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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
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
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
adjacentVerticesOutgoingStream(V) - Method in class GraphWithPayload
afterAllJobsAreExecuted(S, InputOutputContext) - Method in class Task
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
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
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
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
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
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