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absolute() - Method in class Tuple3d
 
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
 
accept(int) - Method in interface CheckedIntConsumer
 
accept(int, int) - Method in interface Histogram.BinConsumer
 
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.
acceptIteration(BinaryVoxels<UnsignedByteBuffer>) - Method in class AcceptIterationList
 
acceptIteration(BinaryVoxels<UnsignedByteBuffer>) - Method in interface AcceptIterationPredicate
 
acceptIteration(BinaryVoxels<UnsignedByteBuffer>) - Method in class RejectIterationIfAllHigh
 
acceptIteration(BinaryVoxels<UnsignedByteBuffer>) - Method in class RejectIterationIfLowDisconnected
 
AcceptIterationList - Class in org.anchoranalysis.image.voxel.object.morphological.predicate
 
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 interface PropertyDefiner
 
accepts(Class<?>) - Method in class SimplePropertyDefiner
 
acceptsAsSource(Class<?>) - Method in class ExtractFromParam
Are the source-parameters acceptable for extraction? *
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.
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(PermutationSetter) - Method in class PermutationSetterList
 
add(String) - Method in interface StringBeanCollection
 
add(String) - Method in class StringList
 
add(String) - Method in class StringSet
 
add(Color) - Method in class ColorList
 
add(RGBColor) - Method in class ColorList
 
add(int, RGBColor) - Method in class ColorList
 
add(NamedProvider<T>) - Method in class NamedProviderCombine
 
add(String, T) - Method in class NameValueSet
 
add(NameValue<T>) - Method in class NameValueSet
 
add(NameValueSet<T>) - Method in class NameValueSet
 
add(String, StoreSupplier<T>) - Method in class EagerEvaluationStore
 
add(String, StoreSupplier<T>) - Method in class LazyEvaluationStore
 
add(String, StoreSupplier<T>) - Method in interface NamedProviderStore
 
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
 
add(double) - Method in class EnergyTotal
 
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(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(ObjectWithProperties) - Method in class ObjectCollectionWithProperties
 
add(Seed) - Method in class SeedCollection
 
add(String, Stack) - Method in class NamedStacks
 
add(String, StoreSupplier<Stack>) - Method in class NamedStacks
 
add(String, Stack) - Method in class NamedStacksUniformSize
 
add(String, StoreSupplier<TimeSequence>) - Method in class WrapStackAsTimeSequenceStore
 
add(Stack) - Method in class TimeSequence
 
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(AcceptIterationPredicate) - Method in class AcceptIterationList
 
add(ObjectMask) - Method in class ObjectCollection
 
add(VoxelStatistics) - Method in class VoxelStatisticsCombined
 
add(VoxelsWrapper) - Method in class VoxelsWrapperList
 
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(int, long) - Method in class VarianceCalculator
 
add(MemoForIndex, VoxelizedMarkMemo) - Method in class SetUpdatable
 
add(MemoForIndex, VoxelizedMarkMemo) - Method in class RandomCollectionWithAddCriteria
 
add(EnergyMemoList, VoxelizedMarkMemo, EnergyStackWithoutParams) - Method in class MarksWithEnergyBreakdown
 
add(VoxelizedMarkMemo) - Method in class MarksWithTotalEnergy
 
add(VoxelizedMarkMemo, EnergyStackWithoutParams) - 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, EnergyStackWithoutParams, 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(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(String, Mark) - Method in class ErrorNode
 
add(Exception) - Method in class ErrorNode
 
add(String) - Method in class ErrorNodeImpl
 
add(String, Mark) - Method in class ErrorNodeImpl
 
add(Exception) - Method in class ErrorNodeImpl
 
add(String) - Method in class ErrorNodeNull
 
add(String, Mark) - Method in class ErrorNodeNull
 
add(Exception) - Method in class ErrorNodeNull
 
add(CreateProposalVisualization) - Method in class CreateProposeVisualizationList
 
add(FeedbackReceiver<T>) - Method in class FeedbackReceiverList
 
add(TerminationCondition) - Method in class TerminationConditionListOr
 
add(WeightedKernel<T, S>) - Method in class WeightedKernelList
 
add(AggregateReceiver<T>) - Method in class AggregateReceiverList
 
add(PeriodReceiver<T>) - Method in class PeriodReceiverList
 
add(IndexByRegion<T>) - Method in class IndexByChannel
 
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(AnnotationGroup<T>) - Method in class AnnotationGroupList
 
add(double) - Method in class RangeSum
 
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(NamedChannelsInput) - Method in class ImageSize
 
add(NamedChannelsInput) - Method in class SummarizerNamedChannelsSimple
 
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
 
add(int, int, int) - Method in class PointRange
 
add(Point2i) - Method in class Point2d
 
add(Point2d) - Method in class Point2d
 
add(Point2i) - Method in class Point2i
 
add(Tuple3d) - Method in class Tuple3d
 
add(double, double, double) - Method in class Tuple3d
 
add(ReadableTuple3i) - Method in class Tuple3d
 
add(ReadableTuple3i) - Method in class Tuple3i
 
add(BoundingBox, T) - Method in class RTree
Adds a bounding-box with a corresponding index.
addAcceptedAnnotation(T) - Method in interface AddAnnotation
 
addAcceptedAnnotation(T) - Method in class AnnotationGroup
 
addAcceptedAnnotation(T) - Method in class AnnotationGroupList
 
addAcceptedAnnotation(AssignmentOverlapFromPairs) - Method in class AnnotationGroupObject
 
addAdditionalOptions(Options) - Method in class LauncherConfig
 
addAdditionalOptions(Options) - Static method in class CommandLineOptions
 
addAll(Define) - Method in class Define
Adds all the named-beans (shallow copy) from source to th ecurrent map
addAll(ColorList) - Method in class ColorList
 
addAll(FeatureList<? extends T>) - Method in class FeatureList
 
addAll(ObjectCollection) - Method in class ObjectCollection
 
addAll(Collection<? extends ObjectMask>) - Method in class ObjectCollection
 
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<AnnotationGroup<T>>) - Method in class AnnotationGroupList
 
addAllOutputNamesTo(OutputEnabledMutable) - Method in class DefineOutputter
Adds all possible output-names to a OutputEnabledMutable.
addAllScaled(ColorList, double) - Method in class ColorList
 
addAllToUpdatablePairList(UpdatableMarksList) - Method in class VoxelizedMarksWithEnergy
 
AddAnnotation<T extends Assignment> - Interface in org.anchoranalysis.plugin.annotation.comparison
 
addAsSeparateChannels(NamedStacks, int, Progress) - Method in interface NamedChannelsForSeries
 
addAsSeparateChannels(NamedProviderStore<TimeSequence>, int) - Method in interface NamedChannelsForSeries
 
addAsSeparateChannels(NamedStacks, int, Progress) - Method in class NamedChannelsForSeriesConcatenate
 
addAsSeparateChannels(NamedProviderStore<TimeSequence>, int) - Method in class NamedChannelsForSeriesConcatenate
 
addAsSeparateChannels(NamedStacks, int, Progress) - Method in class NamedChannelsForSeriesMap
 
addAsSeparateChannels(NamedProviderStore<TimeSequence>, int) - Method in class NamedChannelsForSeriesMap
 
addBasicOptions(Options) - Static method in class CommandLineOptions
 
addBean(String, Object) - Method in class ErrorNode
 
addBean(String, Object) - Method in class ErrorNodeImpl
 
addBean(String, Object) - Method in class ErrorNodeNull
 
addBeansFromList(Define, List<NamedBean<?>>) - Static method in class DefineAdderUtilities
 
addBlankChannel() - Method in class Stack
 
addBoundChangeListener(BoundChangeListener) - Method in class BoundedIndexContainerFromList
 
addBoundChangeListener(BoundChangeListener) - Method in interface BoundedRangeIncompleteDynamic
 
addBoundChangeListener(BoundChangeListener) - Method in class BoundsFromRange
 
addBoundChangeListener(BoundChangeListener) - Method in class BoundedIndexContainerBridge
 
addBoundChangeListener(BoundChangeListener) - Method in class IntegerSequenceContaner
 
addBoundChangeListener(BoundChangeListener) - Method in class SingleContainer
 
addChangeID(Mark, Color) - Method in class ColoredMarks
 
addChangeID(Mark, RGBColor) - Method in class ColoredMarks
 
addChannel(Channel) - Method in class Stack
 
addChannel(Channel) - Method in class StackNotUniformSized
 
addChannelsFrom(Stack) - Method in class Stack
 
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
AddCriteriaDistanceTo - Class in org.anchoranalysis.plugin.mpp.bean.addcriteria
 
AddCriteriaDistanceTo() - Constructor for class AddCriteriaDistanceTo
 
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
 
addCustomNames(FeatureList<?>) - Method in class FeatureNameList
Add the customNames of a feature
addCustomNamesWithPrefix(String, FeatureList<?>) - Method in class FeatureNameList
Add the customNames of a feature with a Prefix
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 an EDT transform by bundling together several other beans
AddDistanceTransform() - Constructor for class AddDistanceTransform
 
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
 
addErrorLevel(String, AnchorBean<?>) - Method in class ProposerContext
 
addField(Field) - Method in class PermutationSetterSingle
 
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
 
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.
addFromProviders(NamedProvider<FeatureList<FeatureInput>>) - Method in class SharedFeatureMulti
 
addFromWithPrefix(NamedProvider<Stack>, String) - Method in class NamedStacks
 
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
 
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.
addIter(int) - Method in class ErrorNode
 
addIter(int) - Method in class ErrorNodeImpl
 
addIter(int) - Method in class ErrorNodeNull
 
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
 
addLeftObject(ObjectMask) - Method in class AssignmentOverlapFromPairs
 
addLeftObjects(ObjectCollection) - Method in class AssignmentOverlapFromPairs
 
addListOfBeansToCollection(String, HierarchicalConfiguration, Collection<T>, Object) - Static method in class HelperListUtilities
 
addManifestExperimentFileSet(Collection<File>, ManifestDeserializer, Logger) - Method in class ManifestCouplingDefinition
 
addMultiple(RGBColor, int) - Method in class ColorList
 
addNewPath(Point3i, Point3i) - Method in class VisitedVoxels
Adds a new path with a point
addNoDuplicate(FeatureList<FeatureInput>) - Method in class SharedFeatureMulti
 
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.
addPair(ObjectMask, ObjectMask, double) - Method in class AssignmentOverlapFromPairs
 
addPointsInMark(MemoForIndex, VoxelizedMarkMemo) - Method in class SetUpdatable
 
addProperties(NameValueSet<String>) - Method in class Orientation
 
addProperties(NameValueSet<String>) - Method in class Orientation2D
 
addProperties(NameValueSet<String>) - Method in class Orientation3DEulerAngles
 
addProperties(NameValueSet<String>) - Method in class OrientationIdentity
 
addPropertiesToMask(ObjectWithProperties) - Method in class Orientation
 
addPropertiesToMask(ObjectWithProperties) - Method in class Orientation2D
 
addPropertiesToMask(ObjectWithProperties) - Method in class Orientation3DEulerAngles
 
addPropertiesToMask(ObjectWithProperties) - Method in class OrientationIdentity
 
addResultsFor(RowLabels, ResultsVector) - Method in class GroupWriter
Adds a result to the group-writer, but doesn't write yet.
addResultsFor(RowLabels, ResultsVector) - Method in class ResultsWriter
Adds feature-calculation results to be written.
addResultsFor(RowLabels, ResultsVectorWithThumbnail) - Method in interface ExportFeatureResultsAdder
Adds labeled results (which makes a row in a feature-table, and possibly other outputs).
addResultsFor(RowLabels, ResultsVectorWithThumbnail) - Method in class InputProcessContext
 
addRightObject(ObjectMask) - Method in class AssignmentOverlapFromPairs
 
addRightObjects(ObjectCollection) - Method in class AssignmentOverlapFromPairs
 
addRow(RowLabels, ResultsVector) - 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
addSkippedAnnotationImage() - Method in interface AddAnnotation
 
addSkippedAnnotationImage() - Method in class AnnotationGroup
 
addSkippedAnnotationImage() - Method in class AnnotationGroupList
 
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.
addTo(Define) - Method in class Concatenate
 
addTo(Define) - Method in interface DefineAdder
 
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
 
addToMarks(ColoredMarks) - Method in interface CreateProposalVisualization
 
addToMarks(ColoredMarks) - Method in class CreateProposeVisualizationList
 
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>) - Method in interface MultiInputSubMap
Copies all the existing entries into a NamedProviderStore.
addToStore(NamedProviderStore<T>) - Method in class OperationMap
 
addToStore(NamedProviderStore<TimeSequence>) - Method in class StackWithMap
 
addToStore(NamedProviderStore<TimeSequence>, int, Progress) - Method in class StackWithMap
 
addToStoreInferNames(NamedProviderStore<TimeSequence>, int, Progress) - Method in class NamedChannelsInput
 
addToStoreInferNames(NamedProviderStore<Stack>) - Method in interface ProvidesStackInput
Adds the current object to a named-store of stacks (using the default series)
addToStoreInferNames(NamedProviderStore<TimeSequence>, int, Progress) - Method in interface ProvidesStackInput
Adds the current object to a named-store of stacks
addToStoreInferNames(NamedProviderStore<TimeSequence>, int, Progress) - Method in class MultiInput
 
addToStoreInferNames(NamedProviderStore<TimeSequence>, int, Progress) - Method in class ConvertNamedChannelsInputToStack
 
addToStoreWithName(String, NamedProviderStore<TimeSequence>, int, Progress) - Method in class NamedChannelsInput
 
addToStoreWithName(String, NamedProviderStore<TimeSequence>, int, Progress) - Method in interface ProvidesStackInput
 
addToStoreWithName(String, NamedProviderStore<TimeSequence>, int, Progress) - Method in class MultiInput
 
addToStoreWithName(String, NamedProviderStore<TimeSequence>, int, Progress) - Method in class ConvertNamedChannelsInputToStack
 
addToTypeValueCollection(Collection<TypedValue>, int) - Method in class ResultsVector
 
addToUpdatablePairList(UpdatableMarksList, VoxelizedMarkMemo) - Method in class VoxelizedMarksWithEnergy
 
addToVoxelList(int, int, int) - Method in class IndexByRegion
 
addUnannotatedImage() - Method in interface AddAnnotation
 
addUnannotatedImage() - Method in class AnnotationGroup
 
addUnannotatedImage() - Method in class AnnotationGroupList
 
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 VoxelPartitionFactoryHistogramReuse
 
addUnused(Histogram) - Method in class VoxelPartitonFactoryHistogram
 
addVertex(V) - Method in class GraphWithoutPayload
Adds a vertex.
addVertex(V) - Method in class GraphWithPayload
Adds a vertex.
addVisitedPoint(Point3i) - Method in class VisitedVoxels
Adds a visited-point to an existing path, or else makes a new one
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
 
addWithIndex(RGBColor) - Method in class ColorList
 
addWithName(Define, String, AnchorBean<?>) - Method in class DefineAdderWithPrefixBean
 
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
afterAllJobsAreExecuted(S, InputOutputContext) - Method in class Task
afterAllJobsAreExecuted(NoSharedState, InputOutputContext) - Method in class TaskWithoutSharedState
 
afterAllJobsAreExecuted(AggregateSharedState, InputOutputContext) - Method in class AggregateAnnotations
 
afterAllJobsAreExecuted(SharedState<T>, InputOutputContext) - Method in class CompareAnnotations
 
afterAllJobsAreExecuted(SharedStateExportFeatures<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) - Method in interface NamedChannelsForSeries
 
allChannelsAsStack(int) - Method in class NamedChannelsForSeriesConcatenate
 
allChannelsAsStack(int) - Method in class NamedChannelsForSeriesMap
 
allChannelsHaveIdenticalType() - Method in class Stack
Determines if all channels have an identical voxel data-type.
allChannelsHaveType(VoxelDataType) - Method in class RGBStack
 
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.
allocateBuffer() - Method in class ToUnsignedByte
 
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.
allSlices(Voxels<U>, Function<U, T>, Function<AbstractNativeImg<S, T>, S>) - Static method in class Wrap
 
AllSlicesMaskEverythingNonZero - Class in org.anchoranalysis.plugin.mpp.bean.region
Only takes pixels where indexNonZero has a nonzero pixel
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.dimensions
 
AllValuesOff() - Constructor for class AllValuesOff
 
AllValuesOn - Class in org.anchoranalysis.plugin.image.bean.mask.provider.dimensions
Creates a new mask of particular dimensionality where all values are ON
AllValuesOn() - Constructor for class AllValuesOn
 
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
 
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
 
AnchorCheckedException(String, Throwable) - Constructor for exception AnchorCheckedException
 
AnchorCheckedException(String) - Constructor for exception AnchorCheckedException
 
AnchorCheckedException(Throwable) - Constructor for exception AnchorCheckedException
 
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
 
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 occur, instead of
AnchorImpossibleSituationException() - Constructor for exception AnchorImpossibleSituationException
 
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
 
AnchorRuntimeException(String, Throwable) - Constructor for exception AnchorRuntimeException
 
AnchorRuntimeException(String) - Constructor for exception AnchorRuntimeException
 
AnchorRuntimeException(Throwable) - Constructor for exception AnchorRuntimeException
 
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
 
AndKernel(BinaryKernel, BinaryKernel) - Constructor for class AndKernel
 
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.anneal
 
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
 
AnnotationBackground() - Constructor for class AnnotationBackground
 
AnnotationComparisonAssigner<T extends Assignment> - Class in org.anchoranalysis.plugin.annotation.bean.comparison.assigner
 
AnnotationComparisonAssigner() - Constructor for class AnnotationComparisonAssigner
 
AnnotationComparisonInput<T extends InputFromManager> - Class in org.anchoranalysis.plugin.annotation.comparison
 
AnnotationComparisonInput(T, Tuple2<Comparer, Comparer>, 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
 
annotationExistsCorrespondTo(Path) - Method in class MarkAnnotationReader
 
AnnotationGroup<T extends Assignment> - Class in org.anchoranalysis.plugin.annotation.comparison
 
AnnotationGroup(String) - Constructor for class AnnotationGroup
 
AnnotationGroupList<T extends Assignment> - Class in org.anchoranalysis.plugin.annotation.comparison
 
AnnotationGroupList() - Constructor for class AnnotationGroupList
 
AnnotationGroupObject - Class in org.anchoranalysis.plugin.annotation.comparison
 
AnnotationGroupObject(String) - Constructor for class AnnotationGroupObject
 
AnnotationInputManager<T extends ProvidesStackInput,S extends AnnotatorStrategy> - Class in org.anchoranalysis.annotation.io.bean
 
AnnotationInputManager() - Constructor for class AnnotationInputManager
 
AnnotationLabel - Class in org.anchoranalysis.plugin.annotation.bean.label
 
AnnotationLabel() - Constructor for class AnnotationLabel
 
annotationLabelFor(ProvidesStackInput) - Method in class AnnotatorStrategy
Returns a label describing the annotation, or empty() if this makes no sense
annotationLabelFor(ProvidesStackInput) - Method in class MarkProposerStrategy
 
annotationLabelFor(ProvidesStackInput) - Method in class WholeImageLabelStrategy
 
AnnotationMarksComparer<T> - Class in org.anchoranalysis.plugin.annotation.bean.comparer
 
AnnotationMarksComparer() - Constructor for class AnnotationMarksComparer
 
annotationPathFor(ProvidesStackInput) - Method in class AnnotatorStrategy
 
annotationPathFor(ProvidesStackInput) - Method in class SinglePathStrategy
 
AnnotationReader<T extends Annotation> - Interface in org.anchoranalysis.annotation.io
 
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
An annotation that has been combined with its strategy.
AnnotationWithStrategy(ProvidesStackInput, T) - Constructor for class AnnotationWithStrategy
 
AnnotationWriter<T extends Annotation> - Interface in org.anchoranalysis.annotation.io
 
AnnotatorStrategy - Class in org.anchoranalysis.annotation.io.bean
 
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 VoxelsWrapper
Returns voxels that are not cast to 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(Optional<FeatureList<T>>) - Method in class FeatureList
Appends one or more additional (optional) feature-lists
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
 
apply(int, int) - Method in interface IntBinaryOperation
 
apply(Integer) - Method in class IndexBridge
 
apply(ImageInitialization) - Static method in class CreateCombinedStack
 
apply(Mask, Mask) - Static method in class MaskAnd
Performs a 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 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 MaskIfHighLow
Performs a iff first==HIGH and second==LOW then LOW operation on each voxel in two masks, writing the result onto the second mask.
apply(Mask, Mask) - Static method in class MaskOr
Performs a 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 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 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.
apply(IFormatReader, ReadOptions, int) - Method in class DimensionsCreator
 
apply(String, Path) - Static method in class WriteStringToFile
 
apply(ObjectMask, double, int, int) - Static method in class SplitContourSmoothingSpline
1.
applyAsDouble(T, U) - Method in interface CheckedToDoubleBiFunction
Applies this function to the given arguments.
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
 
applyGlobal(List<Point3i>) - Method in class OutlineTraverser
Root point is arbitrarily chosen from object
applyGlobal(Point3i, List<Point3i>) - Method in class OutlineTraverser
 
ApplyImageJMorphologicalOperation - Class in org.anchoranalysis.plugin.imagej.mask
Applies an ImageJ (2D) morphological operation to voxels
applyInitializationIfPossibleTo(Object, Object, Logger) - Method in class PropertyInitializer
Applies the initialization to a property using the current or extracted params 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(Dimensions, UnaryOperator<Stack>) - 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
 
ApplyPermutations<T extends AnchorBean<T>> - Class in org.anchoranalysis.bean.permute
Applies a PermuteProperty to a bean to create new duplicated beans each with a permutation
ApplyPermutations(ApplyPermutations.NameGetter<T>, ApplyPermutations.NameSetter<T>) - Constructor for class ApplyPermutations
 
ApplyPermutations.NameGetter<S> - Interface in org.anchoranalysis.bean.permute
 
ApplyPermutations.NameSetter<S> - Interface in org.anchoranalysis.bean.permute
 
applyPermutationsToCreateDuplicates(List<T>, PermuteProperty<S>, PermutationSetter) - Method in class ApplyPermutations
Takes a list of beans, and creates a permuted version, updating the custom names
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
 
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?
areNeighborsDistinct(List<Point3i>) - Static method in class PointsNeighborChecker
Makes sure no successive neighbors are equal
arePointsNeighbors(Point3i, Point3i) - Static method in class PointsNeighborChecker
 
areXmlEqual(Document, Document) - Static method in class TestLoader
Does a check if the XML documents are equal
ArgumentConverter - Class in org.anchoranalysis.launcher.executor.selectparam.path.convert
Converts string passed as arguments.
arithmetic() - Method in class Channel
 
arithmetic() - Method in class BoundedVoxels
 
arithmetic() - Method in class Voxels
Methods to manipulate the voxel-values via arithmetic.
arithmetic() - Method in class VoxelsWrapper
 
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() - Static method in class RGBChannelNames
Creates an array with all channel-names in R-G-B order.
asByte() - Method in class VoxelsWrapper
 
asByte(ImageProcessor) - Static method in class ConvertToVoxelBuffer
Convert a ImageProcessor to VoxelBuffer<UnsignedByteBuffer>
asByteOrCreateEmpty(boolean) - Method in class VoxelsWrapper
Reuses the existing buffer if byte, otherwise creates a new empty byte buffer
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 VoxelsWrapper
 
asInt() - Method in class VoxelsWrapper
 
asList() - Method in class FeatureList
 
asList() - Method in class FeatureNameList
 
asList() - 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
 
asList() - Method in class SegmentedObjects
 
asListChannels() - Method in class Stack
 
asListOrderPreserved(List<T>) - Method in class ScaledElements
Returns a list of scaled-elements corresponding to a list of unscaled-elements
asMap() - Method in class MapCreate
 
AsMark - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
 
AsMark() - Constructor for class AsMark
 
asMarks() - Method in class EnergyMemoList
 
AsObject - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
 
AsObject() - Constructor for class AsObject
 
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
 
asObjects() - Method in class SegmentedObjects
 
asOperationFailedException() - Method in exception GetOperationFailedException
 
asOrderedArray() - Method in class Extent
 
asPath() - Method in class RootPath
 
asPath(boolean) - Method in class DirectoryWithPrefix
A path that combines the directory and fileNamePrefix and delimiter.
asPoint() - Method in class Padding
 
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() - Static method in class RGBChannelNames
Creates a set of the channel names.
asSet(Progress) - Method in interface ProvidesStackInput
Exposes the input as a set of named stacks (inferring the names)
asShort() - Method in class VoxelsWrapper
 
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.
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.
assignFilterExtensions(Set<String>) - Method in class InputArguments
 
assignFilterExtensionsIfMissing(Optional<Set<String>>) - Method in class InputArguments
 
assignFilterGlob(String) - Method in class InputArguments
 
assignFrom(CachedSupplierBase<T>) - Method in class CachedSupplierBase
 
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(IndexRange) - Method in class InputArguments
If defined, this indicates and specifies only a subset of the elements of the identifier to use.
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 - Interface in org.anchoranalysis.annotation.io.assignment
 
AssignmentGenerator - Class in org.anchoranalysis.annotation.io.assignment.generator
Outputs a raster showing an Assignment on a background.
AssignmentGenerator(DisplayStack, IntFunction<ColorPool>, boolean, Tuple2<String, String>, boolean, int) - Constructor for class AssignmentGenerator
 
AssignmentMaskIntersection - Class in org.anchoranalysis.annotation.io.assignment
Calculates statistics (DICE, Jaccard etc.) based upon corresponding two object-masks
AssignmentMaskIntersection(ObjectMask, ObjectMask) - Constructor for class AssignmentMaskIntersection
 
AssignmentObjectFactory - Class in org.anchoranalysis.annotation.io.assignment
 
AssignmentObjectFactory(FeatureEvaluator<FeatureInputPairObjects>, boolean) - Constructor for class AssignmentObjectFactory
 
AssignmentOverlapFromPairs - Class in org.anchoranalysis.annotation.io.assignment
Pairs objects in left with objects in right
AssignmentOverlapFromPairs() - Constructor for class AssignmentOverlapFromPairs
 
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
 
assignOff() - Method in class Mask
 
assignOff() - Method in class BinaryVoxels
 
assignOff() - Method in class ObjectMask
Assigns OFF value to voxels, expecting global coordinates
assignOn() - Method in class Mask
 
assignOn() - Method in class BinaryVoxels
 
assignOn() - Method in class ObjectMask
Assigns ON value to voxels, expecting global coordinates
assignOutputDirectory(Path) - Method in class OutputPrefixerSettings
 
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.
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, RelationToValue) - 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
 
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
 
assignType(String) - Method in class ManifestDescription
Assigns a new type.
assignValue(int) - Method in class Channel
 
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
Provides a means to assign a constant-value to some or all of the voxels.
assignValue(int) - Method in class VoxelsAsFloat
 
assignValue(int) - Method in class VoxelsAsInt
 
assignValue(int) - Method in class VoxelsAsShort
 
assignValue(int) - Method in class VoxelsUnsignedByte
 
assignValue(int) - Method in class VoxelsWrapper
 
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
 
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
 
associateXml(XMLConfiguration) - Method in interface AssociateXmlUponLoad
Associated
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
 
asStack() - Method in class EnergyStackWithoutParams
 
asStack() - Method in class RGBStack
 
asTuple() - Method in class Extent
Exposes the extent as a tuple.
atanHandlingNan(double) - Static method in class EllipseStandardFormConverter
 
atBorder(Extent) - Method in class BoundingBox
 
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
 
AtBorderZ - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.border
 
AtBorderZ() - Constructor for class AtBorderZ
 
atBorderZ(Extent) - Method in class BoundingBox
 
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
 
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
 
AxisAlignedUnitVector - Class in org.anchoranalysis.image.bean.spatial.direction
 
AxisAlignedUnitVector() - Constructor for class AxisAlignedUnitVector
 
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.object.conic
 
AxisRatioEllipsoid() - Constructor for class AxisRatioEllipsoid
 
AxisType - Enum in org.anchoranalysis.spatial.axis
 
AxisTypeConverter - Class in org.anchoranalysis.spatial.axis
Converts to/from AxisType to string representations and integer index (0 for X, 1 for Y, 2 for Z)
AxisTypeException - Exception in org.anchoranalysis.spatial.axis
 
AxisTypeException(String) - Constructor for exception AxisTypeException
 

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
 
backgroundStack() - Method in class RGBStack
 
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
 
Base<T> - Class in org.anchoranalysis.image.voxel.extracter
 
Base(Voxels<T>) - Constructor for class Base
 
BBoxRatio - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
 
BBoxRatio() - Constructor for class BBoxRatio
 
BeanDuplicateException - Exception in org.anchoranalysis.bean.exception
An exception occurs when the duplication of a bean fails
BeanDuplicateException(String) - Constructor for exception BeanDuplicateException
 
BeanDuplicateException(Exception) - Constructor for exception BeanDuplicateException
 
BeanDuplicateException(String, Throwable) - Constructor for exception BeanDuplicateException
 
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.
beanFor(Field, AnchorBean<?>) - Static method in class PermutationSetterUtilities
Finds a bean corresponding to a field (exceptionally handling a List by taking the first item in it)
BeanInitialization - Interface in org.anchoranalysis.bean.initializable.params
Parent class for all state used to initialise beans in InitializableBean
BeanInitializer<T> - Interface in org.anchoranalysis.bean.initializable.params
 
BeanInstanceMap - Class in org.anchoranalysis.bean
Maps a AnchorBean family-type to some beans belong to the family.
BeanInstanceMap() - Constructor for class BeanInstanceMap
 
BeanMisconfiguredException - Exception in org.anchoranalysis.bean.exception
If a Bean is misconfigured
BeanMisconfiguredException(String) - Constructor for exception BeanMisconfiguredException
 
BeanMisconfiguredException(String, Throwable) - Constructor for exception BeanMisconfiguredException
 
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
BeanPathUtilities - Class in org.anchoranalysis.bean.xml.factory
 
BeanProviderAsStackBase<T,S> - Class in org.anchoranalysis.image.bean.provider
A provider base-class that as well as providing type S, also provide 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
 
BeanStrangeException(String, Throwable) - Constructor for exception BeanStrangeException
 
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, Throwable) - Constructor for exception BeanXmlException
 
BeanXmlException(Throwable) - Constructor for exception BeanXmlException
 
BeanXmlException(String) - Constructor for exception BeanXmlException
 
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, int) - Method in class Anonymize
 
beforeCopying(Path, int) - Method in class CopyFilesNaming
beforeCopying(Path, int) - Method in class CopyFilesNamingOne
 
beforeCopying(Path, int) - Method in class CopyFilesNamingWithoutSharedState
 
beforeCopying(Path, int) - 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
 
BidirectionalBound - Class in org.anchoranalysis.mpp.bound
 
BidirectionalBound(Optional<ResolvedBound>, Optional<ResolvedBound>) - Constructor for class BidirectionalBound
 
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
 
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
 
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
 
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 Mask
 
binaryValues() - Method in class BinaryVoxels
Which two intensity values represent OFF and ON states
BinaryValues - Class in org.anchoranalysis.image.voxel.binary.values
Two values representing int binary states in an unsigned-byte buffer e.g.
BinaryValues(int, int) - Constructor for class BinaryValues
 
binaryValues() - Method in class ObjectMask
 
BinaryValuesByte - Class in org.anchoranalysis.image.voxel.binary.values
Two values representing byte binary states in an unsigned-byte buffer e.g.
BinaryValuesByte(int, int) - Constructor for class BinaryValuesByte
 
BinaryValuesByte(byte, byte) - Constructor for class BinaryValuesByte
 
binaryValuesByte() - Method in class ObjectMask
 
binaryVoxels() - Method in class Mask
 
BinaryVoxels<T> - Class in org.anchoranalysis.image.voxel.binary
Like Voxels but should only contain two distinct intensity-values representing ON and OFF states.
BinaryVoxels(Voxels<T>, BinaryValues) - Constructor for class BinaryVoxels
 
binaryVoxels() - Method in class ObjectMask
 
BinaryVoxelsBase - Class in org.anchoranalysis.image.bean.threshold.relation
 
BinaryVoxelsBase() - Constructor for class BinaryVoxelsBase
 
BinaryVoxelsFactory - Class in org.anchoranalysis.image.voxel.binary
 
binaryVoxelsFor(Voxels<T>, BinaryValues) - Method in class BinaryVoxels
 
bind(FeatureList<T>, FeatureInitialization, SharedFeatureMulti, 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
 
BioformatsOpenedRaster - Class in org.anchoranalysis.io.bioformats
 
BioformatsOpenedRaster(IFormatReader, IMetadata, ReadOptions) - Constructor for class BioformatsOpenedRaster
 
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() - Method in class NamedChannelsInput
Bit-depth of image
bitDepth() - Method in interface OpenedImageFile
 
bitDepth() - Method in class VoxelDataType
The number of bits required to represent a voxel.
bitDepth() - Method in class BioformatsOpenedRaster
 
BitDepth - Class in org.anchoranalysis.plugin.io.bean.summarizer.image
 
BitDepth() - Constructor for class BitDepth
 
bitDepth() - Method in class MultiFileReaderOpenedRaster
 
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
 
blur(VoxelsWrapper, Dimensions, MessageLogger) - Method in class BlurGaussian3D
 
blur(VoxelsWrapper, Dimensions, MessageLogger) - Method in class BlurGaussianEachSlice2D
 
blur(VoxelsWrapper, 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
 
bothNameAndParams() - Static method in class NamedFeatureStoreFactory
 
Bound - Class in org.anchoranalysis.mpp.bean.bound
 
Bound() - Constructor for class Bound
 
boundaryMax(SessionInput<T>) - Method in class CompareWithRangeFeature
 
boundaryMax(SessionInput<T>) - Method in class RangeCompareBase
Boundary to define the maximum accepted value in the range
boundaryMax(SessionInput<T>) - Method in class RangeCompareFromScalars
 
boundaryMin(SessionInput<T>) - Method in class CompareWithRangeFeature
 
boundaryMin(SessionInput<T>) - Method in class RangeCompareBase
Boundary to define the minimum accepted value in the range
boundaryMin(SessionInput<T>) - Method in class RangeCompareFromScalars
 
BoundCalculator - Class in org.anchoranalysis.mpp.bean.bound
 
BoundCalculator() - Constructor for class BoundCalculator
 
BoundCalculatorException - Exception in org.anchoranalysis.mpp.bound
 
BoundCalculatorException(String) - Constructor for exception BoundCalculatorException
 
BoundCalculatorException(Exception) - Constructor for exception BoundCalculatorException
 
boundChanged(BoundChangeEvent) - Method in interface BoundChangeListener
 
BoundChangeEvent - Class in org.anchoranalysis.core.index.bounded
 
BoundChangeEvent(Object, BoundChangeEvent.BoundType) - Constructor for class BoundChangeEvent
 
BoundChangeEvent.BoundType - Enum in org.anchoranalysis.core.index.bounded
 
BoundChangeListener - Interface in org.anchoranalysis.core.index.bounded
 
BoundDegrees - Class in org.anchoranalysis.mpp.bean.bound
 
BoundDegrees() - Constructor for class BoundDegrees
 
BoundDegrees(BoundDegrees) - Constructor for class BoundDegrees
 
BoundedIndexContainer<T> - Interface in org.anchoranalysis.core.index.bounded
 
BoundedIndexContainerBridge<H,S,E extends Exception> - Class in org.anchoranalysis.core.index.bounded.bridge
Bridges calls from hidden-type to external-type.
BoundedIndexContainerBridge(BoundedIndexContainer<H>) - Constructor for class BoundedIndexContainerBridge
 
BoundedIndexContainerBridgeWithIndex<H,S,E extends Exception> - Class in org.anchoranalysis.core.index.bounded.bridge
Bridges calls from hidden-type to external-type.
BoundedIndexContainerBridgeWithIndex(BoundedIndexContainer<H>, BridgeElementWithIndex<H, S, E>) - Constructor for class BoundedIndexContainerBridgeWithIndex
 
BoundedIndexContainerBridgeWithoutIndex<H,S,E extends Exception> - Class in org.anchoranalysis.core.index.bounded.bridge
Bridges calls from hidden-type to external-type.
BoundedIndexContainerBridgeWithoutIndex(BoundedIndexContainer<H>, CheckedFunction<H, S, E>) - Constructor for class BoundedIndexContainerBridgeWithoutIndex
 
BoundedIndexContainerFromList<T> - Class in org.anchoranalysis.core.index.bounded
 
BoundedIndexContainerFromList(List<T>) - Constructor for class BoundedIndexContainerFromList
 
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.
BoundedRange - Interface in org.anchoranalysis.core.index.bounded
 
BoundedRangeIncomplete - Interface in org.anchoranalysis.core.index.bounded
A range of discrete integers that is not complete (missing many integers).
BoundedRangeIncompleteDynamic - Interface in org.anchoranalysis.core.index.bounded
 
BoundedVoxels<T> - Class in org.anchoranalysis.image.voxel
Voxel-data that is bounded to exist in 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
 
boundingBox() - Method in class ObjectWithProperties
 
boundingBox() - Method in class BoundedVoxels
A bounding-box that associates voxels to a particular part of an image
boundingBox() - Method in class ObjectMask
 
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 2 or 3 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
 
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? e.g.
BoundingBoxContains(BoundingBox) - Constructor for class BoundingBoxContains
 
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
 
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
 
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
 
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
 
BoundsFromRange<T> - Class in org.anchoranalysis.core.index.bounded
 
BoundsFromRange(GetterFromIndex<T>, BoundedRangeIncomplete) - Constructor for class BoundsFromRange
 
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(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 class Base
 
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(int, H) - Method in class BoundedIndexContainerBridge
 
bridge(int, H) - Method in class BoundedIndexContainerBridgeWithIndex
 
bridge(int, H) - Method in class BoundedIndexContainerBridgeWithoutIndex
 
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
 
bridgeElement(int, S) - Method in interface BridgeElementWithIndex
 
BridgeElementWithIndex<S,D,E extends Exception> - Interface in org.anchoranalysis.core.index
 
buffer() - Method in class VoxelBuffer
The associated buffer for storing the voxels.
buffer() - Method in class VoxelBufferUnsigned
 
buffer(VoxelBuffer<U>, Extent, Function<U, T>, Function<AbstractNativeImg<S, T>, S>) - Static method in class Wrap
 
BufferedImageFactory - Class in org.anchoranalysis.image.core.bufferedimage
 
BufferedImageOverlay - Class in org.anchoranalysis.image.core.bufferedimage
 
bufferListForSlice(int) - Method in class VoxelsWrapperList
 
bufferRelative(int) - Method in class SlidingBuffer
 
BufferRetriever - Interface in org.anchoranalysis.image.voxel.kernel
 
bufferValueEqualTo(T, int) - Method in class Base
Checks if the current value from a buffer is equal to a constant value
bufferValueGreaterThan(T, int) - Method in class Base
Checks if the current value from a buffer is greater than a constant value
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.
byDimension(AxisType) - Method in interface ReadableTuple3i
 
byDimension(int) - Method in interface ReadableTuple3i
 
byDimension(int) - Method in class Tuple3i
 
byDimension(AxisType) - Method in class Tuple3i
 
bySymbol() - Method in interface SessionInput
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.
bytesPerPixel - Variable in class ToUnsignedByte
 
bytesPerPixel() - Method in class FloatFromUnsignedByte
 
bytesPerPixel() - Method in class FloatFromUnsignedInt
 
bytesPerPixel() - Method in class ToFloat
 
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(NamedStacksSupplier) - Static method in interface NamedStacksSupplier
 
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
 
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(FeatureList<T>, SessionInput<T>) - Method in interface FeatureSessionCalculator
Calculates a feature-list throwing an exception if there is an error
calc(FeatureInputObjectCollection) - Method in class FeatureObjectCollection
 
calc(FeatureInputMarkCollection) - Method in class FeatureMarkCollection
 
calc(EnergyMemoList, EnergySchemeWithSharedFeatures, EnergyStackWithoutParams) - Method in class EnergySavedAll
 
calc(FeatureInputObjectCollection) - Method in class NumberObjects
 
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(SessionInput<T>, FeatureCalculation<U, T>, Function<ResolvedCalculation<U, T>, CalculateInputFromDelegateOption<S, T, U>>, Feature<S>, ChildCacheName, double) - Static method in class CalculateInputFromDelegateOption
Calculates a feature using a cached-calculation as delegate, and optional Params return value
calc(FeatureInputMarkCollection) - Method in class NumberMarks
 
calc(double, double, double, boolean, boolean) - Static method in class GaussianScoreCalculator
 
calc(FeatureInputSingleObject, Ellipsoid) - Method in class AxisRatioEllipsoid
 
calc(FeatureInputSingleObject, Ellipsoid) - Method in class EllipsoidBase
 
calc(FeatureInputSingleObject, Ellipsoid) - Method in class Ellipsoidicity
 
calculate(SessionInput<T>) - Method in class Feature
 
calculate(SessionInput<T>) - Method in class Constant
 
calculate(SessionInput<T>) - Method in class Reference
 
calculate(SessionInput<T>) - Method in class Sum
 
calculate(FeatureInputResults) - Method in class Count
 
calculate(SessionInput<FeatureInputResults>) - Method in class FeatureResults
 
calculate(FeatureInputResults) - Method in class FeatureResults
 
calculate(FeatureInputResults) - Method in class StatisticForFeature
 
calculate(Feature<S>, S, ChildCacheName) - Method in interface CalculateForChild
Calculates a feature in a child-cache
calculate(Feature<S>, FeatureCalculation<S, T>, ChildCacheName) - Method in interface CalculateForChild
Calculates a feature in a child-cache using a new input created from a FeatureCalculation
calculate(ChildCacheName, S, Function<CalculationResolver<S>, ResolvedCalculation<U, S>>) - Method in interface CalculateForChild
Calculates a FeatureCalculation in a child-cache
calculate(Feature<T>, SessionInput<T>) - Method in interface FeatureSessionCalculator
Calculate a feature with particular values
calculate(Feature<T>) - Method in interface SessionInput
Calculates the result of a feature using this input
calculate(FeatureList<T>) - Method in interface SessionInput
Calculates the results of several features using this input
calculate(FeatureCalculation<S, T>) - Method in interface SessionInput
Calculates a feature-calculation after resolving it against the main cache
calculate(ResolvedCalculation<S, T>) - Method in interface SessionInput
Calculates a resolved Feature-calculation
calculate(T) - Method in class FeatureCalculatorCachedMulti
 
calculate(T, FeatureList<T>) - Method in class FeatureCalculatorCachedMulti
 
calculate(T) - Method in interface FeatureCalculatorMulti
Performs one calculation throwing an exception if something goes wrong
calculate(T, FeatureList<T>) - Method in interface FeatureCalculatorMulti
Performs one calculation on a sub-set of the feature list throwing an exception if something goes wrong
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 class FeatureCalculatorCachedSingle
 
calculate(T) - Method in interface FeatureCalculatorSingle
Performs one calculation throwing an exception if something goes wrong
calculate(T) - Method in class FeatureCalculatorSingleChangeInput
 
calculate(T) - Method in class FeatureCalculatorSingleFromMulti
 
calculate(T) - Method in class SequentialSession
Calculates one params for each feature.
calculate(T, FeatureList<T>) - Method in class SequentialSession
 
calculate(Feature<T>) - Method in class SessionInputSequential
 
calculate(FeatureList<T>) - Method in class SessionInputSequential
 
calculate(FeatureCalculation<S, T>) - Method in class SessionInputSequential
 
calculate(ResolvedCalculation<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(SessionInput<FeatureInputHistogram>) - Method in class FeatureHistogramStatistic
 
calculate(SessionInput<FeatureInputObjectCollection>) - Method in class FeatureObjectCollection
 
calculate(SessionInput<FeatureInputPairObjects>) - Method in class First
 
calculate(SessionInput<FeatureInputPairObjects>) - Method in class Merged
 
calculate(SessionInput<FeatureInputPairObjects>) - Method in class Minimum
 
calculate(SessionInput<FeatureInputPairObjects>) - Method in class RatioFirstToSecond
 
calculate(SessionInput<FeatureInputPairObjects>) - Method in class Second
 
calculate(SessionInput<FeatureInputPairObjects>) - Method in class SubtractSecondFromFirst
 
calculate(SessionInput<FeatureInputSingleObject>) - Method in class CenterOfGravity
 
calculate(SessionInput<FeatureInputSingleObject>) - Method in class NumberVoxels
 
calculate(SessionInput<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(SessionInput<FeatureInputPairMemo>) - Method in class AsSingle
 
calculate(SessionInput<FeatureInputSingleMemo>) - Method in class FeatureSingleMemo
 
calculate(SessionInput<FeatureInputMarkCollection>) - Method in class FeatureMarkCollection
 
calculate(SessionInput<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 MinimumXYResolution
 
calculate(Optional<Dimensions>, Optional<ImageSizeSuggestion>) - Method in class ToDimensions
 
calculate(Optional<Dimensions>, Optional<ImageSizeSuggestion>) - Method in class ToSuggested
 
calculate(SessionInput<T>) - Method in class FromDimensionsBase
 
calculate(SessionInput<FeatureInputHistogram>) - Method in class LevelFromHistogram
 
calculate(SessionInput<FeatureInputHistogram>) - Method in class ThresholdHistogram
 
calculate(SessionInput<FeatureInputPairObjects>) - Method in class Intersection
 
calculate(SessionInput<FeatureInputPairObjects>) - Method in class CostOverlapWithinMidpointDistance
 
calculate(SessionInput<FeatureInputPairObjects>) - Method in class OverlapRelative
 
calculate(SessionInput<FeatureInputPairObjects>) - Method in class TouchingVoxels
 
calculate(SessionInput<FeatureInputSingleObject>) - Method in class ArbitraryInsidePoint
 
calculate(SessionInput<FeatureInputSingleObject>) - Method in class AtBorderBase
 
calculate(SessionInput<FeatureInputSingleObject>) - Method in class BoundingBoxAlongAxisBase
 
calculate(SessionInput<FeatureInputSingleObject>) - Method in class BoundingBoxNumberVoxels
 
calculate(SessionInput<FeatureInputSingleObject>) - Method in class SpecificEnergyChannelBase
 
calculate(SessionInput<FeatureInputSingleObject>) - Method in class FeatureEnergyChannel
 
calculate(SessionInput<FeatureInputSingleObject>) - Method in class GradientMagnitude
 
calculate(SessionInput<FeatureInputSingleObject>) - Method in class GradientMeanForAxis
 
calculate(SessionInput<FeatureInputSingleObject>) - Method in class ImageMomentsBase
 
calculate(SessionInput<FeatureInputSingleObject>) - Method in class DerivedObject
 
calculate(SessionInput<FeatureInputSingleObject>) - Method in class NumberRemovedVoxelsAfterClosing
 
calculate(SessionInput<FeatureInputSingleObject>) - Method in class OutlineKernelBase
 
calculate(SessionInput<FeatureInputSingleObject>) - Method in class ObjectRadiusStandardDeviation
 
calculate(SessionInput<FeatureInputSingleObject>) - Method in class ShapeRegularityCenterSlice
 
calculate(SessionInput<FeatureInputSingleObject>) - Method in class ShapeRegularityMIP
 
calculate(SessionInput<FeatureInputSingleObject>) - Method in class FeatureIntersectingObjects
 
calculate(SessionInput<FeatureInputSingleObject>) - Method in class PairedWithMask
 
calculate(SessionInput<FeatureInputSingleObject>) - Method in class MaximumNumberContourVoxelsOnSlice
 
calculate(SessionInput<FeatureInputSingleObject>) - Method in class MaximumNumberVoxelsOnSlice
 
calculate(SessionInput<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(SessionInput<T>) - Method in class FeatureSingleObjectFromShared
 
calculate(SessionInput<T>) - Method in class ParamFromCollection
 
calculate(SessionInput<T>) - Method in class DataTypeMaxIntensity
 
calculate(SessionInput<FeatureInputStack>) - Method in class Intensity
 
calculate(SessionInput<FeatureInputStack>) - Method in class NumberChannels
 
calculate(SessionInput<FeatureInputStack>) - Method in class AsObjectMask
 
calculate(SessionInput<FeatureInputStack>) - Method in class QuantileAcrossConnectedComponents
 
calculate(ObjectMask) - Method in interface PayloadCalculator
 
calculate(SessionInput<FeatureInputMark>) - Method in class FeatureMarkDirection
 
calculate(SessionInput<FeatureInputMark>) - Method in class FeatureMarkEccentricity
 
calculate(SessionInput<FeatureInputMark>) - Method in class MaxRatioRadii
 
calculate(SessionInput<FeatureInputMark>) - Method in class OrderedRadius
 
calculate(SessionInput<FeatureInputMark>) - Method in class RadiiRatio
 
calculate(SessionInput<FeatureInputMark>) - Method in class BoundingBoxExtent
 
calculate(SessionInput<FeatureInputMark>) - Method in class MarkEllipseCircumEstimate
 
calculate(SessionInput<FeatureInputMark>) - Method in class Volume
 
calculate(SessionInput<FeatureInputAllMemo>) - Method in class AsCollection
 
calculate(SessionInput<FeatureInputAllMemo>) - Method in class AsSingleMark
 
calculate(SessionInput<FeatureInputAllMemo>) - Method in class CoefficientOfVarianceFromAll
 
calculate(SessionInput<FeatureInputAllMemo>) - Method in class MeanFromAll
 
calculate(SessionInput<FeatureInputAllMemo>) - Method in class NumberMarks
 
calculate(SessionInput<FeatureInputSingleMemo>) - Method in class AsMark
 
calculate(SessionInput<FeatureInputSingleMemo>) - Method in class AsObject
 
calculate(SessionInput<FeatureInputSingleMemo>) - Method in class BBoxRatio
 
calculate(SessionInput<FeatureInputSingleMemo>) - Method in class Intensity
 
calculate(SessionInput<FeatureInputSingleMemo>) - Method in class MaxSliceArea
 
calculate(SessionInput<FeatureInputSingleMemo>) - Method in class MeanIntensityDifference
 
calculate(SessionInput<FeatureInputSingleMemo>) - Method in class Size
 
calculate(SessionInput<FeatureInputSingleMemo>) - Method in class SurfaceSizeMaskNonZero
 
calculate(SessionInput<FeatureInputPairMemo>) - Method in class BoundingBoxZDistance
 
calculate(SessionInput<FeatureInputPairMemo>) - Method in class BoundingBoxZOverlapRatio
 
calculate(SessionInput<FeatureInputPairMemo>) - Method in class MinimumDistanceByDimension
 
calculate(SessionInput<FeatureInputPairMemo>) - Method in class FeatureAsIndividualProportionate
 
calculate(SessionInput<FeatureInputPairMemo>) - Method in class MinFeatureAsIndividual
 
calculate(SessionInput<FeatureInputPairMemo>) - Method in class MaxOverlapRatio
 
calculate(SessionInput<FeatureInputPairMemo>) - Method in class OverlapNumVoxels
 
calculate(SessionInput<FeatureInputPairMemo>) - Method in class OverlapNumVoxelsMask
 
calculate(SessionInput<FeatureInputPairMemo>) - Method in class OverlapRatio
 
calculate(SessionInput<FeatureInputPairMemo>) - Method in class OverlapRatioMask
 
calculate(SessionInput<FeatureInputStack>) - Method in class HOGFeature
 
calculate(SessionInput<T>) - Method in class AbsoluteValue
 
calculate(SessionInput<T>) - Method in class Divide
 
calculate(SessionInput<T>) - Method in class InvertedMax
 
calculate(SessionInput<T>) - Method in class Multiply
 
calculate(SessionInput<T>) - Method in class IfCondition
 
calculate(SessionInput<T>) - Method in class FromDictionary
 
calculate(SessionInput<T>) - Method in class Maximum
 
calculate(SessionInput<T>) - Method in class Mean
 
calculate(SessionInput<T>) - Method in class MeanGeometric
 
calculate(SessionInput<T>) - Method in class Minimum
 
calculate(SessionInput<T>) - Method in class NormalizedRange
 
calculate(SessionInput<T>) - Method in class Range
 
calculate(SessionInput<T>) - Method in class RangeCompareBase
 
calculate(SessionInput<T>) - Method in class StatisticalScoreBase
 
calculate(SessionInput<T>) - Method in class WithValueBase
 
calculate(SessionInput<T>) - Method in class ConvertUnits
 
calculate(SessionInput<FeatureInputSingleObject>) - Method in class EllipsoidBase
 
calculate(SessionInput<FeatureInputSingleObject>) - Method in class Ellipticity
 
calculate(SessionInput<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
 
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
 
calculateBound(Point3d, RotationMatrix) - Method in class BoundCalculator
 
calculateBound(Point3d, RotationMatrix) - Method in class ConstantBoundGenerator
 
calculateBound(Point3d, RotationMatrix) - Method in class LineBoundCalculator
 
calculateBytesPerPixel(int) - Method in class ToUnsignedByte
 
calculateBytesPerPixel(int) - Method in class UnsignedByteFromFloat
 
calculateBytesPerPixel(int) - Method in class UnsignedByteFromUnsignedByteInterleaving
 
calculateBytesPerPixel(int) - Method in class UnsignedByteFromUnsignedByteNoInterleaving
 
calculateBytesPerPixel(int) - Method in class UnsignedByteFromUnsignedInt
 
calculateBytesPerPixel(int) - Method in class UnsignedByteFromUnsignedShort
 
calculateCheckInitialized(SessionInput<T>) - Method in class Feature
 
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.
calculateCountNonZero() - Method in class Histogram
 
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, SessionInput<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, InputProcessContext<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, AxisType) - Method in class Extent
 
calculateForAxis(Dimensions, AxisType) - Method in class ForSpecificAxis
 
calculateForAxis(Dimensions, AxisType) - Method in class VoxelPhysicalSize
 
calculateForChannel(SessionInput<FeatureInputSingleObject>, Channel) - Method in class FeatureEnergyChannel
 
calculateForChannel(SessionInput<FeatureInputSingleObject>, Channel) - Method in class Intensity
 
calculateForChannel(SessionInput<FeatureInputSingleObject>, Channel) - Method in class IntensityMeanMaxSlice
 
calculateForChannel(SessionInput<FeatureInputSingleObject>, Channel) - Method in class IntensityMeanShellBase
 
calculateForChannel(SessionInput<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 KernelBirthPixelized
 
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 Cached-Calculations that generate a Params for feature-calculation using an existing "delegate" calculation
CalculateInputFromDelegate(FeatureCalculation<U, T>, CalculationResolver<T>) - Constructor for class CalculateInputFromDelegate
 
CalculateInputFromDelegate(ResolvedCalculation<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(ResolvedCalculation<U, T>) - Constructor for class CalculateInputFromDelegateOption
The constructor
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(ResolvedCalculation<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 of the histogram values i.e.
calculateMaybeSuppressErrors(FeatureInputPairObjects, ErrorReporter) - Method in class PairsTableCalculator
 
calculateMeanIntensityObject(Channel, ObjectMask) - Static method in class IntensityMeanCalculator
 
calculateMeanIntensityObject(Channel, ObjectMask, boolean) - Static method in class IntensityMeanCalculator
 
calculateMemoryUsage() - Static method in class MemoryUtilities
 
calculateMidpoint(ObjectWithProperties, boolean) - Static method in class Midpoint
 
calculateMinimum() - Method in class Histogram
Calculates the minimum of the histogram values i.e.
calculateMinMax(Optional<Resolution>, boolean) - Method in class MarkBounds
 
calculateMode() - Method in class Histogram
 
calculateMode(int) - Method in class Histogram
Calculates the mode of the histogram values i.e.
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, ResolvedCalculationMap<ObjectMask, FeatureInputSingleObject, Integer>) - Constructor for class CalculateObjectMask
 
calculateOrientation(ObjectWithProperties) - Static method in class Orientation
 
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
 
calculateOverlapRatio(ObjectMask, ObjectMask, ObjectMask) - Static method in class OverlapCalculator
 
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
 
CalculatePointsFromOutline - Class in org.anchoranalysis.plugin.points.calculate
 
CalculatePointsFromOutline() - Constructor for class CalculatePointsFromOutline
 
calculateResultsForInput(FileInput, InputProcessContext<FeatureList<FeatureInputHistogram>>) - Method in class FromHistogram
 
calculateResultsForInput(ProvidesStackInput, InputProcessContext<FeatureList<FeatureInputStack>>) - Method in class FromImage
 
calculateResultsForInput(T, InputProcessContext<FeatureList<S>>) - Method in class SingleRowPerInput
 
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(ResolvedCalculation<ObjectMask, FeatureInputSingleObject>, ResolvedCalculation<ObjectMask, FeatureInputSingleObject>, int, boolean, boolean) - Constructor for class CalculateShellObjectMask
 
calculateSigma(Dimensions, MessageLogger) - Method in class BlurStrategy
 
calculateStatisticFrom(Histogram) - Method in class FeatureHistogramStatistic
 
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
 
calculateSumCubes() - Method in class Histogram
 
calculateSumSquares() - Method in class Histogram
 
calculateSuppressErrors(T, ErrorReporter) - Method in class FeatureCalculatorCachedMulti
 
calculateSuppressErrors(T, ErrorReporter) - Method in interface FeatureCalculatorMulti
Performs one calculation 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 class FeatureCalculatorCachedSingle
 
calculateSuppressErrors(T, ErrorReporter) - Method in interface FeatureCalculatorSingle
Performs one calculation 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
 
calculateVolume() - Method in class Extent
 
calculateVolumeAsInt() - Method in class Extent
 
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 FirstSecondOrderStatistic
 
CalculationResolver<T extends FeatureInput> - Interface in org.anchoranalysis.feature.calculate.cache
Searches a cache to reuses a FeatureCalculation if it already exists.
calculator() - Method in interface FeatureSessionCache
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
 
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
callChannelIfSupported(int, BiConsumer<Channel, ChannelConverterAttached<Channel, UnsignedByteBuffer>>, Consumer<Channel>) - Method in class ChannelMapper
 
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 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 WithPriority
 
canEqual(Object) - Method in class IdentifierModulo
 
canEqual(Object) - Method in class Indexable
 
canEqual(Object) - Method in class ChildCacheName
 
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 Orientation2D
 
canEqual(Object) - Method in class Orientation3DEulerAngles
 
canEqual(Object) - Method in class OrientationAxisAngle
 
canEqual(Object) - Method in class OrientationIdentity
 
canEqual(Object) - Method in class OrientationRotationMatrix
 
canEqual(Object) - Method in class CalculateInputFromPair
 
canEqual(Object) - Method in class CalculateNumberVoxels
 
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 FirstSecondOrderStatistic
 
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 AnnotationGroup
 
canEqual(Object) - Method in class AnnotationGroupObject
 
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 WithConfidence
 
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 CalculatePointsFromOutline
 
canEqual(Object) - Method in class CalculateEllipseLeastSquares
 
canEqual(Object) - Method in class CalculateEllipsoidLeastSquares
 
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
 
canExceptionBeCombined(Throwable) - Method in exception NamedProviderGetException
 
canExceptionBeSkipped(Throwable) - Method in exception BeanMisconfiguredXmlException
 
canExceptionBeSkipped(Throwable) - Method in exception LocalisedBeanException
 
canExceptionBeSkipped(Throwable) - Method in exception AnchorCombinableException
 
canExceptionBeSkipped(Throwable) - Method in exception NamedProviderGetException
 
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
 
castTo() - Method in class VoxelsWrapper
Casts voxels to a particular 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(AxisType) - 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(AxisType) - Method in class ObjectMask
Calculates center-of-gravity for one specific axis only
centerOfGravity() - Method in class BoundingBox
Similar to BoundingBox.midpoint() but not always identical.
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
 
changeExtension(Path, NonImageFileFormat, FileFormat) - Static method in class FormatExtensions
Change the extension in a path.
changeExtent(Extent) - Method in class BoundingBox
 
changeExtentZ(int) - Method in class BoundingBox
 
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
 
Channel - Class in org.anchoranalysis.image.core.channel
A channel from an image.
Channel(Voxels<?>, Optional<Resolution>) - Constructor for class Channel
Constructor
channel() - Method in class Mask
The underlying channel which contains the binary-values.
channel(String) - Static method in class ReferenceFactory
 
channelAt(int) - Method in class RGBStack
 
ChannelConverter<T> - Class in org.anchoranalysis.image.core.channel.convert
Converts a channel 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 attached to a particular object.
ChannelConverterMulti - Class in org.anchoranalysis.image.core.channel.convert
Converts a channel from one type to 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 for one of several data-types
ChannelFactoryByte - Class in org.anchoranalysis.image.core.channel.factory
 
ChannelFactoryByte() - Constructor for class ChannelFactoryByte
 
ChannelFactoryFloat - Class in org.anchoranalysis.image.core.channel.factory
 
ChannelFactoryFloat() - Constructor for class ChannelFactoryFloat
 
ChannelFactoryInt - Class in org.anchoranalysis.image.core.channel.factory
 
ChannelFactoryInt() - Constructor for class ChannelFactoryInt
 
ChannelFactoryShort - Class in org.anchoranalysis.image.core.channel.factory
 
ChannelFactoryShort() - Constructor for class ChannelFactoryShort
 
ChannelFactorySingleType - Class in org.anchoranalysis.image.core.channel.factory
Creates a channel for a specific data-type
ChannelFactorySingleType(VoxelDataType, VoxelsFactoryTypeBound<?>) - Constructor for class ChannelFactorySingleType
 
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 a 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() - Method in interface OpenedImageFile
 
channelNames() - Method in class BioformatsOpenedRaster
 
channelNames() - Method in class MultiFileReaderOpenedRaster
 
ChannelProvider - Class in org.anchoranalysis.image.bean.provider
 
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 EllipseBoundsCheck
 
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
 
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
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
 
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
 
checkUnsupported3D(Channel) - Static method in class SegmentChannelIntoObjects
 
checkUnsupportedObjectMask(Optional<ObjectMask>) - Static method in class SegmentChannelIntoObjects
 
checkUnsupportedSeeds(Optional<SeedCollection>) - 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 FeatureSessionCache
Gets/creates a child-cache for a given name
childCacheFor(FeatureSessionCache<?>, CacheCreator, ChildCacheName, V) - Method in class CheckCacheForSpecificChildren
 
childCacheFor(FeatureSessionCache<?>, CacheCreator, ChildCacheName, V) - Method in interface ChildCacheFinder
Selects a child-cache given a parent and a child-name.
childCacheFor(FeatureSessionCache<?>, CacheCreator, ChildCacheName, V) - Method in class DefaultChildCacheFinder
 
ChildCacheName - Class in org.anchoranalysis.feature.calculate.cache
A unique identifier for a child-cache name, that uses a class and optionally additionally a part-name a class: guaranteed to be unique for the class an optional part-name (string): a further division of the class into different caches
ChildCacheName(Class<?>) - Constructor for class ChildCacheName
Uses only the class as an identifier - and a blank part-name
ChildCacheName(Class<?>, int) - Constructor for class ChildCacheName
Uses only the class as an identifier - and a 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
 
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() - Method in interface VoxelizedMark
 
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
 
clear() - Method in class FeatureList
 
clear() - Method in class StackNotUniformSized
 
clear() - Method in class UnsignedBuffer
Clears the buffer ala Buffer.clear().
clear() - Method in class ObjectCollection
 
clear() - Method in class UpdatableMarksList
 
clearBest() - Method in class DualState
 
clearVisualizationState() - Method in class MergeLists
 
clearVisualizationState() - Method in class PointsFromOrientationProposer
 
clearVisualizationState() - Method in class TraversePointsOnContour
 
clipTo(T, Extent) - Method in interface AccessObjectMask
Ensures the element lies within a certain extent.
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
 
close() - Method in class ProgressConsole
 
close() - Method in class ProgressIgnore
 
close() - Method in class ProgressIncrement
 
close() - Method in class ProgressMultiple
 
close() - Method in class ProgressOneOfMany
 
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 class ResultsWriter
 
close() - Method in interface OpenedImageFile
 
close() - Method in class BioformatsOpenedRaster
 
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 MultiFileReaderOpenedRaster
 
closeAnyOpenIO() - Method in class SharedStateExportFeatures
 
closeAnyOpenIO() - Method in class SharedStateSegmentInstance
 
closeLogger() - Method in class RecordingCounter
Closes the logger.
closestPointOnBorder(Point3d) - Method in class BoundingBox
 
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
 
CoefficientOfVariation - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
 
CoefficientOfVariation() - Constructor for class CoefficientOfVariation
 
CollapseFileName - Class in org.anchoranalysis.plugin.quick.bean.file.path.derive
Takes a file-path of form somedir/somename.ext and converts to somedir.ext
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 pixels
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 pixels
collectResult() - Method in class WrapAbsoluteAsMasked
 
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
 
ColorIndexModulo - Class in org.anchoranalysis.core.color
 
ColorIndexModulo(ColorIndex) - Constructor for class ColorIndexModulo
 
colorLegend(LegendTitle) - Method in class PlotColorScheme
 
ColorList - Class in org.anchoranalysis.core.color
 
ColorList(Color...) - Constructor for class ColorList
 
ColorList(RGBColor...) - Constructor for class ColorList
 
ColorList(RGBColor) - Constructor for class ColorList
 
ColorList() - Constructor for class ColorList
 
colorPlot(XYPlot) - Method in class PlotColorScheme
 
colorPlot(CategoryPlot) - Method in class PlotColorScheme
 
ColorPool - Class in org.anchoranalysis.annotation.io.assignment.generator
 
ColorPool(int, ColorScheme, ColorScheme, boolean) - Constructor for class ColorPool
 
ColorProvider - Class in org.anchoranalysis.image.bean.provider
Provides a list of one or more colors
ColorProvider() - Constructor for class ColorProvider
 
ColorScheme - Class in org.anchoranalysis.bean.shared.color.scheme
Creates a set 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
colorSpaceCode() - Method in class ConvertRGBToHSV
 
colorSpaceCode() - Method in class ConvertRGBToLab
 
column(int) - Method in class RotationMatrix
 
ColumnDefinition - Class in org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition
 
ColumnDefinition() - Constructor for class ColumnDefinition
 
combine(Path, Path) - Static method in class BeanPathUtilities
 
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
 
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.
combineDscr(String, String) - Method in class AddConstantTo
 
combineDscr(String, String) - Method in class ConstantToThePowerOf
 
combineDscr(String, String) - Method in class DivideByConstant
 
combineDscr(String, String) - Method in class MultiplyByConstant
 
combineDscr(String, String) - Method in class SubtractFrom
 
combineDscr(String, String) - Method in class ToThePowerOfConstant
 
combineDscr(String, String) - Method in class ReplaceUnusualValue
 
combineDscr(String, String) - Method in class WithValueBase
 
combineDscrsRecursively(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.
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.image.core.outline.traverser.path.merge
 
combineToOnePath(List<ContiguousVoxelPath>) - Static method in class CombineToOnePath
Combines all the contiguous paths to a single-path
combineToOnePath() - Method in class VisitedVoxels
Combines all the contiguous paths to a single-path
CombineTypes - Class in org.anchoranalysis.image.voxel.datatype
 
combineTypes(VoxelDataType, VoxelDataType) - Static method in class CombineTypes
 
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.
Comparator3d<T extends Tuple3d> - Class in org.anchoranalysis.spatial.point
 
Comparator3d() - Constructor for class Comparator3d
 
Comparator3i<T extends Tuple3i> - Class in org.anchoranalysis.spatial.point
 
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> - 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
 
Comparer - Class in org.anchoranalysis.annotation.io.bean.comparer
 
Comparer() - Constructor for class Comparer
 
compareTo(WithPriority<T>) - Method in class WithPriority
Orders so that hasPriority==true has higher priority in queue to hasPriority==false
compareTo(IndexGetter) - Method in class Indexable
 
compareTo(MultiName) - Method in class CombinedName
 
compareTo(MultiName) - Method in class SimpleName
 
compareTo(EigenvalueAndVector) - Method in class EigenvalueAndVector
 
compareTo(WithConfidence<T>) - Method in class WithConfidence
 
compareTo(SortedSetChannel) - Method in class SortedSetChannel
 
compareTo(SortedSetSlice) - Method in class SortedSetSlice
 
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.feature
Like CompareWithRange but uses features to calculate boundary values
CompareWithRangeFeature() - Constructor for class CompareWithRangeFeature
 
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 CompressAnyTIFF
 
computeInitialFeasibleSolution() - Method in class HungarianAlgorithm
Compute an initial feasible solution by assigning zero labels to the workers and by assigning to each job a label equal to the minimum cost among its incident edges.
Concatenate - Class in org.anchoranalysis.bean.define.adder
Concatenates a list of adders
Concatenate() - Constructor for class Concatenate
 
Concatenate - Class in org.anchoranalysis.plugin.image.bean.color.provider
 
Concatenate() - Constructor for class Concatenate
 
Concatenate - Class in org.anchoranalysis.plugin.image.bean.object.provider
 
Concatenate() - Constructor for class Concatenate
 
Concatenate - Class in org.anchoranalysis.plugin.image.bean.stack.provider
Combines all the channels from one or more sources (stacks, channels etc.)
Concatenate() - Constructor for class Concatenate
 
Concatenate<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input
Concatenates several input-managers
Concatenate() - Constructor for class Concatenate
 
ConcatenateFileTypes - Class in org.anchoranalysis.io.generator
Concatenates the arrays of FileType that may be returned from write operations.
ConcatenateFileTypes() - Constructor for class ConcatenateFileTypes
Creates to always use a list for tracking.
ConcatenateFileTypes(boolean) - Constructor for class ConcatenateFileTypes
Create to use a list for tracking if a flag is true, otherwise to just remember the last result of each call to ConcatenateFileTypes.add(org.anchoranalysis.io.manifest.file.FileType[]).
ConcurrencyPlan - Class in org.anchoranalysis.core.concurrency
How many allocated CPUS and CPUs can be used.
ConcurrentJobMonitor - Class in org.anchoranalysis.experiment.task.processor
 
ConcurrentJobMonitor(long) - Constructor for class ConcurrentJobMonitor
 
ConcurrentModelException - Exception in org.anchoranalysis.core.concurrency
This exception indicates that an error occurred when performing inference from a model concurrently.
ConcurrentModelException(Throwable) - Constructor for exception ConcurrentModelException
 
ConcurrentModelPool<T> - Class in org.anchoranalysis.core.concurrency
Keeps concurrent copies of a model to be used by different threads.
ConcurrentModelPool(ConcurrencyPlan, ConcurrentModelPool.CreateModelForPool<T>) - Constructor for class ConcurrentModelPool
 
ConcurrentModelPool.CreateModelForPool<T> - Interface in org.anchoranalysis.core.concurrency
Creates a model to use in the pool
ConditionalKernel - Class in org.anchoranalysis.image.voxel.kernel
Executes another BinaryKernel iff a predicated is satisfied for a particular point.
ConditionalKernel(BinaryKernel, Predicate<Point3i>) - Constructor for class ConditionalKernel
 
ConditionallyMergeOverlappingObjects - Class in org.anchoranalysis.plugin.image.bean.object.segment.reduce
Where objects overlap, they are merged together if certain conditions are fulfilled.
ConditionallyMergeOverlappingObjects() - Constructor for class ConditionallyMergeOverlappingObjects
 
ConfigureBioformatsLogging - Class in org.anchoranalysis.io.bioformats
Singleton class for making sure Bioformats is configured configured.
configurePermuteProperty(PermutePropertySequenceInteger) - Method in class PermuteDivideByParam
 
configurePermuteProperty(PermutePropertySequenceInteger) - Method in class PermuteFeatureSequenceInteger
 
configurePermuteProperty(PermutePropertySequenceInteger) - Method in class PermuteFirstSecondOrder
 
ConicBase - Class in org.anchoranalysis.mpp.mark.conic
 
ConicBase() - Constructor for class ConicBase
 
ConicBase(MarkWithPosition) - Constructor for class ConicBase
 
ConicFitterBase - Class in org.anchoranalysis.plugin.points.bean.fitter
 
ConicFitterBase() - Constructor for class ConicFitterBase
 
ConnectedComponentsFromBinarySegmentation - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel
Performs a binary-segmentation of the channel and converts its connected-components into objects
ConnectedComponentsFromBinarySegmentation() - Constructor for class ConnectedComponentsFromBinarySegmentation
 
ConnectedComponentsFromMask - Class in org.anchoranalysis.plugin.image.bean.object.provider.connected
Converts a binary-mask into its connected components
ConnectedComponentsFromMask() - Constructor for class ConnectedComponentsFromMask
 
connectedTo(Contour) - Method in class Contour
 
connectedToFirstPointOf(Contour) - Method in class Contour
 
connectedToLastPointOf(Contour) - Method in class Contour
 
ConsiderVisit - Interface in org.anchoranalysis.image.core.outline.traverser
 
considerVisit(Point3i, int) - Method in interface ConsiderVisit
 
considerVisit(Point3i, int, ObjectMask) - Method in class VisitScheduler
 
considerVisit(Point3i, int, ObjectMask) - Method in class VisitSchedulerAnd
 
considerVisit(Point3i, int, ObjectMask) - Method in class VisitSchedulerConvexAboutRoot
 
considerVisit(Point3i, int, ObjectMask) - Method in class VisitSchedulerMaxDistanceAlongContour
 
considerVisit(Point3i, int, ObjectMask) - Method in class VisitSchedulerUniformSample
 
ConsistentChannelChecker - Class in org.anchoranalysis.plugin.image.task.grouped
Checks that the histograms created from channels all have the same data type, res, max-value etc.
ConsistentChannelChecker() - Constructor for class ConsistentChannelChecker
 
ConsoleAccepted - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
 
ConsoleAccepted() - Constructor for class ConsoleAccepted
 
ConsoleAggregatedReporter - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
 
ConsoleAggregatedReporter(double) - Constructor for class ConsoleAggregatedReporter
 
ConsoleAggregatedReporter() - Constructor for class ConsoleAggregatedReporter
 
ConsoleMessageLogger - Class in org.anchoranalysis.experiment.log
 
ConsoleMessageLogger() - Constructor for class ConsoleMessageLogger
 
Constant<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.operator
 
Constant(double) - Constructor for class Constant
Constructor with a particular value
Constant(String, double) - Constructor for class Constant
Constructor with a particular value and a custom-name
Constant() - Constructor for class