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

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absolute() - Method in class Tuple3d
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: Called once after all calls to Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>).
afterAllJobsAreExecuted(NoSharedState, InputOutputContext) - Method in class TaskWithoutSharedState
afterAllJobsAreExecuted(AggregateSharedState, InputOutputContext) - Method in class AggregateAnnotations
afterAllJobsAreExecuted(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: Like ExtensionUtilities.appendExtension(String, Optional) but accepts and returns a Path.
AppendFilePath - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
AppendFilePath() - Constructor for class AppendFilePath
AppendHistogram - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
AppendHistogram() - Constructor for class AppendHistogram
AppendMarks - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
AppendMarks() - Constructor for class AppendMarks
AppendObjects - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
AppendObjects() - Constructor for class AppendObjects
AppendStack - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend: A stack from a stack-collection
AppendStack() - Constructor for class AppendStack
AppendStackDirect - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend: A stack from a stack-collection
AppendStackDirect() - Constructor for class AppendStackDirect
apply(Throwable, Writer, String, int, boolean) - Static method in class RecursivelyDescribeExceptionStack: Incrementally adds a line to a string builder with the message of each exception moving onto the next nested exception until there are no more
apply(S, T) - Method in interface CheckedBiFunction: Calls the function
apply(S) - Method in interface CheckedFunction: Calls the function
apply(int) - Method in interface CheckedIntFunction: Calls the function
apply(T) - Method in interface CheckedUnaryOperator
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: Multiplexes between OutsideKernelPolicy.AS_ON and OutsideKernelPolicy.AS_OFF.
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: Called once before all calls to Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>).
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<T>, ParametersExperiment) - Method in class TaskWithoutSharedState
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<AnnotationWithStrategy<S>>, ParametersExperiment) - Method in class AggregateAnnotations
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<AnnotationComparisonInput<ProvidesStackInput>>, ParametersExperiment) - Method in class CompareAnnotations
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<T>, ParametersExperiment) - Method in class ExportFeatures
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<NamedChannelsInput>, ParametersExperiment) - Method in class ConvertImageFormat
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<ProvidesStackInput>, ParametersExperiment) - Method in class GroupedStackBase
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<ProvidesStackInput>, ParametersExperiment) - Method in class ImageAssignLabel
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<StackSequenceInput>, ParametersExperiment) - Method in class ScaleImage
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<StackSequenceInput>, ParametersExperiment) - Method in class SegmentInstanceWithModel
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<NamedChannelsInput>, ParametersExperiment) - Method in class ExtractSlice
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<NamedChannelsInput>, ParametersExperiment) - Method in class MovieFromSlices
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<FileInput>, ParametersExperiment) - Method in class CombineCSV
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<FileWithDirectoryInput>, ParametersExperiment) - Method in class CopyFiles
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<T>, ParametersExperiment) - Method in class SummarizeBase
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<T>, ParametersExperiment) - Method in class ConvertNamedChannels
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<ManifestCouplingDefinition>, ParametersExperiment) - Method in class ExportReportFeaturesFromManifest
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<MultiInput>, ParametersExperiment) - Method in class ExportReportFeaturesFromMulti
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<MultiInput>, ParametersExperiment) - Method in class ExportObjectsAsCroppedImages
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<FromCSVInput>, ParametersExperiment) - Method in class ExportObjectsFromCSV
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<MultiInput>, ParametersExperiment) - Method in class SegmentMarksFromImage
beforeCalc(FeatureInitialization) - Method in class Feature: Dummy method, that children can optionally override
beforeCalc(FeatureInitialization) - Method in class ConvertToPhysicalDistance
beforeCalc(FeatureInitialization) - Method in class FeatureIntersectingObjects
beforeCalc(FeatureInitialization) - Method in class PairedWithMask
beforeCalc(FeatureInitialization) - Method in class FeatureSingleObjectFromShared
beforeCalc(FeatureInitialization) - Method in class ParamFromCollection
beforeCalc(FeatureInitialization) - Method in class FeatureMarkDirection
beforeCalc(FeatureInitialization) - Method in class FromDictionary
beforeCalcSetup(Histogram, int) - Method in class CalculateLevel
beforeCalcSetup(Histogram, int) - Method in class CalculateLevelBase
beforeCalcSetup(Histogram, int) - Method in class DifferenceCalculateLevelStandardDeviation
beforeCalcWithInitialization(ImageInitialization) - Method in class FeatureSingleObjectFromShared
beforeCalcWithInitialization(ImageInitialization) - Method in class MaskAsSingleObject
beforeCalcWithInitialization(ImageInitialization) - Method in class ObjectAggregationBase
BeforeCondition - Interface in org.anchoranalysis.plugin.image.object.merge.condition
beforeCopying(Path, int) - Method in class Anonymize
beforeCopying(Path, int) - Method in class CopyFilesNaming: To be called once before any calls to CopyFilesNaming.destinationPath(File, DirectoryWithPrefix, int, CopyContext).
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: Performs one calculation, either calling FeatureCalculatorMulti.calculate(T) or FeatureCalculatorMulti.calculateSuppressErrors(T, org.anchoranalysis.core.log.error.ErrorReporter) depending on a flag
calculate(T) - Method in class FeatureCalculatorMultiChangeInput
calculate(T, FeatureList<T>) - Method in class FeatureCalculatorMultiChangeInput
calculate(T) - Method in 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