- 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(String) - Method in class FilePathPattern
-
- 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
-
- 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
-
- 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
-
- addFrom(NamedProvider<Stack>) - Method in class NamedStacks
-
- 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
-
- 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
-
- addOperationRecorder(WriteOperationRecorder) - Method in class Outputter
-
- addOperationRecorder(WriteOperationRecorder) - Method in class OutputterChecked
-
Adds an additional operation recorder alongside any existing recorders.
- 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.
- 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.
- addToSharedObjects(MarksInitialization, ImageInitialization) - Method in interface InputForMarksBean
-
- addToSharedObjects(MarksInitialization, ImageInitialization) - Method in class MultiInput
-
- addToSharedObjects(MarksInitialization, ImageInitialization) - Method in class FromCSVInput
-
- addToStacks(String, Stack) - Method in class ImageInitialization
-
- addToStacks(String, StackProvider) - Method in class ImageInitialization
-
- addToStore(NamedProviderStore<T>) - Method in interface MultiInputSubMap
-
- addToStore(NamedProviderStore<T>) - Method in class OperationMap
-
- addToStore(NamedProviderStore<TimeSequence>) - Method in class StackWithMap
-
- addToStore(NamedProviderStore<TimeSequence>, int, Progress) - Method in class StackWithMap
-
- addToStoreInferNames(NamedProviderStore<TimeSequence>, int, Progress) - Method in class NamedChannelsInput
-
- addToStoreInferNames(NamedProviderStore<Stack>) - Method in interface ProvidesStackInput
-
Adds the current object to a named-store of stacks (using the default series)
- addToStoreInferNames(NamedProviderStore<TimeSequence>, int, Progress) - Method in interface ProvidesStackInput
-
Adds the current object to a named-store of stacks
- addToStoreInferNames(NamedProviderStore<TimeSequence>, int, Progress) - Method in class MultiInput
-
- addToStoreInferNames(NamedProviderStore<TimeSequence>, int, Progress) - Method in class ConvertNamedChannelsInputToStack
-
- addToStoreWithName(String, NamedProviderStore<TimeSequence>, int, Progress) - Method in class NamedChannelsInput
-
- addToStoreWithName(String, NamedProviderStore<TimeSequence>, int, Progress) - Method in interface ProvidesStackInput
-
- addToStoreWithName(String, NamedProviderStore<TimeSequence>, int, Progress) - Method in class MultiInput
-
- addToStoreWithName(String, NamedProviderStore<TimeSequence>, int, Progress) - Method in class ConvertNamedChannelsInputToStack
-
- addToTypeValueCollection(Collection<TypedValue>, int) - Method in class ResultsVector
-
- addToUpdatablePairList(UpdatableMarksList, VoxelizedMarkMemo) - Method in class VoxelizedMarksWithEnergy
-
- addToVoxelList(int, int, int) - Method in class IndexByRegion
-
- addUnannotatedImage() - Method in interface AddAnnotation
-
- addUnannotatedImage() - Method in class AnnotationGroup
-
- addUnannotatedImage() - Method in class AnnotationGroupList
-
- addUncoupledJobs(Collection<File>, ManifestDeserializer, Logger) - Method in class ManifestCouplingDefinition
-
Adds job-manifests that don't have corresponding experiment-manifests.
- addUnused(T) - Method in interface VoxelPartitionFactory
-
- addUnused(Histogram) - Method in class VoxelPartitionFactoryHistogramReuse
-
- addUnused(Histogram) - Method in class VoxelPartitonFactoryHistogram
-
- addVertex(V) - Method in class GraphWithoutPayload
-
Adds a vertex.
- addVertex(V) - Method in class GraphWithPayload
-
Adds a vertex.
- addVisitedPoint(Point3i) - Method in class VisitedVoxels
-
Adds a visited-point to an existing path, or else makes a new one
- addWeightedKernelFactories(List<WeightedKernel<T, S>>) - Method in class KernelProposerOption
-
- addWeightedKernelFactories(List<WeightedKernel<T, S>>) - Method in class KernelProposerOptionDual
-
- addWeightedKernelFactories(List<WeightedKernel<T, S>>) - Method in class KernelProposerOptionSingle
-
- addWithIndex(RGBColor) - Method in class ColorList
-
- addWithName(Define, String, AnchorBean<?>) - Method in class DefineAdderWithPrefixBean
-
- addWithUnits(String, double, DoubleUnaryOperator, SpatialUnits.UnitSuffix) - Method in class OverlayProperties
-
- AdjacentFile - Class in org.anchoranalysis.plugin.quick.bean.input
-
- AdjacentFile() - Constructor for class AdjacentFile
-
- adjacentVerticesOutgoing(V) - Method in class GraphWithoutPayload
-
The vertices that are connected to a particular vertex by an outgoing edge
- adjacentVerticesOutgoing(V) - Method in class GraphWithPayload
-
The vertices that are connected to a particular vertex by an outgoing edge
- afterAllJobsAreExecuted(S, InputOutputContext) - Method in class Task
-
- afterAllJobsAreExecuted(NoSharedState, InputOutputContext) - Method in class TaskWithoutSharedState
-
- afterAllJobsAreExecuted(AggregateSharedState, InputOutputContext) - Method in class AggregateAnnotations
-
- afterAllJobsAreExecuted(SharedState<T>, InputOutputContext) - Method in class CompareAnnotations
-
- afterAllJobsAreExecuted(SharedStateExportFeatures<S>, InputOutputContext) - Method in class ExportFeatures
-
- afterAllJobsAreExecuted(NoSharedState, InputOutputContext) - Method in class ConvertImageFormat
-
- afterAllJobsAreExecuted(GroupedSharedState<S, T>, InputOutputContext) - Method in class GroupedStackBase
-
- afterAllJobsAreExecuted(SharedStateFilteredImageOutput<T>, InputOutputContext) - Method in class ImageAssignLabel
-
- afterAllJobsAreExecuted(NoSharedState, InputOutputContext) - Method in class ScaleImage
-
- afterAllJobsAreExecuted(SharedStateSegmentInstance<T>, InputOutputContext) - Method in class SegmentInstanceWithModel
-
- afterAllJobsAreExecuted(SharedStateSelectedSlice, InputOutputContext) - Method in class ExtractSlice
-
- afterAllJobsAreExecuted(OutputSequenceIncrementing<Stack>, InputOutputContext) - Method in class MovieFromSlices
-
- afterAllJobsAreExecuted(CSVWriter, InputOutputContext) - Method in class CombineCSV
-
- afterAllJobsAreExecuted(RecordingCounter<T>, InputOutputContext) - Method in class CopyFiles
-
- afterAllJobsAreExecuted(Summarizer<S>, InputOutputContext) - Method in class SummarizeBase
-
- afterAllJobsAreExecuted(SharedStateRememberConverted<U, S>, InputOutputContext) - Method in class ConvertNamedChannels
-
- afterAllJobsAreExecuted(NoSharedState, InputOutputContext) - Method in class ExportReportFeaturesFromManifest
-
- afterAllJobsAreExecuted(CSVWriter, InputOutputContext) - Method in class ExportReportFeaturesFromMulti
-
- afterAllJobsAreExecuted(NoSharedState, InputOutputContext) - Method in class ExportObjectsAsCroppedImages
-
- afterAllJobsAreExecuted(FromCSVSharedState, InputOutputContext) - Method in class ExportObjectsFromCSV
-
- afterAllJobsAreExecuted(ExperimentState, InputOutputContext) - Method in class SegmentMarksFromImage
-
- AfterCondition - Interface in org.anchoranalysis.plugin.image.object.merge.condition
-
- afterCreateObject(Point3i, Optional<Resolution>, RandomNumberGenerator) - Method in class VisitScheduler
-
- afterCreateObject(Point3i, Optional<Resolution>, RandomNumberGenerator) - Method in class VisitSchedulerAnd
-
- afterCreateObject(Point3i, Optional<Resolution>, RandomNumberGenerator) - Method in class VisitSchedulerConvexAboutRoot
-
- afterCreateObject(Point3i, Optional<Resolution>, RandomNumberGenerator) - Method in class VisitSchedulerMaxDistanceAlongContour
-
- afterCreateObject(Point3i, Optional<Resolution>, RandomNumberGenerator) - Method in class VisitSchedulerUniformSample
-
- aggEnd(Aggregator) - Method in interface AggregateReceiver
-
- aggEnd(Aggregator) - Method in class AggregateReceiverList
-
- aggEnd(Aggregator) - Method in class ConsoleAggregatedReporter
-
- aggEnd(Aggregator) - Method in class CSVReporterAggregated
-
- aggEnd(Aggregator) - Method in class Log4JReporter
-
- aggEnd(Aggregator) - Method in class OptimizationStepLogReporter
-
- aggEnd(Aggregator) - Method in class TextFile
-
- AggIDCounter - Class in org.anchoranalysis.mpp.segment.optimization.feedback.aggregate
-
- AggIDCounter(int) - Constructor for class AggIDCounter
-
- AggregateAnnotations<S extends AnnotatorStrategy> - Class in org.anchoranalysis.plugin.annotation.bean.aggregate
-
Aggregates many per-image annotations together in form of a CSV file.
- AggregateAnnotations() - Constructor for class AggregateAnnotations
-
- AggregateReceiver<T> - Interface in org.anchoranalysis.mpp.segment.optimization.feedback.aggregate
-
- AggregateReceiverList<T> - Class in org.anchoranalysis.mpp.segment.optimization.feedback.aggregate
-
- AggregateReceiverList() - Constructor for class AggregateReceiverList
-
- aggregateResults(List<Double>) - Method in class FeatureIntersectingObjectsSingleElement
-
- aggregateResults(List<Double>) - Method in class MaxFeatureIntersectingObjects
-
- aggregateResults(List<Double>) - Method in class MinFeatureIntersectingObjectsAboveThreshold
-
- aggregateResults(List<Double>) - Method in class NumberIntersectingObjectsAboveThreshold
-
- AggregateTriggerBank<T> - Class in org.anchoranalysis.mpp.segment.optimization.feedback.aggregate
-
- AggregateTriggerBank(ExtractScoreSize<T>) - Constructor for class AggregateTriggerBank
-
- Aggregator - Class in org.anchoranalysis.mpp.segment.optimization.feedback.aggregate
-
- Aggregator(int) - Constructor for class Aggregator
-
- AggregatorException - Exception in org.anchoranalysis.mpp.segment.optimization.feedback.aggregate
-
- AggregatorException() - Constructor for exception AggregatorException
-
- AggregatorException(String) - Constructor for exception AggregatorException
-
- AggregatorException(Exception) - Constructor for exception AggregatorException
-
- aggReport(Reporting<T>, Aggregator) - Method in interface AggregateReceiver
-
- aggReport(Reporting<T>, Aggregator) - Method in class AggregateReceiverList
-
- aggReport(Reporting<VoxelizedMarksWithEnergy>, Aggregator) - Method in class ConsoleAggregatedReporter
-
- aggReport(Reporting<VoxelizedMarksWithEnergy>, Aggregator) - Method in class CSVReporterAggregated
-
- aggReport(Reporting<VoxelizedMarksWithEnergy>, Aggregator) - Method in class Log4JReporter
-
- aggReport(Reporting<VoxelizedMarksWithEnergy>, Aggregator) - Method in class OptimizationStepLogReporter
-
- aggReport(Reporting<VoxelizedMarksWithEnergy>, Aggregator) - Method in class TextFile
-
- aggStart(FeedbackBeginParameters<T>, Aggregator) - Method in interface AggregateReceiver
-
- aggStart(FeedbackBeginParameters<T>, Aggregator) - Method in class AggregateReceiverList
-
- aggStart(FeedbackBeginParameters<VoxelizedMarksWithEnergy>, Aggregator) - Method in class ConsoleAggregatedReporter
-
- aggStart(FeedbackBeginParameters<VoxelizedMarksWithEnergy>, Aggregator) - Method in class CSVReporterAggregated
-
- aggStart(FeedbackBeginParameters<VoxelizedMarksWithEnergy>, Aggregator) - Method in class Log4JReporter
-
- aggStart(FeedbackBeginParameters<VoxelizedMarksWithEnergy>, Aggregator) - Method in class OptimizationStepLogReporter
-
- aggStart(FeedbackBeginParameters<VoxelizedMarksWithEnergy>, Aggregator) - Method in class TextFile
-
- All - Class in org.anchoranalysis.io.output.bean.enabled
-
All outputs are allowed irrespective of outputName
.
- All - Class in org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels
-
Selects all possible channels from all possible stacks
- All() - Constructor for class All
-
- 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
-
- 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
-
- 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
-
- 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.copyfilesmode.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
-
- 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
-
- 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
-
- array() - Method in class UnsignedShortBuffer
-
- as(boolean) - Static method in enum OutsideKernelPolicy
-
- asArray() - Static method in class RGBChannelNames
-
Creates an array with all channel-names in R-G-B order.
- asByte() - Method in class VoxelsWrapper
-
- asByte(ImageProcessor) - Static method in class ConvertToVoxelBuffer
-
Convert a ImageProcessor
to VoxelBuffer<UnsignedByteBuffer>
- asByteOrCreateEmpty(boolean) - Method in class VoxelsWrapper
-
Reuses the existing buffer if byte, otherwise creates a new empty byte buffer
- asCollection() - Method in class StackSeries
-
- AsCollection - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.all
-
- AsCollection() - Constructor for class AsCollection
-
- asCollectionOrderNotPreserved() - Method in class ScaledElements
-
Returns the scaled-elements as a collection but without preserving the original element
order.
- asExtent() - Method in class SizeXY
-
Creates an extent with identical width and height and depth (z-extent) of 1
- asExtent(int) - Method in class SizeXY
-
Creates an extent with identical width and height and a specific depth (z-extent)
- 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
-
- 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.
- 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
.
- 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.
- assignInputDirectory(Optional<Path>) - Method in class InputArguments
-
Sets an input-directory.
- assignInputFilterExtensions(Set<String>) - Method in class InputArguments
-
- assignInputFilterExtensionsIfMissing(Optional<Set<String>>) - Method in class InputArguments
-
- assignInputFilterGlob(String) - Method in class InputArguments
-
- assignInputPaths(List<Path>) - Method in class InputArguments
-
- 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
-
- 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
-
- 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.
- 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
-
- AsSingle() - Constructor for class AsSingle
-
- AsSingleMark - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.all
-
- AsSingleMark() - Constructor for class AsSingleMark
-
- 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
-
- 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.groupfiles.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
-
- 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
-
- BeanInitializer<T> - Interface in org.anchoranalysis.bean.initializable.params
-
- BeanInstanceMap - Class in org.anchoranalysis.bean
-
Maps a
AnchorBean
family-type to some beans belong to the family.
- BeanInstanceMap() - Constructor for class BeanInstanceMap
-
- BeanMisconfiguredException - Exception in org.anchoranalysis.bean.exception
-
If a Bean is misconfigured
- BeanMisconfiguredException(String) - Constructor for exception BeanMisconfiguredException
-
- BeanMisconfiguredException(String, Throwable) - Constructor for exception BeanMisconfiguredException
-
- BeanMisconfiguredXmlException - Exception in org.anchoranalysis.bean.xml.exception
-
A bean's XML is thrown when a bean has misconfigured XML
- BeanMisconfiguredXmlException(String, Throwable) - Constructor for exception BeanMisconfiguredXmlException
-
Constructor
- BeanMisconfiguredXmlException(Throwable) - Constructor for exception BeanMisconfiguredXmlException
-
Constructor
- BeanPathUtilities - Class in org.anchoranalysis.bean.xml.factory
-
- BeanProviderAsStackBase<T,S> - Class in org.anchoranalysis.image.bean.provider
-
A provider base-class that as well as providing type S, also provide a stack
- BeanProviderAsStackBase() - Constructor for class BeanProviderAsStackBase
-
- BeanStrangeException - Exception in org.anchoranalysis.bean.exception
-
When something quite strange happens that we don't usually want to catch.
- BeanStrangeException(String) - Constructor for exception BeanStrangeException
-
- BeanStrangeException(String, Throwable) - Constructor for exception BeanStrangeException
-
- BeanTestChecker - Class in org.anchoranalysis.test.experiment
-
Checks to see if a bean has been misconfigured, when created manually in tests (thereby skipping
the usual checks during the BeanXML loading process).
- BeanXmlException - Exception in org.anchoranalysis.bean.xml.exception
-
An exception that occurs when one cannot process BeanXML for some reason
- BeanXmlException(String, Throwable) - Constructor for exception BeanXmlException
-
- BeanXmlException(Throwable) - Constructor for exception BeanXmlException
-
- BeanXmlException(String) - Constructor for exception BeanXmlException
-
- BeanXMLLoader - Class in org.anchoranalysis.bean.xml
-
Creates beans based on XML specifying their properties (including nested children).
- beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<T>, ParametersExperiment) - Method in class Task
-
- beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<T>, ParametersExperiment) - Method in class TaskWithoutSharedState
-
- beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<AnnotationWithStrategy<S>>, ParametersExperiment) - Method in class AggregateAnnotations
-
- beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<AnnotationComparisonInput<ProvidesStackInput>>, ParametersExperiment) - Method in class CompareAnnotations
-
- beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<T>, ParametersExperiment) - Method in class ExportFeatures
-
- beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<NamedChannelsInput>, ParametersExperiment) - Method in class ConvertImageFormat
-
- beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<ProvidesStackInput>, ParametersExperiment) - Method in class GroupedStackBase
-
- beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<ProvidesStackInput>, ParametersExperiment) - Method in class ImageAssignLabel
-
- beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<StackSequenceInput>, ParametersExperiment) - Method in class ScaleImage
-
- beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<StackSequenceInput>, ParametersExperiment) - Method in class SegmentInstanceWithModel
-
- beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<NamedChannelsInput>, ParametersExperiment) - Method in class ExtractSlice
-
- beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<NamedChannelsInput>, ParametersExperiment) - Method in class MovieFromSlices
-
- beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<FileInput>, ParametersExperiment) - Method in class CombineCSV
-
- beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<FileWithDirectoryInput>, ParametersExperiment) - Method in class CopyFiles
-
- beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<T>, ParametersExperiment) - Method in class SummarizeBase
-
- beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<T>, ParametersExperiment) - Method in class ConvertNamedChannels
-
- beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<ManifestCouplingDefinition>, ParametersExperiment) - Method in class ExportReportFeaturesFromManifest
-
- beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<MultiInput>, ParametersExperiment) - Method in class ExportReportFeaturesFromMulti
-
- beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<MultiInput>, ParametersExperiment) - Method in class ExportObjectsAsCroppedImages
-
- beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<FromCSVInput>, ParametersExperiment) - Method in class ExportObjectsFromCSV
-
- beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<MultiInput>, ParametersExperiment) - Method in class SegmentMarksFromImage
-
- beforeCalc(FeatureInitialization) - Method in class Feature
-
Dummy method, that children can optionally override
- beforeCalc(FeatureInitialization) - Method in class ConvertToPhysicalDistance
-
- beforeCalc(FeatureInitialization) - Method in class FeatureIntersectingObjects
-
- beforeCalc(FeatureInitialization) - Method in class PairedWithMask
-
- beforeCalc(FeatureInitialization) - Method in class FeatureSingleObjectFromShared
-
- beforeCalc(FeatureInitialization) - Method in class ParamFromCollection
-
- beforeCalc(FeatureInitialization) - Method in class FeatureMarkDirection
-
- beforeCalc(FeatureInitialization) - Method in class FromDictionary
-
- beforeCalcSetup(Histogram, int) - Method in class CalculateLevel
-
- beforeCalcSetup(Histogram, int) - Method in class CalculateLevelBase
-
- beforeCalcSetup(Histogram, int) - Method in class DifferenceCalculateLevelStandardDeviation
-
- beforeCalcWithInitialization(ImageInitialization) - Method in class FeatureSingleObjectFromShared
-
- beforeCalcWithInitialization(ImageInitialization) - Method in class MaskAsSingleObject
-
- beforeCalcWithInitialization(ImageInitialization) - Method in class ObjectAggregationBase
-
- BeforeCondition - Interface in org.anchoranalysis.plugin.image.object.merge.condition
-
- beforeCopying(Path, int) - Method in class Anonymize
-
- beforeCopying(Path, int) - Method in class CopyFilesNaming
-
- beforeCopying(Path, int) - Method in class CopyFilesNamingOne
-
- beforeCopying(Path, int) - Method in class 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
-
- 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
-
- 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
-
- 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.copyfilesmode.copymethod
-
Makes a simple bytewise copy of a file, where no byte is changed.
- Bytewise() - Constructor for class Bytewise
-
- cache(CheckedSupplier<T, E>) - Static method in class CachedSupplier
-
- 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
-
- 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
-
- CachedSupplier<T,E extends Exception> - Class in org.anchoranalysis.core.cache
-
- 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
-
- calculate(ChildCacheName, S, Function<CalculationResolver<S>, ResolvedCalculation<U, S>>) - Method in interface CalculateForChild
-
- calculate(Feature<T>, SessionInput<T>) - Method in interface FeatureSessionCalculator
-
Calculate a feature with particular values
- calculate(Feature<T>) - Method in interface SessionInput
-
Calculates the result of a feature using this input
- calculate(FeatureList<T>) - Method in interface SessionInput
-
Calculates the results of several features using this input
- calculate(FeatureCalculation<S, T>) - Method in interface SessionInput
-
Calculates a feature-calculation after resolving it against the main cache
- calculate(ResolvedCalculation<S, T>) - Method in interface SessionInput
-
Calculates a resolved Feature-calculation
- calculate(T) - Method in class FeatureCalculatorCachedMulti
-
- calculate(T, FeatureList<T>) - Method in class FeatureCalculatorCachedMulti
-
- calculate(T) - Method in interface FeatureCalculatorMulti
-
Performs one calculation throwing an exception if something goes wrong
- calculate(T, FeatureList<T>) - Method in interface FeatureCalculatorMulti
-
Performs one calculation on a sub-set of the feature list throwing an exception if something
goes wrong
- calculate(T, ErrorReporter, boolean) - Method in interface FeatureCalculatorMulti
-
- calculate(T) - Method in class FeatureCalculatorMultiChangeInput
-
- calculate(T, FeatureList<T>) - Method in class FeatureCalculatorMultiChangeInput
-
- calculate(T) - Method in class FeatureCalculatorCachedSingle
-
- calculate(T) - Method in interface FeatureCalculatorSingle
-
Performs one calculation throwing an exception if something goes wrong
- calculate(T) - Method in class FeatureCalculatorSingleChangeInput
-
- calculate(T) - Method in class FeatureCalculatorSingleFromMulti
-
- calculate(T) - Method in class SequentialSession
-
Calculates one params for each feature.
- calculate(T, FeatureList<T>) - Method in class SequentialSession
-
- calculate(Feature<T>) - Method in class SessionInputSequential
-
- calculate(FeatureList<T>) - Method in class SessionInputSequential
-
- calculate(FeatureCalculation<S, T>) - Method in class SessionInputSequential
-
- calculate(ResolvedCalculation<S, T>) - Method in class SessionInputSequential
-
- calculate(Optional<Dimensions>, Optional<ImageSizeSuggestion>) - Method in class ScaleCalculator
-
Calculates a scaling-factor for a source image/entity of particular dimensions.
- calculate(SessionInput<FeatureInputHistogram>) - Method in class FeatureHistogramStatistic
-
- calculate(SessionInput<FeatureInputObjectCollection>) - Method in class FeatureObjectCollection
-
- calculate(SessionInput<FeatureInputPairObjects>) - Method in class First
-
- calculate(SessionInput<FeatureInputPairObjects>) - Method in class Merged
-
- calculate(SessionInput<FeatureInputPairObjects>) - Method in class Minimum
-
- calculate(SessionInput<FeatureInputPairObjects>) - Method in class RatioFirstToSecond
-
- calculate(SessionInput<FeatureInputPairObjects>) - Method in class Second
-
- calculate(SessionInput<FeatureInputPairObjects>) - Method in class SubtractSecondFromFirst
-
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class CenterOfGravity
-
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class NumberVoxels
-
- calculate(SessionInput<T>) - Method in class WithResolutionBase
-
- calculate(int[]) - Method in class VoxelScore
-
- calculate(FeatureInputPairObjects) - Method in class PairsTableCalculator
-
- calculate(FeatureInputPairObjects, FeatureList<FeatureInputPairObjects>) - Method in class PairsTableCalculator
-
- calculate(FeatureInputSingleObject) - Method in class SingleTableCalculator
-
- calculate(FeatureInputSingleObject, FeatureList<FeatureInputSingleObject>) - Method in class SingleTableCalculator
-
- calculate(SessionInput<FeatureInputPairMemo>) - Method in class AsSingle
-
- calculate(SessionInput<FeatureInputSingleMemo>) - Method in class FeatureSingleMemo
-
- calculate(SessionInput<FeatureInputMarkCollection>) - Method in class FeatureMarkCollection
-
- calculate(SessionInput<FeatureInputMark>) - Method in class FeatureMark
-
- calculate(Optional<Dimensions>, Optional<ImageSizeSuggestion>) - Method in class ConstantScaleFactor
-
- calculate(Optional<Dimensions>, Optional<ImageSizeSuggestion>) - Method in class Invert
-
- calculate(Optional<Dimensions>, Optional<ImageSizeSuggestion>) - Method in class MinimumXYResolution
-
- calculate(Optional<Dimensions>, Optional<ImageSizeSuggestion>) - Method in class ToDimensions
-
- calculate(Optional<Dimensions>, Optional<ImageSizeSuggestion>) - Method in class ToSuggested
-
- calculate(SessionInput<T>) - Method in class FromDimensionsBase
-
- calculate(SessionInput<FeatureInputHistogram>) - Method in class LevelFromHistogram
-
- calculate(SessionInput<FeatureInputHistogram>) - Method in class ThresholdHistogram
-
- calculate(SessionInput<FeatureInputPairObjects>) - Method in class Intersection
-
- calculate(SessionInput<FeatureInputPairObjects>) - Method in class CostOverlapWithinMidpointDistance
-
- calculate(SessionInput<FeatureInputPairObjects>) - Method in class OverlapRelative
-
- calculate(SessionInput<FeatureInputPairObjects>) - Method in class TouchingVoxels
-
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class ArbitraryInsidePoint
-
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class AtBorderBase
-
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class BoundingBoxAlongAxisBase
-
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class BoundingBoxNumberVoxels
-
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class SpecificEnergyChannelBase
-
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class FeatureEnergyChannel
-
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class GradientMagnitude
-
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class GradientMeanForAxis
-
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class ImageMomentsBase
-
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class DerivedObject
-
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class NumberRemovedVoxelsAfterClosing
-
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class OutlineKernelBase
-
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class ObjectRadiusStandardDeviation
-
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class ShapeRegularityCenterSlice
-
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class ShapeRegularityMIP
-
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class FeatureIntersectingObjects
-
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class PairedWithMask
-
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class MaximumNumberContourVoxelsOnSlice
-
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class MaximumNumberVoxelsOnSlice
-
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class SurfaceNumberVoxelsBase
-
- calculate(int[]) - Method in class Difference
-
- calculate(int[]) - Method in class Identity
-
- calculate(int[]) - Method in class IdentityImposeValueRelationToHistogram
-
- calculate(int[]) - Method in class OutsideRange
-
- calculate(int[]) - Method in class RejectIfIntensityLessThan
-
- calculate(int[]) - Method in class SingleChannel
-
- calculate(SessionInput<T>) - Method in class FeatureSingleObjectFromShared
-
- calculate(SessionInput<T>) - Method in class ParamFromCollection
-
- calculate(SessionInput<T>) - Method in class DataTypeMaxIntensity
-
- calculate(SessionInput<FeatureInputStack>) - Method in class Intensity
-
- calculate(SessionInput<FeatureInputStack>) - Method in class 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- changePrefix(DirectoryWithPrefix, Optional<WriteOperationRecorder>) - Method in class OutputterChecked
-
- 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
-
- 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
-
- 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
-
- 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
-
- CheckedToIntFunction<S,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked
-
- CheckedUnaryOperator<T,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked
-
- 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
-
- 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.groupfiles.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
-
- 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
-
- 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
-
- 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.provider.file
-
- 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
-
- 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.
- commonPath(Collection<File>) - Static method in class CommonPath
-
- 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
-
- 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.copyfilesmode.copymethod
-
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
-
- 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 Constant
-
- Constant - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold
-
A constant value for thresholding
- Constant() - Constructor for class Constant
-
- Constant(int) - Constructor for class Constant
-
- Constant - Class in org.anchoranalysis.plugin.io.bean.path.derive
-
Always generates a constant path irrespective of the the input
- Constant() - Constructor for class Constant
-
- Constant(String) - Constructor for class Constant
-
- Constant - Class in org.anchoranalysis.plugin.mpp.bean.proposer.scalar
-
- Constant() - Constructor for class Constant
-
- ConstantBoundGenerator - Class in org.anchoranalysis.plugin.mpp.bean.bound
-
- ConstantBoundGenerator() - Constructor for class ConstantBoundGenerator
-
- ConstantBoundGenerator(ResolvedBound) - Constructor for class ConstantBoundGenerator
-
- ConstantScaleFactor - Class in org.anchoranalysis.plugin.image.bean.scale
-
- ConstantScaleFactor() - Constructor for class ConstantScaleFactor
-
- ConstantsInListFixture - Class in org.anchoranalysis.test.feature
-
- ConstantToThePowerOf<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic
-
- ConstantToThePowerOf() - Constructor for class ConstantToThePowerOf
-
- ConstantWeight - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.weight
-
All marks have weight of 1
- ConstantWeight() - Constructor for class ConstantWeight
-
- containerOptional() - Method in class WithContainerBase
-
- containerRequired() - Method in class WithContainerBase
-
- contains(String) - Method in interface StringBeanCollection
-
- contains(String) - Method in class StringList
-
- contains(String) - Method in class StringSet
-
- contains(ChildCacheName) - Method in class CacheTransferSourceCollection
-
- contains(Feature<FeatureInput>) - Method in class SharedFeatureMulti
-
- contains(Point3d) - Metho