
AtLeastZSlices() - Constructor for class AtLeastZSlices
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 AtScale
attachObject(Channel) - Method in class MaxIntensity
attachObject(S) - Method in interface ChannelConverterAttached: Associate the convert with a particular object.
attachObject(Histogram) - Method in class MaxIntensityFromHistogram
attachObject(Histogram) - Method in class QuantileIntensityFromHistogram
attachObject(Histogram) - Method in class UpperLowerQuantileIntensityFromHistogram
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 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 Autoname
Axis - Enum in org.anchoranalysis.spatial.axis: Identifies axis in a Cartesian coordinate system.
AxisAlignedUnitVector - Class in org.anchoranalysis.image.bean.spatial.direction
AxisAlignedUnitVector() - Constructor for class AxisAlignedUnitVector
AxisConversionException - Exception in org.anchoranalysis.spatial.axis: When converting another type to a corresponding Axis fails.
AxisConversionException(String) - Constructor for exception 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.
AxisLimits - Class in org.anchoranalysis.plot
AxisLimits() - Constructor for class AxisLimits
AxisLimits(double, double) - Constructor for class AxisLimits
AxisRatioEllipsoid - Class in org.anchoranalysis.plugin.points.bean.feature
AxisRatioEllipsoid() - Constructor for class AxisRatioEllipsoid

B

background(DisplayStack) - Method in class MarksFlattenedGenerator
background(DisplayStack) - Method in class MarksGenerator
background(DisplayStack) - Method in class MarksGeneratorBase
BackgroundCreator - Class in org.anchoranalysis.mpp.io.output
BackgroundSubtractor - Class in org.anchoranalysis.plugin.imagej.bean.channel.provider
BackgroundSubtractor() - Constructor for class BackgroundSubtractor
BarPlot<T> - Class in org.anchoranalysis.plot.index: A bar plot, stacked or non-stacked.
BarPlot(String, String[], GetForSeries<T, String>, GetForSeries<T, Double>, GetForSeries<T, Paint>, boolean) - Constructor for class BarPlot
BBoxRatio - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
BBoxRatio() - Constructor for class BBoxRatio
BeanCreator - Class in org.anchoranalysis.bean.xml.creator: Creates a single AnchorBean from XML.
BeanDuplicateException - Exception in org.anchoranalysis.bean.exception: An exception occurs when the duplication of a bean fails.
BeanDuplicateException(String) - Constructor for exception BeanDuplicateException: Creates with a message only.
BeanDuplicateException(Throwable) - Constructor for exception BeanDuplicateException: Creates with a cause only.
BeanDuplicateException(String, Throwable) - Constructor for exception BeanDuplicateException: Creates with a message and cause.
BeanField - Annotation Type 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<P> - 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 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 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 BeanInstanceMap
BeanListCreator - Class in org.anchoranalysis.bean.xml.creator: Like BeanCreator but creates a list of beans.
BeanMisconfiguredException - Exception in org.anchoranalysis.bean.exception: If a Bean is misconfigured.
BeanMisconfiguredException(String) - Constructor for exception BeanMisconfiguredException: Creates with a message only.
BeanMisconfiguredException(String, Throwable) - Constructor for exception BeanMisconfiguredException: Creates with a message and a cause.
BeanMisconfiguredXMLException - Exception in org.anchoranalysis.bean.xml.exception: A bean's XML is thrown when a bean has misconfigured XML.
BeanMisconfiguredXMLException(String, Throwable) - Constructor for exception BeanMisconfiguredXMLException: Constructor
BeanMisconfiguredXMLException(Throwable) - Constructor for 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 BeanProviderAsStackBase
BeanStrangeException - Exception in org.anchoranalysis.bean.exception: When something quite strange happens that we don't usually want to catch.
BeanStrangeException(String) - Constructor for exception BeanStrangeException: Creates with a message only.
BeanStrangeException(String, Throwable) - Constructor for 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 in org.anchoranalysis.bean.xml.exception: An exception that occurs when one cannot process BeanXML for some reason.
BeanXMLException(String) - Constructor for exception BeanXMLException: Creates with a message only.
BeanXMLException(Throwable) - Constructor for exception BeanXMLException: Creates with a cause only.
BeanXMLException(String, Throwable) - Constructor for exception BeanXMLException: Creates with a message and cause.
BeanXMLLoader - Class in org.anchoranalysis.bean.xml: Creates beans based on XML specifying their properties (including nested children).
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<T>, ParametersExperiment) - Method in class 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 TaskWithoutSharedState
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<AnnotationWithStrategy<S>>, ParametersExperiment) - Method in class AggregateAnnotations
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<AnnotationComparisonInput<ProvidesStackInput>>, ParametersExperiment) - Method in class CompareAnnotations
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<T>, ParametersExperiment) - Method in class ExportFeatures
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<NamedChannelsInput>, ParametersExperiment) - Method in class ConvertImageFormat
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<ProvidesStackInput>, ParametersExperiment) - Method in class GroupedStackBase
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<ProvidesStackInput>, ParametersExperiment) - Method in class ImageAssignLabel
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<StackSequenceInput>, ParametersExperiment) - Method in class ScaleImage
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<StackSequenceInput>, ParametersExperiment) - Method in class SegmentInstanceWithModel
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<NamedChannelsInput>, ParametersExperiment) - Method in class ExtractSlice
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<NamedChannelsInput>, ParametersExperiment) - Method in class MovieFromSlices
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<FileInput>, ParametersExperiment) - Method in class CombineCSV
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<FileWithDirectoryInput>, ParametersExperiment) - Method in class CopyFiles
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<T>, ParametersExperiment) - Method in class SummarizeBase
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<T>, ParametersExperiment) - Method in class ConvertNamedChannels
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<ManifestCouplingDefinition>, ParametersExperiment) - Method in class ExportReportFeaturesFromManifest
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<MultiInput>, ParametersExperiment) - Method in class ExportReportFeaturesFromMulti
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<MultiInput>, ParametersExperiment) - Method in class ExportObjectsAsCroppedImages
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<FromCSVInput>, ParametersExperiment) - Method in class ExportObjectsFromCSV
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<MultiInput>, ParametersExperiment) - Method in class SegmentMarksFromImage
beforeCalc(FeatureInitialization) - Method in class Feature: Dummy method, that children can optionally override.
beforeCalc(FeatureInitialization) - Method in class ConvertToPhysicalDistance
beforeCalc(FeatureInitialization) - Method in class FeatureIntersectingObjects
beforeCalc(FeatureInitialization) - Method in class PairedWithMask
beforeCalc(FeatureInitialization) - Method in class FeatureSingleObjectFromShared
beforeCalc(FeatureInitialization) - Method in class ParamFromCollection
beforeCalc(FeatureInitialization) - Method in class FeatureMarkDirection
beforeCalc(FeatureInitialization) - Method in class FromDictionary
beforeCalcSetup(Histogram, int) - Method in class CalculateLevel
beforeCalcSetup(Histogram, int) - Method in class CalculateLevelBase
beforeCalcSetup(Histogram, int) - Method in class DifferenceCalculateLevelStandardDeviation
beforeCalcWithInitialization(ImageInitialization) - Method in class FeatureSingleObjectFromShared
beforeCalcWithInitialization(ImageInitialization) - Method in class MaskAsSingleObject
beforeCalcWithInitialization(ImageInitialization) - Method in class ObjectAggregationBase
BeforeCondition - Interface in org.anchoranalysis.plugin.image.object.merge.condition
beforeCopying(Path, List<FileWithDirectoryInput>) - Method in class Anonymize
beforeCopying(Path, List<FileWithDirectoryInput>) - Method in class ClusterByTimestamp
beforeCopying(Path, List<FileWithDirectoryInput>) - Method in class CopyFilesNaming: To be called once before any calls to CopyFilesNaming.destinationPath(File, DirectoryWithPrefix, int, CopyContext).
beforeCopying(Path, List<FileWithDirectoryInput>) - Method in class CopyFilesNamingOne
beforeCopying(Path, List<FileWithDirectoryInput>) - Method in class CopyFilesNamingWithoutSharedState
beforeCopying(Path, List<FileWithDirectoryInput>) - Method in class PreserveName
beforeCreateObject(RandomNumberGenerator, Optional<Resolution>) - Method in class VisitScheduler
beforeCreateObject(RandomNumberGenerator, Optional<Resolution>) - Method in class VisitSchedulerAnd
beforeCreateObject(RandomNumberGenerator, Optional<Resolution>) - Method in class VisitSchedulerConvexAboutRoot
beforeCreateObject(RandomNumberGenerator, Optional<Resolution>) - Method in class VisitSchedulerMaxDistanceAlongContour
beforeCreateObject(RandomNumberGenerator, Optional<Resolution>) - Method in class VisitSchedulerUniformSample
binaryChannel(boolean) - Static method in class StackWriteAttributesFactory
BinaryClassifierImageLabeller - Class in org.anchoranalysis.plugin.image.task.bean.labeller
BinaryClassifierImageLabeller() - Constructor for class 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 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 BinaryKernelMorphological: Creates with a flag for big-neighborhood, and boolean outcomes for certain cases.
BinaryNotOffVoxels - Class in org.anchoranalysis.image.bean.threshold.relation: Selects anything that is not off voxels from a binary mask.
BinaryNotOffVoxels() - Constructor for class BinaryNotOffVoxels
BinaryNotOnVoxels - Class in org.anchoranalysis.image.bean.threshold.relation: Selects anything that is not on voxels from a binary mask.
BinaryNotOnVoxels() - Constructor for class BinaryNotOnVoxels
BinaryOffVoxels - Class in org.anchoranalysis.image.bean.threshold.relation: Selects only the off voxels from a binary mask.
BinaryOffVoxels() - Constructor for class 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 from a binary mask.
BinaryOnVoxels() - Constructor for class BinaryOnVoxels
binaryOperation(Voxels<UnsignedByteBuffer>, Voxels<UnsignedByteBuffer>, Voxels<UnsignedByteBuffer>, IntBinaryOperation) - Static method in class 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
BinaryOutcomeImageLabeller() - Constructor for class BinaryOutcomeImageLabeller
binaryResizing(int) - Method in class InterpolatorFactory: An Interpolator 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
BinarySegmentation() - Constructor for class BinarySegmentation
BinarySegmentationOne - Class in org.anchoranalysis.image.bean.segment.binary
BinarySegmentationOne() - Constructor for class BinarySegmentationOne
BinarySegmentationParameters - Class in org.anchoranalysis.image.bean.nonbean.segment: Parameters that are optionally associated with a BinarySegmentation
BinarySegmentationParameters() - Constructor for class BinarySegmentationParameters
BinarySegmentationParameters(Optional<Resolution>) - Constructor for class BinarySegmentationParameters
BinarySegmentationParameters(Resolution, Optional<Histogram>) - Constructor for class BinarySegmentationParameters: Constructor
BinarySegmentationParameters(Optional<Histogram>, Optional<Resolution>) - Constructor for class BinarySegmentationParameters
BinarySegmentationReference - Class in org.anchoranalysis.image.bean.segment.binary
BinarySegmentationReference() - Constructor for class BinarySegmentationReference
binarySegmentations() - Method in class ImageInitialization
BinarySegmentationThreshold - Class in org.anchoranalysis.image.bean.segment.binary
BinarySegmentationThreshold() - Constructor for class BinarySegmentationThreshold
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 BinarySegmentByObject
binaryValues() - Method in class BinaryVoxels: Which two intensity values represent off and on states.
binaryValues() - Method in class ObjectMask: What values constitute an on and off state in voxels - as ints.
binaryValuesByte() - Method in class Mask: The two states which are permitted to be assigned to the voxels, stored as bytes.
BinaryValuesByte - Class in org.anchoranalysis.image.voxel.binary.values: Two values representing byte binary states in an UnsignedByteBuffer.
BinaryValuesByte(int, int) - Constructor for class BinaryValuesByte: Create with int values for off and on states.
BinaryValuesByte(byte, byte) - Constructor for class BinaryValuesByte
binaryValuesByte() - Method in class ObjectMask: What values constitute an on and off state in voxels - as bytes.
binaryValuesInt() - Method in class 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 BinaryValuesInt
binaryVoxels() - Method in class Mask: The underlying voxels in the mask, exposed as BinaryVoxels.
BinaryVoxels<T> - Class in org.anchoranalysis.image.voxel.binary: Like Voxels but should only contain two distinct intensity-values representing on and off.
BinaryVoxels(Voxels<T>, BinaryValuesInt) - Constructor for class BinaryVoxels
binaryVoxels() - Method in class ObjectMask: The underlying voxel memory buffers for the object-mask, exposed via a BinaryVoxels.
BinaryVoxelsBase - Class in org.anchoranalysis.image.bean.threshold.relation
BinaryVoxelsBase() - Constructor for class BinaryVoxelsBase
BinaryVoxelsFactory - Class in org.anchoranalysis.image.voxel.binary: Creates BinaryVoxels parameterized by size and initial state.
binaryVoxelsFor(Voxels<T>, BinaryValuesInt) - Method in class BinaryVoxels: Creates a BinaryVoxels corresponding to a particular voxels and BinaryValuesInt.
bind(FeatureList<T>, FeatureInitialization, SharedFeatures, Logger) - Method in class BoundReplaceStrategy
BindFailedException - Exception in org.anchoranalysis.io.output.outputter
BindFailedException(String) - Constructor for exception BindFailedException
BindFailedException(Throwable) - Constructor for exception BindFailedException
BioformatsReader - Class in org.anchoranalysis.io.bioformats.bean: Reads a stack using the Bioformats library.
BioformatsReader(ReadOptions) - Constructor for class BioformatsReader: Create with particular options.
BioformatsReader() - Constructor for class BioformatsReader
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 BioformatsWriter
bitDepth(Logger) - Method in class NamedChannelsInput: Bit-depth of image.
bitDepth(Logger) - Method in interface OpenedImageFile: The bit-depth of the image voxels e.g.
bitDepth() - Method in class VoxelDataType: The number of bits required to represent a voxel.
BitDepth - Class in org.anchoranalysis.plugin.io.bean.summarizer.image
BitDepth() - Constructor for class BitDepth
bitDepth(Logger) - Method in class OpenedMultiFile
BitDepthPerChannel - Class in org.anchoranalysis.plugin.image.feature.bean.metadata: The bit-depth of the image per channel.
BitDepthPerChannel() - Constructor for class BitDepthPerChannel
BlackBackgroud - Class in org.anchoranalysis.plot.bean.colorscheme: A black background and white axes.
BlackBackgroud() - Constructor for class BlackBackgroud
blockUntilLoaded() - Static method in class CVInit: Blocks a thread until the initialization has completed.
BLUE - Static variable in class RGBChannelNames: Name for the blue channel.
blue() - Method in class RGBStack: The blue channel.
blur(VoxelsUntyped, Dimensions, MessageLogger) - Method in class BlurGaussian3D
blur(VoxelsUntyped, Dimensions, MessageLogger) - Method in class BlurGaussianEachSlice2D
blur(VoxelsUntyped, Dimensions, MessageLogger) - Method in class BlurStrategy
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 Blur
BlurGaussian3D - Class in org.anchoranalysis.plugin.image.bean.blur: Performs a Gaussian Blur in 3D
BlurGaussian3D() - Constructor for class BlurGaussian3D
BlurGaussianEachSlice2D - Class in org.anchoranalysis.plugin.image.bean.blur: Performs a Gaussian-blur in 2D on each slice independently
BlurGaussianEachSlice2D() - Constructor for class BlurGaussianEachSlice2D
BlurStrategy - Class in org.anchoranalysis.plugin.image.bean.blur: A method for applying blurring to an image
BlurStrategy() - Constructor for class BlurStrategy
BMP - Class in org.anchoranalysis.plugin.io.bean.metadata.header: The headers found in a BMP file.
BMP() - Constructor for class BMP
bothNameAndParameters() - Static method in class NamedFeatureStoreFactory: The custom-names of the features are derived from both their name and their parameters.
Bound - Class in org.anchoranalysis.mpp.bean.bound
Bound() - Constructor for class Bound
boundaryMax(FeatureCalculationInput<T>) - Method in class CompareWithRangeFeature
boundaryMax(FeatureCalculationInput<T>) - Method in class RangeCompareBase: Boundary to define the maximum accepted value in the range
boundaryMax(FeatureCalculationInput<T>) - Method in class RangeCompareFromScalars
boundaryMin(FeatureCalculationInput<T>) - Method in class CompareWithRangeFeature
boundaryMin(FeatureCalculationInput<T>) - Method in class RangeCompareBase: Boundary to define the minimum accepted value in the range
boundaryMin(FeatureCalculationInput<T>) - Method in class RangeCompareFromScalars
BoundDegrees - Class in org.anchoranalysis.mpp.bean.bound
BoundDegrees() - Constructor for class BoundDegrees
BoundDegrees(BoundDegrees) - Constructor for class 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<T> - Class in org.anchoranalysis.image.voxel: Voxels that exist within a particular bounding-box in an image.
BoundedVoxels(Voxels<T>) - Constructor for class BoundedVoxels: Creates voxels bounded to match the entire voxel-data at the origin.
BoundedVoxels(BoundedVoxels<T>) - Constructor for class BoundedVoxels: Copy constructor.
BoundedVoxels(BoundingBox, Voxels<T>) - Constructor for class BoundedVoxels: Creates voxels with a corresponding bounding box.
boundedVoxels() - Method in class ObjectMask: The underlying voxel memory buffers for the object-mask, exposed via BoundedVoxels.
boundingBox() - Method in class ObjectWithProperties: The bounding-box which gives a location for the object-mask on an image.
boundingBox() - Method in class BoundedVoxels: A bounding-box that associates voxels to a particular part of an image.
boundingBox() - Method in class ObjectMask: The bounding-box which gives a location for the object-mask on an image.
boundingBox() - Method in interface VoxelizedMark: A bounding-box enclosing the voxelized representation of the mark
boundingBox() - Method in class 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 BoundingBox: Constructs a bounding-box to cover the entirety of a certain extent.
BoundingBox(Point3d, Point3d) - Constructor for class BoundingBox: Creates from two double points (a minimum corner and a maximum corner).
BoundingBox(ReadableTuple3i, ReadableTuple3i) - Constructor for class BoundingBox: Creates from two int points (a minimum corner and a maximum corner).
BoundingBox(ReadableTuple3i, Extent) - Constructor for class BoundingBox: Creates a bounding-box from a corner and an extent.
BoundingBoxAlongAxisBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox
BoundingBoxAlongAxisBase() - Constructor for class BoundingBoxAlongAxisBase
BoundingBoxCalculator - Class in org.anchoranalysis.mpp.mark.conic: Functions to calculate a bounding-box for a point surrounded by some form of radii
BoundingBoxContains - Class in org.anchoranalysis.spatial.box: Does a bounding box contain other objects?
BoundingBoxContains(BoundingBox) - Constructor for class BoundingBoxContains: Create with the BoundingBox that is queried.
BoundingBoxDistance - Class in org.anchoranalysis.spatial.box: Calculates distance between two bounding boxes.
BoundingBoxesOnPlane - Class in org.anchoranalysis.image.bean.nonbean.spatial.arrange: Describes a set of bounding boxes on top of a plane
BoundingBoxesOnPlane(Extent, BoundingBox) - Constructor for class BoundingBoxesOnPlane
BoundingBoxesOnPlane(Extent) - Constructor for class BoundingBoxesOnPlane
BoundingBoxExtent - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.region
BoundingBoxExtent() - Constructor for class BoundingBoxExtent
BoundingBoxExtentAlongAxis - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox
BoundingBoxExtentAlongAxis() - Constructor for class BoundingBoxExtentAlongAxis
BoundingBoxFactory - Class in org.anchoranalysis.spatial.box: Utility methods to create a BoundingBox.
boundingBoxFlattened() - Method in interface VoxelizedMark: The bounding-box flattened in z dimension
boundingBoxFor(T) - Method in interface AccessObjectMask: A bounding-box for a given element.
boundingBoxForRegion(VoxelizedMark) - Method in class IndexedRegionBase
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
BoundingBoxIntersection() - Constructor for class BoundingBoxIntersection
BoundingBoxIntersection - Class in org.anchoranalysis.spatial.box: Methods for checking intersection between a particular bounding-box and others.
BoundingBoxIntersection(BoundingBox) - Constructor for class BoundingBoxIntersection
BoundingBoxMaximumAlongAxis - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox
BoundingBoxMaximumAlongAxis() - Constructor for class 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
BoundingBoxMinimumAlongAxis() - Constructor for class BoundingBoxMinimumAlongAxis
BoundingBoxNumberVoxels - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox
BoundingBoxNumberVoxels() - Constructor for class BoundingBoxNumberVoxels
BoundingBoxOutline - Class in org.anchoranalysis.image.io.bean.object.draw: Draws the outline of the bounding-box for each object.
BoundingBoxOutline() - Constructor for class BoundingBoxOutline
BoundingBoxOutline(int) - Constructor for class BoundingBoxOutline
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 BoundingBoxRTree: Creates an empty R-Tree.
BoundingBoxRTree(int) - Constructor for class BoundingBoxRTree: Creates an empty R-Tree with a specified number of children.
boundingBoxThatSpansInput(T) - Method in class CombineObjectsForFeatures: Creates a bounding-box that tightly fits the input to a particular table row (could be for one or more objects)
boundingBoxThatSpansInput(FeatureInputSingleObject) - Method in class EachObjectIndependently
boundingBoxThatSpansInput(FeatureInputPairObjects) - Method in class PairNeighbors
BoundingBoxUnion - Class in org.anchoranalysis.spatial.box: Performs union of a bounding-box with other entities
BoundingBoxUnion(BoundingBox) - Constructor for class BoundingBoxUnion
BoundingBoxZDistance - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.distance: Measures the amount of distance in Z for the bounding box.
BoundingBoxZDistance() - Constructor for class BoundingBoxZDistance
BoundingBoxZOverlapRatio - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.distance: Measures the amount of bounding box overlap in the Z dimension
BoundingBoxZOverlapRatio() - Constructor for class BoundingBoxZOverlapRatio
BoundMinMax - Class in org.anchoranalysis.mpp.bean.bound
BoundMinMax() - Constructor for class BoundMinMax
BoundMinMax(double, double) - Constructor for class BoundMinMax
BoundMinMax(BoundMinMax) - Constructor for class 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 BoundOutputter
BoundPhysicalExtent - Class in org.anchoranalysis.mpp.bean.bound
BoundPhysicalExtent(double, double) - Constructor for class BoundPhysicalExtent
BoundPhysicalExtent(BoundPhysicalExtent) - Constructor for class BoundPhysicalExtent
BoundPhysicalExtent() - Constructor for class BoundPhysicalExtent
BoundReplaceStrategy<T extends FeatureInput,S extends ReplaceStrategy<T>> - Class in org.anchoranalysis.feature.session.replace: Attaches a replacement-strategy to a session lazily (i.e.
BoundReplaceStrategy(Function<CacheCreator, S>) - Constructor for class BoundReplaceStrategy
BoundRotation - Class in org.anchoranalysis.mpp.bean.bound.rotation
BoundRotation() - Constructor for class 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 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 BoundRotation3D
BoundUnitless - Class in org.anchoranalysis.mpp.bean.bound
BoundUnitless() - Constructor for class BoundUnitless
BoundUnitless(double, double) - Constructor for class BoundUnitless
BoundUnitless(BoundUnitless) - Constructor for class BoundUnitless
box(Dimensions, int) - Method in class Ellipse
box(Dimensions, int) - Method in class Ellipsoid
box(Dimensions, int) - Method in class MarkWithPositionAndSingleRadius
box(Dimensions, int) - Method in class Mark
box(Dimensions, int) - Method in class LineSegment
box(Dimensions, int) - Method in class PointListBase
box() - Method in class PointListBase
box(Dimensions, int) - Method in class RotatableBoundingBox
box(DrawOverlay, Dimensions) - Method in class OverlayMark: How we create our scaled masks
box(DrawOverlay, Dimensions) - Method in class OverlayObjectMask
box(DrawOverlay, Dimensions) - Method in class Overlay: A bounding-box around the overlay
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 Box
box(FeatureInputPairMemo, Function<FeatureInputPairMemo, VoxelizedMarkMemo>) - Method in class FeaturePairMemoSingleRegion
box(BoundingBox) - Method in class BoundingBoxContains: Is this other bounding-box fully contained within this bounding box?
boxAllRegions(Dimensions) - Method in class Ellipse
boxAllRegions(Dimensions) - Method in class Ellipsoid
boxAllRegions(Dimensions) - Method in class MarkWithPositionAndSingleRadius
boxAllRegions(Dimensions) - Method in class Mark
boxAllRegions(Dimensions) - Method in class LineSegment
boxAllRegions(Dimensions) - Method in class PointList
boxAllRegions(Dimensions) - Method in class Polygon
boxAllRegions(Dimensions) - Method in class PolygonCurve
boxAllRegions(Dimensions) - Method in class RotatableBoundingBox
boxCopyTo(BoundingBox, Voxels<T>, BoundingBox) - Method in interface VoxelsExtracter: Copies a bounding-box area to another Voxels.
boxFromBounds(Point3d, double, boolean, Dimensions) - Static method in class BoundingBoxCalculator: Calculates a bounding box for a point with a scalar radius in all dimensions.
boxFromBounds(Point3d, DoubleMatrix1D, boolean, Dimensions) - Static method in class BoundingBoxCalculator: Calculates a bounding box for a point with varying radii in each dimension (that have already been resolved into a matrix)
boxIterator() - Method in class BoundingBoxesOnPlane
boxList(Dimensions, int) - Method in class MarkCollection
boxList(DrawOverlay, Dimensions) - Method in class ColoredOverlayCollection
boxList(DrawOverlay, Dimensions) - Method in class OverlayCollection
BoxPlot<T> - Class in org.anchoranalysis.plot.index
BoxPlot(String, String[], GetForSeries<T, String>, GetForSeries<T, BoxAndWhiskerItem>, GetForSeries<T, Paint>) - Constructor for class BoxPlot
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 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 BranchExtension
BranchIfDebug<T extends InputFromManager> - 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 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 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 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 Bridge
buffer() - Method in class VoxelBuffer: The associated buffer for storing the voxels.
buffer() - Method in class 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 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 FileFormat: Builds a path which has an existing path but missing an extension.
buildPath(Path) - Method in interface FileFormat: Builds a path which has an existing path but missing an extension.
buildPath(Path, String) - Method in interface FileFormat: Builds a path with a directory and filename component.
buildPath(String, String) - Method in interface FileFormat: Builds a path with a directory and filename component.
buildPath(String, String, String) - Method in interface FileFormat: Builds a path with a directory, subdirectory, and filename component.
bySymbol() - Method in interface FeatureCalculationInput: Calculates a feature if only an symbol (ID/name) is known, which refers to another feature.
bySymbol() - Method in class 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 ByteRepresentationForChannel: The byte-representation of the voxels for a particular slice.
bytesPerVoxel() - Method in class ConvertTo: The number bytes to describe each source-voxel.
bytesPerVoxel() - Method in class UnsignedByteFromFloat
bytesPerVoxel() - Method in class UnsignedByteFromUnsignedByte
bytesPerVoxel() - Method in class UnsignedByteFromUnsignedByteNoInterleavingScale
bytesPerVoxel() - Method in class UnsignedByteFromUnsignedInt
bytesPerVoxel() - Method in class UnsignedByteFromUnsignedShort
bytesPerVoxel() - Method in class FloatFromUnsignedByte
bytesPerVoxel() - Method in class FloatFromUnsignedInt
bytesPerVoxel() - Method in class UnsignedIntFromUnsignedInt
bytesPerVoxel() - Method in class 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 Bytewise

C

cache(CheckedSupplier<T, E>) - Static method in class CachedSupplier: Creates a cached-version of a CheckedSupplier.
cache(StoreSupplier<T>) - Static method in interface StoreSupplier: Memoizes (caches) the supplied object, and returning it with an identical interface.
cache(CheckedProgressingSupplier<T, E>) - Static method in class CachedProgressingSupplier: Creates a cached-version of a CheckedProgressingSupplier
cache(FeatureCalculatorSingle<T>) - Static method in class FeatureCalculatorCache
cache(FeatureCalculatorSingle<T>, int) - Static method in class FeatureCalculatorCache
cache(FeatureCalculatorMulti<T>) - Static method in class FeatureCalculatorCache
cache(FeatureCalculatorMulti<T>, int) - Static method in class FeatureCalculatorCache
cache(NamedStacksSupplier) - Static method in interface NamedStacksSupplier: Caches a NamedStacksSupplier so that its value will be remembered after first execution.
cache(SerializedObjectSupplier<T>) - Static method in interface SerializedObjectSupplier
CACHE_NAME_FIRST - Static variable in class FeatureDeriveFromPair
CACHE_NAME_MERGED - Static variable in class FeatureDeriveFromPair
CACHE_NAME_SECOND - Static variable in class FeatureDeriveFromPair
CacheAndReuseStrategy<T extends FeatureInput> - Class in org.anchoranalysis.feature.session.replace: Reuse (without needing to invalidate) an existing session-input as stored in a least-recently used cache, otherwise create a new one.
CacheAndReuseStrategy(CacheCreator) - Constructor for class CacheAndReuseStrategy
CacheCreator - Interface in org.anchoranalysis.feature.calculate.cache: Creates a FeatureCalculationCache that accepts a particular input type.
CachedProgressingSupplier<T,E extends Exception> - Class in org.anchoranalysis.core.progress: Memoizes (caches) a call to CheckedProgressingSupplier.
CachedSupplier<T,E extends Exception> - 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 CachedSupplierBase
cacheName() - Method in class DerivedObject
cacheName() - Method in class Erode
cacheName() - Method in class Shell
cacheResettable(StoreSupplier<T>) - Static method in interface StoreSupplier: Memoizes (caches) the supplied object, and returning it with a CachedSupplier interface
cachesToAvoidInvalidating() - Method in class CheckCacheForSpecificChildren
cachesToAvoidInvalidating() - Method in interface ChildCacheFinder: If set, these particular-caches are exceptionall NOT invalidated during the typical invalidation operation on their parent.
cachesToAvoidInvalidating() - Method in class DefaultChildCacheFinder
CacheSupplier<T extends FeatureInput,E extends Exception> - Interface in org.anchoranalysis.feature.session.cache.finder
CacheTransferSource<T extends FeatureInput> - 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 CacheTransferSource
CacheTransferSourceCollection - Class in org.anchoranalysis.feature.session.cache.finder
CacheTransferSourceCollection() - Constructor for class CacheTransferSourceCollection
calc(FeatureInputMarkCollection) - Method in class FeatureMarkCollection
calc(EnergyMemoList, EnergySchemeWithSharedFeatures, EnergyStackWithoutParameters) - Method in class EnergySavedAll
calc(CalculateForChild<T>, Feature<FeatureInputSingleObject>) - Method in class FeatureSingleObjectFromShared
calc(CalculateForChild<T>, Feature<FeatureInputSingleObject>) - Method in class MaskAsSingleObject
calc(CalculateForChild<T>, Feature<FeatureInputSingleObject>) - Method in class ObjectAggregationBase
calc(FeatureCalculationInput<T>, CalculationPart<U, T>, Function<ResolvedPart<U, T>, CalculateInputFromDelegateOption<S, T, U>>, Feature<S>, ChildCacheName, double) - Static method in class CalculateInputFromDelegateOption: Calculates a feature using a cached-calculation as delegate.
calc(FeatureInputMarkCollection) - Method in class NumberMarks
calc(FeatureInputSingleObject, Ellipsoid) - Method in class AxisRatioEllipsoid
calc(FeatureInputSingleObject, Ellipsoid) - Method in class EllipsoidBase
calc(FeatureInputSingleObject, Ellipsoid) - Method in class Ellipsoidicity
calculate(FeatureCalculationInput<T>) - Method in class Feature: Calculates a value for some input.
calculate(FeatureCalculationInput<T>) - Method in class Constant
calculate(FeatureCalculationInput<T>) - Method in class Reference
calculate(FeatureCalculationInput<T>) - Method in class Sum
calculate(FeatureInputResults) - Method in class Count
calculate(FeatureCalculationInput<FeatureInputResults>) - Method in class FeatureResults
calculate(FeatureInputResults) - Method in class FeatureResults: Calculates the feature-result given a FeatureInputResults.
calculate(FeatureInputResults) - Method in class FeatureResultsStatistic
calculate(T) - Method in interface FeatureCalculatorMulti: Calculate the results of the features with a particular input.
calculate(T, FeatureList<T>) - Method in interface FeatureCalculatorMulti: Calculates the results of a subset of the features with a particular input.
calculate(T, ErrorReporter, boolean) - Method in interface 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) - Method in class FeatureCalculatorMultiChangeInput
calculate(T, FeatureList<T>) - Method in class FeatureCalculatorMultiChangeInput
calculate(T) - Method in interface FeatureCalculatorSingle: Calculate the results of the feature with a particular input.
calculate(T) - Method in class FeatureCalculatorSingleChangeInput
calculate(T) - Method in class FeatureCalculatorSingleFromMulti
calculate(Feature<S>, S, ChildCacheName) - Method in interface CalculateForChild: Calculates a feature in a child-cache.
calculate(Feature<S>, CalculationPart<S, T>, ChildCacheName) - Method in interface CalculateForChild: Calculates a feature in a child-cache using a new input created from a CalculationPart.
calculate(ChildCacheName, S, Function<CalculationPartResolver<S>, ResolvedPart<U, S>>) - Method in interface CalculateForChild: Calculates a CalculationPart in a child-cache.
calculate(Feature<T>) - Method in interface FeatureCalculationInput: Calculates the result of a feature using this input.
calculate(FeatureList<T>) - Method in interface FeatureCalculationInput: Calculates the results of several features using this input.
calculate(CalculationPart<S, T>) - Method in interface FeatureCalculationInput: Calculates a feature-calculation after resolving it against the main cache.
calculate(ResolvedPart<S, T>) - Method in interface FeatureCalculationInput: Calculates a resolved Feature-calculation.
calculate(Feature<T>, FeatureCalculationInput<T>) - Method in interface FeatureCalculator: Calculate the result of feature with a particular input.
calculate(FeatureList<T>, FeatureCalculationInput<T>) - Method in interface FeatureCalculator: Calculates results for a list of features with a particular input, throwing an exception if a calculation fails.
calculate(T) - Method in class SequentialSession
calculate(T, FeatureList<T>) - Method in class SequentialSession
calculate(Feature<T>) - Method in class SessionInputSequential
calculate(FeatureList<T>) - Method in class SessionInputSequential
calculate(CalculationPart<S, T>) - Method in class SessionInputSequential
calculate(ResolvedPart<S, T>) - Method in class SessionInputSequential
calculate(Optional<Dimensions>, Optional<ImageSizeSuggestion>) - Method in class ScaleCalculator: Calculates a scaling-factor for a source image/entity of particular dimensions.
calculate(FeatureCalculationInput<FeatureInputImageMetadata>) - Method in class FeatureImageMetadata
calculate(ImageMetadata) - Method in class FeatureImageMetadata: Calculates the feature-value for a given ImageMetadata.
calculate(FeatureCalculationInput<FeatureInputHistogram>) - Method in class FeatureHistogramStatistic
calculate(FeatureCalculationInput<FeatureInputObjectCollection>) - Method in class FeatureObjectCollection
calculate(FeatureInputObjectCollection) - Method in class FeatureObjectCollection: Calculates the feature-value for a given FeatureInputObjectCollection.
calculate(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class First
calculate(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class Merged
calculate(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class Minimum
calculate(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class RatioFirstToSecond
calculate(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class Second
calculate(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class SubtractSecondFromFirst
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class CenterOfGravity
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class NumberVoxels
calculate(FeatureCalculationInput<T>) - Method in class WithResolutionBase
calculate(int[]) - Method in class VoxelScore
calculate(FeatureInputPairObjects) - Method in class PairsTableCalculator
calculate(FeatureInputPairObjects, FeatureList<FeatureInputPairObjects>) - Method in class PairsTableCalculator
calculate(FeatureInputSingleObject) - Method in class SingleTableCalculator
calculate(FeatureInputSingleObject, FeatureList<FeatureInputSingleObject>) - Method in class SingleTableCalculator
calculate(FeatureCalculationInput<FeatureInputPairMemo>) - Method in class AsSingle
calculate(FeatureCalculationInput<FeatureInputSingleMemo>) - Method in class FeatureSingleMemo
calculate(FeatureCalculationInput<FeatureInputMarkCollection>) - Method in class FeatureMarkCollection
calculate(FeatureCalculationInput<FeatureInputMark>) - Method in class FeatureMark
calculate(Optional<Dimensions>, Optional<ImageSizeSuggestion>) - Method in class ConstantScaleFactor
calculate(Optional<Dimensions>, Optional<ImageSizeSuggestion>) - Method in class Invert
calculate(Optional<Dimensions>, Optional<ImageSizeSuggestion>) - Method in class LargestMultipleWithin
calculate(Optional<Dimensions>, Optional<ImageSizeSuggestion>) - Method in class MinimumXYResolution
calculate(Optional<Dimensions>, Optional<ImageSizeSuggestion>) - Method in class ToDimensions
calculate(Optional<Dimensions>, Optional<ImageSizeSuggestion>) - Method in class ToSuggested
calculate(FeatureCalculationInput<T>) - Method in class FromDimensionsBase
calculate(FeatureCalculationInput<FeatureInputHistogram>) - Method in class LevelFromHistogram
calculate(FeatureCalculationInput<FeatureInputHistogram>) - Method in class ThresholdHistogram
calculate(ImageMetadata) - Method in class BitDepthPerChannel
calculate(ImageMetadata) - Method in class NumberChannels
calculate(ImageMetadata) - Method in class NumberFrames
calculate(FeatureInputObjectCollection) - Method in class NumberObjects
calculate(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class Intersection
calculate(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class CostOverlapWithinMidpointDistance
calculate(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class OverlapRelative
calculate(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class TouchingVoxels
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class ArbitraryInsidePoint
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class AtBorderBase
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class BoundingBoxAlongAxisBase
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class BoundingBoxNumberVoxels
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class SpecificEnergyChannelBase
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class FeatureEnergyChannel
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class GradientMagnitude
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class GradientMeanForAxis
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class ImageMomentsBase
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class DerivedObject
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class NumberRemovedVoxelsAfterClosing
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class OutlineKernelBase
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class ObjectRadiusStandardDeviation
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class ShapeRegularityCenterSlice
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class ShapeRegularityMIP
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class FeatureIntersectingObjects
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class PairedWithMask
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class MaximumNumberContourVoxelsOnSlice
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class MaximumNumberVoxelsOnSlice
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class SurfaceNumberVoxelsBase
calculate(int[]) - Method in class Difference
calculate(int[]) - Method in class Identity
calculate(int[]) - Method in class IdentityImposeValueRelationToHistogram
calculate(int[]) - Method in class OutsideRange
calculate(int[]) - Method in class RejectIfIntensityLessThan
calculate(int[]) - Method in class SingleChannel
calculate(FeatureCalculationInput<T>) - Method in class FeatureSingleObjectFromShared
calculate(FeatureCalculationInput<T>) - Method in class ParamFromCollection
calculate(FeatureCalculationInput<T>) - Method in class DataTypeMaxIntensity
calculate(FeatureCalculationInput<FeatureInputStack>) - Method in class Intensity
calculate(FeatureCalculationInput<FeatureInputStack>) - Method in class NumberChannels
calculate(FeatureCalculationInput<FeatureInputStack>) - Method in class AsObjectMask
calculate(FeatureCalculationInput<FeatureInputStack>) - Method in class QuantileAcrossConnectedComponents
calculate(ObjectMask) - Method in interface PayloadCalculator
calculate(FeatureCalculationInput<FeatureInputMark>) - Method in class FeatureMarkDirection
calculate(FeatureCalculationInput<FeatureInputMark>) - Method in class FeatureMarkEccentricity
calculate(FeatureCalculationInput<FeatureInputMark>) - Method in class MaxRatioRadii
calculate(FeatureCalculationInput<FeatureInputMark>) - Method in class OrderedRadius
calculate(FeatureCalculationInput<FeatureInputMark>) - Method in class RadiiRatio
calculate(FeatureCalculationInput<FeatureInputMark>) - Method in class BoundingBoxExtent
calculate(FeatureCalculationInput<FeatureInputMark>) - Method in class MarkEllipseCircumEstimate
calculate(FeatureCalculationInput<FeatureInputMark>) - Method in class Volume
calculate(FeatureCalculationInput<FeatureInputAllMemo>) - Method in class AsCollection
calculate(FeatureCalculationInput<FeatureInputAllMemo>) - Method in class AsSingleMark
calculate(FeatureCalculationInput<FeatureInputAllMemo>) - Method in class CoefficientOfVarianceFromAll
calculate(FeatureCalculationInput<FeatureInputAllMemo>) - Method in class MeanFromAll
calculate(FeatureCalculationInput<FeatureInputAllMemo>) - Method in class NumberMarks
calculate(FeatureCalculationInput<FeatureInputSingleMemo>) - Method in class AsMark
calculate(FeatureCalculationInput<FeatureInputSingleMemo>) - Method in class AsObject
calculate(FeatureCalculationInput<FeatureInputSingleMemo>) - Method in class BBoxRatio
calculate(FeatureCalculationInput<FeatureInputSingleMemo>) - Method in class Intensity
calculate(FeatureCalculationInput<FeatureInputSingleMemo>) - Method in class MaxSliceArea
calculate(FeatureCalculationInput<FeatureInputSingleMemo>) - Method in class MeanIntensityDifference
calculate(FeatureCalculationInput<FeatureInputSingleMemo>) - Method in class Size
calculate(FeatureCalculationInput<FeatureInputSingleMemo>) - Method in class SurfaceSizeMaskNonZero
calculate(FeatureCalculationInput<FeatureInputPairMemo>) - Method in class BoundingBoxZDistance
calculate(FeatureCalculationInput<FeatureInputPairMemo>) - Method in class BoundingBoxZOverlapRatio
calculate(FeatureCalculationInput<FeatureInputPairMemo>) - Method in class MinimumDistanceByDimension
calculate(FeatureCalculationInput<FeatureInputPairMemo>) - Method in class FeatureAsIndividualProportionate
calculate(FeatureCalculationInput<FeatureInputPairMemo>) - Method in class MinFeatureAsIndividual
calculate(FeatureCalculationInput<FeatureInputPairMemo>) - Method in class MaxOverlapRatio
calculate(FeatureCalculationInput<FeatureInputPairMemo>) - Method in class OverlapNumberVoxelsMask
calculate(FeatureCalculationInput<FeatureInputPairMemo>) - Method in class OverlapNumVoxels
calculate(FeatureCalculationInput<FeatureInputPairMemo>) - Method in class OverlapRatio
calculate(FeatureCalculationInput<FeatureInputPairMemo>) - Method in class OverlapRatioMask
calculate(FeatureCalculationInput<FeatureInputStack>) - Method in class HOGFeature
calculate(FeatureCalculationInput<T>) - Method in class AbsoluteValue
calculate(FeatureCalculationInput<T>) - Method in class Divide
calculate(FeatureCalculationInput<T>) - Method in class InvertedMax
calculate(FeatureCalculationInput<T>) - Method in class Multiply
calculate(FeatureCalculationInput<T>) - Method in class IfCondition
calculate(FeatureCalculationInput<T>) - Method in class FromDictionary
calculate(FeatureCalculationInput<T>) - Method in class Maximum
calculate(FeatureCalculationInput<T>) - Method in class Mean
calculate(FeatureCalculationInput<T>) - Method in class MeanGeometric
calculate(FeatureCalculationInput<T>) - Method in class Minimum
calculate(FeatureCalculationInput<T>) - Method in class NormalizedRange
calculate(FeatureCalculationInput<T>) - Method in class Range
calculate(FeatureCalculationInput<T>) - Method in class RangeCompareBase
calculate(FeatureCalculationInput<T>) - Method in class StatisticalBase
calculate(FeatureCalculationInput<T>) - Method in class WithValueBase
calculate(FeatureCalculationInput<T>) - Method in class ConvertUnits
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class EllipsoidBase
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class Ellipticity
calculate(FeatureCalculationInput<FeatureInput>) - Method in class MockFeatureWithCalculation
calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class Kernel
calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class KernelBirth
calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class KernelBirthAndKill
calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class KernelDeath
calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class KernelExchange
calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class KernelInitialMarksFromPartition
calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class KernelInitialMarksProposed
calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class KernelInitialMarksVoxelized
calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class KernelMerge
calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class KernelReplace
calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class KernelSplit
calculateAcceptanceProbability(Kernel<?, ?>, Optional<T>, T, int, KernelCalculationContext) - Method in class AcceptanceProbabilityCalculator
calculateAndOutput(T, FeatureCalculationContext<S>) - Method in class FeatureSource: Processes one input to calculate feature-results and output them to the file-system.
calculateAndOutput(T, FeatureCalculationContext<FeatureList<S>>) - Method in class SingleRowPerInput
calculateAndOutput(MultiInput, FeatureCalculationContext<FeatureTableCalculator<T>>) - Method in class FromObjects
calculateAt(KernelPointCursor) - Method in class AndKernel
calculateAt(KernelPointCursor) - Method in class BinaryKernel: Calculates the boolean at a particular point.
calculateAt(KernelPointCursor) - Method in class ConditionalKernel
calculateAt(KernelPointCursor) - Method in class CountKernel: Calculates the count at a particular point.
calculateAt(KernelPointCursor) - Method in class BinaryKernelMorphological
calculateCheckInitialized(FeatureCalculationInput<T>) - Method in class Feature: Calculates the result of a feature and throws an exception if the feature has not been initialized.
calculateConnectedComponentID(Point3i, int) - Method in class EncodedVoxels
calculateContext(MarkFactoryContext) - Method in class OptimizationContext
calculateCornerMax() - Method in class BoundingBox: The maximum (right-most) point inside the box.
calculateCornerMaxExclusive() - Method in class BoundingBox: The maximum (right-most) point just outside the box.
calculateDenominator(FeatureInputPairObjects) - Method in class OverlapRelative
calculateDenominator(FeatureInputPairObjects) - Method in class OverlapRelativeToFirst
calculateDenominator(FeatureInputPairObjects) - Method in class OverlapRelativeToMaxVolume
calculateDenominator(FeatureInputPairObjects) - Method in class OverlapRelativeToMerged
calculateDenominator(FeatureInputPairObjects) - Method in class OverlapRelativeToSecond
calculateDensityRatio(double, double, int) - Method in class AnnealScheme
CalculateDeriveMarkCollectionInput - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.all
CalculateDeriveMarkCollectionInput() - Constructor for class CalculateDeriveMarkCollectionInput
CalculateDeriveMarkInput - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.all
CalculateDeriveMarkInput() - Constructor for class CalculateDeriveMarkInput
CalculateDeriveObjectInput - Class in org.anchoranalysis.plugin.image.feature.bean.stack.object
CalculateDeriveObjectInput(int) - Constructor for class CalculateDeriveObjectInput
CalculateDeriveSingleMemoFromPair - Class in org.anchoranalysis.mpp.feature.bean.energy.element
CalculateDeriveSingleMemoFromPair(boolean) - Constructor for class CalculateDeriveSingleMemoFromPair
CalculateDilation - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological
CalculateDilationMap - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological
CalculateDilationMap(boolean) - Constructor for class CalculateDilationMap
CalculateDilationMap(CalculateIncrementalOperationMap) - Constructor for class CalculateDilationMap
calculateEccentricity(double, double) - Static method in class PrincipalAxisEccentricity
CalculateEllipseLeastSquares - Class in org.anchoranalysis.plugin.points.calculate.ellipse
CalculateEllipseLeastSquares() - Constructor for class CalculateEllipseLeastSquares
CalculateEllipsoidLeastSquares - Class in org.anchoranalysis.plugin.points.calculate.ellipsoid
CalculateErosion - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological
CalculateErosionMap - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological
CalculateErosionMap(boolean) - Constructor for class CalculateErosionMap
CalculateErosionMap(CalculateIncrementalOperationMap) - Constructor for class CalculateErosionMap
calculateFeatureByIdentifier(String, FeatureCalculationInput<T>) - Method in interface FeatureSymbolCalculator: Searches for a feature that matches a particular identifier.
calculateFeatureOn(ObjectCollection, FeatureCalculatorSingle<FeatureInputSingleObject>) - Method in class ReportFeatureOnObject
calculateFeatureOn(ObjectCollection, FeatureCalculatorSingle<FeatureInputObjectCollection>) - Method in class ReportFeatureOnObjectCollection
calculateFeatureOn(ObjectCollection, FeatureCalculatorSingle<T>) - Method in class ReportFeatureOnObjectsBase
CalculateFeaturesForObjects<T extends FeatureInput> - Class in org.anchoranalysis.plugin.image.task.feature.calculator
CalculateFeaturesForObjects(CombineObjectsForFeatures<T>, InitializationWithEnergyStack, boolean, FeatureCalculationContext<FeatureTableCalculator<T>>) - Constructor for class CalculateFeaturesForObjects
calculateFeaturesForObjects(ObjectCollection, EnergyStack, CalculateFeaturesForObjects.LabelsForInput<T>) - Method in class CalculateFeaturesForObjects
CalculateFeaturesForObjects.LabelsForInput<T extends FeatureInput> - Interface in org.anchoranalysis.plugin.image.task.feature.calculator
calculateForAxis(Dimensions, Axis) - Method in class Extent
calculateForAxis(Dimensions, Axis) - Method in class ForSpecificAxis
calculateForAxis(Dimensions, Axis) - Method in class VoxelPhysicalSize
calculateForChannel(FeatureCalculationInput<FeatureInputSingleObject>, Channel) - Method in class FeatureEnergyChannel
calculateForChannel(FeatureCalculationInput<FeatureInputSingleObject>, Channel) - Method in class Intensity
calculateForChannel(FeatureCalculationInput<FeatureInputSingleObject>, Channel) - Method in class IntensityMeanMaxSlice
calculateForChannel(FeatureCalculationInput<FeatureInputSingleObject>, Channel) - Method in class IntensityMeanShellBase
calculateForChannel(FeatureCalculationInput<FeatureInputSingleObject>, Channel) - Method in class TextureScore
CalculateForChild<T extends FeatureInput> - Interface in org.anchoranalysis.feature.calculate.cache: Performs calculations using child-caches instead of the main cache
calculateForEllipsoid(Ellipsoid, Orientation, RotationMatrix, Vector3d) - Method in class DotProductOrientationToVector
calculateForEllipsoid(Ellipsoid, Orientation, RotationMatrix, Vector3d) - Method in class EllipsoidAxisRatio
calculateForEllipsoid(Ellipsoid, Orientation, RotationMatrix, Vector3d) - Method in class EllipsoidMaxAreaIntersectingPlane
calculateForEllipsoid(Ellipsoid, Orientation, RotationMatrix, Vector3d) - Method in class FeatureMarkDirection
calculateForNewMark(MarksFromPartition, Set<Mark>, KernelCalculationContext) - Method in class KernelBirthPartition
calculateForNewMark(T, Set<Mark>, KernelCalculationContext) - Method in class KernelBirth
calculateForNewMark(VoxelizedMarksWithEnergy, Set<Mark>, KernelCalculationContext) - Method in class KernelBirthVoxelized
calculateForShell(ObjectMask, Channel) - Method in class IntensityMeanShell
calculateForShell(ObjectMask, Channel) - Method in class IntensityMeanShellBase
calculateForShell(ObjectMask, Channel) - Method in class IntensityMeanShellMaxSlice
calculateForVoxel(int, int) - Method in class CalculateLevel
calculateForVoxel(int, int) - Method in class CalculateLevelBase
calculateForVoxel(int, int) - Method in class DifferenceCalculateLevelStandardDeviation
calculateFromAllMoments(ImageMoments) - Method in class ImageMomentsBase
calculateFromAllMoments(ImageMoments) - Method in class PrincipalAxisEccentricity
calculateFromAllMoments(ImageMoments) - Method in class RatioPrincipalAxisLength
calculateFromAllMoments(ImageMoments) - Method in class SpecificAxisBase
calculateFromDimensions(Dimensions) - Method in class Area
calculateFromDimensions(Dimensions) - Method in class ForSpecificAxis
calculateFromDimensions(Dimensions) - Method in class FromDimensionsBase
calculateFromDimensions(Dimensions) - Method in class Volume
calculateFromSpecificMoment(EigenvalueAndVector) - Method in class PrincipalAxisLength
calculateFromSpecificMoment(EigenvalueAndVector) - Method in class PrincipalAxisOrientation
calculateFromSpecificMoment(EigenvalueAndVector) - Method in class SpecificAxisBase: Calculates the result for the specific moment identified by index
CalculateHistogram - Class in org.anchoranalysis.plugin.image.feature.stack.calculation
CalculateHistogram(int) - Constructor for class CalculateHistogram
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 CalculateHistogramMasked
CalculateIncrementalOperationMap - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single
CalculateIncrementalOperationMap(boolean) - Constructor for class CalculateIncrementalOperationMap
CalculateIncrementalOperationMap(CalculateIncrementalOperationMap) - Constructor for class CalculateIncrementalOperationMap
CalculateInputFromDelegate<S,T extends FeatureInput,U> - Class in org.anchoranalysis.plugin.image.feature.object.calculation.delegate: A base class for CalculationParts that derive from an existing "delegate" calculation.
CalculateInputFromDelegate(CalculationPart<U, T>, CalculationPartResolver<T>) - Constructor for class CalculateInputFromDelegate
CalculateInputFromDelegate(ResolvedPart<U, T>) - Constructor for class CalculateInputFromDelegate
CalculateInputFromDelegateOption<S extends FeatureInput,T extends FeatureInput,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 CalculateInputFromDelegateOption: Creates with a delegate.
CalculateInputFromPair - Class in org.anchoranalysis.image.feature.calculation: Calculates a single-input from a pair
CalculateInputFromPair(CalculateInputFromPair.Extract) - Constructor for class CalculateInputFromPair
CalculateInputFromPair.Extract - Enum in org.anchoranalysis.image.feature.calculation
CalculateIntersecting - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting
CalculateIntersecting(ResolvedPart<ObjectCollection, FeatureInputSingleObject>, int) - Constructor for class CalculateIntersecting
CalculateLevel - Class in org.anchoranalysis.image.bean.threshold: Calculates a threshold-level from a histogram.
CalculateLevel() - Constructor for class CalculateLevel
calculateLevel(Histogram) - Method in class CalculateLevel: Determines a voxel intensity that can be used for thresholding.
calculateLevel(Histogram) - Method in class CalculateLevelRelativeToThreshold
calculateLevel(Histogram) - Method in class ClampHistogramMax
calculateLevel(Histogram) - Method in class Constant
calculateLevel(Histogram) - Method in class EmptyHistogramConstant
calculateLevel(Histogram) - Method in class Maximum
calculateLevel(Histogram) - Method in class Minimum
calculateLevel(Histogram) - Method in class Otsu
calculateLevel(Histogram) - Method in class OtsuWeighted
calculateLevel(Histogram) - Method in class Quantile
CalculateLevel - Class in org.anchoranalysis.plugin.image.feature.bean.score
CalculateLevel() - Constructor for class CalculateLevel
CalculateLevelBase - Class in org.anchoranalysis.plugin.image.feature.bean.score
CalculateLevelBase() - Constructor for class CalculateLevelBase
calculateLevelIncoming(Histogram) - Method in class CalculateLevelOne
CalculateLevelListBase - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold
CalculateLevelListBase() - Constructor for class CalculateLevelListBase
CalculateLevelOne - Class in org.anchoranalysis.image.bean.threshold
CalculateLevelOne() - Constructor for class CalculateLevelOne
CalculateLevelRelativeToThreshold - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold
CalculateLevelRelativeToThreshold() - Constructor for class CalculateLevelRelativeToThreshold
calculateMaximum() - Method in class Histogram: Calculates the maximum value with non zero-count among the histogram values.
calculateMaybeSuppressErrors(FeatureInputPairObjects, ErrorReporter) - Method in class PairsTableCalculator
calculateMeanIntensityObject(Channel, ObjectMask) - Static method in class IntensityMeanCalculator
calculateMeanIntensityObject(Channel, ObjectMask, boolean) - Static method in class IntensityMeanCalculator
calculateMidpoint(ObjectWithProperties, boolean) - Static method in class Midpoint
calculateMinimum() - Method in class Histogram: Calculates the minimum value with non zero-count among the histogram values.
calculateMinMax(Optional<Resolution>, boolean) - Method in class MarkBounds
calculateMode() - Method in class Histogram: Calculates the mode of the histogram values.
calculateNewMaxCurrentValue() - Method in class PriorityQueueIndexRangeDownhill
CalculateNumberVoxels - Class in org.anchoranalysis.image.feature.calculation
CalculateNumberVoxels(boolean) - Constructor for class CalculateNumberVoxels
CalculateObjectMask - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single
CalculateObjectMask(CalculateObjectMask) - Constructor for class CalculateObjectMask: Copy constructor
CalculateObjectMask(int, ResolvedPartMap<ObjectMask, FeatureInputSingleObject, Integer>) - Constructor for class CalculateObjectMask
calculateOrientation(ObjectWithProperties) - Static method in class Orientation
CalculateOrientationChange - Interface in org.anchoranalysis.image.io.stack: Calculates any needed orientation change.
calculateOrientationChange(Logger) - Method in interface CalculateOrientationChange: Calculates any needed orientation change.
CalculateOverlap - Class in org.anchoranalysis.plugin.mpp.feature.overlap
CalculateOverlap(int) - Constructor for class CalculateOverlap
CalculateOverlapMask - Class in org.anchoranalysis.plugin.mpp.feature.overlap
CalculateOverlapMask(int, int, byte) - Constructor for class CalculateOverlapMask
CalculateOverlapMIP - Class in org.anchoranalysis.plugin.mpp.feature.overlap
CalculateOverlapMIP(int) - Constructor for class CalculateOverlapMIP
CalculateOverlapMIPBase - Class in org.anchoranalysis.plugin.mpp.feature.overlap
CalculateOverlapMIPBase(int) - Constructor for class CalculateOverlapMIPBase
CalculateOverlapMIPRatio - Class in org.anchoranalysis.plugin.mpp.feature.overlap
CalculateOverlapMIPRatio(int) - Constructor for class CalculateOverlapMIPRatio
calculateOverlapResult(double, MaxIntensityProjectionPair) - Method in class CalculateOverlapMIP
calculateOverlapResult(double, MaxIntensityProjectionPair) - Method in class CalculateOverlapMIPBase
calculateOverlapResult(double, MaxIntensityProjectionPair) - Method in class CalculateOverlapMIPRatio
calculatePath() - Method in class MutableDirectory
calculatePath() - Method in class OutputtedFile
calculatePoint(ObjectWithProperties, String) - Static method in class Orientation
calculatePoints(Point3d, Orientation, boolean, RandomNumberGenerator, boolean) - Method in class MergeLists
calculatePoints(Point3d, Orientation, boolean, RandomNumberGenerator, boolean) - Method in class PointsFromOrientationProposer
calculatePoints(Point3d, Orientation, boolean, RandomNumberGenerator, boolean) - Method in class TraversePointsOnContour
calculateResultsForInput(FileInput, FeatureCalculationContext<FeatureList<FeatureInputHistogram>>) - Method in class FromHistogram
calculateResultsForInput(ProvidesStackInput, FeatureCalculationContext<FeatureList<FeatureInputStack>>) - Method in class FromImage
calculateResultsForInput(ImageMetadataInput, FeatureCalculationContext<FeatureList<FeatureInputImageMetadata>>) - Method in class FromImageMetadata
calculateResultsForInput(T, FeatureCalculationContext<FeatureList<S>>) - Method in class SingleRowPerInput: Calculates feature-results for a particular input.
calculateRunningSum(Mask, Voxels<UnsignedByteBuffer>) - Static method in class IterateVoxelsMask: Calculates the sum and count across voxels intensity that correspond to on voxels on a mask
calculateScaleFactor(Optional<Dimensions>) - Method in interface ImageSizeSuggestion: Calculates the scaling factor.
CalculateShellObjectMask - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single
CalculateShellObjectMask(ResolvedPart<ObjectMask, FeatureInputSingleObject>, ResolvedPart<ObjectMask, FeatureInputSingleObject>, int, boolean, boolean) - Constructor for class CalculateShellObjectMask
calculateSigma(Dimensions, MessageLogger) - Method in class BlurStrategy
calculateStatisticFrom(Histogram) - Method in class FeatureHistogramStatistic: Calculates the statistic from the histogram, that is subsequently returned as the feature-value.
calculateStatisticFrom(Histogram) - Method in class Mean
calculateStatisticFrom(Histogram) - Method in class CoefficientOfVariation
calculateStatisticFrom(Histogram) - Method in class Count
calculateStatisticFrom(Histogram) - Method in class Kurtosis
calculateStatisticFrom(Histogram) - Method in class Max
calculateStatisticFrom(Histogram) - Method in class MeanRaisedToPower
calculateStatisticFrom(Histogram) - Method in class Median
calculateStatisticFrom(Histogram) - Method in class Min
calculateStatisticFrom(Histogram) - Method in class Mode
calculateStatisticFrom(Histogram) - Method in class NumberDistinctValues
calculateStatisticFrom(Histogram) - Method in class Quantile
calculateStatisticFrom(Histogram) - Method in class Range
calculateStatisticFrom(Histogram) - Method in class RatioNonMode
calculateStatisticFrom(Histogram) - Method in class Skewness
calculateStatisticFrom(Histogram) - Method in class StdDev
calculateStatisticFrom(Histogram) - Method in class Sum
calculateStatisticFrom(Histogram) - Method in class TotalCount
calculateStatisticFrom(Histogram) - Method in class Variance
calculateStatisticFrom(Histogram) - Method in class RatioThreshold
calculateSum() - Method in class Histogram: Calculates the sum of all values in the distribution considering their counts.
calculateSumCubes() - Method in class Histogram: Calculates the cube of the squares of all values in the distribution considering their counts.
calculateSumSquares() - Method in class Histogram: Calculates the sum of the squares of all values in the distribution considering their counts.
calculateSuppressErrors(T, ErrorReporter) - Method in interface 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 FeatureCalculatorMultiChangeInput
calculateSuppressErrors(T, ErrorReporter) - Method in interface 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 FeatureCalculatorSingleChangeInput
calculateSuppressErrors(T, ErrorReporter) - Method in class FeatureCalculatorSingleFromMulti
calculateSuppressErrors(T, ErrorReporter) - Method in class SequentialSession: Calculates the next-object in our sequential series, reporting any exceptions into a reporter log
calculateSuppressErrors(FeatureInputPairObjects, ErrorReporter) - Method in class PairsTableCalculator
calculateSuppressErrors(FeatureInputSingleObject, ErrorReporter) - Method in class SingleTableCalculator
calculateTemperature(int) - Method in class AnnealScheme
calculateTemperature(int) - Method in class Geometry
calculateTemperature(int) - Method in class NoAnnealing
calculateVolume() - Method in class Dimensions: Calculates the volume of the Extent when considered as a box.
calculateVolume() - Method in class Extent: Calculates the volume of the Extent when considered as a box.
calculateVolumeAsInt() - Method in class Extent: Like Extent.calculateVolume() but uses an int to calculate the volume.
calculateWith(Feature<T>, T, Logger) - Static method in class FeatureSession: Starts a feature-session for a single feature - and performs a calculation.
calculateWithChannel(ObjectMask, Channel) - Method in class CountEqual
calculateWithChannel(ObjectMask, Channel) - Method in class SpecificEnergyChannelBase
calculateWithIntersection(ObjectMask, ObjectMask, BoundingBox) - Method in class HasTouchingVoxels
calculateWithIntersection(ObjectMask, ObjectMask, BoundingBox) - Method in class NumberTouchingVoxelFaces
calculateWithIntersection(ObjectMask, ObjectMask, BoundingBox) - Method in class NumberTouchingVoxels
calculateWithIntersection(ObjectMask, ObjectMask, BoundingBox) - Method in class TouchingVoxels
calculateWithParameters(ObjectMask, KernelApplicationParameters, CheckedSupplier<EnergyStack, FeatureCalculationException>) - Method in class NumberVoxelsAtBorder
calculateWithParameters(ObjectMask, KernelApplicationParameters, CheckedSupplier<EnergyStack, FeatureCalculationException>) - Method in class NumberNeighboringVoxels
calculateWithParameters(ObjectMask, KernelApplicationParameters, CheckedSupplier<EnergyStack, FeatureCalculationException>) - Method in class OutlineKernelBase
calculateWithResolution(double, Resolution) - Method in class FeatureConvertUnits
calculateWithResolution(double, Resolution) - Method in class WithResolutionBase
calculateWithResolution(double, Resolution) - Method in class UnitsWithinRange
calculateZScore(double, double, double) - Static method in class ZScoreCalculator: Calculates a Z-Score for a particular value and parameterization.
CalculationPart<S,T extends FeatureInput> - 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 CalculationPart
CalculationPartMap<S,T extends FeatureInput,U,E extends Exception> - 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 CalculationPartMap: Creates for a particular cache-size.
CalculationPartResolver<T extends FeatureInput> - Interface in org.anchoranalysis.feature.calculate.part: Searches a cache to reuses a CalculationPart if it already exists.
calculator() - Method in interface FeatureCalculationCache: A means of calculating feature values using this cache.
calculatorForAll(FeatureList<T>) - Method in class FeatureCalculatorFromProvider: Calculates all image-features in the feature-store
calculatorSingleFromProvider(FeatureListProvider<T>, String) - Method in class FeatureCalculatorFromProvider: Calculates a single-feature that comes from a provider (but can reference the other features from the store)
call(CheckedSupplier<T, E>) - Method in class CachedSupplierBase: Gets the value supplied by supplier via the cache if it exists, or otherwise via the supplier.
call() - Method in class CallableJob
CallableJob<T extends InputFromManager,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>, JobState, JobDescription, ConcurrentJobMonitor, Optional<MessageLogger>, int) - Constructor for class CallableJob: Constructor.
callEachPointInNeighborhood(Point3i, Neighborhood, boolean, ProcessVoxelNeighbor<T>, int, int) - Static method in class IterateVoxelsNeighbors: Iterate over each point in the neighborhood of an existing point.
canEqual(Object) - Method in class DoubleList
canEqual(Object) - Method in class DoubleSet
canEqual(Object) - Method in class IntegerList
canEqual(Object) - Method in class IntegerSet
canEqual(Object) - Method in class StringList
canEqual(Object) - Method in class StringSet
canEqual(Object) - Method in class RootPath
canEqual(Object) - Method in class EqualToBean
canEqual(Object) - Method in class GreaterThanBean
canEqual(Object) - Method in class GreaterThanEqualToBean
canEqual(Object) - Method in class LessThanBean
canEqual(Object) - Method in class LessThanEqualToBean
canEqual(Object) - Method in class RelationBean
canEqual(Object) - Method in class RelationToConstant
canEqual(Object) - Method in class Indexable
canEqual(Object) - Method in class ChildCacheName
canEqual(Object) - Method in class FeatureInputDimensions
canEqual(Object) - Method in class FeatureInputEnergy
canEqual(Object) - Method in class FeatureInputNull
canEqual(Object) - Method in class SimpleName
canEqual(Object) - Method in class SizeXY
canEqual(Object) - Method in class CalculateLevelOne
canEqual(Object) - Method in class BinaryNotOffVoxels
canEqual(Object) - Method in class BinaryNotOnVoxels
canEqual(Object) - Method in class BinaryOffVoxels
canEqual(Object) - Method in class BinaryOnVoxels
canEqual(Object) - Method in class BinaryVoxelsBase
canEqual(Object) - Method in class CalculateInputFromPair
canEqual(Object) - Method in class CalculateNumberVoxels
canEqual(Object) - Method in class FeatureInputImageMetadata
canEqual(Object) - Method in class FeatureInputObjectCollection
canEqual(Object) - Method in class FeatureInputPairObjects
canEqual(Object) - Method in class FeatureInputSingleObject
canEqual(Object) - Method in class FeatureInputStack
canEqual(Object) - Method in class UnsignedBuffer
canEqual(Object) - Method in class UnsignedBufferAsInt
canEqual(Object) - Method in class UnsignedByteBuffer
canEqual(Object) - Method in class UnsignedIntBuffer
canEqual(Object) - Method in class UnsignedShortBuffer
canEqual(Object) - Method in class QuadraticEquationSolver.QuadraticRoots
canEqual(Object) - Method in class MeanScale
canEqual(Object) - Method in class RegionMap
canEqual(Object) - Method in class RegionMembership
canEqual(Object) - Method in class RegionMembershipWithFlags
canEqual(Object) - Method in class CalculateDeriveSingleMemoFromPair
canEqual(Object) - Method in class FeatureInputMark
canEqual(Object) - Method in class IndexableMarksWithEnergy
canEqual(Object) - Method in class FeatureInputAllMemo
canEqual(Object) - Method in class FeatureInputPairMemo
canEqual(Object) - Method in class FeatureInputSingleMemo
canEqual(Object) - Method in class MemoList
canEqual(Object) - Method in class ColoredMarksWithDisplayStack
canEqual(Object) - Method in class MarksWithDisplayStack
canEqual(Object) - Method in class OverlayMark
canEqual(Object) - Method in class FeedbackBeginParameters
canEqual(Object) - Method in class IndexableOverlays
canEqual(Object) - Method in class AxisLimits
canEqual(Object) - Method in class CalculateLevelListBase
canEqual(Object) - Method in class CalculateLevelRelativeToThreshold
canEqual(Object) - Method in class ClampHistogramMax
canEqual(Object) - Method in class Constant
canEqual(Object) - Method in class EmptyHistogramConstant
canEqual(Object) - Method in class IfGreaterThan
canEqual(Object) - Method in class IfLessThan
canEqual(Object) - Method in class Maximum
canEqual(Object) - Method in class Minimum
canEqual(Object) - Method in class Otsu
canEqual(Object) - Method in class OtsuWeighted
canEqual(Object) - Method in class Quantile
canEqual(Object) - Method in class MorphologicalIterations
canEqual(Object) - Method in class CalculateIntersecting
canEqual(Object) - Method in class CalculateDeriveObjectInput
canEqual(Object) - Method in class CalculateInputFromDelegate
canEqual(Object) - Method in class CalculateInputFromDelegateOption
canEqual(Object) - Method in class CalculateIncrementalOperationMap
canEqual(Object) - Method in class CalculateObjectMask
canEqual(Object) - Method in class CalculateShellObjectMask
canEqual(Object) - Method in class CalculateDilation
canEqual(Object) - Method in class CalculateDilationMap
canEqual(Object) - Method in class CalculateErosion
canEqual(Object) - Method in class CalculateErosionMap
canEqual(Object) - Method in class CalculateHistogram
canEqual(Object) - Method in class CalculateHistogramMasked
canEqual(Object) - Method in class ChangeableOutputSequence
canEqual(Object) - Method in class SortedSetChannel
canEqual(Object) - Method in class SortedSetSlice
canEqual(Object) - Method in class AllSlicesMaskEverythingNonZero
canEqual(Object) - Method in class AllSlicesMaskNonZero
canEqual(Object) - Method in class CenterSlice
canEqual(Object) - Method in class CenterSliceBase
canEqual(Object) - Method in class CenterSliceWindow
canEqual(Object) - Method in class GreatestAreaSlice
canEqual(Object) - Method in class IndexedRegionBase
canEqual(Object) - Method in class SelectSlicesBase
canEqual(Object) - Method in class SelectSlicesWithIndexBase
canEqual(Object) - Method in class Specific
canEqual(Object) - Method in class CalculateDeriveMarkCollectionInput
canEqual(Object) - Method in class CalculateDeriveMarkInput
canEqual(Object) - Method in class CalculateOverlap
canEqual(Object) - Method in class CalculateOverlapMask
canEqual(Object) - Method in class CalculateOverlapMIP
canEqual(Object) - Method in class CalculateOverlapMIPBase
canEqual(Object) - Method in class CalculateOverlapMIPRatio
canEqual(Object) - Method in class HOGParameters
canEqual(Object) - Method in class FitResult
canEqual(Object) - Method in class CalculateEllipseLeastSquares
canEqual(Object) - Method in class CalculateEllipsoidLeastSquares
canEqual(Object) - Method in class Orientation2D
canEqual(Object) - Method in class Orientation3DEulerAngles
canEqual(Object) - Method in class OrientationAxisAngle
canEqual(Object) - Method in class OrientationRotationMatrix
canEqual(Object) - Method in class Point3d
canEqual(Object) - Method in class Point3f
canEqual(Object) - Method in class Point3i
canEqual(Object) - Method in class Tuple3d
canEqual(Object) - Method in class Tuple3f
canEqual(Object) - Method in class Tuple3i
canEqual(Object) - Method in class Vector3d
canExceptionBeCombined(Throwable) - Method in exception BeanMisconfiguredXMLException
canExceptionBeCombined(Throwable) - Method in exception LocalisedBeanException
canExceptionBeCombined(Throwable) - Method in exception AnchorCombinableException: Can another exception be combined with this exception?
canExceptionBeCombined(Throwable) - Method in exception NamedProviderGetException
canExceptionBeSkipped(Throwable) - Method in exception BeanMisconfiguredXMLException
canExceptionBeSkipped(Throwable) - Method in exception LocalisedBeanException
canExceptionBeSkipped(Throwable) - Method in exception AnchorCombinableException: Can another exception be skipped, when we combine with the current exception?
canExceptionBeSkipped(Throwable) - Method in exception NamedProviderGetException
canValueRangeChange() - Method in interface Interpolator: 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 InterpolatorImgLib2Lanczos
canValueRangeChange() - Method in class InterpolatorImgLib2Linear
canValueRangeChange() - Method in class InterpolatorImgLib2NearestNeighbor
canValueRangeChange() - Method in class InterpolatorNone
canValueRangeChange() - Method in class InterpolatorImageJ
capacity() - Method in class UnsignedBuffer: The capacity of the buffer ala Buffer.capacity.
capacity() - Method in class VoxelBuffer: The capacity (i.e.
capacity() - Method in class VoxelBufferUnsigned
castAs() - Method in class Feature: Casts the feature to having a different input-type.
Cell - Class in org.anchoranalysis.image.bean.spatial.arrange
Cell() - Constructor for class Cell
CenterOfGravity - Class in org.anchoranalysis.image.feature.bean.object.single
CenterOfGravity(Axis) - Constructor for class CenterOfGravity: Creates for a specific axis.
CenterOfGravity() - Constructor for class CenterOfGravity
centerOfGravity() - Method in class ObjectMask: Calculates center-of-gravity across all axes.
centerOfGravity(Axis) - Method in class ObjectMask: Calculates center-of-gravity for one specific axis only.
centerOfGravity() - Method in class BoundingBox: A mid-point in the bounding-box, corresponding to the mean of all points inside the box.
CenterOnMask - Class in org.anchoranalysis.plugin.mpp.bean.check
CenterOnMask() - Constructor for class CenterOnMask
centerPoint() - Method in class Mark
centerPoint() - Method in class MarkWithPosition
centerPoint() - Method in class LineSegment
centerPoint() - Method in class PointList
centerPoint() - Method in class Polygon
centerPoint() - Method in class PolygonCurve
centerPoint() - Method in class EllipseStandardFormConverter
CenterSlice - Class in org.anchoranalysis.plugin.mpp.bean.region
CenterSlice() - Constructor for class CenterSlice
CenterSliceBase - Class in org.anchoranalysis.plugin.mpp.bean.region
CenterSliceBase() - Constructor for class CenterSliceBase
CenterSliceWindow - Class in org.anchoranalysis.plugin.mpp.bean.region: Like {#link org.anchoranalysis.plugin.mpp.bean.region.CenterSlice} but considers more than one slice, specifically centerSlice+- windowSize
CenterSliceWindow() - Constructor for class CenterSliceWindow
chainCode(int, int, int) - Static method in class ChainCodesDirection
chainCodes(int) - Method in class WatershedEncoding: Decodes a chain-code into a point
ChainCodesDirection - Class in org.anchoranalysis.plugin.image.segment.watershed.encoding: Maps directions to chain codes
ChangeableOutputSequence<T,S> - Class in org.anchoranalysis.plugin.image.task.bean.format
ChangeableOutputSequence() - Constructor for class ChangeableOutputSequence
changedMarkIDArray() - Method in class Kernel: The mark ids that were changed in the last energy calculation for the kernel
changedMarkIDArray() - Method in class KernelBirth
changedMarkIDArray() - Method in class KernelBirthAndKill
changedMarkIDArray() - Method in class KernelDeath
changedMarkIDArray() - Method in class KernelExchange
changedMarkIDArray() - Method in class KernelInitialMarksFromPartition
changedMarkIDArray() - Method in class KernelInitialMarksProposed
changedMarkIDArray() - Method in class KernelInitialMarksVoxelized
changedMarkIDArray() - Method in class KernelMerge
changedMarkIDArray() - Method in class KernelReplace
changedMarkIDArray() - Method in class KernelSplit
changedOffset(int, int) - Method in class 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 FormatExtensions: Change the extension in a path.
changeExtent(Extent) - Method in class BoundingBox: Creates a copied BoundingBox but with a different extent.
changeExtentZ(int) - Method in class BoundingBox: Creates a copied BoundingBox but with a different extent in the Z-dimension.
changeInput(U) - Method in class InputBound: Immutably changes the input-object
changeInputAndSharedState(U, V) - Method in class InputBound: Immutably changes the input-object and shared-state
changeIntensity(Voxels<?>, IntUnaryOperator) - Static method in class IterateVoxelsAll: Changes each voxel, reading and writing the buffer as an int.
changePrefix(DirectoryWithPrefix) - Method in class OutputterTarget: Creates a new OutputterTarget with a changed prefix.
changePrefix(DirectoryWithPrefix, Optional<WriteOperationRecorder>) - Method in class OutputterChecked: Creates a OutputterChecked with a changed prefix and WriteOperationRecorder.
changeZ(int, int) - Method in class BoundingBox: Creates a copied BoundingBox but with a different corner and extent in the Z-dimension.
Channel - Class in org.anchoranalysis.image.core.channel: A channel from an image.
Channel(Voxels<?>, Optional<Resolution>) - Constructor for class Channel: Creates for particular voxels and resolution.
channel() - Method in class Mask: The underlying channel which contains the binary-values.
channel(String) - Static method in class ReferenceFactory
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 ChannelConverter
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 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 ChannelConvertStyle
ChannelEntry - Class in org.anchoranalysis.image.io.bean.channel
ChannelEntry(String, int) - Constructor for class ChannelEntry
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 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 ChannelFactorySingleType
ChannelFactoryUnsignedByte - Class in org.anchoranalysis.image.core.channel.factory: Creates a Channel with voxel-type UnsignedByteVoxelType.
ChannelFactoryUnsignedByte() - Constructor for class ChannelFactoryUnsignedByte: Default constructor.
ChannelFactoryUnsignedInt - Class in org.anchoranalysis.image.core.channel.factory: Creates a Channel with voxel-type UnsignedIntVoxelType.
ChannelFactoryUnsignedInt() - Constructor for class ChannelFactoryUnsignedInt: Default constructor.
ChannelFactoryUnsignedShort - Class in org.anchoranalysis.image.core.channel.factory: Creates a Channel with voxel-type UnsignedShortVoxelType.
ChannelFactoryUnsignedShort() - Constructor for class ChannelFactoryUnsignedShort: Default constructor.
ChannelFilter - Class in org.anchoranalysis.image.io.bean.channel: Applies a filter to a particular channel
ChannelFilter() - Constructor for class ChannelFilter
ChannelGenerator - Class in org.anchoranalysis.image.io.channel.output: Writes a single channel to a file.
ChannelGenerator(String) - Constructor for class ChannelGenerator
ChannelGetter - Interface in org.anchoranalysis.image.io.channel.input
ChannelGetterForTimepoint - Class in org.anchoranalysis.plugin.image.task.stack
ChannelGetterForTimepoint(ChannelGetter, int) - Constructor for class ChannelGetterForTimepoint
ChannelMap - Class in org.anchoranalysis.image.io.bean.channel
ChannelMap() - Constructor for class ChannelMap
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 ChannelMapper
channelNames() - Method in interface NamedChannelsForSeries
channelNames() - Method in class NamedChannelsForSeriesConcatenate
channelNames() - Method in class NamedChannelsForSeriesMap
channelNames(Logger) - Method in interface OpenedImageFile: The names of each channel, if they are known.
channelNames(Logger) - Method in class 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 ChannelProvider
ChannelProviderBinary - Class in org.anchoranalysis.image.bean.provider: A channel-provider based-on two input channel-providers that must be of the same dimensionality
ChannelProviderBinary() - Constructor for class ChannelProviderBinary
ChannelProviderTernary - Class in org.anchoranalysis.image.bean.provider
ChannelProviderTernary() - Constructor for class ChannelProviderTernary
ChannelProviderUnary - Class in org.anchoranalysis.image.bean.provider
ChannelProviderUnary() - Constructor for class ChannelProviderUnary
channels() - Method in class ImageInitialization
ChannelSource - Class in org.anchoranalysis.plugin.image.task.grouped: Source of channels for aggregating.
ChannelSource(NamedStacks, ConsistentChannelChecker, Optional<SizeXY>) - Constructor for class ChannelSource
channelsPerByteArray(IFormatReader) - Method in class Default
channelsPerByteArray(IFormatReader) - Method in class ForceChannelsPerByteArray
channelsPerByteArray(IFormatReader) - Method in class ReadOptions: The number of channels returned with each call to IFormatReader.openBytes(int).
channelsPerByteArray(IFormatReader) - Method in class ReadOptionsDelegate
check(Mark, RegionMap, EnergyStack) - Method in class CheckMark: Checks a mark
check(Channel, Mask) - Static method in class DimensionsChecker
check(Channel, String, Dimensions) - Static method in class DimensionsChecker: Checks a channel to make sure it's the same size as an an existing channel
check(Mask, String, Dimensions) - Static method in class DimensionsChecker: Checks a channel to make sure it's the same size as an an existing channel
check(Mark, RegionMap, EnergyStack) - Method in class AndList
check(Mark, RegionMap, EnergyStack) - Method in class AnySliceCenterOnMask
check(Mark, RegionMap, EnergyStack) - Method in class CenterOnMask
check(Mark, RegionMap, EnergyStack) - Method in class FeatureValueCheckMark
check(Mark, RegionMap, EnergyStack) - Method in class Not
check(Mark, RegionMap, EnergyStack) - Method in class RadiiMinRatio
check(Mark, RegionMap, EnergyStack) - Method in class VolumeMin
Check - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
Check() - Constructor for class Check
Check - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection
Check() - Constructor for class Check
check(T) - Static method in class BeanTestChecker: Checks if a bean has all necessary items, throwing a run-time exception if it does not.
checkAbsolutePath() - Method in class OutputPrefixerSettings
checkAndInit(T, P, Logger) - Static method in class 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 session-input is available from another LRU-cache and reuse.
CheckCacheForSpecificChildren(Class<?>, CacheTransferSourceCollection) - Constructor for class CheckCacheForSpecificChildren
checkChannelType(VoxelDataType) - Method in class ConsistentChannelChecker: Checks that a channel has the same type (max value) as the others
checkCompatibleWith(Mark) - Method in class KernelProposer
CheckedBiConsumer<S,T,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked: Like BiConsumer but can also throw a checked exception.
CheckedBiFunction<S,T,V,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked: Like BiFunction but can also throw a checked exception.
CheckedBooleanSupplier<E extends Exception> - Interface in org.anchoranalysis.core.functional.checked: Like BooleanSupplier but can also throw an exception.
CheckedConsumer<S,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked: Consumes a value and throws an exception.
CheckedFunction<S,V,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked: Like Function but can also thrown an exception.
CheckedIntConsumer<E extends Exception> - Interface in org.anchoranalysis.core.functional.checked: Consumes an int and throws an exception.
CheckedIntFunction<T,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked: Like IntFunction but can also thrown an exception.
CheckedPredicate<T,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked: Like Predicate but can also throw an exception.
CheckedProgressingSupplier<R,E extends Exception> - Interface in org.anchoranalysis.core.progress: Like CheckedSupplier but can update a progress-reporter as the operation progresses.
CheckedRunnable<E extends Exception> - 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 in org.anchoranalysis.core.functional: An exception that wraps another exception, but exposes itself as a RuntimeException.
CheckedSupplier<T,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked: Like Supplier but can also throw an exception.
CheckedToDoubleBiFunction<T,U,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked: Like ToDoubleBiFunction but can also thrown an exception.
CheckedToIntFunction<S,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked: Like ToIntFunction but can also thrown an exception.
CheckedUnaryOperator<T,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked: Like a UnaryOperator but allows an exception to be thrown.
CheckedUnsupportedOperationException - Exception in org.anchoranalysis.core.exception: When a particular operation is unsupported in particular circumstances.
CheckedUnsupportedOperationException() - Constructor for exception CheckedUnsupportedOperationException: Creates with a default message indicating that the operation is unsupported.
CheckedUnsupportedOperationException(String) - Constructor for exception CheckedUnsupportedOperationException: Creates with a message explaining that the operation is unsupported.
CheckException - Exception in org.anchoranalysis.mpp.feature.error
CheckException(String) - Constructor for exception CheckException
CheckException(String, Throwable) - Constructor for exception CheckException
CheckException(Throwable) - Constructor for exception CheckException
checkExtentMatch(BoundingBox, BoundingBox) - Static method in class ExtentMatchHelper: Checks that the Extents of two bounding boxes are identical.
checkIdenticalDataType(VoxelDataType) - Method in class 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 CheckIfAllowed
checkIfConnected() - Method in class ObjectMask: Determines if an object-mask is connected.
CheckMark - Class in org.anchoranalysis.mpp.feature.bean.mark: A predicate on a mark to check if a condition has been satisfied.
CheckMark() - Constructor for class CheckMark
CheckMarkWithMask - Class in org.anchoranalysis.plugin.mpp.bean.check
CheckMarkWithMask() - Constructor for class CheckMarkWithMask
checkMisconfigured(BeanInstanceMap) - Method in class AnchorBean: Checks that a bean's properties conform to expectations.
CheckMisconfigured - Class in org.anchoranalysis.bean.initializable: Routines for checking that particular patterns exist with bean-properties.
checkMisconfigured(BeanInstanceMap) - Method in class SequenceInteger
checkMisconfigured(BeanInstanceMap) - Method in class FeatureEvaluator
checkMisconfigured(BeanInstanceMap) - Method in class OutputWriteSettings
checkMisconfigured(BeanInstanceMap) - Method in interface FeedbackReceiver
checkMisconfigured(BeanInstanceMap) - Method in class FromStack
checkMisconfigured(BeanInstanceMap) - Method in class ExtractSliceRange
checkMisconfigured(BeanInstanceMap) - Method in class Erode
checkMisconfigured(BeanInstanceMap) - Method in class Sequence
checkMisconfigured(BeanInstanceMap) - Method in class ThreeChannels
checkMisconfigured(BeanInstanceMap) - Method in class ThreeColoredObjects
checkMisconfigured(BeanInstanceMap) - Method in class FromChannelOrMask
checkMisconfigured(BeanInstanceMap) - Method in class PermuteFeature
checkMisconfigured(BeanInstanceMap) - Method in class PermuteFeatureSequenceInteger
checkMisconfigured(BeanInstanceMap) - Method in class Intersection
checkMisconfigured(BeanInstanceMap) - Method in class IntensityMeanShellBase
checkMisconfigured(BeanInstanceMap) - Method in class LastDirectories
checkMisconfigured(BeanInstanceMap) - Method in class CoupledManifestsInputManager
checkMisconfigured(BeanInstanceMap) - Method in class HOGFeature
checkMisconfigured(BeanInstanceMap) - Method in class FromDictionary
checkMisconfigured(BeanInstanceMap) - Method in class QuickExperiment
checkMisconfigured(BeanInstanceMap) - Method in class QuickMultiDatasetExperiment
checkMisconfigured(BeanInstanceMap) - Method in class MultiInputManagerQuick
checkMisconfigured(BeanInstanceMap) - Method in class NamedChannelsQuick
checkMisconfigured(BeanInstanceMap) - Method in class ExperimentResultsExperimentStructure
checkMisconfigured(BeanInstanceMap) - Method in class ExperimentStructure
checkMisconfigured(BeanInstanceMap) - Method in class QuickMultiDatasetStructuredExperiment
CheckParsedFilePathBag - Class in org.anchoranalysis.plugin.io.bean.file.group.check
CheckParsedFilePathBag() - Constructor for class CheckParsedFilePathBag
checkResultVector(ResultsVector) - Static method in class ConstantsInListFixture: checks that a result-vector has the results we expect from the feature-list associated with this fixture
checkSize(Extent) - Method in class HOGParameters: Throws an exception if an image of size extent cannot be described by these parameters.
checkUnsupported3D(Channel) - Static method in class SegmentChannelIntoObjects
checkUnsupportedObjectMask(Optional<ObjectMask>) - Static method in class SegmentChannelIntoObjects
checkUnsupportedSeeds(Optional<ObjectCollection>) - Static method in class SegmentChannelIntoObjects
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 FeatureCalculationCache: Gets/creates a child-cache for a given name.
childCacheFor(FeatureCalculationCache<?>, CacheCreator, ChildCacheName, V) - Method in class CheckCacheForSpecificChildren
childCacheFor(FeatureCalculationCache<?>, CacheCreator, ChildCacheName, V) - Method in interface ChildCacheFinder: Selects a child-cache given a parent and a child-name.
childCacheFor(FeatureCalculationCache<?>, CacheCreator, ChildCacheName, V) - Method in class 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 ChildCacheName: Uses only the class as an identifier.
ChildCacheName(Class<?>, int) - Constructor for class ChildCacheName: Uses only the class combines with an integer part-name.
ChildCacheName(Class<?>, String) - Constructor for class ChildCacheName: Uses both the class and a part-name as an identifier.
children() - Method in class ErrorNodeImpl
ChooseOneList - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
ChooseOneList() - Constructor for class ChooseOneList
Circle - Class in org.anchoranalysis.mpp.mark.conic: A circle
Circle(Bound) - Constructor for class Circle: Creates with a radius within particular bounds.
Circle(Circle) - Constructor for class Circle: Copy constructor
Circle() - Constructor for class Circle
circleAt(Point2i, double) - Static method in class CircleObjectFixture
CircleObjectFixture - Class in org.anchoranalysis.test.feature.plugins.objects
circumference(int) - Method in class Ellipse
clamp(Point3i, Dimensions) - Static method in class PointClamper
clamp(Point3d, Dimensions) - Static method in class PointClamper
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 ClampHistogramMax
clampTo(Extent) - Method in class 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 BinaryOutcomeImageLabeller
classInCurrentJar() - Method in class LauncherConfig: A class which we use to determine the base location for pathRelativeProperties.
clean() - Method in class VoxelizedMarksWithEnergy
clean() - Method in class EnergyMemoList
cleanUp(VoxelPartitionFactory<T>) - Method in class IndexByChannel
cleanUp(VoxelPartitionFactory<T>) - Method in class IndexByRegion
cleanUp(VoxelPartitionFactory<T>) - Method in interface VoxelPartition
cleanUp(VoxelPartitionFactory<Histogram>) - Method in class VoxelPartitionHistogram
cleanUp() - Method in interface VoxelizedMark
clear() - Method in class FeatureList: Removes all of the elements from this list.
clear() - Method in class UnsignedBuffer: Clears the buffer ala Buffer.clear().
clear() - Method in class UpdatableMarksList
clearBest() - Method in class DualState
clipTo(T, Extent) - Method in interface AccessObjectMask: Ensures the element lies within a certain extent.
clipTo(ObjectMask, Extent) - Method in class AccessObjectMaskSimple
clipTo(Extent) - Method in class ObjectMask: Makes sure an object fits inside an extent, removing any parts which do not.
close() - Method in interface Progress: Ends tracking progress, to be called after any calls to Progress.update(int).
close() - Method in class ProgressConsole
close() - Method in class ProgressIgnore
close() - Method in class ProgressIncrement: Ends tracking progress, to be called after any calls to ProgressIncrement.update().
close() - Method in class ProgressMultiple
close(boolean, boolean) - Method in class StatefulNullMessageLogger
close(boolean, boolean) - Method in class ConsoleMessageLogger
close(boolean, boolean) - Method in class FailureOnlyMessageLogger
close(boolean, boolean) - Method in class MessageLoggerList
close(boolean, boolean) - Method in interface StatefulMessageLogger
close(boolean, boolean) - Method in class TextFileMessageLogger
close() - Method in class FeatureCSVWriter: Closes any open file-handles.
close() - Method in interface OpenedImageFile: Closes the opened image-file, removing any intermediate data-structures.
close() - Method in class CSVWriter
close() - Method in class CSVReader.OpenedCSVFile
close() - Method in class ReadByLine: Closes any opened-files
close(ErrorReporter) - Method in interface InputFromManager: Performs all tidying up, file-closing etc.
close(ErrorReporter) - Method in class InputFromManagerDelegate
close(ErrorReporter) - Method in class MultiInput
close(ErrorReporter) - Method in class StackWithMap
close() - Method in class SharedStateFilteredImageOutput
close() - Method in class SharedStateSelectedSlice
close() - Method in class OpenedMultiFile
close() - Method in class OpenCVModel
closeAnyOpenIO() - Method in class FeatureExporter: Closes any open IO and removes redundant structures stored in memory.
closeAnyOpenIO() - Method in class SharedStateSegmentInstance: Closes any open IO and removes redundant structures stored in memory.
closeLogger() - Method in class 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 ClusterByTimestamp
clusterFor(File) - Method in class 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(ZoneOffset) - Constructor for class ClusterIdentifier: Creates with no name.
ClusterIdentifier(String, ZoneOffset) - Constructor for class ClusterIdentifier: Creates with a constant-name.
ClusterMembership - Class in org.anchoranalysis.plugin.io.file.copy: A mapping of files to membership of particular clusters.
ClusterMembership(ClusterIdentifier) - Constructor for class ClusterMembership
CODE_MINIMA - Static variable in class WatershedEncoding
CODE_PLATEAU - Static variable in class WatershedEncoding
CODE_TEMPORARY - Static variable in class WatershedEncoding
CODE_UNVISITED - Static variable in class WatershedEncoding
CoefficientOfVarianceFromAll - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.all
CoefficientOfVarianceFromAll() - Constructor for class CoefficientOfVarianceFromAll
coefficientOfVariation(Histogram) - Static method in class 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 CoefficientOfVariation
CollapseFileName - Class in org.anchoranalysis.plugin.quick.bean.file.path.derive: Removes the file-name from a path, but keeps the directories and preserves the file-extension.
CollapseFileName() - Constructor for class 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 CollectionGenerator
collectResult() - Method in interface ProcessChangedPointAbsoluteMasked: Collects the result of the operation after processing neighbor voxels.
collectResult() - Method in interface ProcessVoxelNeighbor: Collects the result of the operation after processing neighbor pixels.
collectResult() - Method in interface ProcessVoxelNeighborAbsolute: Collects the result of the operation after processing neighbor voxels.
colorAxis(Axis) - Method in class PlotColorScheme
colorChart(JFreeChart) - Method in class PlotColorScheme
ColorConverterBase - Class in org.anchoranalysis.plugin.opencv.bean.color: Converts a RGB stack into another color space using OpenCV.
ColorConverterBase() - Constructor for class 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 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 ColoredBaseWithGenerator
ColoredMarks - Class in org.anchoranalysis.mpp.mark
ColoredMarks() - Constructor for class ColoredMarks
ColoredMarks(MarkCollection, ColorIndex, IdentifierGetter<Mark>) - Constructor for class ColoredMarks
ColoredMarks(Mark, RGBColor) - Constructor for class ColoredMarks
ColoredMarks(MarkCollection, ColorList) - Constructor for class ColoredMarks
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 ColoredMarks
ColoredMarksWithDisplayStack - Class in org.anchoranalysis.mpp.io.marks
ColoredMarksWithDisplayStack(MarksWithDisplayStack, ColorIndex, IdentifierGetter<Mark>) - Constructor for class ColoredMarksWithDisplayStack
ColoredMarksWithDisplayStack(ColoredMarks, DisplayStack) - Constructor for class ColoredMarksWithDisplayStack
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 ColoredMask
ColoredObjectCollection - Class in org.anchoranalysis.plugin.image.object: Associates a ColorList with a ObjectCollection
ColoredObjectCollection() - Constructor for class ColoredObjectCollection: Create with an empty collection.
ColoredObjectCollection(ObjectMask, RGBColor) - Constructor for class ColoredObjectCollection: Create with a single object and color.
ColoredObjectCollection(ObjectCollection, ColorList) - Constructor for class ColoredObjectCollection: Create with an existing object and color list.
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 ColoredObjects
coloredObjectsToDraw(Dimensions) - Method in class ColoredBase: Creates colored-objects to be drawn.
coloredObjectsToDraw(Dimensions) - Method in class ColoredBaseWithGenerator
coloredObjectsToDraw(Dimensions) - Method in class ColoredMask
coloredObjectsToDraw(Dimensions) - Method in class ThreeColoredObjects
ColoredOverlayCollection - Class in org.anchoranalysis.overlay.collection
ColoredOverlayCollection() - Constructor for class ColoredOverlayCollection
ColoredOverlayCollection(OverlayCollection, ColorList) - Constructor for class ColoredOverlayCollection
colorFor(ObjectWithProperties, int) - Method in class ObjectDrawAttributes: A color for a particular object
colorForEachIndex(int) - Method in class 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 ColorIndexModulo
colorLegend(LegendTitle) - Method in class PlotColorScheme
ColorList - Class in org.anchoranalysis.core.color: A list of colors, each corresponding to a particular index position.
ColorList(Color...) - Constructor for class ColorList: Create for one or more colors of type Color.
ColorList(RGBColor...) - Constructor for class ColorList: Create for one or more colors of type RGBColor.
ColorList() - Constructor for class ColorList
colorPlot(XYPlot) - Method in class PlotColorScheme
colorPlot(CategoryPlot) - Method in class PlotColorScheme
ColorProvider - Class in org.anchoranalysis.image.bean.provider: Base class for beans that implement Provider to provide a ColorList.
ColorProvider() - Constructor for class ColorProvider
ColorScheme - Class in org.anchoranalysis.bean.shared.color.scheme: Creates a sequence of related colors.
ColorScheme() - Constructor for class 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 ColorSchemeUnary
ColorSchemeUnary(ColorScheme) - Constructor for class ColorSchemeUnary
colorSpaceCode() - Method in class ColorConverterBase: The color space conversion code to use from OpenCV, that defines the color-space to convert to.
colorSpaceCode() - Method in class ConvertRGBToHSV
colorSpaceCode() - Method in class ConvertRGBToLab
column(int) - Method in class RotationMatrix: Extracts a column from the rotation-matrix as a point.
ColumnDefinition - Class in org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition
ColumnDefinition() - Constructor for class ColumnDefinition
combine(List<PermutationAssigner>) - Static method in class PermutationAssignerFactory: Combines multiple existing assigners into a single PermutationAssigners.
Combine - Class in org.anchoranalysis.image.io.bean.object.draw
Combine() - Constructor for class Combine
Combine(List<DrawObject>) - Constructor for class Combine
combine(boolean, boolean) - Method in class MultiLevelAnd
combine(boolean, boolean) - Method in class MultiLevelBinary
combine(boolean, boolean) - Method in class MultiLevelOr
combine(boolean, boolean) - Method in class SingleLevelAnd
combine(boolean, boolean) - Method in class SingleLevelBinary
combine(boolean, boolean) - Method in class SingleLevelOr
Combine - Class in org.anchoranalysis.plugin.io.bean.file.provider
Combine() - Constructor for class Combine
CombineBase - Class in org.anchoranalysis.plugin.image.bean.mask.provider.combine
CombineBase() - Constructor for class CombineBase
CombineCSV - Class in org.anchoranalysis.plugin.io.bean.task: Combines multiple CSV files into a single CSV file.
CombineCSV() - Constructor for class CombineCSV
combined() - Method in class PathDifference: The directory-component (if it exists) and filename-component combined.
combined() - Method in class SplitPath: A path that combines the root together with the remainder.
combineDescription(String, String) - Method in class AddConstantTo
combineDescription(String, String) - Method in class ConstantToThePowerOf
combineDescription(String, String) - Method in class DivideByConstant
combineDescription(String, String) - Method in class MultiplyByConstant
combineDescription(String, String) - Method in class SubtractFrom
combineDescription(String, String) - Method in class ToThePowerOfConstant
combineDescription(String, String) - Method in class ReplaceUnusualValue
combineDescription(String, String) - Method in class WithValueBase
combineDescriptionsRecursively(String, String) - Method in exception 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(NameValue<Generator<T>>) - Constructor for class CombinedListGenerator
CombinedListGenerator(Stream<NameValue<Generator<T>>>) - Constructor for class CombinedListGenerator
CombinedListGenerator(Generator<T>...) - Constructor for class CombinedListGenerator
CombinedListGenerator() - Constructor for class CombinedListGenerator
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 CombinedName: Creates with explicit strings for both parts.
CombineObjectsForFeatures<T extends FeatureInput> - 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 CombineObjectsForFeatures
CombineRasterGenerator<T> - Class in org.anchoranalysis.image.io.bean.stack.combine: Combines a number of generators of Raster images by tiling their outputs together
CombineRasterGenerator() - Constructor for class CombineRasterGenerator
combineSecond(SingleLevelOutputEnabled, SingleLevelOutputEnabled) - Method in class MultiLevelAnd
combineSecond(SingleLevelOutputEnabled, SingleLevelOutputEnabled) - Method in class MultiLevelBinary
combineSecond(SingleLevelOutputEnabled, SingleLevelOutputEnabled) - Method in class MultiLevelOr
CombineToOnePath - Class in org.anchoranalysis.plugin.mpp.contour.path.merge
combineToOnePath(List<ContiguousVoxelPath>) - Static method in class CombineToOnePath: Combines all the contiguous paths to a single-path.
CombineTypes - Class in org.anchoranalysis.image.voxel.datatype: Calculates which VoxelDataType to use when combining two other voxel-data types, but without losing precision.
combineTypes(VoxelDataType, VoxelDataType) - Static method in class CombineTypes: What data-type to use to represent voxels of both type1 and type2?
combineValueAndFeature(double, double) - Method in class AddConstantTo
combineValueAndFeature(double, double) - Method in class ConstantToThePowerOf
combineValueAndFeature(double, double) - Method in class DivideByConstant
combineValueAndFeature(double, double) - Method in class MultiplyByConstant
combineValueAndFeature(double, double) - Method in class SubtractFrom
combineValueAndFeature(double, double) - Method in class ToThePowerOfConstant
combineValueAndFeature(double, double) - Method in class ReplaceUnusualValue
combineValueAndFeature(double, double) - Method in class WithValueBase
combineWithSuffix(String) - Method in class FilenameSplitExtension: Inserts a suffix after the base-name, but before the extension, immutably.
CommandLineException - Exception in org.anchoranalysis.launcher: An exception thrown at run-time while processing command-line args
CommandLineException(String) - Constructor for exception CommandLineException
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 CommandLineExtracter
CommandLineOptions - Class in org.anchoranalysis.launcher.options: All command-line options used by the launcher.
common() - Method in class InitializationContext
common() - Method in interface 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 CommonContext
CommonPath - Class in org.anchoranalysis.core.system.path: Finds the common root directory of a set of paths.
commonType(Stream<VoxelDataType>) - Static method in class FindCommonVoxelType: Finds a common type to represent (ideally without loss of precision} of a stream of types.
commonType(VoxelDataType, VoxelDataType) - Static method in class 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 ComparableSource
Comparator3d<T extends Tuple3d> - Class in org.anchoranalysis.spatial.point: Imposes an ordering on any sub-type of Tuple3d.
Comparator3d() - Constructor for class Comparator3d
Comparator3i<T extends Tuple3i> - Class in org.anchoranalysis.spatial.point: Imposes an ordering on any sub-type of Tuple3i.
Comparator3i() - Constructor for class 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 ComparatorOrderByName
compare(NameValue<V>, NameValue<V>) - Method in class ComparatorOrderByName
compare(T, T) - Method in class Comparator3d
compare(T, T) - Method in class Comparator3i
CompareAnnotations<T extends Assignment<ObjectMask>> - 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 CompareAnnotations
compareTo(AssociatedIndex) - Method in class Indexable
compareTo(MultiName) - Method in class CombinedName
compareTo(MultiName) - Method in class SimpleName
compareTo(EigenvalueAndVector) - Method in class EigenvalueAndVector
compareTo(SortedSetChannel) - Method in class SortedSetChannel
compareTo(SortedSetSlice) - Method in class SortedSetSlice
compareTo(BoundingBox) - Method in class BoundingBox: Exposed via ReadableTuple3i to keep it read-only
compareTo(Extent) - Method in class Extent
compareTo(ReadableTuple3i) - Method in interface ReadableTuple3i
CompareWithRange<T extends FeatureInput> - 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 CompareWithRange
CompareWithRangeFeature<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.range: Like CompareWithRange but uses features to calculate boundary values
CompareWithRangeFeature() - Constructor for class CompareWithRangeFeature
CompareXML - Class in org.anchoranalysis.test: Compares two XML documents to see if they are equal.
comparison() - Method in interface ImageCounterWithStatistics: Creates statistics from counted images and the payload T passed for annotated images.
ComparisonSharedState<T extends Assignment<ObjectMask>> - Class in org.anchoranalysis.plugin.annotation.bean.comparison
ComparisonSharedState(CSVAssignment, int, Function<String, ImageCounterWithStatistics<T>>) - Constructor for class ComparisonSharedState
CompatibleWithMark - Interface in org.anchoranalysis.mpp.mark
completeProjection() - Method in interface ProjectableBuffer: Performs any final operation before turning the projected buffer.
Compose<S,T,U> - Class in org.anchoranalysis.mpp.segment.transformer: Combines a transformation from S to U with one from U to T
Compose() - Constructor for class Compose
Compose(StateTransformerBean<S, U>, StateTransformerBean<U, T>) - Constructor for class Compose
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