- absolute() - Method in class Tuple3d
-
Convert each dimension's component into its absolute value.
- AbsoluteValue<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic
-
- AbsoluteValue() - Constructor for class AbsoluteValue
-
- accept(S, T) - Method in interface CheckedBiConsumer
-
Calls the function.
- accept(S) - Method in interface CheckedConsumer
-
Like Consumer.accept(T)
but throws an exception.
- accept(int) - Method in interface CheckedIntConsumer
-
Like IntConsumer.accept(int)
but throws an exception.
- accept(BinaryVoxels<UnsignedByteBuffer>) - Method in class AcceptIterationList
-
- accept(BinaryVoxels<UnsignedByteBuffer>) - Method in interface AcceptIterationPredicate
-
Whether a particular voxels
fulfills the condition or not.
- accept(int, int) - Method in interface Histogram.BinConsumer
-
Accepts a particular bin and corresponding count.
- accept(ObjectMask, ObjectMask, ObjectMask) - Method in interface AfterCondition
-
- accept(ObjectMask) - Method in class AndCondition
-
- accept(ObjectMask, ObjectMask, Optional<UnitConverter>) - Method in interface BeforeCondition
-
- accept(ObjectMask, ObjectMask, Optional<UnitConverter>) - Method in class DistanceCondition
-
- accept(ObjectMask, ObjectMask, ObjectMask) - Method in class IncreaseFeatureCondition
-
- accept(ObjectMask) - Method in class NeighborhoodCondition
-
- accept(ObjectMask) - Method in interface UpdatableBeforeCondition
-
- accept(ObjectMask) - Method in class WrapAsUpdatable
-
- accept(ParsedFilePathBag) - Method in class AtLeastZSlices
-
- accept(ParsedFilePathBag) - Method in class CheckParsedFilePathBag
-
- accept(Point2i, int) - Method in interface OffsettedPointTwoDimensionalConsumer
-
Accepts a point like with a
Consumer
in general.
- accept(int, int, int) - Method in interface OffsettedScalarTwoDimensionalConsumer
-
Accepts a point
- accept(Point2i) - Method in interface PointTwoDimensionalConsumer
-
Accepts a point like with a
Consumer
in general.
- accept(int, int, int) - Method in interface ScalarThreeDimensionalConsumer
-
Accepts a point like with a
Consumer
in general.
- accept(int, int) - Method in interface ScalarTwoDimensionalConsumer
-
Accepts a point like with a
Consumer
in general.
- acceptableProbability(AnnealScheme) - Method in class AssignMode
-
- acceptableProbability(AnnealScheme) - Method in class DirectAssignMode
-
- acceptableProbability(AnnealScheme) - Method in class TransformationAssignMode
-
- AcceptanceProbabilityCalculator<T> - Class in org.anchoranalysis.plugin.mpp.segment.optimization
-
- AcceptanceProbabilityCalculator(AnnealScheme, ExtractScoreSize<T>) - Constructor for class AcceptanceProbabilityCalculator
-
- accepted() - Method in interface DualMarks
-
The accepted marks.
- AcceptIterationList - Class in org.anchoranalysis.image.voxel.object.morphological.predicate
-
- 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.
- acceptProposal(ToDoubleFunction<T>) - Method in class OptimizationStep
-
- accepts(Class<?>) - Method in class AssignerMatchClass
-
- accepts(Class<?>) - Method in interface InitializationParameterAssigner
-
Whether a particular type of initialization parameters is accepted?
- AccessObjectMask<T> - Interface in org.anchoranalysis.image.core.object.scale
-
Provides functions to provide access and creation to/from the object-mask representation of a
generic type.
- AccessObjectMaskSimple - Class in org.anchoranalysis.image.core.object.scale
-
Provides access to the simple-case of a list of
ObjectMask
s.
- AccessObjectMaskSimple() - Constructor for class AccessObjectMaskSimple
-
- AcquisitionDateReader - Class in org.anchoranalysis.io.bioformats.metadata
-
Reads the image acquisition-date.
- activateDebugMode(String) - Method in class ExecutionArguments
-
Activates debug-mode.
- add(NamedBean<?>) - Method in class Define
-
Adds a named-bean to our definitions, using the {#link GroupingRoot} annotation to determine
a group where definitions are stored.
- add(Double) - Method in class DoubleList
-
- add(Double) - Method in class DoubleSet
-
- add(Integer) - Method in class IntegerList
-
- add(Integer) - Method in class IntegerSet
-
- add(T) - Method in interface PrimitiveBeanCollection
-
Add an element to the collection.
- add(String) - Method in class StringList
-
- add(String) - Method in class StringSet
-
- add(String) - Method in class StringSetTrie
-
Adds an string to the set.
- add(Color) - Method in class ColorList
-
Appends a
Color
to the list.
- add(RGBColor) - Method in class ColorList
-
- add(int, RGBColor) - Method in class ColorList
-
Inserts a
Color
into the list, at a particular index.
- add(String, T) - Method in class NameValueMap
-
Adds an element.
- add(NameValue<T>) - Method in class NameValueMap
-
Adds an element.
- add(String, StoreSupplier<T>) - Method in class EagerEvaluationStore
-
- add(String, StoreSupplier<T>) - Method in class LazyEvaluationStore
-
- add(String, StoreSupplier<T>) - Method in interface NamedProviderStore
-
Adds an element to the store.
- add(Class<? extends InputFromManager>) - Method in class InputTypesExpected
-
Appends an input-type class to the existing list.
- add(SubmittedJob) - Method in class ConcurrentJobMonitor
-
Adds a job to be considered in the aggregate view.
- add(Feature<? extends T>) - Method in class FeatureList
-
Adds a feature to the current list.
- add(LabelledResultsVector) - Method in class LabelledResultsCSVWriter
-
Adds a results-element to be written.
- add(LabelledResultsVector) - Method in interface LabelledResultsCollector
-
Adds a results-element to be written.
- add(String) - Method in class FeatureNameList
-
Adds a feature-name.
- add(String, int) - Method in class FeatureNameMapToIndex
-
Adds a new featureName and index
- add(ResultsVector) - Method in class ResultsVectorList
-
- add(CacheTransferSource<? extends FeatureInput>) - Method in class CacheTransferSourceCollection
-
Adds a source.
- add(String, Feature<T>) - Method in class NamedFeatureStore
-
Adds a named-feature to the store.
- add(BoundingBox) - Method in class StackArrangement
-
Adds a new
BoundingBox
to the arrangement, with no padding.
- add(BoundingBoxEnclosed) - Method in class StackArrangement
-
- add(ObjectMask) - Method in class ObjectCollectionWithProperties
-
Add an
ObjectMask
to the collection, assigning empty properties to it.
- add(ObjectWithProperties) - Method in class ObjectCollectionWithProperties
-
- add(String, Stack) - Method in class NamedStacks
-
Add a stack.
- add(String, StoreSupplier<Stack>) - Method in class NamedStacks
-
- add(String, Stack) - Method in class NamedStacksUniformSize
-
Adds an element to the store.
- add(IndexedChannel) - Method in class ChannelMap
-
- add(String, StoreSupplier<TimeSeries>) - Method in class ExtractFrameStore
-
- add(ReadableTuple3i) - Method in class DeriveObjectFromPoints
-
Adds a point to the object.
- add(AcceptIterationPredicate) - Method in class AcceptIterationList
-
Adds an item to the list of predicates.
- add(VoxelStatistics) - Method in class VoxelStatisticsCombined
-
Adds an element.
- add(String, Generator<T>) - Method in class CombinedListGenerator
-
- 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(String, boolean) - Method in class RecordedOutputs
-
Adds a new output-name to the set of recorded names.
- add(RunningSum) - Method in class RunningSum
-
Adds the values of another
RunningSum
to the current values.
- add(double) - Method in class RunningSumExtrema
-
Adds a value to the running-sum, also remembering if value
is the minimum or maximum
of calls to this method.
- add(double) - Method in class VarianceCalculatorDouble
-
Adds a value to the running sum.
- add(int) - Method in class VarianceCalculatorLong
-
Adds a value to the running sum.
- add(int, int) - Method in class VarianceCalculatorLong
-
Adds a multiple instances of a value to the running sum.
- add(MemoForIndex, VoxelizedMarkMemo) - Method in class RandomCollectionWithAddCriteria
-
- add(double) - Method in class EnergyTotal
-
- add(EnergyMemoList, VoxelizedMarkMemo, EnergyStackWithoutParameters) - Method in class MarksWithEnergyBreakdown
-
- add(VoxelizedMarkMemo) - Method in class MarksWithTotalEnergy
-
- add(VoxelizedMarkMemo, EnergyStackWithoutParameters) - Method in class VoxelizedMarksWithEnergy
-
- add(EnergyTotal) - Method in class EnergySavedInd
-
- add(MemoForIndex, VoxelizedMarkMemo) - Method in class EnergySavedPairs
-
- add(String, EnergyScheme) - Method in class EnergySchemeSet
-
- add(EnergySavedInd, VoxelizedMarkMemo, EnergyStackWithoutParameters, EnergySchemeWithSharedFeatures) - Method in class EnergyMemoList
-
- add(VoxelizedMarkMemo) - Method in class MemoList
-
- add(UpdatableMarks) - Method in class UpdatableMarksList
-
- add(MemoForIndex, VoxelizedMarkMemo) - Method in class UpdatableMarksList
-
- add(MemoForIndex) - Method in class UpdatableMarksList
-
- add(int, UpdatableMarks) - Method in class UpdatableMarksList
-
- add(IndexByRegion<T>) - Method in class IndexByChannel
-
- add(String, StoreSupplier<T>) - Method in interface MultiInputSubMap
-
Adds an entry to the map
- add(String, StoreSupplier<T>) - Method in class OperationMap
-
- add(String, StoreSupplier<TimeSeries>) - Method in class StackWithMap
-
- add(Mark, Color) - Method in class ColoredMarks
-
- add(Mark, RGBColor) - Method in class ColoredMarks
-
- add(Mark) - Method in class MarkCollection
-
- add(MemoForIndex, VoxelizedMarkMemo) - Method in interface UpdatableMarks
-
- add(String) - Method in class ErrorNode
-
- add(Exception) - Method in class ErrorNode
-
- add(String) - Method in class ErrorNodeImpl
-
- add(Exception) - Method in class ErrorNodeImpl
-
- add(String) - Method in class ErrorNodeNull
-
- add(Exception) - Method in class ErrorNodeNull
-
- add(FeedbackReceiver<T>) - Method in class FeedbackReceiverList
-
- add(TerminationCondition) - Method in class TerminationConditionListOr
-
- add(AggregateReceiver<T>) - Method in class AggregateReceiverList
-
- add(PeriodReceiver<T>) - Method in class PeriodReceiverList
-
- add(WeightedKernel<T, S>) - Method in class WeightedKernelList
-
- add(Overlay, RGBColor) - Method in class ColoredOverlayCollection
-
Append an overlay and its respective color to the end of the list..
- add(Overlay) - Method in class OverlayCollection
-
Append an overlay to the end of the list.
- add(ImageCounter<T>) - Method in class ImageCounterList
-
- add(LevelResult) - Method in class LevelResultCollection
-
- add(String, Channel) - Method in class NamedChannels
-
- add(CheckedSupplier<LabelledResultsVector, OperationFailedException>, CheckedSupplier<Optional<DisplayStack>, OperationFailedException>) - Method in class FeatureResultsAndThumbnails
-
Adds results, together with a thumbnail.
- add(S, T) - Method in interface AddToAggregateItem
-
- add(Optional<String>, List<Pair<String, S>>) - Method in class GroupMapByName
-
Adds an item with a non-group identifier, and also optionally a group identifier.
- add(T, String) - Method in class FileLabelMap
-
- add(ImageMetadataInput) - Method in class ImageSize
-
- add(ImageMetadataInput) - Method in class SummarizerImageMetadataSimple
-
- add(T) - Method in class SummarizerInputFromManager
-
- add(Path) - Method in class ExtensionCount
-
- add(Path) - Method in class FilePathPattern
-
- add(Path) - Method in class FileSizeStatistics
-
- add(T) - Method in class Summarizer
-
Adds a element to the summary.
- add(T) - Method in class SummarizerAggregate
-
- add(T) - Method in class SummarizerCount
-
- add(T) - Method in class SummarizerListMultiline
-
- add(T) - Method in class SummarizerSplitMoreThan
-
- add(FileDetails) - Method in class ParsedFilePathBag
-
- add(int, String) - Method in class SortedSetChannel
-
- add(ReadableTuple3i) - Method in class PointRange
-
Adds a new point to be considered in the range.
- add(int, int, int) - Method in class PointRange
-
Adds a new point to be considered in the range.
- add(Point2i) - Method in class Point2d
-
Arithmetically adds a
Point2i
's values across each dimension.
- add(Point2d) - Method in class Point2d
-
Arithmetically adds a
Point2d
's values across each dimension.
- add(int, int) - Method in class Point2d
-
Arithmetically adds two int
values, to the X- and Y- dimensions.
- add(double, double) - Method in class Point2d
-
Arithmetically adds two double
values, to the X- and Y- dimensions.
- add(Point2i) - Method in class Point2i
-
Adds values from a
Point2i
across each corresponding dimension.
- add(double, double, double) - Method in class Tuple3d
-
Arithmetically adds values to each dimension's component.
- add(Tuple3d) - Method in class Tuple3d
-
Arithmetically adds a
Tuple3d
's values across each dimension.
- add(ReadableTuple3i) - Method in class Tuple3d
-
- add(ReadableTuple3i) - Method in class Tuple3i
-
- add(BoundingBox, T) - Method in class BoundingBoxRTree
-
Adds a bounding-box with a corresponding payload.
- add(double, double, T) - Method in class IntervalRTree
-
Adds a bounding-box with a corresponding index.
- add(Rectangle, T) - Method in class RTree
-
Adds a Rectangle
with a corresponding payload.
- addAdditionalOptions(Options) - Method in class LauncherConfig
-
- addAdditionalOptions(Options) - Static method in class CommandLineOptions
-
- addAll(Define) - Method in class Define
-
Adds all the named-beans from source to the current map.
- addAll(List<NamedBean<T>>) - Method in class Define
-
Adds all the named-beans from source to the current map.
- addAll(ColorList) - Method in class ColorList
-
Appends
Color
s to the list.
- addAll(FeatureList<? extends T>) - Method in class FeatureList
-
Add all the features in other
to the current list.
- 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(Collection<S>) - Method in class ImageCounterList
-
- addAll(Collection<T>) - Method in class Summarizer
-
Adds the elements to the summary.
- addAllOutputNamesTo(OutputEnabledMutable) - Method in class DefineOutputter
-
- addAllToUpdatablePairList(UpdatableMarksList) - Method in class VoxelizedMarksWithEnergy
-
- addAnnotatedImage(T) - Method in interface ImageCounter
-
Add an image that had an associated annotation.
- addAnnotatedImage(T) - Method in class ImageCounterList
-
- addAsSeparateChannels(NamedStacks, int, Logger) - Method in class NamedChannelsConcatenate
-
- addAsSeparateChannels(NamedProviderStore<TimeSeries>, int, Logger) - Method in class NamedChannelsConcatenate
-
- addAsSeparateChannels(NamedStacks, int, Logger) - Method in interface NamedChannelsMap
-
- addAsSeparateChannels(NamedProviderStore<TimeSeries>, int, Logger) - Method in interface NamedChannelsMap
-
- addAsSeparateChannels(NamedStacks, int, Logger) - Method in class OpenedNamedChannels
-
- addAsSeparateChannels(NamedProviderStore<TimeSeries>, int, Logger) - Method in class OpenedNamedChannels
-
- addAssignedPair(ObjectMask, ObjectMask, double) - Method in class OverlappingObjects
-
Adds an assigned pair of objects with a particular overlap-ratio.
- addAsynchronously(T) - Method in class OutputSequenceIncrementing
-
- addBasicOptions(Options) - Static method in class CommandLineOptions
-
- addBlankChannel() - Method in class Stack
-
Adds a new empty
Channel
in the final-most position in the list.
- addChangeID(Mark, Color) - Method in class ColoredMarks
-
- addChangeID(Mark, RGBColor) - Method in class ColoredMarks
-
- addChannel(Channel, Logger) - Method in class ChannelAggregator
-
- addChannel(Channel) - Method in class Stack
-
Appends a channel to the stack, as the new final-most channel position-wise.
- addChannel(Channel) - Method in class StackNotUniformSized
-
Appends a channel to the stack, as the new final-most channel position-wise.
- addChannelAfterCheck(Channel) - Method in class ChannelAggregator
-
Adds a
Channel
to the aggregation - after checking
channel
has acceptable
dimensions.
- addChannelAfterCheck(Channel) - Method in class ProjectableBufferAggregator
-
- addChannelsFrom(Stack) - Method in class Stack
-
Add the channels from another instance into this instance.
- AddConstant - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
-
- AddConstant() - Constructor for class AddConstant
-
- AddConstantTo<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic
-
- AddConstantTo() - Constructor for class AddConstantTo
-
- AddCriteria<T> - Interface in org.anchoranalysis.mpp.feature.addcriteria
-
Add Criteria
- AddCriteriaEnergyPair - Class in org.anchoranalysis.mpp.feature.addcriteria
-
- AddCriteriaEnergyPair(FeatureList<FeatureInputPairMemo>, AddCriteriaPair) - Constructor for class AddCriteriaEnergyPair
-
- AddCriteriaFeatureRelationThreshold - Class in org.anchoranalysis.plugin.mpp.bean.addcriteria
-
- AddCriteriaFeatureRelationThreshold() - Constructor for class AddCriteriaFeatureRelationThreshold
-
- AddCriteriaNever<T> - Class in org.anchoranalysis.mpp.feature.addcriteria
-
- AddCriteriaNever() - Constructor for class AddCriteriaNever
-
- AddCriteriaOr - Class in org.anchoranalysis.mpp.feature.addcriteria
-
- AddCriteriaOr() - Constructor for class AddCriteriaOr
-
- AddCriteriaPair - Class in org.anchoranalysis.mpp.feature.addcriteria
-
- AddCriteriaPair() - Constructor for class AddCriteriaPair
-
- addDefaultOutputs(OutputEnabledMutable) - Method in class AnnotationComparisonAssigner
-
Adds any default outputs that should occur from the assigner.
- addDefaultOutputs(OutputEnabledMutable) - Method in class FeatureCostAssigner
-
- addDefaultOutputs(OutputEnabledMutable) - Method in class MaskIntersectionAssigner
-
- addDictionary(String, Dictionary) - Method in class ImageInitialization
-
Adds a
Dictionary
to the corresponding named-collection of dictionaries.
- AddDistanceTransform - Class in org.anchoranalysis.plugin.fiji.bean.define
-
- AddDistanceTransform() - Constructor for class AddDistanceTransform
-
- addDouble(String, double) - Method in class StatisticsToExport
-
Adds a statistic that is a double
.
- 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
-
- addExtension(String, String) - Static method in class ExtensionAdder
-
- 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
-
- addFrom(CommandLineExtracter, InputArguments) - Static method in class AddInputOptions
-
Adds options to change the inputs from the command-line.
- addFrom(CommandLineExtracter, OutputArguments) - Static method in class AddOutputOptions
-
Adds options to add/remove change the outputs the inputs from the command-line.
- addFromList(FeatureList<FeatureInput>) - Method in class SharedFeatures
-
Add features from a feature-list.
- addFromProviders(NamedProvider<FeatureList<FeatureInput>>) - Method in class SharedFeatures
-
- 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
-
Adds the counts from another histogram to the current object.
- addIndexToRetain(int) - Method in class ReductionOutcome
-
Adds an index to be retained after reduction.
- addInputOptions(Options) - Static method in class CommandLineOptions
-
- AddInputOptions - Class in org.anchoranalysis.launcher.options.process
-
Adds options relating to inputting from the command-line.
- addInt(String, int) - Method in class StatisticsToExport
-
Adds a statistic that is an int
.
- additionalLabelsFor(FileInput) - Method in class FromHistogram
-
- additionalLabelsFor(ProvidesStackInput) - Method in class FromImage
-
- additionalLabelsFor(ImageMetadataInput) - Method in class FromImageMetadata
-
- additionalLabelsFor(T) - Method in class SingleRowPerInput
-
Additional labels for an input to include (after the identifier, and before any group
labels).
- addMeanExtrema(String, double, double, double) - Method in class StatisticsToExport
-
Adds three statistics a mean, min and max.
- addMeanExtrema(String, RunningSumExtrema) - Method in class StatisticsToExport
-
- addMultiple(RGBColor, int) - Method in class ColorList
-
Append multiple entries for the same color to the end of the list.
- addNewlyAdded(T) - Method in class ReductionOutcome
-
Adds a newly-added element, that didn't exist in the input list for reduction, but should
exist in the output list.
- addObjectsFrom(NamedProvider<ObjectCollection>) - Method in class ImageInitialization
-
- 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
-
- addOptionsFromCommandLine() - Method in class AddInputOptions
-
- AddOptionsFromCommandLine<T> - Class in org.anchoranalysis.launcher.options.process
-
Base class for adding options from command-line arguments.
- AddOptionsFromCommandLine(CommandLineExtracter, T) - Constructor for class AddOptionsFromCommandLine
-
- addOptionsFromCommandLine() - Method in class AddOptionsFromCommandLine
-
Maybe add options to the arguments from the command-line.
- addOptionsFromCommandLine() - Method in class AddOutputOptions
-
- AddOutputOptions - Class in org.anchoranalysis.launcher.options.process
-
Adds options relating to outputting from the command-line.
- addResultsFor(LabelledResultsVector) - Method in class GroupedResults
-
Adds a result to the group-writer, but doesn't write yet.
- addRow(LabelledResultsVector) - Method in class FeatureCSVWriter
-
Directly adds a row of feature-values.
- addRow(List<TypedValue>) - Method in class FeatureCSVWriter
-
Directly adds a row in the form of typed-values.
- addSharedObjectsDictionary(Optional<SharedObjects>, Optional<Dictionary>) - Method in class ImageInitialization
-
Adds stacks and object-collections from a
SharedObjects
using the respective
identifiers, and also adds a
Dictionary
.
- addShift(ReadableTuple3i) - Method in class ContiguousVoxelPath
-
Adds a shift to each point (modifying the existing points in memory), and returns them as a
list
- addStack(String, Stack) - Method in class ImageInitialization
-
Adds a
Stack
to the corresponding named-collection of stacks.
- addStack(Provider<Stack>) - Method in class Arrange
-
Adds a stack to the existing list of stack-providers.
- addStacksFrom(NamedProvider<Stack>) - Method in class ImageInitialization
-
- addString(String, String) - Method in class StatisticsToExport
-
Adds a statistic that is a
String
.
- addTimestamp(long) - Method in class ClusterIdentifier
-
Adds a timestamp to the cluster.
- addTo(Define) - Method in class Concatenate
-
- addTo(Define) - Method in interface DefineAdder
-
Adds items to define
.
- addTo(Define) - Method in class FromXMLList
-
- addTo(ObjectMask, int) - Method in interface VoxelsArithmetic
-
Adds a constant-value to each voxel but only for voxels inside an object-mask.
- addTo(Define) - Method in class AddDistanceTransform
-
- addTo(Define) - Method in class AddEdgeFilters
-
- addTo(Define) - Method in class VisualizeOnBackground
-
- AddToAggregateItem<S,T> - Interface in org.anchoranalysis.plugin.image.task.grouped
-
Adds an individual-item to an aggregate-item
- AddToDefaults - Class in org.anchoranalysis.io.output.bean.rules
-
Adds additional outputs-names to be enabled to the defaults.
- AddToDefaults() - Constructor for class AddToDefaults
-
- addToErrorNode(ErrorNode) - Method in exception ErrorNodeException
-
- addToManager(MultiInputManager, String, String) - Method in class FilePathBaseAppendToManager
-
- addToRow(List<TypedValue>) - Method in class RowLabels
-
Adds the identifiers to a row to be outputted in a features CSV.
- addToStore(NamedProviderStore<T>, Logger) - Method in interface MultiInputSubMap
-
- addToStore(NamedProviderStore<T>, Logger) - Method in class OperationMap
-
- addToStore(NamedProviderStore<TimeSeries>, Logger) - Method in class StackWithMap
-
- addToStore(NamedProviderStore<TimeSeries>, int, Logger) - Method in class StackWithMap
-
- addToStoreInferNames(NamedProviderStore<TimeSeries>, int, Logger) - Method in class NamedChannelsInput
-
- addToStoreInferNames(NamedProviderStore<Stack>, Logger) - Method in interface ProvidesStackInput
-
Adds the current object to a named-store of stacks (using the default series).
- addToStoreInferNames(NamedProviderStore<TimeSeries>, int, Logger) - Method in interface ProvidesStackInput
-
Adds any stacks exposed by the current element to a named-store of stacks - inferring the
names of the
Stack
s.
- addToStoreInferNames(NamedProviderStore<TimeSeries>, int, Logger) - Method in class MultiInput
-
- addToStoreInferNames(NamedProviderStore<TimeSeries>, int, Logger) - Method in class ConvertNamedChannelsInputToStack
-
- addToStoreWithName(String, NamedProviderStore<TimeSeries>, int, Logger) - Method in class NamedChannelsInput
-
- addToStoreWithName(String, NamedProviderStore<TimeSeries>, int, Logger) - Method in interface ProvidesStackInput
-
Adds any stacks exposed by the current element to a named-store of stacks - with a particular
name.
- addToStoreWithName(String, NamedProviderStore<TimeSeries>, int, Logger) - Method in class MultiInput
-
- addToStoreWithName(String, NamedProviderStore<TimeSeries>, int, Logger) - Method in class ConvertNamedChannelsInputToStack
-
- addToUpdatablePairList(UpdatableMarksList, VoxelizedMarkMemo) - Method in class VoxelizedMarksWithEnergy
-
- addToVoxelList(int, int, int) - Method in class IndexByRegion
-
- addTypedValuesTo(Collection<TypedValue>, int) - Method in class ResultsVector
-
- addUnannotatedImage() - Method in interface ImageCounter
-
Add an image that did not have an associated annotation.
- addUnannotatedImage() - Method in class ImageCounterList
-
- addUnassignedLeft(ObjectMask) - Method in class OverlappingObjects
-
Add an unassigned object to the left set.
- addUnassignedLeft(ObjectCollection) - Method in class OverlappingObjects
-
Add unassigned objects to the left set.
- addUnassignedRight(ObjectMask) - Method in class OverlappingObjects
-
Add an unassigned object to the right set.
- addUnassignedRight(ObjectCollection) - Method in class OverlappingObjects
-
Add unassigned objects to the right set.
- addUnused(T) - Method in interface VoxelPartitionFactory
-
- addUnused(Histogram) - Method in class VoxelPartitonFactoryHistogram
-
- addVertex(V) - Method in class GraphWithoutPayload
-
Adds a vertex.
- addVertex(V) - Method in class GraphWithPayload
-
Adds a vertex.
- addVoxelBuffer(VoxelBuffer<T>) - Method in interface ProjectableBuffer
-
Adds a
VoxelBuffer
to the projection, as a single entity.
- addVoxels(Voxels<T>) - Method in interface ProjectableBuffer
-
Adds a
Voxels
to the projection, as a single entity.
- addWeightedKernelFactories(List<WeightedKernel<T, S>>) - Method in class KernelProposerOption
-
- addWeightedKernelFactories(List<WeightedKernel<T, S>>) - Method in class KernelProposerOptionDual
-
- addWeightedKernelFactories(List<WeightedKernel<T, S>>) - Method in class KernelProposerOptionSingle
-
- addWithName(Define, String, AnchorBean<?>) - Method in class DefineAdderWithPrefixBean
-
Add an item to define
with a name being added.
- 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.
- adjacentVerticesOutgoing(ObjectForReduction) - Method in class ReduceObjectsGraph
-
The vertices that are connected to a particular vertex by an outgoing edge.
- adjacentVerticesOutgoingStream(V) - Method in class GraphWithoutPayload
-
- adjacentVerticesOutgoingStream(V) - Method in class GraphWithPayload
-
- adjacentVerticesOutgoingStream(ObjectForReduction) - Method in class ReduceObjectsGraph
-
- afterAllJobsAreExecuted(S, InputOutputContext) - Method in class Task
-
- afterAllJobsAreExecuted(NoSharedState, InputOutputContext) - Method in class TaskWithoutSharedState
-
- afterAllJobsAreExecuted(AggregateSharedState, InputOutputContext) - Method in class AggregateAnnotations
-
- afterAllJobsAreExecuted(ComparisonSharedState<T>, InputOutputContext) - Method in class CompareAnnotations
-
- afterAllJobsAreExecuted(MontageSharedState, InputOutputContext) - Method in class Montage
-
- afterAllJobsAreExecuted(FeatureExporter<S>, InputOutputContext) - Method in class ExportFeatures
-
- afterAllJobsAreExecuted(NoSharedState, InputOutputContext) - Method in class ConvertImageFormat
-
- afterAllJobsAreExecuted(GroupedSharedState<S, T>, InputOutputContext) - Method in class GroupedStackBase
-
- afterAllJobsAreExecuted(SharedStateFilteredImageOutput<T>, InputOutputContext) - Method in class ImageAssignLabel
-
- afterAllJobsAreExecuted(S, InputOutputContext) - Method in class ScaleImage
-
- afterAllJobsAreExecuted(SharedStateSegmentInstance<T>, InputOutputContext) - Method in class SegmentInstanceWithModel
-
- afterAllJobsAreExecuted(SharedStateSelectedSlice, InputOutputContext) - Method in class ExtractSlice
-
- 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(CSVWriter, InputOutputContext) - Method in class ExportReportFeatures
-
- 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
-
- AggregateChannelTask - Class in org.anchoranalysis.plugin.image.task.bean.combine
-
Creates a an aggregated-image for each group, where each voxel-value is aggregated across each
channel in each image in the group.
- AggregateChannelTask() - Constructor for class AggregateChannelTask
-
- aggregatedChannel() - Method in class ChannelAggregator
-
Retrieve or create a
Channel
with containing the aggregated values.
- 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
-
- align(int, int, int) - Method in enum AlignmentOnDimension
-
Determine the minimum value after alignment.
- Align - Class in org.anchoranalysis.image.bean.spatial.arrange.align
-
Align the bounding-box to the larger
without resizing.
- Align(String, String, String) - Constructor for class Align
-
Creates with alignment text for each axis.
- Align() - Constructor for class Align
-
- align(BoundingBox, BoundingBox) - Method in class BoxAligner
-
- align(Extent, Extent) - Method in class BoxAligner
-
- align(Extent, BoundingBox) - Method in class BoxAligner
-
- alignAfterCheck(BoundingBox, BoundingBox) - Method in class Align
-
- alignAfterCheck(Extent, Extent) - Method in class Align
-
- alignAfterCheck(Extent, BoundingBox) - Method in class Align
-
- alignAfterCheck(BoundingBox, BoundingBox) - Method in class BoxAligner
-
- alignAfterCheck(Extent, Extent) - Method in class BoxAligner
-
- alignAfterCheck(Extent, BoundingBox) - Method in class BoxAligner
-
- alignAfterCheck(BoundingBox, BoundingBox) - Method in class Grow
-
- alignAfterCheck(Extent, Extent) - Method in class Grow
-
- alignAfterCheck(Extent, BoundingBox) - Method in class Grow
-
- alignCorner(BoundingBox, Extent) - Method in class Align
-
The minimum corner at which the entity should be locate after alignment, ignoring the space
to the left.
- alignmentForDimension(String, String) - Method in class PositionChoices
-
Calculates how to align a particular axis.
- AlignmentOnDimension - Enum in org.anchoranalysis.image.bean.nonbean.spatial.align
-
How the alignment will occur for a particular dimension.
- alignX(String) - Static method in class PositionChoicesConstants
-
How to align on the X-axis.
- alignY(String) - Static method in class PositionChoicesConstants
-
How to align on the Y-axis.
- alignZ(String) - Static method in class PositionChoicesConstants
-
How to align on the Z-axis.
- 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
-
- ALL_SUPPORTED_VOXEL_TYPES - Static variable in class PNGTestBase
-
All possible voxel types that can be supported.
- ALL_SUPPORTED_VOXEL_TYPES - Static variable in class StackWriterTestBase
-
All possible voxel types that can be supported.
- allAssociatedPaths() - Method in interface InputFromManager
-
- allChannelsAsStack(int, Logger) - Method in class NamedChannelsConcatenate
-
- allChannelsAsStack(int, Logger) - Method in interface NamedChannelsMap
-
Combines all channels as a single
Stack
at a particular time-frame.
- allChannelsAsStack(int, Logger) - Method in class OpenedNamedChannels
-
- allChannelsEightBit() - Method in class StackWriteAttributes
-
Mark the attributes to indicate that channels are no longer guaranteed to be 8-bit.
- allChannelsHaveIdenticalType() - Method in class Stack
-
Determines if all channels have an identical voxel data-type.
- allChannelsHaveType(VoxelDataType) - Method in class RGBStack
-
Determines if all channels have a specific data-type.
- allChannelsHaveType(VoxelDataType) - Method in class Stack
-
Determines if all channels have a specific data-type.
- allChannelsHaveType(VoxelDataType) - Method in class TimeSeries
-
Whether all
Channel
s in all frames in the times-series have a particular voxel-data
type?
- allExtensions() - Method in enum ImageFileFormat
-
All extensions associated with a file-format.
- 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.
- allocateFloat(int) - Static method in class VoxelBufferFactory
-
Allocates a new float voxel-buffers of given size.
- allocateFloatArray(int) - Static method in class VoxelBufferFactory
-
Creates an array of float voxel-buffers of given size.
- allocateUnsignedByte(int) - Static method in class VoxelBufferFactory
-
Allocates a new unsigned byte voxel-buffer of given size.
- allocateUnsignedByteArray(int) - Static method in class VoxelBufferFactory
-
Creates an array of unsigned byte voxel-buffers of given size.
- allocateUnsignedInt(int) - Static method in class VoxelBufferFactory
-
Allocates a new unsigned int voxel-buffers of given size.
- allocateUnsignedIntArray(int) - Static method in class VoxelBufferFactory
-
Creates an array of unsigned int voxel-buffers of given size.
- allocateUnsignedShort(int) - Static method in class VoxelBufferFactory
-
Allocates a new unsigned short voxel-buffers of given size.
- allocateUnsignedShortArray(int) - Static method in class VoxelBufferFactory
-
Creates an array of unsigned short voxel-buffers of given size.
- AllowEmpty - Annotation Type in org.anchoranalysis.bean.annotation
-
Indicates that a String is allowed be empty, otherwise by default it must be non-empty.
- AllSlicesMaskEverythingNonZero - Class in org.anchoranalysis.plugin.mpp.bean.region
-
Only considers voxels with non-zero intensity.
- AllSlicesMaskEverythingNonZero() - Constructor for class AllSlicesMaskEverythingNonZero
-
- AllSlicesMaskNonZero - Class in org.anchoranalysis.plugin.mpp.bean.region
-
Gets all slices where indexNonZero has at least one non-zero pixel in that slice
- AllSlicesMaskNonZero() - Constructor for class AllSlicesMaskNonZero
-
- allSuccessful() - Method in class TaskStatistics
-
Did all jobs execute and completely successfully?
- AllValuesOff - Class in org.anchoranalysis.plugin.image.bean.mask.provider
-
Creates a new mask of particular dimensionality where all values are off.
- AllValuesOff() - Constructor for class AllValuesOff
-
- AllValuesOn - Class in org.anchoranalysis.plugin.image.bean.mask.provider
-
Creates a new mask of particular dimensionality where all values are on.
- AllValuesOn() - Constructor for class AllValuesOn
-
- ALPHA - Static variable in class RGBChannelNames
-
Name for the alpha channel.
- Always - Class in org.anchoranalysis.plugin.image.bean.object.match
-
Specifies a single object that will always be the "match" for whatever source object.
- Always() - Constructor for class Always
-
- always2D() - 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
-
- AlwaysNew(CacheCreator) - Constructor for class AlwaysNew
-
- AlwaysNew(CacheCreator, ChildCacheFinder) - Constructor for class AlwaysNew
-
- AlwaysReject - Class in org.anchoranalysis.plugin.io.bean.metadata.reader
-
- AlwaysReject() - Constructor for class AlwaysReject
-
- AnchorBean<F> - Class in org.anchoranalysis.bean
-
The base class of all beans used in
Anchor.
- AnchorBean() - Constructor for class AnchorBean
-
- AnchorBeanFactory - Class in org.anchoranalysis.bean.xml.factory
-
Base class for all Anchor-specific bean factories.
- AnchorBeanFactory() - Constructor for class AnchorBeanFactory
-
- AnchorCheckedException - Exception in org.anchoranalysis.core.exception
-
A base class for all checked exceptions used on the Anchor platform.
- AnchorCheckedException() - Constructor for exception AnchorCheckedException
-
Creates without message or cause.
- AnchorCheckedException(String, Throwable) - Constructor for exception AnchorCheckedException
-
Creates with message and cause.
- AnchorCheckedException(String) - Constructor for exception AnchorCheckedException
-
Creates with only a message.
- AnchorCheckedException(Throwable) - Constructor for exception AnchorCheckedException
-
Creates with only a cause.
- AnchorCombinableException - Exception in org.anchoranalysis.core.exception.combinable
-
An exception that can be combined with similar exceptions and summarized.
- AnchorCombinableException(String, Throwable) - Constructor for exception AnchorCombinableException
-
Creates with a description and a cause.
- AnchorDefaultBeanFactory - Class in org.anchoranalysis.bean.xml.factory
-
The default bean factory used for initializing
AnchorBean
s.
- AnchorDefaultBeanFactory(BeanInstanceMap) - Constructor for class AnchorDefaultBeanFactory
-
- AnchorFriendlyCheckedException - Exception in org.anchoranalysis.core.exception.friendly
-
A base class for particular checked-exceptions which are guaranteed to provide a user-friendly
error description.
- AnchorFriendlyCheckedException(String, Throwable) - Constructor for exception AnchorFriendlyCheckedException
-
A user-friendly error message and its cause.
- AnchorFriendlyCheckedException(String) - Constructor for exception AnchorFriendlyCheckedException
-
A user-friendly error message WITHOUT a cause.
- AnchorFriendlyCheckedException(Throwable) - Constructor for exception AnchorFriendlyCheckedException
-
A wrapped exception.
- AnchorFriendlyRuntimeException - Exception in org.anchoranalysis.core.exception.friendly
-
A base class for particular runtime-exceptions which are guaranteed to provide a user-friendly
error description.
- AnchorFriendlyRuntimeException(String, Throwable) - Constructor for exception AnchorFriendlyRuntimeException
-
A user-friendly error message and its cause.
- AnchorFriendlyRuntimeException(String) - Constructor for exception AnchorFriendlyRuntimeException
-
A user-friendly error message without a cause.
- AnchorFriendlyRuntimeException(Throwable) - Constructor for exception AnchorFriendlyRuntimeException
-
A wrapped exception.
- AnchorImpossibleSituationException - Exception in org.anchoranalysis.core.exception.friendly
-
A run-time exception to throw in situations which should never logically occur by design.
- AnchorImpossibleSituationException() - Constructor for exception AnchorImpossibleSituationException
-
Default constructor.
- AnchorImpossibleSituationException(String) - Constructor for exception AnchorImpossibleSituationException
-
Creates with a specific message explaining the exception.
- AnchorNeverOccursException - Exception in org.anchoranalysis.core.exception
-
This is an exception that should never be thrown, but can be used for type-safety where an
exception is needed.
- AnchorNeverOccursException() - Constructor for exception AnchorNeverOccursException
-
- AnchorRuntimeException - Exception in org.anchoranalysis.core.exception
-
A base class for all unchecked (runtime) exceptions used on the Anchor platform.
- AnchorRuntimeException() - Constructor for exception AnchorRuntimeException
-
Creates without message or cause.
- AnchorRuntimeException(String, Throwable) - Constructor for exception AnchorRuntimeException
-
Creates with message and cause.
- AnchorRuntimeException(String) - Constructor for exception AnchorRuntimeException
-
Creates with only a message.
- AnchorRuntimeException(Throwable) - Constructor for exception AnchorRuntimeException
-
Creates with only a cause.
- AnchorWebsiteLinks - Class in org.anchoranalysis.launcher
-
A centralized location for hyperlinks to the Anchor website.
- and(StackWriteAttributes) - Method in class StackWriteAttributes
-
- And - Class in org.anchoranalysis.plugin.image.bean.mask.provider.combine
-
Outputs the logical operation and voxelwise on both masks, modifying {mask} with the
result.
- And() - Constructor for class And
-
- And - Class in org.anchoranalysis.plugin.image.bean.object.filter.combine
-
Applies multiples filter with logical AND i.e.
- And() - Constructor for class And
-
- AndCondition - Class in org.anchoranalysis.plugin.image.object.merge.condition
-
Combines two UpdatableBeforeConditions as LOGICAL ANDs
- AndCondition(UpdatableBeforeCondition, UpdatableBeforeCondition) - Constructor for class AndCondition
-
- AndKernel - Class in org.anchoranalysis.image.voxel.kernel
-
Combines two
BinaryKernel
s so that they only a true value exists only at a point where
both kernels return true.
- AndKernel(BinaryKernel, BinaryKernel) - Constructor for class AndKernel
-
Create for the two kernels.
- AndList - Class in org.anchoranalysis.plugin.mpp.bean.check
-
- AndList() - Constructor for class AndList
-
- AndObjectsWithMasks - Class in org.anchoranalysis.plugin.image.bean.object.provider.mask
-
Reduce the size of individual objects (if neccessary, and minimally) to fit within a binary-mask.
- AndObjectsWithMasks() - Constructor for class AndObjectsWithMasks
-
- AnisotropicDiffusion - Class in org.anchoranalysis.plugin.fiji.bean.channel.provider
-
- AnisotropicDiffusion() - Constructor for class AnisotropicDiffusion
-
- AnnealScheme - Class in org.anchoranalysis.mpp.bean
-
- AnnealScheme() - Constructor for class AnnealScheme
-
- Annotation - Interface in org.anchoranalysis.annotation
-
Base class for types of image annotations.
- AnnotationAggregateCSVGenerator - Class in org.anchoranalysis.plugin.annotation.bean.aggregate
-
- AnnotationAggregateCSVGenerator() - Constructor for class AnnotationAggregateCSVGenerator
-
- AnnotationBackground - Class in org.anchoranalysis.annotation.io.bean
-
How to display one or more
Stack
s as background during an annotation process.
- AnnotationBackground() - Constructor for class AnnotationBackground
-
- AnnotationComparisonAssigner<T extends Assignment<ObjectMask>> - Class in org.anchoranalysis.plugin.annotation.bean.comparison.assigner
-
Compares elements in an annotation to elements from an experiment.
- AnnotationComparisonAssigner() - Constructor for class AnnotationComparisonAssigner
-
- AnnotationComparisonInput<T extends InputFromManager> - Class in org.anchoranalysis.plugin.annotation.comparison
-
- AnnotationComparisonInput(T, Tuple2<ComparableSource, ComparableSource>, Tuple2<String, String>, StackReader) - Constructor for class AnnotationComparisonInput
-
- AnnotationComparisonInputManager<T extends InputFromManager> - Class in org.anchoranalysis.plugin.annotation.bean.comparison
-
- AnnotationComparisonInputManager() - Constructor for class AnnotationComparisonInputManager
-
- AnnotationDeleter - Interface in org.anchoranalysis.annotation.io
-
Allows an annotation to be deleted from the file-system.
- annotationExistsAt(Path) - Method in class DualMarksAnnotationReader
-
Whether an annotation exists at a particular path on the file-system.
- AnnotationInputManager<T extends ProvidesStackInput,S extends AnnotatorStrategy> - Class in org.anchoranalysis.annotation.io.bean
-
An
InputManager
that provides annotations corresponding to images.
- AnnotationInputManager() - Constructor for class AnnotationInputManager
-
- AnnotationLabel - Class in org.anchoranalysis.plugin.annotation.bean.label
-
- AnnotationLabel() - Constructor for class AnnotationLabel
-
- annotationLabelFor(ProvidesStackInput, OperationContext) - Method in class AnnotatorStrategy
-
A human-friendly textual description of the annotation, or
Optional.empty()
if no
label is available.
- annotationLabelFor(ProvidesStackInput, OperationContext) - Method in class ImageLabelStrategy
-
- annotationLabelFor(ProvidesStackInput, OperationContext) - Method in class MarkProposerStrategy
-
- AnnotationReader<T extends Annotation> - Interface in org.anchoranalysis.annotation.io
-
Allows an annotation to be read from the file-system.
- AnnotationWithMarks - Interface in org.anchoranalysis.annotation.mark
-
An image-annotation that involves a mark-collection.
- AnnotationWithStrategy<T extends AnnotatorStrategy> - Class in org.anchoranalysis.annotation.io
-
One particular annotation, associated with its strategy.
- AnnotationWithStrategy(ProvidesStackInput, T) - Constructor for class AnnotationWithStrategy
-
Creates for a particular input and associated annotation strategy.
- AnnotationWriter<T extends Annotation> - Interface in org.anchoranalysis.annotation.io
-
Allows an annotation to be written to the file-system.
- AnnotatorStrategy - Class in org.anchoranalysis.annotation.io.bean
-
How an input is associated with annotations on the file-system, and how this is presented
visually.
- AnnotatorStrategy() - Constructor for class AnnotatorStrategy
-
- Anonymize - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming
-
Copies files to a number 001, 002
etc.
- Anonymize() - Constructor for class Anonymize
-
- AnonymizeSharedState - Class in org.anchoranalysis.plugin.io.shared
-
- AnonymizeSharedState(NumberToStringConverter, Map<Integer, Integer>) - Constructor for class AnonymizeSharedState
-
- any() - Method in class VoxelsUntyped
-
Exposes without any specific buffer type.
- anyDimensionIsLargerThan(Extent) - Method in class Extent
-
Returns true if any dimension in this extent is larger than the corresponding dimension in
other
extent.
- anyExists() - Method in class PredicateAtCorner
-
- anyExists() - Method in class PredicateImplementation
-
- anyExists() - Method in interface VoxelsPredicate
-
Does at least one value satisfy the predicate - across all voxels?
- anyMatch(Predicate<ObjectMask>) - Method in class ObjectMaskStream
-
Does the predicate evaluate to true on any object in the collection?
- anyPredicateMatch(Voxels<T>, Predicate<T>) - Static method in class IterateVoxelsAll
-
Tries to apply a predicate to all the remaining buffer locations, returning true if the
predicate matches.
- AnySliceCenterOnMask - Class in org.anchoranalysis.plugin.mpp.bean.check
-
The center ps of at least one slice should be on the stack Tries overall center point first, and
then projects it onto each slice
- AnySliceCenterOnMask() - Constructor for class AnySliceCenterOnMask
-
- append(StatisticsToExport) - Method in class StatisticsToExport
-
Appends the names and values from another AnnotationComparison
to the existing.
- append(Optional<FeatureList<T>>) - Method in class FeatureList
-
Appends the features one or more (optional) feature-lists to the existing list.
- AppendCsv - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
-
A CSV that is appended from the root of a project
- AppendCsv() - Constructor for class AppendCsv
-
- AppendDictionary - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
-
- AppendDictionary() - Constructor for class AppendDictionary
-
- appendExtension(String, Optional<String>) - Static method in class ExtensionUtilities
-
Appends an (optional) extension to a string, adding in the leading period if the extension is
defined.
- appendExtension(Path, Optional<String>) - Static method in class ExtensionUtilities
-
- AppendFilePath - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
-
- AppendFilePath() - Constructor for class AppendFilePath
-
- AppendHistogram - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
-
- AppendHistogram() - Constructor for class AppendHistogram
-
- AppendMarks - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
-
- AppendMarks() - Constructor for class AppendMarks
-
- AppendObjects - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
-
- AppendObjects() - Constructor for class AppendObjects
-
- AppendStack - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
-
A stack from a stack-collection
- AppendStack() - Constructor for class AppendStack
-
- AppendStackDirect - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
-
A stack from a stack-collection
- AppendStackDirect() - Constructor for class AppendStackDirect
-
- apply(Throwable, Writer, String, int, boolean) - Static method in class RecursivelyDescribeExceptionStack
-
Incrementally adds a line to a string builder with the message of each exception moving onto
the next nested exception until there are no more
- apply(S, T) - Method in interface CheckedBiFunction
-
Calls the function.
- apply(S) - Method in interface CheckedFunction
-
Calls the function.
- apply(S, int) - Method in interface CheckedFunctionWithInt
-
Calls the function.
- apply(int) - Method in interface CheckedIntFunction
-
Calls the function
- apply(T) - Method in interface CheckedUnaryOperator
-
Applies the operation.
- apply(S, int) - Method in interface FunctionWithInt
-
Calls the function.
- apply(int) - Method in interface UnaryIntOperator
-
Apply the operator.
- apply(Mask, Mask) - Static method in class MaskAnd
-
Performs a logical and operation on each voxel in two masks, writing the result onto
the second mask.
- apply(Voxels<UnsignedByteBuffer>, Voxels<UnsignedByteBuffer>, BinaryValuesByte, BinaryValuesByte) - Static method in class MaskAnd
-
Performs a logical
and operation on each voxel in two
Voxels
(considered to be
masks), writing the result onto the second mask.
- apply(Mask, Mask) - Static method in class MaskOr
-
Performs a logical or operation on each voxel in two masks, writing the result onto
the first mask.
- apply(Mask, Mask) - Static method in class MaskXor
-
Performs a logical xor (exclusive or) operation on each voxel in two masks, writing
the result onto the first mask.
- apply(BinaryVoxels<UnsignedByteBuffer>, BinaryVoxels<UnsignedByteBuffer>) - Static method in class MaskXor
-
Performs a logical
xor (exclusive or) operation on each voxel in two
Voxels
(considered to be masks), writing the result onto the second mask.
- apply(BiFunction<T, T, R>) - Method in class DualScale
-
- apply(BinaryKernel, BinaryVoxels<UnsignedByteBuffer>, KernelApplicationParameters) - Static method in class ApplyKernel
-
Apply the kernel to BinaryVoxels<UnsignedByteBuffer>
using the same binary-values as
voxels
to calculate a value for each voxel.
- apply(IFormatReader, ReadOptions, int) - Method in class DimensionsCreator
-
- apply(String, Path) - Static method in class WriteStringToFile
-
- applyAsDouble(T, U) - Method in interface CheckedToDoubleBiFunction
-
Applies this function to the given arguments.
- applyAsDouble(T) - Method in interface CheckedToDoubleFunction
-
Applies this function to the given arguments.
- applyAsFloat(int) - Method in interface IntToFloatFunction
-
Applies this function to the given argument.
- applyAsInt(S) - Method in interface CheckedToIntFunction
-
Calls the function.
- applyCoefficientsToMark(DoubleMatrix2D, Mark, Dimensions) - Method in class LinearLeastSquaresViaNormalEquationBase
-
- applyDelta(MultiLevelOutputEnabled) - Method in class OutputEnabledDelta
-
Applies the changes to enable or disable additional outputs, if they are defined.
- applyFitResultToMark(Ellipsoid, Dimensions, double) - Method in class FitResult
-
- applyForCount(CountKernel, BinaryVoxels<UnsignedByteBuffer>, KernelApplicationParameters) - Static method in class ApplyKernel
-
Applies the kernel to voxels and sums the returned value.
- applyForCount(CountKernel, BinaryVoxels<UnsignedByteBuffer>, BoundingBox, KernelApplicationParameters) - Static method in class ApplyKernel
-
Applies the kernel to voxels and sums the returned value.
- applyForCount(BinaryKernel, BinaryVoxels<UnsignedByteBuffer>, KernelApplicationParameters) - Static method in class ApplyKernel
-
Applies a
BinaryKernel
to voxels and counts how many true values occur en aggregate.
- ApplyImageJMorphologicalOperation - Class in org.anchoranalysis.plugin.imagej.mask
-
Applies an ImageJ (2D) morphological operation to voxels.
- applyInitializationIfPossibleTo(Object, Object, Logger) - Method in class BeanInitializer
-
Applies the initialization to a bean if possible.
- ApplyKernel - Class in org.anchoranalysis.image.voxel.kernel
-
- applyMorphologicalOperation(Mask, boolean) - Method in class Dilate
-
- applyMorphologicalOperation(Mask, boolean) - Method in class Erode
-
- applyMorphologicalOperation(Mask, boolean) - Method in class MorphologicalOperatorBase
-
- applyMorphologicalOperation(ObjectMask, Optional<Extent>) - Method in class Dilate
-
- applyMorphologicalOperation(ObjectMask, Optional<Extent>) - Method in class Erode
-
- applyMorphologicalOperation(ObjectMask, Optional<Extent>) - Method in class ObjectCollectionProviderMorphological
-
- applyOperation(UnaryOperator<Stack>, Optional<Dimensions>) - Method in class NamedStacks
-
Applies an operation on each
Stack
in the collection and returns a new derived
collection.
- applyOperation(ObjectMask, Extent, boolean) - Method in class CalculateIncrementalOperationMap
-
- applyOperation(ObjectMask, Extent, boolean) - Method in class CalculateDilationMap
-
- applyOperation(ObjectMask, Extent, boolean) - Method in class CalculateErosionMap
-
- applyOperation(BinaryVoxels<UnsignedByteBuffer>, String, int) - Static method in class ApplyImageJMorphologicalOperation
-
- applyRadiiSubtractScale(double, double) - Method in class FitResult
-
- applyRankFilter(Channel, int, int) - Static method in class FilterHelper
-
Applies a 2D rank-filter to each slice independently.
- applyStrategy(MergeCandidate) - Method in class MergeStrategy
-
- applyUntilPositive(CountKernel, BinaryVoxels<UnsignedByteBuffer>, BoundingBox, KernelApplicationParameters) - Static method in class ApplyKernel
-
Applies the kernel to voxels until a positive value is returned, then exits with true.
- arbitraryElement() - Method in class RTree
-
Any arbitrary element from the tree.
- 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 square meters, or units thereof.
- AreaPhysical() - Constructor for class AreaPhysical
-
- AreaPixels - Class in org.anchoranalysis.image.bean.unitvalue.extent.area
-
Area expressed in pixels.
- AreaPixels(double) - Constructor for class AreaPixels
-
Creates with a particular area value.
- AreaPixels() - Constructor for class AreaPixels
-
- areaXY() - Method in class Dimensions
-
Size in X multiplied by size in Y.
- areaXY() - Method in class Extent
-
Size in X multiplied by size in Y.
- areCsvFilesEqual(Path, Path, PrintStream) - Method in class CSVComparer
-
Are two CSV files equal?
- areDocumentsEqual(Document, Document) - Static method in class CompareXML
-
Are two XML-documents equal in content, ignoring whitespace and comments?
- areEqual(double, double) - Static method in class DoubleUtilities
-
Are the two numbers equal, within a tolerance?
- areEqual(float, float) - Static method in class FloatUtilities
-
Are the two numbers equal?
- arePointsNeighbors(Point3i, Point3i) - Static method in class PointsNeighborChecker
-
Do two points have a big neighbor relationship to each other?
- ArgumentConverter - Class in org.anchoranalysis.launcher.executor.selectparam.path.convert
-
Converts string passed as arguments.
- arithmetic() - Method in class Channel
-
Interface that allows manipulation of voxel intensities via arithmetic operations.
- arithmetic() - Method in class BoundedVoxels
-
Interface that allows manipulation of voxel intensities via arithmetic operations.
- arithmetic() - Method in class Voxels
-
Interface that allows manipulation of voxel intensities via arithmetic operations.
- arithmetic() - Method in class VoxelsUntyped
-
Interface that allows manipulation of voxel intensities via arithmetic operations.
- ArithmeticWithConstantBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
-
Base-class for operations that perform a binary arithmetic operation with each voxel-value and a
constant.
- ArithmeticWithConstantBase() - Constructor for class ArithmeticWithConstantBase
-
- ArithmeticWithConstantConditionallyWriteBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
-
- ArithmeticWithConstantConditionallyWriteBase() - Constructor for class ArithmeticWithConstantConditionallyWriteBase
-
- Arrange - Class in org.anchoranalysis.image.bean.provider.stack
-
Creates a stack that combines other stacks.
- Arrange(boolean, boolean) - Constructor for class Arrange
-
Shortcut to create with some explicit parameters.
- Arrange() - Constructor for class Arrange
-
- ArrangeStackException - Exception in org.anchoranalysis.image.bean.nonbean.spatial.arrange
-
When the position of a particular
RGBStack
cannot be determined, when combined with
others onto a single plane.
- ArrangeStackException(String) - Constructor for exception ArrangeStackException
-
Create with a message.
- ArrangeStackException(Exception) - Constructor for exception ArrangeStackException
-
Create with a cause.
- ArrangeStackException(String, Exception) - Constructor for exception ArrangeStackException
-
Create with a message and cause.
- arrangeStacks(Iterator<Extent>, OperationContext) - Method in class Fill
-
- arrangeStacks(Iterator<Extent>, OperationContext) - Method in class Overlay
-
- arrangeStacks(Iterator<Extent>, OperationContext) - Method in class Single
-
- arrangeStacks(Iterator<Extent>, OperationContext) - Method in class StackArranger
-
Arranges stacks to that they fit together in a single raster.
- arrangeStacks(Iterator<Extent>, OperationContext) - Method in class Tile
-
- array() - Method in class UnsignedByteBuffer
-
- array() - Method in class UnsignedIntBuffer
-
- array() - Method in class UnsignedShortBuffer
-
- as(boolean) - Static method in enum OutsideKernelPolicy
-
- asArray(boolean) - Static method in class RGBChannelNames
-
Creates an array with all channel-names in R-G-B order.
- asByte() - Method in class BinaryValuesInt
-
- asByte() - Method in class VoxelsUntyped
-
- asByte(ImageProcessor) - Static method in class ConvertToVoxelBuffer
-
Convert a ImageProcessor
to VoxelBuffer<UnsignedByteBuffer>
- AsCollection - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.all
-
- AsCollection() - Constructor for class AsCollection
-
- asCollectionOrderNotPreserved() - Method in class ScaledElements
-
Returns the scaled-elements as a collection but without preserving the original element
order.
- asExtent() - Method in class SizeXY
-
Creates an extent with identical width and height and depth (z-extent) of 1.
- asExtent(int) - Method in class SizeXY
-
Creates an extent with identical width and height and a specific depth (z-extent).
- asFile() - Method in interface InputFromManager
-
Expresses the input as a file with a name (the unique identifier).
- asFloat() - Method in class VoxelsUntyped
-
- asFloat(ImageProcessor) - Static method in class ConvertToVoxelBuffer
-
Convert a ImageProcessor
to VoxelBuffer<FloatBuffer>
- asGraph() - Method in class IntersectingObjects
-
Constructs a graph where each vertex is an element and an edge exists between any elements
that intersect.
- asInt() - Method in class BinaryValuesByte
-
- asInt() - Method in class VoxelsUntyped
-
- asList() - Method in class StringList
-
Exposes the underlying list of values.
- asList() - Method in class ColorList
-
Exposes the underlying
List
in the data-structure.
- asList() - Method in class FeatureList
-
Exposes the underlying list of features in this data-structure.
- asList() - Method in class FeatureNameList
-
Exposes the underlying list of names.
- asList(boolean) - Static method in class RGBChannelNames
-
Creates a list with all channel-names in R-G-B order.
- asList() - Method in class ObjectCollection
-
Exposes the underlying objects as a
ArrayList
.
- 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 ScaledElements
-
The underlying map used to map an unscaled object to its scaled counterpart.
- AsMark - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
-
- AsMark() - Constructor for class AsMark
-
- asMarks() - Method in class EnergyMemoList
-
- asNamedStacks() - Method in class NamedStacksUniformSize
-
- AsObject - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
-
- AsObject() - Constructor for class AsObject
-
- asObjectMask() - Method in class ObjectWithProperties
-
Exposes the underlying
ObjectMask
ignoring any properties.
- AsObjectMask - Class in org.anchoranalysis.plugin.image.feature.bean.stack.object
-
Treats a channel as an object-mask, assuming binary values of 0 and 255 and calls an object-mask
feature
- AsObjectMask() - Constructor for class AsObjectMask
-
- asOperationFailedException() - Method in exception GetOperationFailedException
-
- asPath() - Method in class RootPath
-
Exposes the
path
field as a
Path
.
- asPath(boolean) - Method in class DirectoryWithPrefix
-
A path that combines the directory
and fileNamePrefix
and delimiter
.
- aspectRatioInverted() - Method in class ExtentToArrange
-
Returns the ratio of *image height to width*.
- aspectRatioXY() - Method in class Extent
-
Derives an aspect-ratio, by dividing the X-dimension by the Y-dimension value.
- asPoint() - Method in class Padding
-
- asPredicateDouble() - Method in class RelationToThreshold
-
Expresses the relation as a predicate on values, where only values that fulfill the relation
to threshold are true.
- asPredicateInt() - Method in class RelationToThreshold
-
- asScaleFactor() - Method in class ScaleFactorInt
-
Converts to a
ScaleFactor
that accepts floating-point values.
- assertCalc(ResultsVector, Object...) - Static method in class ResultsVectorTestUtilities
-
- assertDoubleResult(String, Feature<T>, T, double) - Static method in class FeatureTestCalculator
-
- assertDoubleResult(String, Feature<T>, T, Optional<SharedObjects>, double) - Static method in class FeatureTestCalculator
-
- assertDoubleResult(String, Feature<T>, T, T, double, double) - Static method in class FeatureTestCalculatorDuo
-
- assertExpectedTaskOutputs(T, V, Path, String, Iterable<String>) - Method in class ExecuteTaskHelper
-
Executes a task on a single-input.
- assertExpectedTaskOutputs(List<T>, V, Path, String, Iterable<String>) - Method in class ExecuteTaskHelper
-
Executes a task on a multiple inputs and asserts expected outputs - with task arguments.
- assertIdentical(String, String, Path) - Method in interface ImageComparer
-
Asserts that two stacks being compared are identical.
- assertIntResult(String, Feature<T>, T, int) - Static method in class FeatureTestCalculator
-
- assertIntResult(String, Feature<T>, T, Optional<SharedObjects>, int) - Static method in class FeatureTestCalculator
-
- assertIntResult(String, Feature<T>, T, T, int, int) - Static method in class FeatureTestCalculatorDuo
-
- assertValid() - Method in class MarksWithEnergyBreakdown
-
- assertValid() - Method in class EnergySavedInd
-
- assertValid() - Method in class EnergySavedPairs
-
- asSet(boolean) - Static method in class RGBChannelNames
-
Creates a set of the channel names.
- asSet(Logger) - Method in interface ProvidesStackInput
-
Exposes the input as a set of named stacks (inferring the names).
- asSet() - Method in class RTree
-
All elements contained within the tree, as a
Set
.
- asShort() - Method in class VoxelsUntyped
-
- 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.
- assignAllVoxels(RGBColor) - Method in class RGBStack
-
Assigns a
RGBColor
to all voxels in the respective channels.
- 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.
- assignCallUponDirectoryCreation(Consumer<Path>) - Method in class InputArguments
-
Indicates that consumer
will be called when an output directory is first created.
- assignCopyNonInputs() - Method in class InputArguments
-
Activates a toggle where any files in the input directory that are unused as inputs, are
copied to the output directory.
- assignCurrent(Optional<T>) - Method in class DualState
-
- assignEachMatchingPoint(Voxels<?>, IntPredicate, int) - Static method in class IterateVoxelsAll
-
Assigns a value to any voxel whose intensity matches a predicate, reading and writing the
buffer as an int
.
- AssignerMatchClass<P extends BeanInitialization> - Class in org.anchoranalysis.bean.initializable.property
-
Allows assignment of parameters if they are are of type paramTypeMatch
or subclass of it.
- AssignerMatchClass(Class<?>) - Constructor for class AssignerMatchClass
-
- assignExtent(Extent) - Method in class SizeMapping
-
Replace the existing
Extent
with a new value.
- AssignFeatureNameUtilities - Class in org.anchoranalysis.feature.name
-
Utilities for assigning a name to a feature.
- assignFilterGlob(String) - Method in class InputContextParameters
-
Assigns a glob that can be used by beans to filter input.
- assignFixedLimit(int) - Method in class InputContextParameters
-
Assigns a fixed upper limit of number of inputs.
- 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
-
- assignGroup(String) - Method in class TaskArguments
-
Assigns an index-range to use to form groups, by subsetting components from each input's
identifier.
- assignIdentifierSubrange(IndexRangeNegative) - Method in class InputContextParameters
-
If defined, this indicates and specifies only a subset of the elements of the identifier to
use.
- assignInitializationToProperties(Object, Object, Object, Logger) - Method in class AssignerMatchClass
-
- assignInitializationToProperties(Object, Object, Object, Logger) - Method in interface InitializationParameterAssigner
-
Assigns the parameter to the bean.
- assignInputDirectory(Optional<Path>) - Method in class InputContextParameters
-
Sets an input-directory.
- assignInputFilterExtensions(StringSetTrie) - Method in class InputContextParameters
-
Assigns extensions that can be used filter inputs, but irrespective of whether
extensions have already been set.
- assignInputFilterExtensionsIfMissing(Supplier<Optional<StringSetTrie>>) - Method in class InputContextParameters
-
Assigns extensions that can be used filter inputs, but only when no extensions have
already been set.
- assignLogger(Logger) - Method in class OutputterChecked
-
Assigns a logger to the outputter, which is used to output warnings or messages when
outputting.
- assignMaxNumberProcessors(String) - Method in class TaskArguments
-
Assigns a suggested maximum number of processors (CPUs) for a task.
- Assignment<T> - Interface in org.anchoranalysis.annotation.io.assignment
-
A one-to-one pairing between items in two respective sets.
- AssignmentColorPool - Class in org.anchoranalysis.annotation.io.assignment.generator
-
Different
ColorScheme
s that can be used to select colors for paired and unpaired objects.
- AssignmentColorPool(int, ColorScheme) - Constructor for class AssignmentColorPool
-
Creates with a number and colors for the paired objects, and defaults colors for unpaired.
- AssignmentColorPool(int, ColorScheme, ColorScheme, boolean) - Constructor for class AssignmentColorPool
-
- AssignmentGenerator - Class in org.anchoranalysis.annotation.io.assignment.generator
-
Outputs a raster showing an
Assignment
on a background.
- AssignmentGenerator(DrawColoredObjects, IntFunction<AssignmentColorPool>, Tuple2<String, String>, boolean) - Constructor for class AssignmentGenerator
-
- AssignMode<S,T,U> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode
-
How assignments and other decisions are made in the SimulatedAnnealing optimizaton
- AssignMode() - Constructor for class AssignMode
-
- assignModelDirectory(Path) - Method in class InputArguments
-
Assigns a directory indicating where models can be located.
- assignName(String) - Method in class ClusterIdentifier
-
Assigns a name for the cluster.
- assignOff() - Method in class Mask
-
Interface that allows assignment of an off state to all or subsets of the voxels.
- assignOff() - Method in class BinaryVoxels
-
Creates an assigner that may set the off state in subsequently specified regions of
the voxels.
- assignOff() - Method in class ObjectMask
-
Assigns the off value to voxels, expecting global coordinates.
- assignOn() - Method in class Mask
-
Interface that allows assignment of an on state to all or subsets of the voxels.
- assignOn() - Method in class BinaryVoxels
-
Creates an assigner that may set the on state in subsequently specified regions of the
voxels.
- assignOn() - Method in class ObjectMask
-
Assigns the on value to voxels, expecting global coordinates.
- assignOutputDirectory(Path) - Method in class OutputPrefixerSettings
-
- AssignOverlappingObjects - Class in org.anchoranalysis.annotation.io.assignment
-
Creates a one-to-one
assignment between two sets of
ObjectMask
s.
- AssignOverlappingObjects(FeatureEvaluator<FeatureInputPairObjects>, boolean) - Constructor for class AssignOverlappingObjects
-
- assignPaths(List<Path>) - Method in class InputContextParameters
-
Assigns a specific list of paths that are used for the inputs.
- assignPaused(DualMarks) - Method in class DualMarksAnnotation
-
Assigns marks with an overall paused state.
- AssignPermutationException - Exception in org.anchoranalysis.bean.permute.assign
-
When the assignment of a permuted value to a property cannot succeed.
- AssignPermutationException(String) - Constructor for exception AssignPermutationException
-
Create with an error message.
- assignPrevious(double, int) - Method in class UnchangedBase
-
Assigns the previous value to be remembered for comparison next time.
- assignPrevious(double, int) - Method in class UnchangedScore
-
- assignPrevious(double, int) - Method in class UnchangedSize
-
- AssignPriority - Class in org.anchoranalysis.plugin.image.object.merge.priority
-
- AssignPriority() - Constructor for class AssignPriority
-
- assignPriority(ObjectVertex, ObjectVertex, GraphLogger) - Method in class AssignPriority
-
Assigns a priority to a potential merge
- AssignPriorityFromImprovement - Class in org.anchoranalysis.plugin.image.object.merge.priority
-
Allows merges if there is an increase in the payload i.e.
- AssignPriorityFromImprovement(PayloadCalculator) - Constructor for class AssignPriorityFromImprovement
-
- AssignPriorityFromPair - Class in org.anchoranalysis.plugin.image.object.merge.priority
-
Calculates pair-feature on each potential merge, and this value determines priority..
- AssignPriorityFromPair(FeatureCalculatorSingle<FeatureInputPairObjects>, double, DoubleBiPredicate) - Constructor for class AssignPriorityFromPair
-
- assignPriorityToEdge(ObjectVertex, ObjectVertex, ObjectMask, ErrorReporter) - Method in class AssignPriority
-
- assignPriorityToEdge(ObjectVertex, ObjectVertex, ObjectMask, ErrorReporter) - Method in class AssignPriorityFromImprovement
-
- assignPriorityToEdge(ObjectVertex, ObjectVertex, ObjectMask, ErrorReporter) - Method in class AssignPriorityFromPair
-
- assignProposal(OptimizationStep<S, T, U>, TransformationContext, KernelWithIdentifier<S, U>) - Method in interface KernelAssigner
-
- assignProposal(Optional<T>, KernelWithIdentifier<S, V>) - Method in class OptimizationStep
-
- assignProposal(OptimizationStep<S, T, U>, TransformationContext, KernelWithIdentifier<S, U>) - Method in class KernelAssignerAddErrorLevel
-
- assignProposal(OptimizationStep<S, T, V>, TransformationContext, KernelWithIdentifier<S, V>) - Method in class KernelAssignerCalculateEnergyFromKernel
-
- assignRatioLimit(double) - Method in class InputContextParameters
-
Assigns a fixed upper limit that is a ratio of the number of inputs allowed.
- assignRejected(DualMarks, T) - Method in class DualMarksAnnotation
-
Assigns marks with an overall rejected state.
- assignRelativeForIdentifier() - Method in class InputContextParameters
-
Specify that the entire filename or relative path (excluding extension) is used to determine
a unique identifier.
- assignResolution(Optional<Resolution>) - Method in class Channel
-
Assigns a new resolution.
- assignResolution(Resolution) - Method in class Stack
-
Assigns a new resolution.
- assignShuffle() - Method in class InputContextParameters
-
Indicates that the order of the inputs should be shuffled (randomized).
- assignSize(String) - Method in class TaskArguments
-
Assign dimensions or scaling factor or size for an image, as may be used by a task.
- assignSuggestedImageOutputFormat(ImageFileFormat) - Method in class OutputArguments
-
Assigns a suggestion for a preferred image-output format.
- assignSuggestedImageOutputFormat(ImageFileFormat) - Method in class OutputPrefixerSettings
-
Assigns a suggestion for a preferred image-output format.
- assignTaskName(Optional<String>) - Method in class TaskArguments
-
Assigns a name for the task.
- assignTo(Feature<FeatureInput>) - Method in class Feature
-
Copies fields in this (base) class to target
.
- assignTo(KernelPosNeg<T, S>) - Method in class KernelPosNeg
-
Copies fields in this (base) class to target
.
- assignTo(ConicFitterBase) - Method in class ConicFitterBase
-
Copies fields in this (base) class to target
.
- assignValue(AnchorBean<?>, Object) - Method in interface PermutationAssigner
-
Assigns value
to one or more properties in bean
.
- assignValue(int) - Method in class Channel
-
Interface that allows assignment of a particular value to all or subsets of the voxels.
- assignValue(int) - Method in class BoundedVoxels
-
Assigns a value to a bounded-voxels accepting global coordinates for objects, boxes
etc.
- assignValue(int) - Method in class Voxels
-
Interface that allows assignment of a particular value to all or subsets of the voxels.
- assignValue(int) - Method in class VoxelsFloat
-
- assignValue(int) - Method in class VoxelsUnsignedByte
-
- assignValue(int) - Method in class VoxelsUnsignedInt
-
- assignValue(int) - Method in class VoxelsUnsignedShort
-
- assignValue(int) - Method in class VoxelsUntyped
-
Interface that allows assignment of a particular value to all or subsets of the voxels.
- AssignValue - Class in org.anchoranalysis.plugin.image.bean.channel.provider.assign
-
Assigns a constant (scalar) value to the portion of the image covered by a mask
- AssignValue() - Constructor for class AssignValue
-
- assignVoxel(Point3i, RGBColor) - Method in class RGBStack
-
Assigns a
RGBColor
to a single voxel in the respective channels.
- assignWithPrefix(Feature<? extends FeatureInput>, String, String) - Static method in class AssignFeatureNameUtilities
-
Assigns a new custom-name to a feature, by combining an existing-name with a prefix.
- AsSingle - Class in org.anchoranalysis.mpp.feature.bean.energy.element
-
- AsSingle() - Constructor for class AsSingle
-
- AsSingleMark - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.all
-
- AsSingleMark() - Constructor for class AsSingleMark
-
- associated - Variable in class AddOptionsFromCommandLine
-
An associated entity which consumers accept.
- associatedFile() - Method in class AnnotationWithStrategy
-
The file associated with the annotation, if such a file exists.
- AssociatedIndex - Interface in org.anchoranalysis.core.index
-
Associated an index with the object.
- associateFileWithCluster(File, long, ClusterIdentifier) - Method in class ClusterMembership
-
Indicates a particular file is a member of a particular cluster.
- associateXML(XMLConfiguration) - Method in interface AssociateXMLUponLoad
-
Associated an XML configuration with an object.
- associateXML(XMLConfiguration) - Method in class Experiment
-
- associateXML(XMLConfiguration) - Method in class QuickMultiDatasetStructuredExperiment
-
- AssociateXMLUponLoad - Interface in org.anchoranalysis.bean.xml
-
For classes that wish to have a XmlConfiguration associated with them.
- asStack() - Method in class EnergyStack
-
Derive a
Stack
representation containing the identical channels to the current
instance.
- asStack() - Method in class EnergyStackWithoutParameters
-
Derive a
Stack
representation containing the identical channels to the current
instance.
- asStack() - Method in class RGBStack
-
Exposes the underlying stack, storing the three RGB channels in respective order.
- asStack(Logger) - Method in interface ProvidesStackInput
-
Exposes the input as a single
Stack
throw an error if more than one exists.
- asTuple() - Method in class Extent
-
Exposes the extent as a tuple.
- asVector3d() - Method in class DirectionVector
-
- at(int, int, int, int) - Static method in class BoundingBoxFactory
-
Short-hand factory method for creating a 2D bounding-box.
- at(int, int, int, int, int, int) - Static method in class BoundingBoxFactory
-
Short-hand factory method for creating a 3D bounding-box.
- atanHandlingNan(double) - Static method in class EllipseStandardFormConverter
-
- atBorder(Extent) - Method in class BoundingBox
-
Does the bounding-box have an edge at the border of an image of size extent
?
- AtBorderBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.border
-
- AtBorderBase() - Constructor for class AtBorderBase
-
- AtBorderXY - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.border
-
- AtBorderXY() - Constructor for class AtBorderXY
-
- atBorderXY(Extent) - Method in class BoundingBox
-
- 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
-
Extract a single
ObjectMask
into a new collection.
- AtIndex() - Constructor for class AtIndex
-
- atInputScale() - Method in class DualScale
-
The element scaled to match the size of the input-image.
- atInputScale() - Method in class SegmentedBackground
-
The background scaled to match the size of the input-image.
- atLeastOne(String, String, boolean, boolean) - Static method in class CheckMisconfigured
-
Checks that one of two properties is defined, or both.
- AtLeastZSlices - Class in org.anchoranalysis.plugin.io.bean.file.group.check
-
- AtLeastZSlices() - Constructor for class AtLeastZSlices
-
- atModelScale() - Method in class DualScale
-
The element scaled to match the size of the input for model inference.
- atModelScale() - Method in class SegmentedBackground
-
The background scaled to match the size of the input for model inference.
- 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 IntensityRange
-
- attachObject(Channel) - Method in class MaxIntensity
-
- attachObject(S) - Method in interface ChannelConverterAttached
-
Associate the convert with a particular object.
- attachObject(Histogram) - Method in class MaxIntensityFromHistogram
-
- attachObject(Histogram) - Method in class QuantileIntensityFromHistogram
-
- attachObject(Histogram) - Method in class UpperLowerQuantileIntensityFromHistogram
-
- AutoLocalThreshold - Class in org.anchoranalysis.plugin.fiji.bean.mask.provider
-
Applies local thresholding algorithm using Fiji's {link Auto_Local_Threshold} plugin
- AutoLocalThreshold() - Constructor for class AutoLocalThreshold
-
- Autoname - Class in org.anchoranalysis.plugin.io.bean.channel.map
-
Names of the channels from the metadata if it exists, or after RGB, or by index.
- Autoname() - Constructor for class Autoname
-
- Axis - Enum in org.anchoranalysis.spatial.axis
-
- AxisAlignedUnitVector - Class in org.anchoranalysis.image.bean.spatial.direction
-
Creates a
DirectionVector
that is a unit-vector along a particular image-axis.
- AxisAlignedUnitVector() - Constructor for class AxisAlignedUnitVector
-
- AxisConversionException - Exception in org.anchoranalysis.spatial.axis
-
When converting another type to a corresponding
Axis
fails.
- AxisConversionException(String) - Constructor for exception AxisConversionException
-
Create with a messsage, without an underlying cause.
- AxisConverter - Class in org.anchoranalysis.spatial.axis
-
Converts to/from
Axis
to a
String
and
int
representations, checking for
invalid input.
- AxisRatioEllipsoid - Class in org.anchoranalysis.plugin.points.bean.feature
-
- AxisRatioEllipsoid() - Constructor for class AxisRatioEllipsoid
-
- cache(Supplier<T>) - 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(FeatureCalculatorSingle<T>) - Static method in class FeatureCalculatorCache
-
- cache(FeatureCalculatorSingle<T>, int) - Static method in class FeatureCalculatorCache
-
- cache(FeatureCalculatorMulti<T>) - Static method in class FeatureCalculatorCache
-
- cache(FeatureCalculatorMulti<T>, int) - Static method in class FeatureCalculatorCache
-
- cache(NamedStacksSupplier) - Static method in interface NamedStacksSupplier
-
- 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
-
- CacheAndReuseStrategy(CacheCreator) - Constructor for class CacheAndReuseStrategy
-
- cacheChecked(CheckedSupplier<T, E>) - Static method in class CachedSupplier
-
- CacheCreator - Interface in org.anchoranalysis.feature.calculate.cache
-
- 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 exceptionally 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
-
A collection of existing caches that can collectively be used as sources for child-caches
elsewhere.
- CacheTransferSourceCollection() - Constructor for class CacheTransferSourceCollection
-
- calc(FeatureInputMarkCollection) - Method in class FeatureMarkCollection
-
- calc(EnergyMemoList, EnergySchemeWithSharedFeatures, EnergyStackWithoutParameters) - Method in class EnergySavedAll
-
- calc(CalculateForChild<T>, Feature<FeatureInputSingleObject>) - Method in class FeatureSingleObjectFromShared
-
- calc(CalculateForChild<T>, Feature<FeatureInputSingleObject>) - Method in class MaskAsSingleObject
-
- calc(CalculateForChild<T>, Feature<FeatureInputSingleObject>) - Method in class ObjectAggregationBase
-
- calc(FeatureCalculationInput<T>, CalculationPart<U, T>, Function<ResolvedPart<U, T>, CalculateInputFromDelegateOption<S, T, U>>, Feature<S>, ChildCacheName, double) - Static method in class CalculateInputFromDelegateOption
-
Calculates a feature using a cached-calculation as delegate.
- calc(FeatureInputMarkCollection) - Method in class NumberMarks
-
- calc(FeatureInputSingleObject, Ellipsoid) - Method in class AxisRatioEllipsoid
-
- calc(FeatureInputSingleObject, Ellipsoid) - Method in class EllipsoidBase
-
- calc(FeatureInputSingleObject, Ellipsoid) - Method in class Ellipsoidicity
-
- calculate(FeatureCalculationInput<T>) - Method in class Feature
-
Calculates a value for some input.
- calculate(FeatureCalculationInput<T>) - Method in class Constant
-
- calculate(FeatureCalculationInput<T>) - Method in class Reference
-
- calculate(FeatureCalculationInput<T>) - Method in class Sum
-
- calculate(FeatureInputResults) - Method in class Count
-
- calculate(FeatureCalculationInput<FeatureInputResults>) - Method in class FeatureResults
-
- calculate(FeatureInputResults) - Method in class FeatureResults
-
- calculate(FeatureInputResults) - Method in class FeatureResultsStatistic
-
- calculate(T) - Method in interface FeatureCalculatorMulti
-
Calculate the results of the features with a particular input.
- calculate(T, FeatureList<T>) - Method in interface FeatureCalculatorMulti
-
Calculates the results of a subset of the features with a particular input.
- calculate(T, ErrorReporter, boolean) - Method in interface FeatureCalculatorMulti
-
- calculate(T) - Method in class FeatureCalculatorMultiChangeInput
-
- calculate(T, FeatureList<T>) - Method in class FeatureCalculatorMultiChangeInput
-
- calculate(T) - Method in interface FeatureCalculatorSingle
-
Calculate the results of the feature with a particular input.
- calculate(T) - Method in class FeatureCalculatorSingleChangeInput
-
- calculate(T) - Method in class FeatureCalculatorSingleFromMulti
-
- calculate(Feature<S>, S, ChildCacheName) - Method in interface CalculateForChild
-
Calculates a feature in a child-cache.
- calculate(Feature<S>, CalculationPart<S, T>, ChildCacheName) - Method in interface CalculateForChild
-
Calculates a feature in a child-cache using a new input created from a
CalculationPart
.
- calculate(ChildCacheName, S, Function<CalculationPartResolver<S>, ResolvedPart<U, S>>) - Method in interface CalculateForChild
-
- calculate(Feature<T>) - Method in interface FeatureCalculationInput
-
Calculates the result of a feature using this input.
- calculate(FeatureList<T>) - Method in interface FeatureCalculationInput
-
Calculates the results of several features using this input.
- calculate(CalculationPart<S, T>) - Method in interface FeatureCalculationInput
-
Calculates a feature-calculation after resolving it against the main cache.
- calculate(ResolvedPart<S, T>) - Method in interface FeatureCalculationInput
-
Calculates a resolved Feature-calculation.
- calculate(Feature<T>, FeatureCalculationInput<T>) - Method in interface FeatureCalculator
-
Calculate the result of feature with a particular input.
- calculate(FeatureList<T>, FeatureCalculationInput<T>) - Method in interface FeatureCalculator
-
Calculates results for a list of features with a particular input, throwing an exception if a
calculation fails.
- calculate(T) - Method in class SequentialSession
-
- calculate(T, FeatureList<T>) - Method in class SequentialSession
-
- calculate(Feature<T>) - Method in class SessionInputSequential
-
- calculate(FeatureList<T>) - Method in class SessionInputSequential
-
- calculate(CalculationPart<S, T>) - Method in class SessionInputSequential
-
- calculate(ResolvedPart<S, T>) - Method in class SessionInputSequential
-
- calculate(Optional<Dimensions>, Optional<ImageSizeSuggestion>) - Method in class ScaleCalculator
-
Calculates a scaling-factor for a source image/entity of particular dimensions.
- calculate(FeatureCalculationInput<FeatureInputImageMetadata>) - Method in class FeatureImageMetadata
-
- calculate(ImageMetadata) - Method in class FeatureImageMetadata
-
- calculate(FeatureCalculationInput<FeatureInputHistogram>) - Method in class FeatureHistogramStatistic
-
- calculate(FeatureCalculationInput<FeatureInputObjectCollection>) - Method in class FeatureObjectCollection
-
- calculate(FeatureInputObjectCollection) - Method in class FeatureObjectCollection
-
- calculate(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class First
-
- calculate(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class Merged
-
- calculate(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class Minimum
-
- calculate(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class RatioFirstToSecond
-
- calculate(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class Second
-
- calculate(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class SubtractSecondFromFirst
-
- calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class CenterOfGravity
-
- calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class NumberVoxels
-
- calculate(FeatureCalculationInput<T>) - Method in class WithResolutionBase
-
- calculate(int[]) - Method in class VoxelScore
-
- calculate(FeatureInputPairObjects) - Method in class PairsTableCalculator
-
- calculate(FeatureInputPairObjects, FeatureList<FeatureInputPairObjects>) - Method in class PairsTableCalculator
-
- calculate(FeatureInputSingleObject) - Method in class SingleTableCalculator
-
- calculate(FeatureInputSingleObject, FeatureList<FeatureInputSingleObject>) - Method in class SingleTableCalculator
-
- calculate(int) - Method in interface SearchClosestValueMonoticallyIncreasing.ValueFunction
-
Calculate the output value, for a particular input-value.
- calculate(FeatureCalculationInput<FeatureInputPairMemo>) - Method in class AsSingle
-
- calculate(FeatureCalculationInput<FeatureInputSingleMemo>) - Method in class FeatureSingleMemo
-
- calculate(FeatureCalculationInput<FeatureInputMarkCollection>) - Method in class FeatureMarkCollection
-
- calculate(FeatureCalculationInput<FeatureInputMark>) - Method in class FeatureMark
-
- calculate(Optional<Dimensions>, Optional<ImageSizeSuggestion>) - Method in class ConstantScaleFactor
-
- calculate(Optional<Dimensions>, Optional<ImageSizeSuggestion>) - Method in class FitTo
-
- 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(FeatureCalculationInput<T>) - Method in class FromDimensionsBase
-
- calculate(FeatureCalculationInput<FeatureInputHistogram>) - Method in class LevelFromHistogram
-
- calculate(FeatureCalculationInput<FeatureInputHistogram>) - Method in class ThresholdHistogram
-
- calculate(ImageMetadata) - Method in class BitDepthPerChannel
-
- calculate(ImageMetadata) - Method in class NumberChannels
-
- calculate(ImageMetadata) - Method in class NumberFrames
-
- calculate(ImageMetadata) - Method in class NumberResolutionLevels
-
- calculate(ImageMetadata) - Method in class NumberSeries
-
- calculate(FeatureInputObjectCollection) - Method in class NumberObjects
-
- calculate(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class Intersection
-
- calculate(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class CostOverlapWithinMidpointDistance
-
- calculate(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class OverlapRelative
-
- calculate(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class TouchingVoxels
-
- calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class ArbitraryInsidePoint
-
- calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class AtBorderBase
-
- calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class BoundingBoxAlongAxisBase
-
- calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class BoundingBoxNumberVoxels
-
- calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class SpecificEnergyChannelBase
-
- calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class FeatureEnergyChannel
-
- calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class GradientMagnitude
-
- calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class GradientMeanForAxis
-
- calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class ImageMomentsBase
-
- calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class DerivedObject
-
- calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class NumberRemovedVoxelsAfterClosing
-
- calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class OutlineKernelBase
-
- calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class ObjectRadiusStandardDeviation
-
- calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class ShapeRegularityCenterSlice
-
- calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class ShapeRegularityMIP
-
- calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class FeatureIntersectingObjects
-
- calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class PairedWithMask
-
- calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class MaximumNumberContourVoxelsOnSlice
-
- calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class MaximumNumberVoxelsOnSlice
-
- calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class SurfaceNumberVoxelsBase
-
- calculate(int[]) - Method in class Difference
-
- calculate(int[]) - Method in class Identity
-
- calculate(int[]) - Method in class IdentityImposeValueRelationToHistogram
-
- calculate(int[]) - Method in class OutsideRange
-
- calculate(int[]) - Method in class RejectIfIntensityLessThan
-
- calculate(int[]) - Method in class SingleChannel
-
- calculate(FeatureCalculationInput<T>) - Method in class FeatureSingleObjectFromShared
-
- calculate(FeatureCalculationInput<T>) - Method in class ParamFromCollection
-
- calculate(FeatureCalculationInput<T>) - Method in class DataTypeMaxIntensity
-
- calculate(FeatureCalculationInput<FeatureInputStack>) - Method in class Intensity
-
- calculate(FeatureCalculationInput<FeatureInputStack>) - Method in class NumberChannels
-
- calculate(FeatureCalculationInput<FeatureInputStack>) - Method in class AsObjectMask
-
- calculate(FeatureCalculationInput<FeatureInputStack>) - Method in class QuantileAcrossConnectedComponents
-
- calculate(ObjectMask) - Method in interface PayloadCalculator
-
- calculate(FeatureCalculationInput<FeatureInputMark>) - Method in class FeatureMarkDirection
-
- calculate(FeatureCalculationInput<FeatureInputMark>) - Method in class EccentricityAxisAligned
-
- calculate(FeatureCalculationInput<FeatureInputMark>) - Method in class MaxRatioRadii
-
- calculate(FeatureCalculationInput<FeatureInputMark>) - Method in class OrderedRadius
-
- calculate(FeatureCalculationInput<FeatureInputMark>) - Method in class RadiiRatio
-
- calculate(FeatureCalculationInput<FeatureInputMark>) - Method in class BoundingBoxExtent
-
- calculate(FeatureCalculationInput<FeatureInputMark>) - Method in class MarkEllipseCircumEstimate
-
- calculate(FeatureCalculationInput<FeatureInputMark>) - Method in class Volume
-
- calculate(FeatureCalculationInput<FeatureInputAllMemo>) - Method in class AsCollection
-
- calculate(FeatureCalculationInput<FeatureInputAllMemo>) - Method in class AsSingleMark
-
- calculate(FeatureCalculationInput<FeatureInputAllMemo>) - Method in class CoefficientOfVarianceFromAll
-
- calculate(FeatureCalculationInput<FeatureInputAllMemo>) - Method in class MeanFromAll
-
- calculate(FeatureCalculationInput<FeatureInputAllMemo>) - Method in class NumberMarks
-
- calculate(FeatureCalculationInput<FeatureInputSingleMemo>) - Method in class AsMark
-
- calculate(FeatureCalculationInput<FeatureInputSingleMemo>) - Method in class AsObject
-
- calculate(FeatureCalculationInput<FeatureInputSingleMemo>) - Method in class BBoxRatio
-
- calculate(FeatureCalculationInput<FeatureInputSingleMemo>) - Method in class Intensity
-
- calculate(FeatureCalculationInput<FeatureInputSingleMemo>) - Method in class MaxSliceArea
-
- calculate(FeatureCalculationInput<FeatureInputSingleMemo>) - Method in class MeanIntensityDifference
-
- calculate(FeatureCalculationInput<FeatureInputSingleMemo>) - Method in class Size
-
- calculate(FeatureCalculationInput<FeatureInputSingleMemo>) - Method in class SurfaceSizeMaskNonZero
-
- calculate(FeatureCalculationInput<FeatureInputPairMemo>) - Method in class BoundingBoxZDistance
-
- calculate(FeatureCalculationInput<FeatureInputPairMemo>) - Method in class BoundingBoxZOverlapRatio
-
- calculate(FeatureCalculationInput<FeatureInputPairMemo>) - Method in class MinimumDistanceByDimension
-
- calculate(FeatureCalculationInput<FeatureInputPairMemo>) - Method in class FeatureAsIndividualProportionate
-
- calculate(FeatureCalculationInput<FeatureInputPairMemo>) - Method in class MinFeatureAsIndividual
-
- calculate(FeatureCalculationInput<FeatureInputPairMemo>) - Method in class MaxOverlapRatio
-
- calculate(FeatureCalculationInput<FeatureInputPairMemo>) - Method in class OverlapNumberVoxelsMask
-
- calculate(FeatureCalculationInput<FeatureInputPairMemo>) - Method in class OverlapNumVoxels
-
- calculate(FeatureCalculationInput<FeatureInputPairMemo>) - Method in class OverlapRatio
-
- calculate(FeatureCalculationInput<FeatureInputPairMemo>) - Method in class OverlapRatioMask
-
- calculate(FeatureCalculationInput<FeatureInputStack>) - Method in class HOGFeature
-
- calculate(FeatureCalculationInput<T>) - Method in class AbsoluteValue
-
- calculate(FeatureCalculationInput<T>) - Method in class Divide
-
- calculate(FeatureCalculationInput<T>) - Method in class InvertedMax
-
- calculate(FeatureCalculationInput<T>) - Method in class Multiply
-
- calculate(FeatureCalculationInput<T>) - Method in class IfCondition
-
- calculate(FeatureCalculationInput<T>) - Method in class FromDictionary
-
- calculate(FeatureCalculationInput<T>) - Method in class Maximum
-
- calculate(FeatureCalculationInput<T>) - Method in class Mean
-
- calculate(FeatureCalculationInput<T>) - Method in class MeanGeometric
-
- calculate(FeatureCalculationInput<T>) - Method in class Minimum
-
- calculate(FeatureCalculationInput<T>) - Method in class NormalizedRange
-
- calculate(FeatureCalculationInput<T>) - Method in class Range
-
- calculate(FeatureCalculationInput<T>) - Method in class RangeCompareBase
-
- calculate(FeatureCalculationInput<T>) - Method in class StatisticalBase
-
- calculate(FeatureCalculationInput<T>) - Method in class WithValueBase
-
- calculate(FeatureCalculationInput<T>) - Method in class ConvertUnits
-
- calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class EllipsoidBase
-
- calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class Ellipticity
-
- calculate(FeatureCalculationInput<FeatureInput>) - Method in class MockFeatureWithCalculation
-
- calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class Kernel
-
- calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class KernelBirth
-
- calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class KernelBirthAndKill
-
- calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class KernelDeath
-
- calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class KernelExchange
-
- calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class KernelInitialMarksFromPartition
-
- calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class KernelInitialMarksProposed
-
- calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class KernelInitialMarksVoxelized
-
- calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class KernelMerge
-
- calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class KernelReplace
-
- calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class KernelSplit
-
- calculateAcceptanceProbability(Kernel<?, ?>, Optional<T>, T, int, KernelCalculationContext) - Method in class AcceptanceProbabilityCalculator
-
- calculateAndOutput(T, FeatureCalculationContext<S>) - Method in class FeatureSource
-
Processes one input to calculate feature-results and output them to the file-system.
- calculateAndOutput(T, FeatureCalculationContext<FeatureList<S>>) - Method in class SingleRowPerInput
-
- calculateAndOutput(MultiInput, FeatureCalculationContext<FeatureTableCalculator<T>>) - Method in class FromObjects
-
- calculateAreaXYAsDouble() - Method in class Extent
-
Calculates the area freshly by multiplying the x-size with y-size, as doubles.
- calculateAt(KernelPointCursor) - Method in class AndKernel
-
- calculateAt(KernelPointCursor) - Method in class BinaryKernel
-
Calculates the boolean at a particular point.
- calculateAt(KernelPointCursor) - Method in class ConditionalKernel
-
- calculateAt(KernelPointCursor) - Method in class CountKernel
-
Calculates the count at a particular point.
- calculateAt(KernelPointCursor) - Method in class BinaryKernelMorphological
-
- calculateCheckInitialized(FeatureCalculationInput<T>) - Method in class Feature
-
Calculates the result of a feature and throws an exception if the feature has not been
initialized.
- calculateConnectedComponentID(Point3i, int) - Method in class EncodedVoxels
-
- calculateContext(MarkFactoryContext) - Method in class OptimizationContext
-
- calculateCornerMaxExclusive() - Method in class BoundingBox
-
The maximum (right-most) point just outside the box.
- calculateCornerMaxInclusive() - Method in class BoundingBox
-
The maximum (right-most) point inside the box.
- calculateDenominator(FeatureInputPairObjects) - Method in class OverlapRelative
-
- calculateDenominator(FeatureInputPairObjects) - Method in class OverlapRelativeToFirst
-
- calculateDenominator(FeatureInputPairObjects) - Method in class OverlapRelativeToMaxVolume
-
- calculateDenominator(FeatureInputPairObjects) - Method in class OverlapRelativeToMerged
-
- calculateDenominator(FeatureInputPairObjects) - Method in class OverlapRelativeToSecond
-
- calculateDensityRatio(double, double, int) - Method in class AnnealScheme
-
- CalculateDeriveMarkCollectionInput - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.all
-
- CalculateDeriveMarkCollectionInput() - Constructor for class CalculateDeriveMarkCollectionInput
-
- CalculateDeriveMarkInput - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.all
-
- CalculateDeriveMarkInput() - Constructor for class CalculateDeriveMarkInput
-
- CalculateDeriveObjectInput - Class in org.anchoranalysis.plugin.image.feature.bean.stack.object
-
- CalculateDeriveObjectInput(int) - Constructor for class CalculateDeriveObjectInput
-
- CalculateDeriveSingleMemoFromPair - Class in org.anchoranalysis.mpp.feature.bean.energy.element
-
- CalculateDeriveSingleMemoFromPair(boolean) - Constructor for class CalculateDeriveSingleMemoFromPair
-
- CalculateDilation - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological
-
- CalculateDilationMap - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological
-
- CalculateDilationMap(boolean) - Constructor for class CalculateDilationMap
-
- CalculateDilationMap(CalculateIncrementalOperationMap) - Constructor for class CalculateDilationMap
-
- calculateEccentricity(double, double) - Static method in class PrincipalAxisEccentricity
-
- CalculateEllipseLeastSquares - Class in org.anchoranalysis.plugin.points.calculate.ellipse
-
- CalculateEllipseLeastSquares() - Constructor for class CalculateEllipseLeastSquares
-
- CalculateEllipsoidLeastSquares - Class in org.anchoranalysis.plugin.points.calculate.ellipsoid
-
- CalculateErosion - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological
-
- CalculateErosionMap - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological
-
- CalculateErosionMap(boolean) - Constructor for class CalculateErosionMap
-
- CalculateErosionMap(CalculateIncrementalOperationMap) - Constructor for class CalculateErosionMap
-
- calculateFeatureByIdentifier(String, FeatureCalculationInput<T>) - Method in interface FeatureSymbolCalculator
-
Searches for a feature that matches a particular identifier.
- calculateFeatureOn(ObjectCollection, FeatureCalculatorSingle<FeatureInputSingleObject>) - Method in class ReportFeatureOnObject
-
- calculateFeatureOn(ObjectCollection, FeatureCalculatorSingle<FeatureInputObjectCollection>) - Method in class ReportFeatureOnObjectCollection
-
- calculateFeatureOn(ObjectCollection, FeatureCalculatorSingle<T>) - Method in class ReportFeatureOnObjectsBase
-
- CalculateFeaturesForObjects<T extends FeatureInput> - Class in org.anchoranalysis.plugin.image.task.feature.calculator
-
- CalculateFeaturesForObjects(CombineObjectsForFeatures<T>, InitializationWithEnergyStack, boolean, FeatureCalculationContext<FeatureTableCalculator<T>>) - Constructor for class CalculateFeaturesForObjects
-
- calculateForAxis(Dimensions, Axis) - Method in class Extent
-
- calculateForAxis(Dimensions, Axis) - Method in class ForSpecificAxis
-
- calculateForAxis(Dimensions, Axis) - Method in class VoxelPhysicalSize
-
- calculateForChannel(FeatureCalculationInput<FeatureInputSingleObject>, Channel) - Method in class FeatureEnergyChannel
-
- calculateForChannel(FeatureCalculationInput<FeatureInputSingleObject>, Channel) - Method in class Intensity
-
- calculateForChannel(FeatureCalculationInput<FeatureInputSingleObject>, Channel) - Method in class IntensityMeanMaxSlice
-
- calculateForChannel(FeatureCalculationInput<FeatureInputSingleObject>, Channel) - Method in class IntensityMeanShellBase
-
- calculateForChannel(FeatureCalculationInput<FeatureInputSingleObject>, Channel) - Method in class TextureScore
-
- CalculateForChild<T extends FeatureInput> - Interface in org.anchoranalysis.feature.calculate.cache
-
Performs calculations using child-caches instead of the main cache
- calculateForEllipsoid(Ellipsoid, Orientation, Vector3d) - Method in class DotProductOrientationToVector
-
- calculateForEllipsoid(Ellipsoid, Orientation, Vector3d) - Method in class EllipsoidAxisRatio
-
- calculateForEllipsoid(Ellipsoid, Orientation, Vector3d) - Method in class EllipsoidMaxAreaIntersectingPlane
-
- calculateForEllipsoid(Ellipsoid, Orientation, Vector3d) - Method in class FeatureMarkDirection
-
- calculateForNewMark(MarksFromPartition, Set<Mark>, KernelCalculationContext) - Method in class KernelBirthPartition
-
- calculateForNewMark(T, Set<Mark>, KernelCalculationContext) - Method in class KernelBirth
-
- calculateForNewMark(VoxelizedMarksWithEnergy, Set<Mark>, KernelCalculationContext) - Method in class KernelBirthVoxelized
-
- calculateForObjects(ObjectCollectionProvider, LabelsForInput) - Method in class CalculateFeaturesForObjects
-
- calculateForObjects(ObjectCollection, EnergyStack, LabelsForInput) - Method in class CalculateFeaturesForObjects
-
Calculates the feature-results for objects
, and stores the results.
- 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
CalculationPart
s that derive from an existing "delegate" calculation.
- CalculateInputFromDelegate(CalculationPart<U, T>, CalculationPartResolver<T>) - Constructor for class CalculateInputFromDelegate
-
- CalculateInputFromDelegate(ResolvedPart<U, T>) - Constructor for class CalculateInputFromDelegate
-
- CalculateInputFromDelegateOption<S extends FeatureInput,T extends FeatureInput,U> - Class in org.anchoranalysis.plugin.image.feature.object.calculation.delegate
-
- CalculateInputFromDelegateOption(ResolvedPart<U, T>) - Constructor for class CalculateInputFromDelegateOption
-
Creates with a delegate.
- CalculateInputFromPair - Class in org.anchoranalysis.image.feature.calculation
-
Calculates a single-input from a pair
- CalculateInputFromPair(CalculateInputFromPair.Extract) - Constructor for class CalculateInputFromPair
-
- CalculateInputFromPair.Extract - Enum in org.anchoranalysis.image.feature.calculation
-
- CalculateIntersecting - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting
-
- CalculateIntersecting(ResolvedPart<ObjectCollection, FeatureInputSingleObject>, int) - Constructor for class CalculateIntersecting
-
- CalculateLevel - Class in org.anchoranalysis.image.bean.threshold
-
Calculates a threshold-level from a histogram.
- CalculateLevel() - Constructor for class CalculateLevel
-
- calculateLevel(Histogram) - Method in class CalculateLevel
-
Determines a voxel intensity that can be used for thresholding.
- calculateLevel(Histogram) - Method in class CalculateLevelRelativeToThreshold
-
- calculateLevel(Histogram) - Method in class ClampHistogramMax
-
- calculateLevel(Histogram) - Method in class Constant
-
- calculateLevel(Histogram) - Method in class EmptyHistogramConstant
-
- calculateLevel(Histogram) - Method in class Maximum
-
- calculateLevel(Histogram) - Method in class Minimum
-
- calculateLevel(Histogram) - Method in class Otsu
-
- calculateLevel(Histogram) - Method in class OtsuWeighted
-
- calculateLevel(Histogram) - Method in class Quantile
-
- CalculateLevel - Class in org.anchoranalysis.plugin.image.feature.bean.score
-
- CalculateLevel() - Constructor for class CalculateLevel
-
- CalculateLevelBase - Class in org.anchoranalysis.plugin.image.feature.bean.score
-
- CalculateLevelBase() - Constructor for class CalculateLevelBase
-
- calculateLevelFromDelegate(Histogram) - Method in class CalculateLevelUnary
-
Determines a voxel intensity that can be used for thresholding from the delegate calculateLevel
.
- CalculateLevelListBase - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold
-
- CalculateLevelListBase() - Constructor for class CalculateLevelListBase
-
- CalculateLevelRelativeToThreshold - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold
-
- CalculateLevelRelativeToThreshold() - Constructor for class CalculateLevelRelativeToThreshold
-
- CalculateLevelUnary - Class in org.anchoranalysis.image.bean.threshold
-
- CalculateLevelUnary() - Constructor for class CalculateLevelUnary
-
- calculateMaximum() - Method in class Histogram
-
Calculates the maximum value with non zero-count among the histogram values.
- calculateMaybeSuppressErrors(FeatureInputPairObjects, ErrorReporter) - Method in class PairsTableCalculator
-
- calculateMeanIntensityObject(Channel, ObjectMask) - Static method in class IntensityMeanCalculator
-
- calculateMeanIntensityObject(Channel, ObjectMask, boolean) - Static method in class IntensityMeanCalculator
-
- calculateMinimum() - Method in class Histogram
-
Calculates the minimum value with non zero-count among the histogram values.
- calculateMinMax(Optional<Resolution>, boolean) - Method in class MarkBounds
-
- calculateMode() - Method in class Histogram
-
Calculates the mode of the histogram values.
- calculateNewMaxCurrentValue() - Method in class PriorityQueueIndexRangeDownhill
-
- CalculateNumberVoxels - Class in org.anchoranalysis.image.feature.calculation
-
- CalculateNumberVoxels(boolean) - Constructor for class CalculateNumberVoxels
-
- CalculateObjectMask - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single
-
- CalculateObjectMask(CalculateObjectMask) - Constructor for class CalculateObjectMask
-
Copy constructor
- CalculateObjectMask(int, ResolvedPartMap<ObjectMask, FeatureInputSingleObject, Integer>) - Constructor for class CalculateObjectMask
-
- CalculateOrientationChange - Interface in org.anchoranalysis.image.io.stack
-
Calculates any needed orientation change.
- calculateOrientationChange(Logger) - Method in interface CalculateOrientationChange
-
Calculates any needed orientation change.
- CalculateOverlap - Class in org.anchoranalysis.plugin.mpp.feature.overlap
-
- CalculateOverlap(int) - Constructor for class CalculateOverlap
-
- CalculateOverlapMask - Class in org.anchoranalysis.plugin.mpp.feature.overlap
-
- CalculateOverlapMask(int, int, byte) - Constructor for class CalculateOverlapMask
-
- CalculateOverlapMIP - Class in org.anchoranalysis.plugin.mpp.feature.overlap
-
- CalculateOverlapMIP(int) - Constructor for class CalculateOverlapMIP
-
- CalculateOverlapMIPBase - Class in org.anchoranalysis.plugin.mpp.feature.overlap
-
- CalculateOverlapMIPBase(int) - Constructor for class CalculateOverlapMIPBase
-
- CalculateOverlapMIPRatio - Class in org.anchoranalysis.plugin.mpp.feature.overlap
-
- CalculateOverlapMIPRatio(int) - Constructor for class CalculateOverlapMIPRatio
-
- calculateOverlapResult(double, MaxIntensityProjectionPair) - Method in class CalculateOverlapMIP
-
- calculateOverlapResult(double, MaxIntensityProjectionPair) - Method in class CalculateOverlapMIPBase
-
- calculateOverlapResult(double, MaxIntensityProjectionPair) - Method in class CalculateOverlapMIPRatio
-
- calculatePoints(Point3d, Orientation, boolean, RandomNumberGenerator, boolean) - Method in class MergeLists
-
- calculatePoints(Point3d, Orientation, boolean, RandomNumberGenerator, boolean) - Method in class PointsFromOrientationProposer
-
- calculatePoints(Point3d, Orientation, boolean, RandomNumberGenerator, boolean) - Method in class TraversePointsOnContour
-
- calculateResultsForInput(FileInput, FeatureCalculationContext<FeatureList<FeatureInputHistogram>>) - Method in class FromHistogram
-
- calculateResultsForInput(ProvidesStackInput, FeatureCalculationContext<FeatureList<FeatureInputStack>>) - Method in class FromImage
-
- calculateResultsForInput(ImageMetadataInput, FeatureCalculationContext<FeatureList<FeatureInputImageMetadata>>) - Method in class FromImageMetadata
-
- calculateResultsForInput(T, FeatureCalculationContext<FeatureList<S>>) - Method in class SingleRowPerInput
-
Calculates feature-results for a particular input.
- calculateRunningSum(Mask, Voxels<UnsignedByteBuffer>) - Static method in class IterateVoxelsMask
-
Calculates the sum and count across voxels intensity that correspond to on voxels on a
mask
- calculateScaleFactor(Optional<Extent>) - Method in interface ImageSizeSuggestion
-
Calculates the scaling factor.
- CalculateShellObjectMask - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single
-
- CalculateShellObjectMask(ResolvedPart<ObjectMask, FeatureInputSingleObject>, ResolvedPart<ObjectMask, FeatureInputSingleObject>, int, boolean, boolean) - Constructor for class CalculateShellObjectMask
-
- calculateSigma(Dimensions, MessageLogger) - Method in class BlurStrategy
-
- calculateStatisticFrom(Histogram) - Method in class FeatureHistogramStatistic
-
Calculates the statistic from the histogram, that is subsequently returned as the
feature-value.
- calculateStatisticFrom(Histogram) - Method in class Mean
-
- calculateStatisticFrom(Histogram) - Method in class CoefficientOfVariation
-
- calculateStatisticFrom(Histogram) - Method in class Count
-
- calculateStatisticFrom(Histogram) - Method in class Kurtosis
-
- calculateStatisticFrom(Histogram) - Method in class Maximum
-
- calculateStatisticFrom(Histogram) - Method in class MeanRaisedToPower
-
- calculateStatisticFrom(Histogram) - Method in class Median
-
- calculateStatisticFrom(Histogram) - Method in class Minimum
-
- 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 StandardDeviation
-
- calculateStatisticFrom(Histogram) - Method in class Sum
-
- calculateStatisticFrom(Histogram) - Method in class TotalCount
-
- calculateStatisticFrom(Histogram) - Method in class Variance
-
- calculateStatisticFrom(Histogram) - Method in class RatioThreshold
-
- calculateSum() - Method in class Histogram
-
Calculates the sum of all values in the distribution considering their counts.
- calculateSumCubes() - Method in class Histogram
-
Calculates the cube of the squares of all values in the distribution considering their
counts.
- calculateSumSquares() - Method in class Histogram
-
Calculates the sum of the squares of all values in the distribution considering their
counts.
- calculateSuppressErrors(T, ErrorReporter) - Method in interface FeatureCalculatorMulti
-
Calculates the results for an
input
recording the error to an
ErrorReporter
if anything goes wrong, but throwing no exception.
- calculateSuppressErrors(T, ErrorReporter) - Method in class FeatureCalculatorMultiChangeInput
-
- calculateSuppressErrors(T, ErrorReporter) - Method in interface FeatureCalculatorSingle
-
Calculates the result for an
input
recording the error to an
ErrorReporter
if
anything goes wrong, but throwing no exception.
- calculateSuppressErrors(T, ErrorReporter) - Method in class FeatureCalculatorSingleChangeInput
-
- calculateSuppressErrors(T, ErrorReporter) - Method in class FeatureCalculatorSingleFromMulti
-
- calculateSuppressErrors(T, ErrorReporter) - Method in class SequentialSession
-
Calculates the results for the next input in the session, reporting any exceptions into an
ErrorReporter
.
- calculateSuppressErrors(FeatureInputPairObjects, ErrorReporter) - Method in class PairsTableCalculator
-
- calculateSuppressErrors(FeatureInputSingleObject, ErrorReporter) - Method in class SingleTableCalculator
-
- calculateTemperature(int) - Method in class AnnealScheme
-
- calculateTemperature(int) - Method in class Geometry
-
- calculateTemperature(int) - Method in class NoAnnealing
-
- calculateVolume() - Method in class Dimensions
-
Calculates the volume of the
Extent
when considered as a box.
- calculateVolume() - Method in class Extent
-
Calculates the volume of the
Extent
when considered as a box.
- calculateVolumeAsInt() - Method in class Extent
-
- calculateWith(Feature<T>, T, Logger) - Static method in class FeatureSession
-
Starts a feature-session for a single feature - and performs a calculation.
- calculateWithChannel(ObjectMask, Channel) - Method in class CountEqual
-
- calculateWithChannel(ObjectMask, Channel) - Method in class SpecificEnergyChannelBase
-
- calculateWithIntersection(ObjectMask, ObjectMask, BoundingBox) - Method in class HasTouchingVoxels
-
- calculateWithIntersection(ObjectMask, ObjectMask, BoundingBox) - Method in class NumberTouchingVoxelFaces
-
- calculateWithIntersection(ObjectMask, ObjectMask, BoundingBox) - Method in class NumberTouchingVoxels
-
- calculateWithIntersection(ObjectMask, ObjectMask, BoundingBox) - Method in class TouchingVoxels
-
- calculateWithParameters(ObjectMask, KernelApplicationParameters, CheckedSupplier<EnergyStack, FeatureCalculationException>) - Method in class NumberVoxelsAtBorder
-
- calculateWithParameters(ObjectMask, KernelApplicationParameters, CheckedSupplier<EnergyStack, FeatureCalculationException>) - Method in class NumberNeighboringVoxels
-
- calculateWithParameters(ObjectMask, KernelApplicationParameters, CheckedSupplier<EnergyStack, FeatureCalculationException>) - Method in class OutlineKernelBase
-
- calculateWithResolution(double, Resolution) - Method in class FeatureConvertUnits
-
- calculateWithResolution(double, Resolution) - Method in class WithResolutionBase
-
- calculateWithResolution(double, Resolution) - Method in class UnitsWithinRange
-
- calculateZScore(double, double, double) - Static method in class ZScoreCalculator
-
Calculates a Z-Score for a particular value and parameterization.
- CalculationPart<S,T extends FeatureInput> - Class in org.anchoranalysis.feature.calculate.part
-
A sub-part of the calculation of a feature, that can be cached, and reused by other features.
- CalculationPart() - Constructor for class CalculationPart
-
- CalculationPartMap<S,T extends FeatureInput,U,E extends Exception> - Class in org.anchoranalysis.feature.calculate.part
-
Similar to a
CalculationPart
but stores several evaluation results, differentiated by a
key.
- CalculationPartMap(int) - Constructor for class CalculationPartMap
-
Creates for a particular cache-size.
- CalculationPartResolver<T extends FeatureInput> - Interface in org.anchoranalysis.feature.calculate.part
-
- calculationResultsNeeded(MultiLevelOutputEnabled) - Method in class FeatureOutputNames
-
If any output is enabled that requires calculation of feature results?
- calculator() - Method in interface FeatureCalculationCache
-
A means of calculating feature values using this cache.
- calculatorForAll(FeatureList<T>) - Method in class FeatureCalculatorFromProvider
-
Calculates all image-features in the feature-store
- calculatorSingleFromProvider(FeatureListProvider<T>, String) - Method in class FeatureCalculatorFromProvider
-
Calculates a single-feature that comes from a provider (but can reference the other features
from the store)
- call(CheckedSupplier<T, E>) - Method in class CachedSupplierBase
-
Gets the value supplied by supplier
via the cache if it exists, or otherwise via the
supplier.
- call() - Method in class CallableJob
-
- CallableJob<T extends InputFromManager,S> - Class in org.anchoranalysis.experiment.task.processor
-
A job derived from a
Task
that can be placed on different threads
- CallableJob(Task<T, S>, ParametersUnbound<T, S>, JobStateMonitor, JobDescription, ConcurrentJobMonitor, Optional<MessageLogger>, int) - Constructor for class CallableJob
-
Constructor.
- callEachPointInNeighborhood(Point3i, Neighborhood, boolean, ProcessVoxelNeighbor<T>, int, int) - Static method in class IterateVoxelsNeighbors
-
Iterate over each point in the neighborhood of an existing point.
- canEqual(Object) - Method in class DoubleList
-
- canEqual(Object) - Method in class DoubleSet
-
- canEqual(Object) - Method in class IntegerList
-
- canEqual(Object) - Method in class IntegerSet
-
- canEqual(Object) - Method in class StringList
-
- canEqual(Object) - Method in class StringSet
-
- canEqual(Object) - Method in class RootPath
-
- canEqual(Object) - Method in class EqualToBean
-
- canEqual(Object) - Method in class GreaterThanBean
-
- canEqual(Object) - Method in class GreaterThanEqualToBean
-
- canEqual(Object) - Method in class LessThanBean
-
- canEqual(Object) - Method in class LessThanEqualToBean
-
- canEqual(Object) - Method in class RelationBean
-
- canEqual(Object) - Method in class RelationToConstant
-
- canEqual(Object) - Method in class Indexable
-
- canEqual(Object) - Method in class ChildCacheName
-
- canEqual(Object) - Method in class FeatureInputDimensions
-
- canEqual(Object) - Method in class FeatureInputEnergy
-
- canEqual(Object) - Method in class FeatureInputNull
-
- canEqual(Object) - Method in class SimpleName
-
- canEqual(Object) - Method in class SizeXY
-
- canEqual(Object) - Method in class CalculateLevelUnary
-
- canEqual(Object) - Method in class BinaryNotOffVoxels
-
- canEqual(Object) - Method in class BinaryNotOnVoxels
-
- canEqual(Object) - Method in class BinaryOffVoxels
-
- canEqual(Object) - Method in class BinaryOnVoxels
-
- canEqual(Object) - Method in class BinaryVoxelsBase
-
- canEqual(Object) - Method in class CalculateInputFromPair
-
- canEqual(Object) - Method in class CalculateNumberVoxels
-
- canEqual(Object) - Method in class FeatureInputImageMetadata
-
- canEqual(Object) - Method in class FeatureInputObjectCollection
-
- canEqual(Object) - Method in class FeatureInputPairObjects
-
- canEqual(Object) - Method in class FeatureInputSingleObject
-
- canEqual(Object) - Method in class FeatureInputStack
-
- canEqual(Object) - Method in class LabelledWithConfidence
-
- canEqual(Object) - Method in class WithConfidence
-
- 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 WithPriority
-
- canEqual(Object) - Method in class QuadraticEquationSolver.QuadraticRoots
-
- canEqual(Object) - Method in class MeanScale
-
- canEqual(Object) - Method in class RegionMap
-
- canEqual(Object) - Method in class RegionMembership
-
- canEqual(Object) - Method in class RegionMembershipWithFlags
-
- canEqual(Object) - Method in class CalculateDeriveSingleMemoFromPair
-
- canEqual(Object) - Method in class FeatureInputMark
-
- canEqual(Object) - Method in class IndexableMarksWithEnergy
-
- canEqual(Object) - Method in class FeatureInputAllMemo
-
- canEqual(Object) - Method in class FeatureInputPairMemo
-
- canEqual(Object) - Method in class FeatureInputSingleMemo
-
- canEqual(Object) - Method in class MemoList
-
- canEqual(Object) - Method in class ColoredMarksWithDisplayStack
-
- canEqual(Object) - Method in class MarksWithDisplayStack
-
- canEqual(Object) - Method in class OverlayMark
-
- canEqual(Object) - Method in class FeedbackBeginParameters
-
- canEqual(Object) - Method in class CalculateLevelListBase
-
- canEqual(Object) - Method in class CalculateLevelRelativeToThreshold
-
- canEqual(Object) - Method in class ClampHistogramMax
-
- canEqual(Object) - Method in class Constant
-
- canEqual(Object) - Method in class EmptyHistogramConstant
-
- canEqual(Object) - Method in class IfGreaterThan
-
- canEqual(Object) - Method in class IfLessThan
-
- canEqual(Object) - Method in class Maximum
-
- canEqual(Object) - Method in class Minimum
-
- canEqual(Object) - Method in class Otsu
-
- canEqual(Object) - Method in class OtsuWeighted
-
- canEqual(Object) - Method in class Quantile
-
- canEqual(Object) - Method in class MorphologicalIterations
-
- canEqual(Object) - Method in class CalculateIntersecting
-
- canEqual(Object) - Method in class CalculateDeriveObjectInput
-
- canEqual(Object) - Method in class CalculateInputFromDelegate
-
- canEqual(Object) - Method in class CalculateInputFromDelegateOption
-
- canEqual(Object) - Method in class CalculateIncrementalOperationMap
-
- canEqual(Object) - Method in class CalculateObjectMask
-
- canEqual(Object) - Method in class CalculateShellObjectMask
-
- canEqual(Object) - Method in class CalculateDilation
-
- canEqual(Object) - Method in class CalculateDilationMap
-
- canEqual(Object) - Method in class CalculateErosion
-
- canEqual(Object) - Method in class CalculateErosionMap
-
- canEqual(Object) - Method in class CalculateHistogram
-
- canEqual(Object) - Method in class CalculateHistogramMasked
-
- canEqual(Object) - Method in class ChangeableOutputSequence
-
- canEqual(Object) - Method in class SortedSetChannel
-
- canEqual(Object) - Method in class SortedSetSlice
-
- canEqual(Object) - Method in class AllSlicesMaskEverythingNonZero
-
- canEqual(Object) - Method in class AllSlicesMaskNonZero
-
- canEqual(Object) - Method in class CenterSlice
-
- canEqual(Object) - Method in class CenterSliceBase
-
- canEqual(Object) - Method in class CenterSliceWindow
-
- canEqual(Object) - Method in class GreatestAreaSlice
-
- canEqual(Object) - Method in class IndexedRegionBase
-
- canEqual(Object) - Method in class SelectSlicesBase
-
- canEqual(Object) - Method in class SelectSlicesWithIndexBase
-
- canEqual(Object) - Method in class Specific
-
- canEqual(Object) - Method in class CalculateDeriveMarkCollectionInput
-
- canEqual(Object) - Method in class CalculateDeriveMarkInput
-
- canEqual(Object) - Method in class CalculateOverlap
-
- canEqual(Object) - Method in class CalculateOverlapMask
-
- canEqual(Object) - Method in class CalculateOverlapMIP
-
- canEqual(Object) - Method in class CalculateOverlapMIPBase
-
- canEqual(Object) - Method in class CalculateOverlapMIPRatio
-
- canEqual(Object) - Method in class HOGParameters
-
- canEqual(Object) - Method in class FitResult
-
- canEqual(Object) - Method in class CalculateEllipseLeastSquares
-
- canEqual(Object) - Method in class CalculateEllipsoidLeastSquares
-
- canEqual(Object) - Method in class Orientation2D
-
- canEqual(Object) - Method in class Orientation3DEulerAngles
-
- canEqual(Object) - Method in class OrientationAxisAngle
-
- canEqual(Object) - Method in class OrientationRotationMatrix
-
- canEqual(Object) - Method in class Point3d
-
- canEqual(Object) - Method in class Point3f
-
- canEqual(Object) - Method in class Point3i
-
- canEqual(Object) - Method in class Tuple3d
-
- canEqual(Object) - Method in class Tuple3f
-
- canEqual(Object) - Method in class Tuple3i
-
- canEqual(Object) - Method in class Vector3d
-
- canExceptionBeCombined(Throwable) - Method in exception BeanMisconfiguredXMLException
-
- canExceptionBeCombined(Throwable) - Method in exception LocalisedBeanException
-
- canExceptionBeCombined(Throwable) - Method in exception AnchorCombinableException
-
Can another exception be combined with this exception?
- canExceptionBeCombined(Throwable) - Method in exception NamedProviderGetException
-
- canExceptionBeSkipped(Throwable) - Method in exception BeanMisconfiguredXMLException
-
- canExceptionBeSkipped(Throwable) - Method in exception LocalisedBeanException
-
- canExceptionBeSkipped(Throwable) - Method in exception AnchorCombinableException
-
Can another exception be skipped, when we combine with the current exception?
- canExceptionBeSkipped(Throwable) - Method in exception NamedProviderGetException
-
- canMatchSubdirectories() - Method in class FilePathMatcher
-
Determines if it possible to match a file in a subdirectory.
- canMatchSubdirectories() - Method in class MatchExtensions
-
- canMatchSubdirectories() - Method in class MatchGlob
-
- canMatchSubdirectories() - Method in class MatchRegularExpression
-
- canValueRangeChange() - Method in class Lanczos
-
- canValueRangeChange() - Method in class Linear
-
- canValueRangeChange() - Method in class NearestNeighbor
-
- canValueRangeChange() - Method in class VoxelsResizer
-
Returns true if it's possible for values to be created after interpolation that aren't found
in the input-image.
- canValueRangeChange() - Method in class VoxelsResizerExecutionTime
-
- canValueRangeChange() - Method in class VoxelsResizerNone
-
- canValueRangeChange() - Method in class VoxelsResizerImageJ
-
- canValueRangeChange() - Method in class VoxelsResizerOpenCV
-
- capacity() - Method in class UnsignedBuffer
-
- capacity() - Method in class VoxelBuffer
-
The capacity (i.e.
- capacity() - Method in class VoxelBufferUnsigned
-
- carGrayscale16Bit() - Method in class CarImageLoader
-
- carGrayscale16BitAsEnergy() - Method in class CarImageLoader
-
- carGrayscale8Bit() - Method in class CarImageLoader
-
- carGrayscale8BitAsEnergy() - Method in class CarImageLoader
-
- CarImageLoader - Class in org.anchoranalysis.test.image.load
-
Loads some images of a car.
- CarImageLoader() - Constructor for class CarImageLoader
-
- carRGB() - Method in class CarImageLoader
-
- carRGBAsEnergy() - Method in class CarImageLoader
-
- castAs() - Method in class Feature
-
Casts the feature to having a different input-type.
- Cell - Class in org.anchoranalysis.image.bean.spatial.arrange.tile
-
Indicates how to arrange one or more
RGBStack
s in a cell in a table.
- Cell(StackArranger, int, int) - Constructor for class Cell
-
- Cell() - Constructor for class Cell
-
- CENTER - Static variable in class PositionChoicesConstants
-
Align to the center (middle) in the respective dimension.
- CenterOfGravity - Class in org.anchoranalysis.image.feature.bean.object.single
-
- CenterOfGravity(Axis) - Constructor for class CenterOfGravity
-
Creates for a specific axis.
- CenterOfGravity() - Constructor for class CenterOfGravity
-
- centerOfGravity() - Method in class ObjectMask
-
Calculates center-of-gravity across all axes.
- centerOfGravity(Axis) - Method in class ObjectMask
-
Calculates center-of-gravity for one specific axis only.
- centerOfGravity() - Method in class BoundingBox
-
A mid-point in the bounding-box, corresponding to the mean of all points inside the box.
- CenterOnMask - Class in org.anchoranalysis.plugin.mpp.bean.check
-
- CenterOnMask() - Constructor for class CenterOnMask
-
- centerPoint() - Method in class Mark
-
- centerPoint() - Method in class MarkWithPosition
-
- centerPoint() - Method in class LineSegment
-
- centerPoint() - Method in class PointList
-
- centerPoint() - Method in class Polygon
-
- centerPoint() - Method in class PolygonCurve
-
- centerPoint() - Method in class EllipseStandardFormConverter
-
- CenterSlice - Class in org.anchoranalysis.plugin.mpp.bean.region
-
- CenterSlice() - Constructor for class CenterSlice
-
- CenterSliceBase - Class in org.anchoranalysis.plugin.mpp.bean.region
-
- CenterSliceBase() - Constructor for class CenterSliceBase
-
- CenterSliceWindow - Class in org.anchoranalysis.plugin.mpp.bean.region
-
Like {#link org.anchoranalysis.plugin.mpp.bean.region.CenterSlice} but considers more than one
slice, specifically centerSlice+- windowSize
- CenterSliceWindow() - Constructor for class CenterSliceWindow
-
- chainCode(int, int, int) - Static method in class ChainCodesDirection
-
- chainCodes(int) - Method in class WatershedEncoding
-
Decodes a chain-code into a point
- ChainCodesDirection - Class in org.anchoranalysis.plugin.image.segment.watershed.encoding
-
Maps directions to chain codes
- ChangeableOutputSequence<T,S> - Class in org.anchoranalysis.plugin.image.task.bean.format
-
- ChangeableOutputSequence() - Constructor for class ChangeableOutputSequence
-
- changedMarkIDArray() - Method in class Kernel
-
The mark ids that were changed in the last energy calculation for the kernel
- changedMarkIDArray() - Method in class KernelBirth
-
- changedMarkIDArray() - Method in class KernelBirthAndKill
-
- changedMarkIDArray() - Method in class KernelDeath
-
- changedMarkIDArray() - Method in class KernelExchange
-
- changedMarkIDArray() - Method in class KernelInitialMarksFromPartition
-
- changedMarkIDArray() - Method in class KernelInitialMarksProposed
-
- changedMarkIDArray() - Method in class KernelInitialMarksVoxelized
-
- changedMarkIDArray() - Method in class KernelMerge
-
- changedMarkIDArray() - Method in class KernelReplace
-
- changedMarkIDArray() - Method in class KernelSplit
-
- changedOffset(int, int) - Method in class ProcessVoxelNeighborAbsoluteWithSlidingBuffer
-
Calculates the offset in the buffer for a voxel, indicated by its relative-change in
position.
- changeExtension(Path, NonImageFileFormat, FileFormat) - Static method in class FormatExtensions
-
Change the extension in a path.
- changeExtent(Extent) - Method in class BoundingBox
-
Creates a copied
BoundingBox
but with a different extent.
- changeExtent(UnaryOperator<Extent>) - Method in class BoundingBox
-
Creates a copied
BoundingBox
but with a different extent.
- changeExtentZ(int) - Method in class BoundingBox
-
Creates a copied
BoundingBox
but with a different extent in the Z-dimension.
- changeInput(U) - Method in class InputBound
-
Copies the current instance but changes the input.
- changeInputAndSharedState(U, V) - Method in class InputBound
-
Copies the current instance but changes both the input 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) - Method in class OutputterChecked
-
- changeZ(int, int) - Method in class BoundingBox
-
Creates a copied
BoundingBox
but with a different corner and extent in the
Z-dimension.
- Channel - Class in org.anchoranalysis.image.core.channel
-
A channel from an image.
- Channel(Voxels<?>, Optional<Resolution>) - Constructor for class Channel
-
Creates for particular voxels and resolution.
- channel() - Method in class Mask
-
The underlying channel which contains the binary-values.
- channel(String) - Static method in class ReferenceFactory
-
- CHANNEL_TO_SKIP_WHEN_TWO - Static variable in class DisplayStack
-
Index of channel to leave blank when there are only two channels.
- ChannelAggregator - Class in org.anchoranalysis.image.bean.channel
-
A method of aggregating the voxels from many identically-sized
Channel
s into one.
- ChannelAggregator() - Constructor for class ChannelAggregator
-
- ChannelConverter<T> - Class in org.anchoranalysis.image.core.channel.convert
-
Base class to convert
Channel
s from one type to another specific type.
- ChannelConverter(VoxelDataType, VoxelsConverter<T>, VoxelsFactoryTypeBound<T>) - Constructor for class ChannelConverter
-
- ChannelConverterAttached<S,T> - Interface in org.anchoranalysis.image.core.channel.convert.attached
-
A channel-converter that has been permanently associated with a particular object.
- ChannelConverterMulti - Class in org.anchoranalysis.image.core.channel.convert
-
Converts a channel from one voxel data-type to one of multiple other types.
- ChannelConverterMulti() - Constructor for class ChannelConverterMulti
-
- ChannelConvertStyle - Class in org.anchoranalysis.plugin.image.task.bean.format.convertstyle
-
Converts a channel(s) at a particular timepoint into a stack(s).
- ChannelConvertStyle() - Constructor for class ChannelConvertStyle
-
- ChannelFactory - Class in org.anchoranalysis.image.core.channel.factory
-
Creates a
Channel
corresponding to one of several data-types.
- ChannelFactoryFloat - Class in org.anchoranalysis.image.core.channel.factory
-
- ChannelFactoryFloat() - Constructor for class ChannelFactoryFloat
-
Default constructor.
- ChannelFactorySingleType - Class in org.anchoranalysis.image.core.channel.factory
-
Creates a
Channel
for a specific data-type.
- ChannelFactorySingleType(VoxelDataType, VoxelsFactoryTypeBound<?>) - Constructor for class ChannelFactorySingleType
-
- ChannelFactoryUnsignedByte - Class in org.anchoranalysis.image.core.channel.factory
-
- ChannelFactoryUnsignedByte() - Constructor for class ChannelFactoryUnsignedByte
-
Default constructor.
- ChannelFactoryUnsignedInt - Class in org.anchoranalysis.image.core.channel.factory
-
- ChannelFactoryUnsignedInt() - Constructor for class ChannelFactoryUnsignedInt
-
Default constructor.
- ChannelFactoryUnsignedShort - Class in org.anchoranalysis.image.core.channel.factory
-
- ChannelFactoryUnsignedShort() - Constructor for class ChannelFactoryUnsignedShort
-
Default constructor.
- ChannelFixture - Class in org.anchoranalysis.test.image
-
- ChannelFixture() - Constructor for class ChannelFixture
-
- ChannelFixture(boolean) - Constructor for class ChannelFixture
-
- ChannelFixture.IntensityFunction - Interface in org.anchoranalysis.test.image
-
- ChannelGenerator - Class in org.anchoranalysis.image.io.channel.output
-
Writes a single channel to a file.
- ChannelGenerator() - Constructor for class ChannelGenerator
-
- ChannelGetter - Interface in org.anchoranalysis.image.io.channel.input
-
Retrieves a
Channel
by name from a particular time-point.
- ChannelGetterForTimepoint - Class in org.anchoranalysis.plugin.image.task.stack
-
- ChannelGetterForTimepoint(ChannelGetter, int) - Constructor for class ChannelGetterForTimepoint
-
- ChannelMap - Class in org.anchoranalysis.image.io.channel.input
-
A mapping of assigned channel-names to particular indices.
- ChannelMap() - Constructor for class ChannelMap
-
- ChannelMapCreator - Class in org.anchoranalysis.image.io.bean.channel
-
- ChannelMapCreator() - Constructor for class ChannelMapCreator
-
- ChannelMapper - Class in org.anchoranalysis.image.core.stack
-
Helps retrieve channel and an associated converter and apply operation on them jointly.
- ChannelMapper(IntFunction<Channel>, IntFunction<Optional<ChannelConverterAttached<Channel, UnsignedByteBuffer>>>) - Constructor for class ChannelMapper
-
- channelNames() - Method in class NamedChannelsConcatenate
-
- channelNames() - Method in interface NamedChannelsMap
-
All channel-names.
- channelNames() - Method in class OpenedNamedChannels
-
- channelNames(Logger) - Method in interface OpenedImageFile
-
The names of each channel, if they are known.
- channelNames(Logger) - Method in class OpenedMultiFile
-
- ChannelProvider - Class in org.anchoranalysis.image.bean.provider
-
- ChannelProvider() - Constructor for class ChannelProvider
-
- ChannelProviderBinary - Class in org.anchoranalysis.image.bean.provider
-
- 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
-
A collection of
Channel
s, indexed by name.
- ChannelSource - Class in org.anchoranalysis.plugin.image.task.grouped
-
- ChannelSource(NamedStacks, ConsistentChannelChecker, Optional<SizeXY>, VoxelsResizer) - Constructor for class ChannelSource
-
- ChannelSpecification - Class in org.anchoranalysis.test.image.stackwriter
-
Specifies a type and number of channels in a stack.
- ChannelSpecification(VoxelDataType, int, boolean) - Constructor for class ChannelSpecification
-
- channelsPerByteArray(IFormatReader) - Method in class Default
-
- channelsPerByteArray(IFormatReader) - Method in class ForceChannelsPerByteArray
-
- channelsPerByteArray(IFormatReader) - Method in class ReadOptions
-
The number of channels returned with each call to IFormatReader.openBytes(int)
.
- channelsPerByteArray(IFormatReader) - Method in class ReadOptionsDelegate
-
- check(Mark, RegionMap, EnergyStack) - Method in class CheckMark
-
Checks a mark
- check(Channel, Mask) - Static method in class DimensionsChecker
-
- check(Channel, String, Dimensions) - Static method in class DimensionsChecker
-
Checks a channel to make sure it's the same size as an an existing channel.
- check(Mask, String, Dimensions) - Static method in class DimensionsChecker
-
Checks a channel to make sure it's the same size as an an existing channel
- check(Mark, RegionMap, EnergyStack) - Method in class AndList
-
- check(Mark, RegionMap, EnergyStack) - Method in class AnySliceCenterOnMask
-
- check(Mark, RegionMap, EnergyStack) - Method in class CenterOnMask
-
- check(Mark, RegionMap, EnergyStack) - Method in class FeatureValueCheckMark
-
- check(Mark, RegionMap, EnergyStack) - Method in class Not
-
- check(Mark, RegionMap, EnergyStack) - Method in class RadiiMinRatio
-
- check(Mark, RegionMap, EnergyStack) - Method in class VolumeMin
-
- Check - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
-
- Check() - Constructor for class Check
-
- Check - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection
-
- Check() - Constructor for class Check
-
- check(T) - Static method in class BeanTestChecker
-
Checks if a bean has all necessary items, throwing a run-time exception if it does not.
- check(T) - Static method in class BeanInstanceMapFixture
-
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
-
- CheckCacheForSpecificChildren(Class<?>, CacheTransferSourceCollection) - Constructor for class CheckCacheForSpecificChildren
-
- checkChannelNames(Set<String>, boolean) - Method in class ConsistentChannelNamesChecker
-
Checks that the channel-names are consistent.
- checkChannelType(Channel) - 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.
- CheckedFunctionWithInt<S,V,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked
-
- 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.
- CheckedRunnable<E extends Exception> - Interface in org.anchoranalysis.core.functional.checked
-
Like
Runnable
but can also throw an exception.
- CheckedStream - Class in org.anchoranalysis.core.functional
-
Map operations for streams that can throw checked-exceptions.
- CheckedStream.ConvertedToRuntimeException - Exception in org.anchoranalysis.core.functional
-
An exception that wraps another exception, but exposes itself as a
RuntimeException
.
- CheckedSupplier<T,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked
-
Like
Supplier
but can also throw an exception.
- CheckedToDoubleBiFunction<T,U,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked
-
- CheckedToDoubleFunction<T,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
-
- CheckedUnsupportedOperationException - Exception in org.anchoranalysis.core.exception
-
When a particular operation is unsupported in particular circumstances.
- CheckedUnsupportedOperationException() - Constructor for exception CheckedUnsupportedOperationException
-
Creates with a default message indicating that the operation is unsupported.
- CheckedUnsupportedOperationException(String) - Constructor for exception CheckedUnsupportedOperationException
-
Creates with a message explaining that the operation is unsupported.
- CheckException - Exception in org.anchoranalysis.mpp.feature.error
-
- CheckException(String) - Constructor for exception CheckException
-
- CheckException(String, Throwable) - Constructor for exception CheckException
-
- CheckException(Throwable) - Constructor for exception CheckException
-
- checkExtentMatch(BoundingBox, BoundingBox) - Static method in class ExtentMatchHelper
-
Checks that the
Extent
s of two bounding boxes are identical.
- checkIdenticalDataType(VoxelDataType) - Method in class VoxelsUntyped
-
Do the voxels have a data-type that is equal to match
?
- CheckIfAllowed - Class in org.anchoranalysis.io.output.writer
-
- 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 IntensityQuantiles
-
- checkMisconfigured(BeanInstanceMap) - Method in class Align
-
- checkMisconfigured(BeanInstanceMap) - Method in class Fill
-
- checkMisconfigured(BeanInstanceMap) - Method in class FeatureEvaluator
-
- checkMisconfigured(BeanInstanceMap) - Method in class MatchRegularExpression
-
- checkMisconfigured(BeanInstanceMap) - Method in class NameElementRange
-
- 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 CombineObjectsForFeatures
-
- checkMisconfigured(BeanInstanceMap) - Method in class Intersection
-
- checkMisconfigured(BeanInstanceMap) - Method in class IntensityMeanShellBase
-
- checkMisconfigured(BeanInstanceMap) - Method in class LastDirectories
-
- checkMisconfigured(BeanInstanceMap) - Method in class HOGFeature
-
- checkMisconfigured(BeanInstanceMap) - Method in class OpenCVReader
-
- checkMisconfigured(BeanInstanceMap) - Method in class FromDictionary
-
- checkMisconfigured(BeanInstanceMap) - Method in class QuickExperiment
-
- checkMisconfigured(BeanInstanceMap) - Method in class QuickMultiDatasetExperiment
-
- checkMisconfigured(BeanInstanceMap) - Method in class MultiInputManagerQuick
-
- checkMisconfigured(BeanInstanceMap) - Method in class NamedChannelsQuick
-
- checkMisconfigured(BeanInstanceMap) - Method in class ExperimentResultsExperimentStructure
-
- checkMisconfigured(BeanInstanceMap) - Method in class ExperimentStructure
-
- checkMisconfigured(BeanInstanceMap) - Method in class QuickMultiDatasetStructuredExperiment
-
- CheckParsedFilePathBag - Class in org.anchoranalysis.plugin.io.bean.file.group.check
-
- CheckParsedFilePathBag() - Constructor for class CheckParsedFilePathBag
-
- checkResultsVector(ResultsVector) - Static method in class ConstantsInListFixture
-
Checks that a result-vector has the results we expect from the feature-list associated with
this fixture.
- checkSize(Extent) - Method in class HOGParameters
-
Throws an exception if an image of size extent
cannot be described by these
parameters.
- checkUnsupported3D(Channel) - Static method in class SegmentChannelIntoObjects
-
Throws an exception if the channel has more than one z-slice, as 3D is unsupported by the
implementation.
- checkUnsupportedObjectMask(Optional<ObjectMask>) - Static method in class SegmentChannelIntoObjects
-
Throws an exception if object
is present, as it is unsupported by the implementation.
- checkUnsupportedSeeds(Optional<ObjectCollection>) - Static method in class SegmentChannelIntoObjects
-
Throws an exception if seeds
is present, as it is unsupported by the implementation.
- ChildCacheFinder - Interface in org.anchoranalysis.feature.session.cache.finder
-
Strategy to determine which child-cache (among hierarchy) to employ for a particular feature
calculation.
- childCacheFor(ChildCacheName, Class<? extends FeatureInput>, CacheCreator) - Method in interface FeatureCalculationCache
-
Gets/creates a child-cache for a given name.
- childCacheFor(FeatureCalculationCache<?>, CacheCreator, ChildCacheName, V) - Method in class CheckCacheForSpecificChildren
-
- childCacheFor(FeatureCalculationCache<?>, CacheCreator, ChildCacheName, V) - Method in interface ChildCacheFinder
-
Selects a child-cache given a parent and a child-name.
- childCacheFor(FeatureCalculationCache<?>, CacheCreator, ChildCacheName, V) - Method in class DefaultChildCacheFinder
-
- ChildCacheName - Class in org.anchoranalysis.feature.calculate.cache
-
A unique identifier for a child-cache's name commposed potentially of two elements.
- ChildCacheName(Class<?>) - Constructor for class ChildCacheName
-
Uses only the class as an identifier.
- ChildCacheName(Class<?>, int) - Constructor for class ChildCacheName
-
Uses only the class combines with an integer part-name.
- ChildCacheName(Class<?>, String) - Constructor for class ChildCacheName
-
Uses both the class and a part-name as an identifier.
- children() - Method in class ErrorNodeImpl
-
- ChooseOneList - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
-
- ChooseOneList() - Constructor for class ChooseOneList
-
- Circle - Class in org.anchoranalysis.mpp.mark.conic
-
A circle
- Circle(Bound) - Constructor for class Circle
-
Creates with a radius within particular bounds.
- Circle(Circle) - Constructor for class Circle
-
Copy constructor
- Circle() - Constructor for class Circle
-
- circleAt(Point2i, double) - Static method in class CircleObjectFixture
-
- circleAt(Point2d, int) - Static method in class CircleObjectFixture
-
Creates a single circular mask at a particular center point and radius.
- CircleObjectFixture - Class in org.anchoranalysis.test.feature.plugins.objects
-
- CircleObjectFixture - Class in org.anchoranalysis.test.image.object
-
Creates object-masks that are circles in different ways
- 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 ObjectMask
-
Makes sure an object fits inside an extent, removing any parts which do not.
- clampTo(Extent) - Method in class BoundingBox
-
Ensures that the box fits inside a
Extent
by reducing any values to their limits in
the respective dimension.
- classificationString(boolean) - Static method in class BinaryOutcomeImageLabeller
-
- classInCurrentJar() - Method in class LauncherConfig
-
A class which we use to determine the base location for pathRelativeProperties.
- clean() - Method in class VoxelizedMarksWithEnergy
-
- clean() - Method in class EnergyMemoList
-
- cleanUp(VoxelPartitionFactory<T>) - Method in class IndexByChannel
-
- cleanUp(VoxelPartitionFactory<T>) - Method in class IndexByRegion
-
- cleanUp(VoxelPartitionFactory<T>) - Method in interface VoxelPartition
-
- cleanUp(VoxelPartitionFactory<Histogram>) - Method in class VoxelPartitionHistogram
-
- cleanUp() - Method in interface VoxelizedMark
-
- cleanUpRemaining() - Method in class MapCreateCountdown
-
Applies the clean-up function on any keys remaining in the map.
- clear() - Method in class FeatureList
-
Removes all of the elements from this list.
- clear() - Method in class UnsignedBuffer
-
- clear() - Method in class UpdatableMarksList
-
- clearBest() - Method in class DualState
-
- clipTo(T, Extent) - Method in interface AccessObjectMask
-
Ensures the element lies within a certain extent.
- clipTo(ObjectMask, Extent) - Method in class AccessObjectMaskSimple
-
- 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 MultipleLoggers
-
- close(boolean, boolean) - Method in interface StatefulMessageLogger
-
Stops logging.
- close(boolean, boolean) - Method in class TextFileMessageLogger
-
- close() - Method in class FeatureCSVWriter
-
Closes any open file-handles.
- close() - Method in interface OpenedImageFile
-
Closes the opened image-file, removing any intermediate data-structures.
- close() - Method in class ConcurrentModelPool
-
Close all models, to indicate they are no longer in use, and to perform tidy-up.
- close() - Method in interface InferenceModel
-
Indicates that the model will no longer be used, and does appropriate tidying up and freeing
of resources.
- close() - Method in class CSVWriter
-
- close() - Method in class CSVReader.OpenedCSVFile
-
- close() - Method in class ReadByLine
-
Closes any opened-files
- close(ErrorReporter) - Method in interface InputFromManager
-
Performs all tidying up, file-closing etc.
- close(ErrorReporter) - Method in class InputFromManagerDelegate
-
- close(ErrorReporter) - Method in class MultiInput
-
- close(ErrorReporter) - Method in class StackWithMap
-
- close() - Method in class SharedStateFilteredImageOutput
-
- close() - Method in class SharedStateSelectedSlice
-
- close() - Method in class OpenedMultiFile
-
- close() - Method in class OnnxModel
-
- close() - Method in class OpenCVModel
-
- closeAndWriteOutputs(Optional<NamedFeatureStore<FeatureInputResults>>, boolean, Function<InputOutputContext, FeatureCSVWriterFactory>, InputOutputContext) - Method in class FeatureExporter
-
Writes all the results that have been collected as a CSV file, and closes open I/O handles
and memory structures.
- closeAndWriteOutputs(ExportFeaturesStyle) - Method in class SharedStateSegmentInstance
-
Writes all the results that have been collected as a CSV file, and closes open I/O handles
and memory structures.
- closeAnyOpenIO() - Method in class FeatureResultsAndThumbnails
-
Closes any open IO and removes redundant structures stored in memory.
- closeLogger() - Method in class RecordingCounter
-
Closes the logger.
- ClusterByTimestamp - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster
-
Associates particular timestamp with each file, and clusters.
- ClusterByTimestamp() - Constructor for class ClusterByTimestamp
-
- clusterFor(File) - Method in class ClusterMembership
-
Finds the corresponding cluster for a particular file.
- ClusterIdentifier - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster
-
Uniquely identifies a cluster.
- ClusterIdentifier(ZoneOffset) - Constructor for class ClusterIdentifier
-
Creates with no name.
- ClusterIdentifier(String, ZoneOffset) - Constructor for class ClusterIdentifier
-
Creates with a constant-name.
- ClusterMembership - Class in org.anchoranalysis.plugin.io.file.copy
-
A mapping of files to membership of particular clusters.
- ClusterMembership(ClusterIdentifier) - Constructor for class ClusterMembership
-
- CODE_MINIMA - Static variable in class WatershedEncoding
-
- CODE_PLATEAU - Static variable in class WatershedEncoding
-
- CODE_TEMPORARY - Static variable in class WatershedEncoding
-
- CODE_UNVISITED - Static variable in class WatershedEncoding
-
- CoefficientOfVarianceFromAll - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.all
-
- CoefficientOfVarianceFromAll() - Constructor for class CoefficientOfVarianceFromAll
-
- coefficientOfVariation(Histogram) - Static method in class HistogramStatistics
-
Calculates the coefficient-of-variation of a distribution of values, represented by
their histogram.
- CoefficientOfVariation - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
-
- CoefficientOfVariation() - Constructor for class CoefficientOfVariation
-
- CollapseFileName - Class in org.anchoranalysis.plugin.io.bean.path.derive
-
Removes the file-name from a path, but keeps the directories and preserves the file-extension.
- CollapseFileName() - Constructor for class CollapseFileName
-
- CollectionGenerator<T> - Class in org.anchoranalysis.io.generator.collection
-
Writes a collection of elements as a subdirectory with each element as a single file in the
subdirectory.
- CollectionGenerator(Generator<T>, String) - Constructor for class CollectionGenerator
-
- collectResult() - Method in interface ProcessChangedPointAbsoluteMasked
-
Collects the result of the operation after processing neighbor voxels.
- collectResult() - Method in interface ProcessVoxelNeighbor
-
Collects the result of the operation after processing neighbor pixels.
- collectResult() - Method in interface ProcessVoxelNeighborAbsolute
-
Collects the result of the operation after processing neighbor voxels.
- colorAtVoxel(ReadableTuple3i) - Method in class RGBStack
-
Gets the color at a particular voxel.
- 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
-
- ColoredObject - Class in org.anchoranalysis.plugin.image.object
-
- ColoredObject(ObjectMask, RGBColor) - Constructor for class ColoredObject
-
- ColoredObjectCollection - Class in org.anchoranalysis.plugin.image.object
-
- ColoredObjectCollection() - Constructor for class ColoredObjectCollection
-
Create with an empty collection.
- ColoredObjectCollection(Stream<ColoredObject>) - Constructor for class ColoredObjectCollection
-
- 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
-
Create an empty collection.
- ColoredOverlayCollection(OverlayCollection, ColorList) - Constructor for class ColoredOverlayCollection
-
- colorFor(ObjectWithProperties, int) - Method in class ObjectDrawAttributes
-
A color for a particular object
- colorForEachIndex(int) - Method in class ColorScheme
-
Assigns a color to each index value from a list of size numberColors
.
- ColorIndex - Interface in org.anchoranalysis.core.color
-
Associates an RGB-color with each index.
- ColorIndexModulo - Class in org.anchoranalysis.core.color
-
Derives a new
ColorIndex
from an existing
ColorIndex
applying a modulo operation
to each index call.
- ColorIndexModulo(ColorIndex) - Constructor for class ColorIndexModulo
-
- ColorList - Class in org.anchoranalysis.core.color
-
A list of colors, each corresponding to a particular index position.
- ColorList(Color...) - Constructor for class ColorList
-
Create for one or more colors of type
Color
.
- ColorList(RGBColor...) - Constructor for class ColorList
-
Create for one or more colors of type
RGBColor
.
- ColorList(Stream<RGBColor>) - Constructor for class ColorList
-
Create for one or more colors of type
RGBColor
.
- ColorList() - Constructor for class ColorList
-
- ColorProvider - Class in org.anchoranalysis.image.bean.provider
-
- ColorProvider() - Constructor for class ColorProvider
-
- ColorScheme - Class in org.anchoranalysis.bean.shared.color.scheme
-
Creates a sequence of related colors.
- ColorScheme() - Constructor for class ColorScheme
-
- ColorSchemeUnary - Class in org.anchoranalysis.bean.shared.color.scheme
-
- ColorSchemeUnary() - Constructor for class ColorSchemeUnary
-
- ColorSchemeUnary(ColorScheme) - Constructor for class ColorSchemeUnary
-
- colorSpaceCode() - Method in class ColorConverterBase
-
The color space conversion code to use from OpenCV, that defines the color-space to convert
to.
- colorSpaceCode() - Method in class ConvertRGBToHSV
-
- colorSpaceCode() - Method in class ConvertRGBToLab
-
- column(int) - Method in class RotationMatrix
-
Extracts a column from the rotation-matrix as a point.
- ColumnDefinition - Class in org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition
-
- ColumnDefinition() - Constructor for class ColumnDefinition
-
- combine(List<PermutationAssigner>) - Static method in class PermutationAssignerFactory
-
- combine(List<RGBStack>, VoxelsResizer, OperationContext) - Method in class StackArranger
-
Creates a new
RGBStack
of voxel data type
unsigned byte that is a combination
of other
RGBStack
s.
- combine(List<RGBStack>, VoxelsResizer, ChannelFactorySingleType, OperationContext) - Method in class StackArranger
-
- combine(DualScale<U>, BiFunction<T, U, S>) - Method in class DualScale
-
Create a derived
DualScale
by combining the respective elements of this instance with
another.
- combine(boolean, boolean) - Method in class MultiLevelAnd
-
- combine(boolean, boolean) - Method in class MultiLevelBinary
-
- combine(boolean, boolean) - Method in class MultiLevelOr
-
- combine(boolean, boolean) - Method in class SingleLevelAnd
-
- combine(boolean, boolean) - Method in class SingleLevelBinary
-
- combine(boolean, boolean) - Method in class SingleLevelOr
-
- Combine - Class in org.anchoranalysis.plugin.io.bean.file.provider
-
- Combine() - Constructor for class Combine
-
- CombineBase - Class in org.anchoranalysis.plugin.image.bean.mask.provider.combine
-
- CombineBase() - Constructor for class CombineBase
-
- CombineCSV - Class in org.anchoranalysis.plugin.io.bean.task
-
Combines multiple CSV files into a single CSV file.
- CombineCSV() - Constructor for class CombineCSV
-
- combined() - Method in class PathDifference
-
The directory-component (if it exists) and filename-component combined.
- combined() - Method in class SplitPath
-
A path that combines the root
together with the remainder
.
- combineDescription(String, String) - Method in class AddConstantTo
-
- combineDescription(String, String) - Method in class ConstantToThePowerOf
-
- combineDescription(String, String) - Method in class DivideByConstant
-
- combineDescription(String, String) - Method in class MultiplyByConstant
-
- combineDescription(String, String) - Method in class SubtractFrom
-
- combineDescription(String, String) - Method in class ToThePowerOfConstant
-
- combineDescription(String, String) - Method in class ReplaceUnusualValue
-
- combineDescription(String, String) - Method in class WithValueBase
-
- combineDescriptionsRecursively(String, String) - Method in exception AnchorCombinableException
-
Traverses through a set of nested-exceptions creating a description for each "combined"
exception, and combining them into a single string.
- CombinedListGenerator<T> - Class in org.anchoranalysis.io.generator.combined
-
Several generators combined together with a common element-type.
- CombinedListGenerator(NameValue<Generator<T>>) - Constructor for class CombinedListGenerator
-
- CombinedListGenerator(Stream<NameValue<Generator<T>>>) - Constructor for class CombinedListGenerator
-
- CombinedListGenerator(Generator<T>...) - Constructor for class CombinedListGenerator
-
- CombinedListGenerator() - Constructor for class CombinedListGenerator
-
- CombinedName - Class in org.anchoranalysis.feature.io.name
-
A name which is unique when a primaryName is combined with a secondaryName
- CombinedName(String, String) - Constructor for class CombinedName
-
Creates with explicit strings for both parts.
- combinedStacks() - Method in class ImageInitialization
-
Exposes several entities that have natural
Stack
representations as a unified
NamedProvider
.
- 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(Interpolator) - Constructor for class CombineObjectsForFeatures
-
Create with a specific interpolator.
- CombineObjectsForFeatures() - Constructor for class CombineObjectsForFeatures
-
- combineSecond(SingleLevelOutputEnabled, SingleLevelOutputEnabled) - Method in class MultiLevelAnd
-
- combineSecond(SingleLevelOutputEnabled, SingleLevelOutputEnabled) - Method in class MultiLevelBinary
-
- combineSecond(SingleLevelOutputEnabled, SingleLevelOutputEnabled) - Method in class MultiLevelOr
-
- CombineToOnePath - Class in org.anchoranalysis.plugin.mpp.contour.path.merge
-
- combineToOnePath(List<ContiguousVoxelPath>) - Static method in class CombineToOnePath
-
Combines all the contiguous paths to a single-path.
- CombineTypes - Class in org.anchoranalysis.image.voxel.datatype
-
Calculates which
VoxelDataType
to use when combining two other voxel-data types, but
without losing precision.
- combineTypes(VoxelDataType, VoxelDataType) - Static method in class CombineTypes
-
What data-type to use to represent voxels of both type1
and type2
?
- combineValueAndFeature(double, double) - Method in class AddConstantTo
-
- combineValueAndFeature(double, double) - Method in class ConstantToThePowerOf
-
- combineValueAndFeature(double, double) - Method in class DivideByConstant
-
- combineValueAndFeature(double, double) - Method in class MultiplyByConstant
-
- combineValueAndFeature(double, double) - Method in class SubtractFrom
-
- combineValueAndFeature(double, double) - Method in class ToThePowerOfConstant
-
- combineValueAndFeature(double, double) - Method in class ReplaceUnusualValue
-
- combineValueAndFeature(double, double) - Method in class WithValueBase
-
- combineWithSuffix(String) - Method in class FilenameSplitExtension
-
Inserts a suffix after the base-name, but before the extension, immutably.
- CommandLineException - Exception in org.anchoranalysis.launcher
-
An exception thrown at run-time while processing command-line args
- CommandLineException(String) - Constructor for exception CommandLineException
-
- CommandLineExtracter - Class in org.anchoranalysis.launcher.options
-
Adds methods to CommandLine
for querying and extracting options, with and without
arguments.
- CommandLineExtracter(CommandLine) - Constructor for class CommandLineExtracter
-
- CommandLineOptions - Class in org.anchoranalysis.launcher.options
-
All command-line options used by the launcher.
- common() - Method in class InitializationContext
-
Creates a
CommonContext
a context that contains a subset of this context.
- 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.
- CommonSize - Class in org.anchoranalysis.plugin.image.task.size
-
Shared-state that exposes a common-size to all images.
- CommonSize(Extent) - Constructor for class CommonSize
-
- commonType(Stream<VoxelDataType>) - Static method in class FindCommonVoxelType
-
Finds a common type to represent (ideally without loss of precision} of a stream of types.
- commonType(VoxelDataType, VoxelDataType) - Static method in class FindCommonVoxelType
-
Finds a common type to represent (ideally without loss of precision} both first
and
second
.
- ComparableSource - Class in org.anchoranalysis.annotation.io.bean.comparer
-
A set of elements, loaded from the file-system, to be compared to another set.
- ComparableSource() - Constructor for class ComparableSource
-
- Comparator3d<T extends Tuple3d> - Class in org.anchoranalysis.spatial.point
-
Imposes an ordering on any sub-type of
Tuple3d
.
- Comparator3d() - Constructor for class Comparator3d
-
- Comparator3i<T extends Tuple3i> - Class in org.anchoranalysis.spatial.point
-
Imposes an ordering on any sub-type of
Tuple3i
.
- Comparator3i() - Constructor for class Comparator3i
-
- ComparatorOrderByName<V> - Class in org.anchoranalysis.core.identifier.name
-
- ComparatorOrderByName() - Constructor for class ComparatorOrderByName
-
- compare(NameValue<V>, NameValue<V>) - Method in class ComparatorOrderByName
-
- compare(T, T) - Method in class Comparator3d
-
- compare(T, T) - Method in class Comparator3i
-
- CompareAnnotations<T extends Assignment<ObjectMask>> - Class in org.anchoranalysis.plugin.annotation.bean.comparison
-
Task to compare a set of annotations to a segmentation or another set of annotations.
- CompareAnnotations() - Constructor for class CompareAnnotations
-
- compareExplicitDirectoryToTest(Path, String) - Static method in class DualComparerFactory
-
- compareTemporaryDirectoryToTest(Path, Optional<String>, String) - Static method in class DualComparerFactory
-
Compares a directory in a temporary-folder to a directory in Maven's test/resources
.
- compareTo(AssociatedIndex) - Method in class Indexable
-
- compareTo(MultiName) - Method in class CombinedName
-
- compareTo(MultiName) - Method in class SimpleName
-
- compareTo(ExtentToArrange) - Method in class ExtentToArrange
-
Sorts in descending order by extent
.
- compareTo(ObjectForReduction) - Method in class ObjectForReduction
-
- compareTo(LabelledWithConfidence<T>) - Method in class LabelledWithConfidence
-
- compareTo(WithConfidence<T>) - Method in class WithConfidence
-
- compareTo(WithPriority<T>) - Method in class WithPriority
-
Orders so that gpu==true
has higher priority in queue to gpu==false
.
- compareTo(EigenvalueAndVector) - Method in class EigenvalueAndVector
-
- compareTo(SortedSetChannel) - Method in class SortedSetChannel
-
- compareTo(SortedSetSlice) - Method in class SortedSetSlice
-
- compareTo(BoundingBox) - Method in class BoundingBox
-
- compareTo(Extent) - Method in class Extent
-
- compareTo(ReadableTuple3i) - Method in interface ReadableTuple3i
-
- compareTwoBinaryFiles(String) - Method in class DualComparer
-
Compare two binary-files.
- compareTwoCsvFiles(String, CSVComparer, PrintStream) - Method in class DualComparer
-
Compare two CSV files, ignoring the first numFirstColumnsToIgnore.
- compareTwoImages(String) - Method in class DualComparer
-
Compare two images that have an identical path, but in two different test loaders.
- compareTwoImages(String, String, boolean) - Method in class DualComparer
-
Compare two images with different paths, but in two different test loaders.
- compareTwoImages(String, String) - Method in class TestLoaderImage
-
Compare two images that are located on the file system in the same test-folder
- compareTwoImages(TestLoaderImage, String, TestLoaderImage, String, boolean) - Static method in class TestLoaderImage
-
Compare two images that are located on the file system (possibly in different test folders)
- compareTwoObjectCollections(String) - Method in class DualComparer
-
Compare two object-mask-collections.
- compareTwoObjectCollections(String, String) - Method in class TestLoaderImage
-
Compare two obj-mask-collection that are located on the file system in the test-folder
- compareTwoSubdirectories(String) - Method in class DualComparer
-
- compareTwoSubdirectoriesInLoader(TestLoader, String, String) - Static method in class DualComparerFactory
-
- compareTwoSubdirectoriesInLoader(TestLoader, String, TestLoader, String) - Static method in class DualComparerFactory
-
- compareTwoXmlDocuments(String) - Method in class DualComparer
-
Compare two XML documents.
- 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
-
- CompareWithRangeFeature() - Constructor for class CompareWithRangeFeature
-
- CompareXML - Class in org.anchoranalysis.test
-
Compares two XML documents to see if they are equal.
- comparison() - Method in interface ImageCounterWithStatistics
-
Creates statistics from counted images and the payload T
passed for annotated images.
- ComparisonPlan - Class in org.anchoranalysis.test.image.rasterwriter.comparison
-
A plan on which comparisons to execute for a test.
- ComparisonPlan(boolean, Optional<ImageFileFormat>, boolean) - Constructor for class ComparisonPlan
-
Creates a plan for particular settings.
- ComparisonPlan(boolean, Optional<ImageFileFormat>, boolean, String) - Constructor for class ComparisonPlan
-
Creates a plan for particular settings - and which copies any missing images to a particular
directory.
- ComparisonSharedState<T extends Assignment<ObjectMask>> - Class in org.anchoranalysis.plugin.annotation.bean.comparison
-
- ComparisonSharedState(CSVAssignment, int, Function<String, ImageCounterWithStatistics<T>>) - Constructor for class ComparisonSharedState
-
- CompatibleWithMark - Interface in org.anchoranalysis.mpp.mark
-
- completeProjection() - Method in interface ProjectableBuffer
-
Performs any final operation before turning the projected buffer.
- Compose<S,T,U> - Class in org.anchoranalysis.mpp.segment.transformer
-
Combines a transformation from S
to U
with one from U
to T
- Compose() - Constructor for class Compose
-
- Compose(StateTransformerBean<S, U>, StateTransformerBean<U, T>) - Constructor for class Compose
-
- CompressAnyTIFF - Class in org.anchoranalysis.plugin.io.bean.file.copy.method
-
Create a voxelwise
compressed copy of any TIFF file being copied, and otherwise do a
Bytewise
copy.
- CompressAnyTIFF() - Constructor for class CompressAnyTIFF
-
- computeIfAbsent(K) - Method in class MapCreate
-
Gets an existing element from the map, newly creating and storing the element if it's absent.
- 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 the inputs from multiple
InputManager
s that all provide the same input-type.
- Concatenate() - Constructor for class Concatenate
-
- ConcurrencyPlan - Class in org.anchoranalysis.inference.concurrency
-
How many allocated CPUs and CPUs can be used concurrently for inference.
- ConcurrentJobMonitor - Class in org.anchoranalysis.experiment.task.processor
-
Monitors all submitted jobs and their current state of execution.
- ConcurrentJobMonitor(long) - Constructor for class ConcurrentJobMonitor
-
- ConcurrentModel<T extends InferenceModel> - Class in org.anchoranalysis.inference.concurrency
-
An instance of model that can be used concurrently for inference.
- ConcurrentModel(T, boolean) - Constructor for class ConcurrentModel
-
- ConcurrentModelException - Exception in org.anchoranalysis.inference.concurrency
-
This exception indicates that an error occurred when performing inference from a model
concurrently.
- ConcurrentModelException(Throwable) - Constructor for exception ConcurrentModelException
-
Creates with a cause.
- ConcurrentModelPool<T extends InferenceModel> - Class in org.anchoranalysis.inference.concurrency
-
Keeps concurrent copies of a model to be used by different threads.
- ConcurrentModelPool(ConcurrencyPlan, CreateModelForPool<T>, Logger) - Constructor for class ConcurrentModelPool
-
Creates with a particular plan and function to create models.
- ConditionalKernel - Class in org.anchoranalysis.image.voxel.kernel
-
Executes another
BinaryKernel
iff a predicate is satisfied for a particular point.
- ConditionalKernel(BinaryKernel, Predicate<Point3i>) - Constructor for class ConditionalKernel
-
Creates with a particular delegate
BinaryKernel
and a predicate that tests each
point.
- 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
-
- 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
-
- ConsiderVisit - Interface in org.anchoranalysis.plugin.mpp.contour
-
Whether to visit a point or not.
- ConsistentChannelChecker - Class in org.anchoranalysis.image.bean.nonbean
-
Checks that all
Channel
s have the same voxel-data-type.
- ConsistentChannelChecker() - Constructor for class ConsistentChannelChecker
-
- ConsistentChannelNamesChecker - Class in org.anchoranalysis.plugin.image.task.grouped
-
Checks that each image has an identical set of
Channel
-names, and RGB-state.
- ConsistentChannelNamesChecker() - Constructor for class ConsistentChannelNamesChecker
-
- 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
-
Logs messages to the console, STDOUT.
- ConsoleMessageLogger() - Constructor for class ConsoleMessageLogger
-
- Constant<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.operator
-
A constant value that is entirely invariant to the feature-input.
- 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
-
- ConstantScaleFactor - Class in org.anchoranalysis.plugin.image.bean.scale
-
Scale X and Y dimension by a constant floating-point number.
- ConstantScaleFactor() - Constructor for class ConstantScaleFactor
-
- ConstantScaleFactor(double) - 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
-
- consumeChannelIfSupported(int, BiConsumer<Channel, ChannelConverterAttached<Channel, UnsignedByteBuffer>>, Consumer<Channel>) - Method in class ChannelMapper
-
- consumeMatchingFiles(List<Path>, Consumer<File>) - Method in class DualPathPredicates
-
Calls a
Consumer
on any path that matches the predicate
file
.
- containerOptional() - Method in class WithContainerBase
-
- containerRequired() - Method in class WithContainerBase
-
- contains(Double) - Method in class DoubleList
-
- contains(Double) - Method in class DoubleSet
-
- contains(Integer) - Method in class IntegerList
-
- contains(Integer) - Method in class IntegerSet
-
- contains(T) - Method in interface PrimitiveBeanCollection
-
Whether the collection contains a particular element?
- contains(String) - Method in class StringList
-
- contains(String) - Method in class StringSet
-
- contains(String) - Method in class StringSetTrie
-
Does the set contain a particular string?
- contains(ChildCacheName) - Method in class CacheTransferSourceCollection
-
Whether a particular child-cache exists in the source?
- contains(Feature<FeatureInput>) - Method in class SharedFeatures
-
Whether a particular feature is contained in this instance.
- contains(Point3d) - Method in class Dimensions
-
Is a point of type
Point3d
contained within the extent?
- contains(Point3i) - Method in class Dimensions
-
- contains(BoundingBox) - Method in class Dimensions
-
Is box
entirely contained within the extent?
- contains(Point3i) - Method in class IntersectingObjects
-
All elements that contain a particular point.
- contains(Point3i) - Method in class ObjectMask
-
Whether a particular point exists within the object-mask?
- contains(double) - Method in class ResolvedBound
-
- contains(Object) - Method in class UpdatableMarksList
-
- contains(Object) - Method in class MarkCollection
-
- contains() - Method in class BoundingBox
-
For evaluating whether this bounding-box contains other points, boxes etc.?
- contains(Point2i) - Method in class Extent
-
Is a point of type
Point2i
contained within the extent in the XY plane?
- contains(Point3d) - Method in class Extent
-
Is a point of type
Point3d
contained within the extent?
- contains(ReadableTuple3i) - Method in class Extent
-
- contains(int, int, int) - Method in class Extent
-
Is a point contained within the extent?
- contains(BoundingBox) - Method in class Extent
-
Is box
entirely contained within the extent?
- contains(ReadableTuple3i) - Method in class BoundingBoxRTree
-
Which objects contain a particular point?
- contains(double) - Method in class IntervalRTree
-
Which objects contain a particular point?
- containsAll(Collection<?>) - Method in class UpdatableMarksList
-
- containsChild(ChildCacheName) - Method in class CacheTransferSource
-
Whether a particular child-cache exists in the source?
- containsEdge(V, V) - Method in class GraphWithoutPayload
-
Does the graph contain a particular edge?
- containsEdge(V, V) - Method in class GraphWithPayload
-
Does the graph contain a particular edge?
- containsFamily(Class<?>) - Method in class BeanInstanceMap
-
Is a particular family-type contained in the map?
- containsKey(String) - Method in class Dictionary
-
Does a parameter exist with a particular key?
- containsMark(Mark) - Method in class RandomCollectionWithAddCriteria
-
- containsOrEmpty() - Method in class DebugModeParameters
-
- containsStream(ReadableTuple3i) - Method in class BoundingBoxRTree
-
- containsStream(double) - Method in class IntervalRTree
-
- containsStream(Point) - Method in class RTree
-
Which objects contain a particular point?
- containsVertex(V) - Method in class GraphWithoutPayload
-
Does the graph contain a particular vertex?
- containsVertex(V) - Method in class GraphWithPayload
-
Does the graph contain a particular vertex?
- containsX(double) - Method in class Extent
-
Is a value contained within the extent on the X-axis?
- containsX(int) - Method in class Extent
-
Is a value contained within the extent on the X-axis?
- containsY(double) - Method in class Extent
-
Is a value contained within the extent on the Y-axis?
- containsY(int) - Method in class Extent
-
Is a value contained within the extent on the Y-axis?
- containsZ(double) - Method in class Extent
-
Is a value contained within the extent on the Z-axis?
- containsZ(int) - Method in class Extent
-
Is a value contained within the extent on the Z-axis?
- ContiguousVoxelPath - Class in org.anchoranalysis.plugin.mpp.contour.path
-
A list of visited pixels which forms one contiguous path where each voxel neighbors each other.
- ContiguousVoxelPath(Point3i, Point3i) - Constructor for class ContiguousVoxelPath
-
With a single initial-point, and maybe a connection point
- ContiguousVoxelPath() - Constructor for class ContiguousVoxelPath
-
Without any connection-point
- continueFurther(int, double, int, MessageLogger) - Method in class TerminationCondition
-
Whether to continue for an additional iteration step or not.
- continueFurther(int, double, int, MessageLogger) - Method in class TerminationConditionListOr
-
- continueFurther(int, double, int, MessageLogger) - Method in class TriggerTerminationCondition
-
- continueFurther(int, double, int, MessageLogger) - Method in class NumberIterations
-
- continueFurther(int, double, int, MessageLogger) - Method in class UnchangedBase
-
- Contour - Class in org.anchoranalysis.spatial.point
-
A path of successively-neighbored points.
- Contour() - Constructor for class Contour
-
- contoursForObject(ObjectMask) - Static method in class CVFindContours
-
- ContourTraverser - Class in org.anchoranalysis.plugin.mpp.contour
-
Iteratively moves around a
ObjectMask
that describes the contour of an object.
- ContourTraverser(ObjectMask, ConsiderVisit, boolean, boolean) - Constructor for class ContourTraverser
-
- ConversionPolicy - Enum in org.anchoranalysis.image.core.channel.convert
-
The different ways of converting the voxel-data-type in a
Channel
.
- convert(Channel, ConversionPolicy) - Method in class IntensityRange
-
- convert(Channel, ConversionPolicy) - Method in class MaxIntensity
-
- convert(Channel, ConversionPolicy) - Method in interface ChannelConverterAttached
-
Converts the voxel-type in a
Channel
.
- convert(Channel, ConversionPolicy) - Method in class MaxIntensityFromHistogram
-
- convert(Channel, ConversionPolicy) - Method in class QuantileIntensityFromHistogram
-
- convert(Channel, ConversionPolicy) - Method in class UpperLowerQuantileIntensityFromHistogram
-
- convert(Stack, ConversionPolicy) - Method in class ChannelConverter
-
- convert(Channel, ConversionPolicy) - Method in class ChannelConverter
-
Converts channel
to have voxels with data-type T
.
- convert(Channel, VoxelDataType) - Method in class ChannelConverterMulti
-
Converts a
Channel
's voxels to another type.
- convert(Stack, StackDisplayer, boolean) - Static method in class ConvertStackToRGB
-
- convert(DisplayStack, boolean) - Static method in class ConvertStackToRGB
-
- convert(VoxelsUntyped, VoxelsFactoryTypeBound<T>) - Method in class VoxelsConverterMulti
-
Converts a
Voxels
to another type.
- convert(ByteBuffer, int, OrientationChange, boolean) - Method in class ConvertTo
-
- convert(ByteBuffer, int, OrientationChange, boolean) - Method in class UnsignedByteFromUnsignedByte
-
- convert(Mark) - Method in class MarkToObjectConverter
-
- Convert<T> - Class in org.anchoranalysis.plugin.image.bean.channel.provider.convert
-
Converts a channel by applying a converter (no histogram is involved in the conversion).
- Convert() - Constructor for class Convert
-
- convert(Set<String>, ChannelGetterForTimepoint, Logger) - Method in class ChannelConvertStyle
-
Converts a particular set of channels.
- convert(Set<String>, ChannelGetterForTimepoint, Logger) - Method in class ExtractToRGB
-
- convert(Set<String>, ChannelGetterForTimepoint, Logger) - Method in class IndependentChannels
-
- convert(Set<String>, ChannelGetterForTimepoint, Logger) - Method in class RGBIfNamesMatch
-
- convert(int) - Method in class NumberToStringConverter
-
Converts number
to a string, padding with leading zeros if necessary to ensure the
desired width.
- convert2iTo3d(List<Point2i>) - Static method in class PointConverter
-
- convert2iTo3f(List<Point2i>) - Static method in class PointConverter
-
- convert3dTo3f(List<Point3d>) - Static method in class PointConverter
-
- convert3fTo3d(List<Point3f>) - Static method in class PointConverter
-
- convert3i(List<Point3f>, boolean) - Static method in class PointConverter
-
Convert a list of
Point3f
to a list of
Point3i
, optionally rounding values.
- convert3i(List<Point3d>) - Static method in class PointConverter
-
- convert3iTo3f(List<Point3i>) - Static method in class PointConverter
-
- ConvertBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider.convert
-
- ConvertBase() - Constructor for class ConvertBase
-
- convertBeforeAssign(DisplayStack) - Method in class DisplayStackGenerator
-
- convertBeforeAssign(Stack) - Method in class FlattenStackGenerator
-
- convertBeforeAssign(T) - Method in class RasterGeneratorBridge
-
- convertBeforeAssign(T) - Method in class RasterGeneratorDelegateToRaster
-
Converts an element before setting it on the delegate
.
- convertBeforeTransform(Stack) - Method in class DisplayStackGenerator
-
- convertBeforeTransform(Stack) - Method in class FlattenStackGenerator
-
- convertBeforeTransform(Stack) - Method in class RasterGeneratorBridge
-
- convertBeforeTransform(Stack) - Method in class RasterGeneratorDelegateToRaster
-
- ConvertChannelTo<T> - Class in org.anchoranalysis.image.bean.channel
-
- ConvertChannelTo() - Constructor for class ConvertChannelTo
-
- ConvertChannelToWithHistogram<T> - Class in org.anchoranalysis.image.bean.channel
-
Creates a
ChannelConverterAttached<Histogram, T>
for converting a channel to a particular
type, making use of a
Histogram
.
- ConvertChannelToWithHistogram() - Constructor for class ConvertChannelToWithHistogram
-
- convertCode(int, int, EncodedVoxels, Point3i) - Method in class EncodedIntBuffer
-
Convert code to connected-component
- convertCropped(DisplayStack, BoundingBox) - Static method in class ConvertStackToRGB
-
- ConvertedInput<U extends InputFromManager> - Class in org.anchoranalysis.plugin.mpp.experiment.shared
-
A converted-input, together with any logged messages associated with it.
- ConvertedInput(U, StringBuilder) - Constructor for class ConvertedInput
-
- ConvertedToRuntimeException(Throwable) - Constructor for exception CheckedStream.ConvertedToRuntimeException
-
Creates for any exception.
- convertFloat(FloatBuffer, FloatBuffer) - Method in class ToFloatNoScaling
-
- convertFloat(FloatBuffer, UnsignedByteBuffer) - Method in class ToUnsignedByteNoScaling
-
- convertFloat(FloatBuffer, UnsignedByteBuffer) - Method in class ToUnsignedByteScaleByMaxValue
-
- convertFloat(FloatBuffer, UnsignedByteBuffer) - Method in class ToUnsignedByteScaleByMinMaxValue
-
- convertFloat(FloatBuffer, UnsignedByteBuffer) - Method in class ToUnsignedByteScaleByType
-
- convertFloat(FloatBuffer, UnsignedIntBuffer) - Method in class ToUnsignedInt
-
- convertFloat(FloatBuffer, UnsignedShortBuffer) - Method in class ToUnsignedShortNoScaling
-
- convertFloat(FloatBuffer, UnsignedShortBuffer) - Method in class ToUnsignedShortScaleByType
-
- convertFloat(FloatBuffer, T) - Method in class VoxelsConverter
-
Copies a value from the current position in a
FloatBuffer
to the current position in
a buffer of type
T
.
- convertFrom(VoxelsUntyped, VoxelsFactoryTypeBound<T>) - Method in class VoxelsConverter
-
Creates a new voxels of type T
and copies the voxels from from
.
- ConvertFromImagePlus - Class in org.anchoranalysis.io.imagej.convert
-
Converts an ImagePlus
into a channel or voxels.
- ConvertFromMat - Class in org.anchoranalysis.plugin.opencv.convert
-
Convert from the OpenCV
Mat
to a
Stack
.
- ConvertFromPhysicalVolume<T extends FeatureInputWithResolution> - Class in org.anchoranalysis.image.feature.bean.physical
-
converts a feature to a physical distance in a XY place that is isometric
- ConvertFromPhysicalVolume() - Constructor for class ConvertFromPhysicalVolume
-
- convertFromUnits(double, String) - Static method in class SpatialUnits
-
Converts a value from another unit-type to base units.
- convertFromUnits(double, SpatialUnits.UnitSuffix) - Static method in class SpatialUnits
-
Converts a value from another unit-type to base units.
- ConvertImageFormat - Class in org.anchoranalysis.plugin.image.task.bean.format
-
Converts each input-image to an output format, optionally changing the bit depth.
- ConvertImageFormat() - Constructor for class ConvertImageFormat
-
- ConvertNamedChannels<T extends NamedChannelsInput,S,U extends InputFromManager> - Class in org.anchoranalysis.plugin.mpp.experiment.bean.convert
-
- ConvertNamedChannels() - Constructor for class ConvertNamedChannels
-
- ConvertNamedChannelsInputToStack - Class in org.anchoranalysis.plugin.io.bean.input.stack
-
- ConvertNamedChannelsInputToStack(NamedChannelsInput, ExecutionTimeRecorder) - Constructor for class ConvertNamedChannelsInputToStack
-
Create with an input.
- ConvertNamedChannelsInputToStack(NamedChannelsInput, int, Optional<String>, ExecutionTimeRecorder) - Constructor for class ConvertNamedChannelsInputToStack
-
Create with an input.
- ConvertNamedChannelsToStack - Class in org.anchoranalysis.plugin.io.bean.input.stack
-
- ConvertNamedChannelsToStack() - Constructor for class ConvertNamedChannelsToStack
-
- ConvertRGBToHSV - Class in org.anchoranalysis.plugin.opencv.bean.color
-
- ConvertRGBToHSV() - Constructor for class ConvertRGBToHSV
-
- ConvertRGBToLab - Class in org.anchoranalysis.plugin.opencv.bean.color
-
- ConvertRGBToLab() - Constructor for class ConvertRGBToLab
-
- convertSliceOfSingleChannel(ByteBuffer, int, OrientationChange) - Method in class ConvertTo
-
Converts a slice of single-channel into a newly created
VoxelBuffer
.
- ConvertStackToRGB - Class in org.anchoranalysis.image.io.stack
-
- ConvertTo<T> - Class in org.anchoranalysis.io.bioformats.copyconvert
-
Converts a subset of raw voxel bytes in a buffer to a possibly a buffer with different data-type.
- ConvertTo(Function<VoxelsUntyped, Voxels<T>>, IntFunction<T>, Function<T, VoxelBuffer<T>>) - Constructor for class ConvertTo
-
- convertTo3d(Point2d) - Static method in class PointConverter
-
Convert a
Point2d
to a
Point3d
using
0
as the value of the Z-axis
component.
- convertTo3i(Point2i) - Static method in class PointConverter
-
Convert a
Point2i
to a
Point3i
using
0
as the value of the Z-axis
component.
- convertTo3i(Point2i, int) - Static method in class PointConverter
-
Convert a
Point3i
to a
Point2i
using an explicit value for the Z-axis
component.
- ConvertToFactory - Class in org.anchoranalysis.io.bioformats.copyconvert
-
- ConvertToImagePlus - Class in org.anchoranalysis.io.imagej.convert
-
Converts a channel or voxels into a ImagePlus
.
- ConvertToImageProcessor - Class in org.anchoranalysis.io.imagej.convert
-
Converts other voxel data-structures (as used by Anchor) to an ImageJ ImageProcessor
.
- ConvertToImg - Class in org.anchoranalysis.image.voxel.convert.imglib2
-
- ConvertToMat - Class in org.anchoranalysis.plugin.opencv.convert
-
Converts common image data-structures used by Anchor to the Mat
class used by OpenCV.
- ConvertToNativeImg - Class in org.anchoranalysis.image.voxel.convert.imglib2
-
- convertToObjects(Dimensions) - Method in interface AnnotationWithMarks
-
Creates an object-collection that is a voxelized representation of the marks in the
annotation.
- convertToOutputType(Channel) - Method in class GradientBase
-
- convertToPhysical(double, UnitConverter) - Method in class ConvertFromPhysicalVolume
-
- convertToPhysical(double, UnitConverter) - Method in class ConvertToPhysicalAreaXY
-
- convertToPhysical(double, UnitConverter) - Method in class ConvertToPhysicalDistance
-
- convertToPhysical(double, UnitConverter) - Method in class ConvertToPhysicalVolume
-
- convertToPhysical(double, UnitConverter) - Method in class FeatureConvertUnits
-
- ConvertToPhysicalAreaXY<T extends FeatureInputWithResolution> - Class in org.anchoranalysis.image.feature.bean.physical
-
- ConvertToPhysicalAreaXY() - Constructor for class ConvertToPhysicalAreaXY
-
- ConvertToPhysicalDistance<T extends FeatureInputWithResolution> - Class in org.anchoranalysis.image.feature.bean.physical
-
- ConvertToPhysicalDistance(Feature<T>, SpatialUnits.UnitSuffix, DirectionVector) - Constructor for class ConvertToPhysicalDistance
-
- ConvertToPhysicalDistance() - Constructor for class ConvertToPhysicalDistance
-
- ConvertToPhysicalVolume<T extends FeatureInputWithResolution> - Class in org.anchoranalysis.image.feature.bean.physical
-
converts a feature to a physical distance in a XY place that is isometric
- ConvertToPhysicalVolume() - Constructor for class ConvertToPhysicalVolume
-
- convertToString(Path) - Static method in class PathOperations
-
Converts a path to a string, making sure it uses UNIX-style separators.
- convertToUnits(double, String) - Static method in class SpatialUnits
-
Converts a value in base-units to another unit-type.
- convertToUnits(double, SpatialUnits.UnitSuffix) - Static method in class SpatialUnits
-
Converts a value in base-units to another unit-type.
- ConvertToVoxelBuffer - Class in org.anchoranalysis.io.imagej.convert
-
Converts a ImageProcessor
to a voxel-buffer of particular data-type.
- ConvertUnits<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.physical
-
- ConvertUnits() - Constructor for class ConvertUnits
-
- convertUnsignedByte(UnsignedByteBuffer, FloatBuffer) - Method in class ToFloatNoScaling
-
- convertUnsignedByte(UnsignedByteBuffer, UnsignedByteBuffer) - Method in class ToUnsignedByte
-
- convertUnsignedByte(UnsignedByteBuffer, UnsignedIntBuffer) - Method in class ToUnsignedInt
-
- convertUnsignedByte(UnsignedByteBuffer, UnsignedShortBuffer) - Method in class ToUnsignedShortNoScaling
-
- convertUnsignedByte(UnsignedByteBuffer, UnsignedShortBuffer) - Method in class ToUnsignedShortScaleByType
-
- convertUnsignedByte(UnsignedByteBuffer, T) - Method in class VoxelsConverter
-
Copies a value from the current position in a
UnsignedByteBuffer
to the current
position in a buffer of type
T
.
- convertUnsignedInt(UnsignedIntBuffer, FloatBuffer) - Method in class ToFloatNoScaling
-
- convertUnsignedInt(UnsignedIntBuffer, UnsignedByteBuffer) - Method in class ToUnsignedByteNoScaling
-
- convertUnsignedInt(UnsignedIntBuffer, UnsignedByteBuffer) - Method in class ToUnsignedByteScaleByMaxValue
-
- convertUnsignedInt(UnsignedIntBuffer, UnsignedByteBuffer) - Method in class ToUnsignedByteScaleByMinMaxValue
-
- convertUnsignedInt(UnsignedIntBuffer, UnsignedByteBuffer) - Method in class ToUnsignedByteScaleByType
-
- convertUnsignedInt(UnsignedIntBuffer, UnsignedIntBuffer) - Method in class ToUnsignedInt
-
- convertUnsignedInt(UnsignedIntBuffer, UnsignedShortBuffer) - Method in class ToUnsignedShortNoScaling
-
- convertUnsignedInt(UnsignedIntBuffer, UnsignedShortBuffer) - Method in class ToUnsignedShortScaleByType
-
- convertUnsignedInt(UnsignedIntBuffer, T) - Method in class VoxelsConverter
-
Copies a value from the current position in a
UnsignedIntBuffer
to the current
position in a buffer of type
T
.
- convertUnsignedShort(UnsignedShortBuffer, FloatBuffer) - Method in class ToFloatNoScaling
-
- convertUnsignedShort(UnsignedShortBuffer, UnsignedByteBuffer) - Method in class ToUnsignedByteNoScaling
-
- convertUnsignedShort(UnsignedShortBuffer, UnsignedByteBuffer) - Method in class ToUnsignedByteScaleByMaxValue
-
- convertUnsignedShort(UnsignedShortBuffer, UnsignedByteBuffer) - Method in class ToUnsignedByteScaleByMinMaxValue
-
- convertUnsignedShort(UnsignedShortBuffer, UnsignedByteBuffer) - Method in class ToUnsignedByteScaleByType
-
- convertUnsignedShort(UnsignedShortBuffer, UnsignedIntBuffer) - Method in class ToUnsignedInt
-
- convertUnsignedShort(UnsignedShortBuffer, UnsignedShortBuffer) - Method in class ToUnsignedShortNoScaling
-
- convertUnsignedShort(UnsignedShortBuffer, UnsignedShortBuffer) - Method in class ToUnsignedShortScaleByType
-
- convertUnsignedShort(UnsignedShortBuffer, T) - Method in class VoxelsConverter
-
Copies a value from the current position in a
UnsignedShortBuffer
to the current
position in a buffer of type
T
.
- convertValue(short) - Method in class ToUnsignedShort
-
- convertValue(short) - Method in class UnsignedShortFromSignedShort
-
- convertValue(short) - Method in class UnsignedShortFromUnsignedShort
-
- ConvertWithHistogram<T> - Class in org.anchoranalysis.plugin.image.bean.channel.provider.convert
-
Converts a channel to a different voxel data-type by applying a converter with an associated
histogram.
- ConvertWithHistogram() - Constructor for class ConvertWithHistogram
-
- ConvexHull2D - Class in org.anchoranalysis.plugin.points.bean.convexhull
-
Sets particular voxels to high only if they exist on the convex-hull of the outline of a mask.
- ConvexHull2D() - Constructor for class ConvexHull2D
-
- convexHull2D(List<Point2i>) - Static method in class ConvexHullUtilities
-
- convexHull2D(List<Point2i>, int) - Static method in class ConvexHullUtilities
-
Apply a convex-hull algorithm to filter a set of points.
- ConvexHull3D - Class in org.anchoranalysis.plugin.points.bean.convexhull
-
- ConvexHull3D() - Constructor for class ConvexHull3D
-
- ConvexHullBase - Class in org.anchoranalysis.plugin.points.bean.convexhull
-
- ConvexHullBase() - Constructor for class ConvexHullBase
-
- ConvexHullUtilities - Class in org.anchoranalysis.plugin.points.convexhull
-
- copyAllChannels(Dimensions, ByteBuffer, DestinationChannelForIndex, int, ImageFileEncoding, OrientationChange) - Method in class ConvertTo
-
- copyAllFrames(IFormatReader, List<Channel>, ImageFileShape, ConvertTo<?>, ReadOptions, OrientationChange) - Static method in class CopyConvert
-
Copies all frames, channels, z-slices (in a byte-array) into a destination set of
Channel
s converting them if necessary along the way.
- copyChange(MarkCollection) - Method in class MarksFromPartition
-
Makes a copy, with different marks
- copyChangeDictionary(Dictionary) - Method in class EnergyStack
-
- copyChangeIterationsDilation(int) - Method in class MorphologicalIterations
-
Copies the bean setting an new value for iterationsDilation
- copyChangeOrientation(ByteBuffer, boolean, int, T, OrientationChange) - Method in class ConvertTo
-
Copy the bytes, changing orientation.
- copyChangeOrientation(ByteBuffer, boolean, int, UnsignedByteBuffer, OrientationChange) - Method in class ToUnsignedByteWithScaling
-
- copyChangeOrientation(ByteBuffer, boolean, int, UnsignedByteBuffer, OrientationChange) - Method in class UnsignedByteFromFloat
-
- copyChangeOrientation(ByteBuffer, boolean, int, UnsignedByteBuffer, OrientationChange) - Method in class UnsignedByteFromUnsignedByteInterleaving
-
- copyChangeOrientation(ByteBuffer, boolean, int, UnsignedByteBuffer, OrientationChange) - Method in class UnsignedByteFromUnsignedByteNoInterleaving
-
- copyChangeOrientation(ByteBuffer, boolean, int, FloatBuffer, OrientationChange) - Method in class FloatFromUnsignedByte
-
- copyChangeOrientation(ByteBuffer, boolean, int, FloatBuffer, OrientationChange) - Method in class FloatFromUnsignedInt
-
- copyChangeOrientation(ByteBuffer, boolean, int, UnsignedIntBuffer, OrientationChange) - Method in class UnsignedIntFromUnsignedInt
-
- copyChangeOrientation(ByteBuffer, boolean, int, UnsignedShortBuffer, OrientationChange) - Method in class ToUnsignedShort
-
- CopyContext<T> - Class in org.anchoranalysis.plugin.io.input.path
-
Context parameters when copying many files from a source directory to a destination directory.
- CopyContext(Path, Path, T) - Constructor for class CopyContext
-
- CopyConvert - Class in org.anchoranalysis.io.bioformats.copyconvert
-
Copies the bytes from a IFormatReader
to a list of channels, converting if necessary.
- CopyFiles<T> - Class in org.anchoranalysis.plugin.io.bean.task
-
Copy files to the output-directory, possibly changing the name or performing other operations
like compression in the process.
- CopyFiles() - Constructor for class CopyFiles
-
- CopyFilesMethod - Class in org.anchoranalysis.plugin.io.bean.file.copy.method
-
A method used for copying files (e.g.
- CopyFilesMethod() - Constructor for class CopyFilesMethod
-
- CopyFilesNaming<T> - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming
-
How an output name (and path) is selected for an input file when copying.
- CopyFilesNaming() - Constructor for class CopyFilesNaming
-
- CopyFilesNamingOne - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming
-
- CopyFilesNamingOne() - Constructor for class CopyFilesNamingOne
-
- CopyFilesNamingWithoutSharedState - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming
-
Base class for implementations of
CopyFilesNaming
where each file is copied independently
of the others.
- CopyFilesNamingWithoutSharedState() - Constructor for class CopyFilesNamingWithoutSharedState
-
- copyFrom(int, int, ResultsVector, int) - Method in class ResultsVector
-
Copies a contiguous subset of results from another vector.
- copyFrom(VoxelsUntyped, Voxels<T>) - Method in class VoxelsConverter
-
Copies voxels from a source (of any type) to voxels of type T
.
- copyFromFloat(Voxels<FloatBuffer>, Voxels<T>) - Method in class VoxelsConverter
-
Copies voxels from a source of type @{link FloatBuffer} to voxels of type T
.
- copyFromPath1ToPath2(String) - Method in class DualComparer
-
Copies a file from its path in the first loader, to its path in the second loader.
- copyFromUnsignedByte(Voxels<UnsignedByteBuffer>, Voxels<T>) - Method in class VoxelsConverter
-
Copies voxels from a source of type @{link UnsignedByteBuffer} to voxels of type T
.
- copyFromUnsignedInt(Voxels<UnsignedIntBuffer>, Voxels<T>) - Method in class VoxelsConverter
-
Copies voxels from a source of type @{link UnsignedIntBuffer} to voxels of type T
.
- copyFromUnsignedShort(Voxels<UnsignedShortBuffer>, Voxels<T>) - Method in class VoxelsConverter
-
Copies voxels from a source of type @{link UnsignedShortBuffer} to voxels of type T
.
- copyImageInto(Stack, Stack, BoundingBox) - Static method in class StackCopierAtBox
-
Copies a
source
stack into a
destination
stack at a particular
BoundingBox
.
- copyInitialize(Class<?>, NamedProviderStore<S>) - Method in class PopulateStoreFromDefine
-
Copies objects of a particular class from the define and initializes.
- copyKeepOrientation(ByteBuffer, boolean, int, T) - Method in class ConvertTo
-
Copy the bytes, without changing orientation.
- copyKeepOrientation(ByteBuffer, boolean, int, UnsignedByteBuffer) - Method in class ToUnsignedByteWithScaling
-
- copyKeepOrientation(ByteBuffer, boolean, int, UnsignedByteBuffer) - Method in class UnsignedByteFromFloat
-
- copyKeepOrientation(ByteBuffer, boolean, int, UnsignedByteBuffer) - Method in class UnsignedByteFromUnsignedByteInterleaving
-
- copyKeepOrientation(ByteBuffer, boolean, int, UnsignedByteBuffer) - Method in class UnsignedByteFromUnsignedByteNoInterleaving
-
- copyKeepOrientation(ByteBuffer, boolean, int, FloatBuffer) - Method in class FloatFromUnsignedByte
-
- copyKeepOrientation(ByteBuffer, boolean, int, FloatBuffer) - Method in class FloatFromUnsignedInt
-
- copyKeepOrientation(ByteBuffer, boolean, int, UnsignedIntBuffer) - Method in class UnsignedIntFromUnsignedInt
-
- copyKeepOrientation(ByteBuffer, boolean, int, UnsignedShortBuffer) - Method in class ToUnsignedShort
-
- copyPixelsTo(int, BoundingBox, Voxels<UnsignedByteBuffer>, BoundingBox) - Method in class DisplayStack
-
Copies pixels from a particular channel to an output buffer.
- copyProviderInitialize(Class<?>, NamedProviderStore<T>) - Method in class PopulateStoreFromDefine
-
Copies objects of a particular class (which must be a
Provider
) from
define
and initializes each.
- copyStackInto(CheckedSupplier<RGBStack, InputReadFailedException>, String, Path, Optional<String>) - Method in class MontageSharedState
-
- copyTo(SharedObjects, Logger) - Method in interface ExportSharedObjects
-
Adds any exported shared-objects to sharedObjects
.
- copyTo(SharedObjects, Logger) - Method in class MultiInput
-
- copyTo(SharedObjects, Logger) - Method in class FromCSVInput
-
- copyToDirectory(File) - Method in class TestLoader
-
Copies all the data in the test-data folder (recursively), preserving file modification
times.
- copyToDirectory(String[], File) - Method in class TestLoader
-
Copies specific subdirectories from the test-data folder (recursively), preserving file
modification times.
- copyVoxelFrom(int, VoxelBuffer<T>, int) - Method in class VoxelBuffer
-
Copies one particular intensity-value from another
VoxelBuffer
into this buffer.
- copyVoxelsTo(BoundingBox, VoxelsUntyped, BoundingBox) - Method in class VoxelsUntyped
-
Copies the voxels into a destination
, but only those voxels inside a bounding-box.
- copyVoxelsTo(ObjectMask, VoxelsUntyped, BoundingBox) - Method in class VoxelsUntyped
-
Copies the voxels into a
destination
, but only those voxels inside an
ObjectMask
.
- copyWithoutInitialize(Class<?>, NamedProviderStore<S>) - Method in class PopulateStoreFromDefine
-
Copies objects of a particular class from the define without performing any
initialization.
- cornerMin() - Method in class BoundedVoxels
-
The minimum corner of the bounding box in each dimension.
- cornerMin() - Method in class BoundingBox
-
The minimum corner of the bounding box in each dimension.
- correctedEndIndex(int) - Method in class IndexRangeNegative
-
The end-index, maybe corrected so that it is no longer negative.
- correctedStartIndex(int) - Method in class IndexRangeNegative
-
The start-index, maybe corrected so that it is no longer negative.
- CostMatrix<T> - Class in org.anchoranalysis.annotation.io.assignment
-
Stores costs between all possible pairings between elements from two lists.
- CostOverlapWithinMidpointDistance - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap
-
TODO the center-of-gravity calculation can be turned into a FeatureCalculation which is cacheable
- CostOverlapWithinMidpointDistance() - Constructor for class CostOverlapWithinMidpointDistance
-
- Count - Class in org.anchoranalysis.feature.bean.results
-
The sum of the results from a particular feature.
- Count() - Constructor for class Count
-
- count() - Method in class PredicateAtCorner
-
- count() - Method in class PredicateImplementation
-
- count() - Method in interface VoxelsPredicate
-
Counts the number of values satisfying the predicate - across all voxels.
- count(BoundedVoxels<UnsignedByteBuffer>, BoundedVoxels<UnsignedByteBuffer>) - Method in class CountIntersectingVoxels
-
- Count - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
-
Counts the number of items in a histogram (posssibly in relation to a threshold: above, below
etc.)
- Count() - Constructor for class Count
-
- countByte(BoundedVoxels<UnsignedByteBuffer>, BoundedVoxels<UnsignedByteBuffer>, PredicateTwoBytes) - Static method in class CountVoxelsIntersectingBounded
-
Counts all voxels in the intersection of two bounded-voxels of type
BoundedVoxels
that match a predicate.
- countByteMasked(Voxels<UnsignedByteBuffer>, byte, BoundedVoxels<UnsignedByteBuffer>, BoundedVoxels<UnsignedByteBuffer>, PredicateTwoBytes) - Static method in class CountVoxelsIntersectingBounded
-
Counts all voxels intersection of two bounded-voxels of type
BoundedVoxels
but only
voxels that lie on an object-mask and match a predicate.
- CountEqual - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.energy
-
- CountEqual() - Constructor for class CountEqual
-
- Counter - Class in org.anchoranalysis.math.arithmetic
-
A simple counter that increments.
- Counter(int) - Constructor for class Counter
-
- Counter() - Constructor for class Counter
-
- countForObject(ObjectMask) - Method in class PredicateAtCorner
-
- countForObject(ObjectMask) - Method in class PredicateImplementation
-
- countForObject(ObjectMask) - Method in interface VoxelsPredicate
-
Counts the number of values satisfying the predicate - but restricted to voxels corresponding
to on in an object-mask.
- countIntersectingVoxels(ObjectMask, ObjectMask) - Static method in class CountVoxelsIntersectingObjects
-
Counts the number of intersecting-voxels between two object-masks.
- countIntersectingVoxels(ObjectMask) - Method in class ObjectMask
-
Counts the number of intersecting-voxels between two object-masks.
- CountIntersectingVoxels - Class in org.anchoranalysis.mpp.overlap
-
Counts the number of intersecting-pixels where bytes are encoded as region memberships
- CountIntersectingVoxels(byte) - Constructor for class CountIntersectingVoxels
-
- CountIntersectingVoxels(PredicateRegionMembership) - Constructor for class CountIntersectingVoxels
-
- countIntersectingVoxels() - Method in class MaxIntensityProjectionPair
-
- CountKernel - Class in org.anchoranalysis.image.voxel.kernel.count
-
Base class for kernels that return a count (positive integer) for every voxel.
- CountKernel() - Constructor for class CountKernel
-
Creates with a kernel-size of three.
- CountKernelNeighborhood - Class in org.anchoranalysis.image.voxel.kernel.count
-
For every voxel on the outline, count all neighbors that are adjacent.
- CountKernelNeighborhood() - Constructor for class CountKernelNeighborhood
-
- CountKernelNeighborhoodMask - Class in org.anchoranalysis.image.voxel.kernel.count
-
The number of touching-faces of a voxel with a neighbor, so long as the neighbor is part of an
ObjectMask
.
- CountKernelNeighborhoodMask(ObjectMask) - Constructor for class CountKernelNeighborhoodMask
-
Create with object-mask.
- countMasked(BoundedVoxels<UnsignedByteBuffer>, BoundedVoxels<UnsignedByteBuffer>, Voxels<UnsignedByteBuffer>, byte) - Method in class CountIntersectingVoxels
-
- countMatching(IntPredicate) - Method in class Histogram
-
Gets the total count of all values that match a predicate.
- countOff() - Method in class BinaryVoxels
-
Counts the number of voxels with an off state.
- countOn() - Method in class BinaryVoxels
-
Counts the number of voxels with an on state.
- countThreshold(RelationToThreshold) - Method in interface VoxelStatistics
-
Counts the number of voxels that exist, relative to a threshold.
- countThreshold(RelationToThreshold) - Method in class VoxelStatisticsCombined
-
- countThreshold(RelationToThreshold) - Method in class VoxelStatisticsFromHistogram
-
- CountVoxelsIntersectingBounded - Class in org.anchoranalysis.image.voxel.iterator.intersecting
-
- CountVoxelsIntersectingObjects - Class in org.anchoranalysis.image.voxel.iterator.intersecting
-
- countXY() - Method in class RunningSumPoint
-
The count for the X or Y dimensions.
- countZ() - Method in class RunningSumPoint
-
The count for the Z dimension.
- create(List<T>, List<T>, boolean, CheckedToDoubleBiFunction<T, T, CreateException>) - Static method in class CostMatrix
-
Creates by calculating the cost between elements.
- create(Provider<T>) - Static method in class OptionalProviderFactory
-
Creates from a provider if non-null.
- create() - Method in class RandomNumberGeneratorBean
-
- create() - Method in class EqualToBean
-
- create() - Method in class GreaterThanBean
-
- create() - Method in class GreaterThanEqualToBean
-
- create() - Method in class LessThanBean
-
- create() - Method in class LessThanEqualToBean
-
- create() - Method in class RelationBean
-
- create() - Method in class StringMap
-
Derives a
Map
representation for the mapping.
- create(boolean, T) - Static method in class OptionalFactory
-
Creates only if a boolean flag is true, otherwise returns Optional.empty()
.
- create(boolean, Supplier<T>) - Static method in class OptionalFactory
-
Creates only if a boolean flag is true, otherwise returns Optional.empty()
.
- create(String) - Static method in class OptionalFactory
-
Creates Optional.empty()
for an empty string, or otherwise Optional.of()
.
- create(OutputterChecked, ErrorReporter, ExecutionArguments, boolean) - Method in class LoggingDestination
-
Creates a logger for this destination
- create(OutputterChecked, ErrorReporter, ExecutionArguments, boolean) - Method in class OnlyIf
-
- create(OutputterChecked, ErrorReporter, ExecutionArguments, boolean) - Method in class SwitchDetailedLogging
-
- create(OutputterChecked, ErrorReporter, ExecutionArguments, boolean) - Method in class ToConsole
-
- create(OutputterChecked, ErrorReporter, ExecutionArguments, boolean) - Method in class ToMultiple
-
- create(OutputterChecked, ErrorReporter, ExecutionArguments, boolean) - Method in class ToTextFile
-
- create(OutputterChecked, ErrorReporter, ExecutionArguments, boolean) - Method in class ToTextFileOnlyIfFailure
-
- create(boolean) - Static method in class ExecutionTimeRecorderFactory
-
Creates either a
ExecutionTimeRecorder
that records times, or ignores the recording
depending on whether any output is enabled that needs the execution-time.
- create(Class<? extends FeatureInput>) - Method in interface CacheCreator
-
- create(SharedObjects) - Static method in class FeatureRelatedInitialization
-
Creates with shared-objects, and otherwise empty initialization.
- create(Logger, Path) - Static method in class FeatureRelatedInitialization
-
Creates a log and a model-directory, and otherwise empty initialization.
- create(FeatureCSVMetadata, Outputter, boolean) - Static method in class FeatureCSVWriter
-
- create(FeatureCSVMetadata) - Method in interface FeatureCSVWriterFactory
-
- create(FeatureCSVMetadataForOutput, FeatureCSVWriterFactory, Optional<Consumer<LabelledResultsVector>>, boolean) - Static method in class LabelledResultsCSVWriterFactory
-
Creates with appropriate support classes for outputting.
- create(FeatureNameList, boolean) - Static method in class FeatureTableCSVGeneratorFactory
-
- create(Optional<String>, String) - Static method in class MultiNameFactory
-
Creates either a multi-name that is either has a single part or a double part.
- create(Class<? extends FeatureInput>) - Method in class HorizontalCacheCreator
-
- create(Stack) - Static method in class BufferedImageFromStack
-
- create(Dimensions, VoxelDataType) - Method in class ChannelFactory
-
Creates an empty initialized channel for a particular data-type.
- create(Voxels<?>) - Method in class ChannelFactory
-
Create a
Channel
from particular voxels.
- create(Voxels<?>, Optional<Resolution>) - Method in class ChannelFactory
-
Create a
Channel
from particular voxels.
- create(Voxels<?>, Optional<Resolution>) - Method in class ChannelFactorySingleType
-
Create a
Channel
from voxels and a resolution.
- create(String) - Static method in class ImageSizeSuggestionFactory
-
Creates a suggestion for how to resize an image.
- create(Map<Integer, T>, UnaryOperator<T>) - Method in class DecodeLabels
-
Creates a map of elements to other elements that are labelled with unique integers
(sequentially increasing) in voxels.
- create(int) - Method in class DecodeLabels
-
Creates a list of elements from voxels that are labelled with unique integers (sequentially
increasing).
- create(Collection<Point3i>) - Static method in class ObjectFromPointsFactory
-
- create(Optional<SharedObjects>, Optional<EnergyStack>) - Static method in class InitializationFactory
-
- create(OpenedImageFile, Logger) - Method in class ChannelMapCreator
-
- create(InputOutputContext) - Static method in class ImageInitializationFactory
-
- create(InputOutputContext, Optional<ImageSizeSuggestion>) - Static method in class ImageInitializationFactory
-
- create() - Static method in class RasterDirectoryObjectsGenerator
-
Creates the
Generator
to write each object as a binary
Mask
in a directory.
- create(SliceBufferIndex<T>) - Method in interface VoxelsFactoryTypeBound
-
- create(ObjectCollection, Extent, boolean, boolean) - Static method in class NeighborGraph
-
Create the graph with object-masks as vertices, where edges represent the number of
neighboring voxels between objects.
- create(List<V>, Function<V, ObjectMask>, Extent, boolean, boolean) - Static method in class NeighborGraph
-
- create(ObjectCollection) - Static method in class IntersectingObjects
-
- create(VoxelDataType, Extent) - Static method in class MaxIntensityProjection
-
Creates a buffer for a maximum-intensity projection for unsigned byte voxels.
- create(VoxelDataType, Extent) - Static method in class MinIntensityProjection
-
Creates a buffer for a minimum-intensity projection for unsigned byte voxels.
- create(VoxelDataType, Extent) - Static method in class MeanIntensityProjection
-
Creates a buffer for a mean-intensity projection for unsigned byte voxels.
- create(VoxelDataType, Extent) - Static method in class StandardDeviationIntensityProjection
-
Creates a buffer for a standard-deviation projection for unsigned byte voxels.
- create(boolean) - Method in interface CreateModelForPool
-
Creates a model.
- create(IFormatReader, VoxelDataType, int) - Static method in class ConvertToFactory
-
- create(Path) - Static method in class CSVWriter
-
Creates and starts a CSVWriter (it's always allowed, so will never return null)
- create(String, OutputterChecked, String) - Static method in class TextFileOutputter
-
- create(InputManagerParameters) - Method in class FilesProvider
-
Creates or provides a list of files.
- create(InputManagerParameters) - Method in class FilesProviderUnary
-
- create(InputManagerParameters) - Method in class FilesProviderWithDirectory
-
- create(InputManagerParameters) - Method in class SpecificPathList
-
- create(Optional<MultiLevelOutputEnabled>) - Method in class AddToDefaults
-
- create(Optional<MultiLevelOutputEnabled>) - Method in class IgnoreUnderscorePrefixUnless
-
- create(Optional<MultiLevelOutputEnabled>) - Method in class NoneExcept
-
- create(Optional<MultiLevelOutputEnabled>) - Method in class OutputEnabledRules
-
Creates rules for determining whether an output is enabled or disabled.
- create(Optional<MultiLevelOutputEnabled>) - Method in class Permissive
-
- create(Optional<MultiLevelOutputEnabled>) - Method in class PermissiveExcept
-
- create(CommandLine, Path, Path) - Static method in class ExperimentExecutorFactory
-
Creates an experiment-executor from a command line that EITHER: uses a default-experiment OR
accepts a path passed as the first command-line argument
- create() - Method in class MarkEllipseFactory
-
- create() - Method in class MarkEllipsoidFactory
-
- create() - Method in class MarkFactory
-
- create() - Method in class MarkPointListFactory
-
- create() - Method in class EnergySchemeCreator
-
- create() - Method in class EnergySchemeCreatorByElement
-
- create(EnergyStackWithoutParameters) - Method in class DictionaryForImageCreator
-
- create(int) - Method in interface VoxelPartitionFactory
-
- create(int) - Method in class VoxelPartitonFactoryHistogram
-
- create(ImageInitialization, SharedObjects) - Static method in class PointsInitialization
-
- create(Optional<? extends ExportSharedObjects>, InitializationContext, Optional<Define>) - Static method in class MarksInitializationFactory
-
- create(List<Point3d>) - Static method in class PointListFactory
-
- create(List<Point3d>, int) - Static method in class PointListFactory
-
- create(IntToFloatFunction, Point2i) - Static method in class RotatableBoundingBoxFactory
-
Builds a bounding-box from the 5-element floating-point vector returned from the EAST
algorithm.
- create(Mark, EnergyStackWithoutParameters, RegionMap) - Static method in class PxlMarkMemoFactory
-
- create(Mark, EnergyStackWithoutParameters, RegionMap) - Static method in class VoxelizedMarkFactory
-
- create(Mark) - Method in class ProposerContext
-
- create(InputManagerParameters) - Method in class FromAnnotations
-
- create(VoxelDataType, Extent) - Method in class MaxProjection
-
- create(VoxelDataType, Extent) - Method in class MeanProjection
-
- create(VoxelDataType, Extent) - Method in class MinProjection
-
- create(VoxelDataType, Extent) - Method in class ProjectableBufferAggregator
-
- create(VoxelDataType, Extent) - Method in class StandardDeviationProjection
-
- create() - Method in interface PermuteFirstSecondOrder.CreateFirstSecondOrder
-
- create(List<NamedBean<FeatureListProvider<T>>>, LabelHeaders, FeatureOutputNames, Optional<InputGrouper>, FeatureExporterContext) - Static method in class FeatureExporter
-
Alternative static constructor that creates a shared-state from a list of named
FeatureListProvider
s.
- create(NamedFeatureStore<T>, LabelHeaders, FeatureOutputNames, Optional<InputGrouper>, FeatureExporterContext) - Static method in class FeatureExporter
-
- create(FeatureOutputNames, FeatureTableCalculator<T>, LabelHeaders, Optional<InputGrouper>, FeatureExporterContext) - Static method in class FeatureExporter
-
- create(OpenedImageFile, Logger) - Method in class Autoname
-
- create(OpenedImageFile, Logger) - Method in class FromEntries
-
- create(OpenedImageFile, Logger) - Method in class FromMetadata
-
- create(OpenedImageFile, Logger) - Method in class SingleChannel
-
- create(InputManagerParameters) - Method in class Combine
-
- create(InputManagerParameters) - Method in class Rooted
-
- create(InputManagerParameters) - Method in class ExperimentResultsExperimentStructure
-
- create() - Static method in class ConstantsInListFixture
-
Creates a feature-list associated with the fixture.
- create(boolean, boolean) - Static method in class EnergyStackFixture
-
Creates the energy-stack to use.
- create(boolean, boolean, boolean, boolean) - Static method in class EnergyStackFixture
-
Creates the energy-stack to use.
- create(boolean) - Static method in class MaskFixture
-
Creates the
Mask
with
the default corner and no assigned resolution.
- create(boolean, Optional<Resolution>) - Static method in class MaskFixture
-
Creates the
Mask
with
the default corner and a particular resolution.
- create(Point3i, boolean) - Static method in class MaskFixture
-
Creates the
Mask
with
a particular corner and no assigned resolution.
- create(Point3i, boolean, Optional<Resolution>) - Static method in class MaskFixture
-
Creates the
Mask
with
a particular corner and a particular resolution.
- create(ChannelSpecification, Extent) - Method in class StackFixture
-
Creates a stack with a particular number of the channels of particular size.
- create() - Static method in class OutputterCheckedFixture
-
- create1() - Method in class CutOffCornersObjectFixture
-
Create the first object.
- create2() - Method in class CutOffCornersObjectFixture
-
Create the second object.
- create3() - Method in class CutOffCornersObjectFixture
-
Create the third object.
- createAddCriteria() - Method in class EnergySchemeWithSharedFeatures
-
- createAggregateFeature(Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>) - Method in class FeatureListProviderAggregatePair
-
- createAggregateFeature(Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>) - Method in class ReduceFirstAndSecond
-
- createAggregateFeature(Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>) - Method in class ReduceRatioFirstAndSecond
-
- createAggregateFeature(Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>) - Method in class SubtractReducedFromMerged
-
- createAll() - Method in class CutOffCornersObjectFixture
-
Creates all three objects.
- createAndConsumeListBeans(String, HierarchicalConfiguration, Object, Collection<T>) - Static method in class BeanListCreator
-
Extracts a list of instantiated bean objects from an XML configuration, and adds them to
addTo
.
- createAndStartSession() - Method in class ReportFeatureEvaluator
-
- createArguments(CommandLine) - Method in class LauncherConfig
-
- createAscending() - Static method in class HistogramFixture
-
a histogram from 0 to 255 (inclusive) where each bin is equal to its index (value 5 has count
5, value 100 has count 100 etc.)
- createAssignment(ObjectCollection, ObjectCollection, double, Dimensions) - Method in class AssignOverlappingObjects
-
Creates an assignment from the objects in left
to those in right
.
- createAssignment(ObjectsToCompare, Dimensions, boolean, InputOutputContext) - Method in class AnnotationComparisonAssigner
-
- createAssignment(ObjectsToCompare, Dimensions, boolean, InputOutputContext) - Method in class FeatureCostAssigner
-
- createAssignment(ObjectsToCompare, Dimensions, boolean, InputOutputContext) - Method in class MaskIntersectionAssigner
-
- createAxisArray() - Method in class GradientBaseAddSum
-
- createAxisArray() - Method in class GradientForAxis
-
- createAxisArray() - Method in class GradientXY
-
- createBackground(NamedProviderStore<Stack>, String, StackDisplayer) - Static method in class BackgroundCreator
-
- createBean(Class, BeanDeclaration, Object) - Method in class DefineFactory
-
- createBean(Class<?>, BeanDeclaration, Object) - Method in class AnchorDefaultBeanFactory
-
- createBean(Class, BeanDeclaration, Object) - Method in class IncludeBeanFactory
-
- createBean(Class, BeanDeclaration, Object) - Method in class IncludeListBeanFactory
-
- createBean(Class, BeanDeclaration, Object) - Method in class ListBeanFactory
-
- createBean(Class, BeanDeclaration, Object) - Method in class DoubleListFactory
-
- createBean(Class, BeanDeclaration, Object) - Method in class DoubleSetFactory
-
- createBean(Class, BeanDeclaration, Object) - Method in class IntegerListFactory
-
- createBean(Class, BeanDeclaration, Object) - Method in class IntegerSetFactory
-
- createBean(Class, BeanDeclaration, Object) - Method in class StringListFactory
-
- createBean(Class, BeanDeclaration, Object) - Method in class StringSetFactory
-
- createBean(Class, BeanDeclaration, Object) - Method in class ReplacePropertyBeanFactory
-
- createBeanFromConfig(HierarchicalConfiguration, Object) - Static method in class BeanCreator
-
Creates a bean from a HierarchicalConfiguration
.
- createBeanFromXML(XMLBeanDeclaration, String, Object) - Static method in class BeanCreator
-
Creates a bean from XML.
- createBetweenTwoPoints(Point3d, Point3d) - Static method in class DirectionVector
-
- createBetweenTwoPoints(Point3i, Point3i) - Static method in class DirectionVector
-
- createBounded(BoundingBox) - Method in interface VoxelsFactoryTypeBound
-
Creates and initializes voxels that correspond to a particular bounding-box region.
- createBuilderWithDefaultErrorHandler() - Static method in class XMLParser
-
Creates a document-builder with default error-handling.
- createCachedCalculationForDerived(CalculationPartResolver<FeatureInputSingleObject>) - Method in class DerivedObject
-
- createCachedCalculationForDerived(CalculationPartResolver<FeatureInputSingleObject>) - Method in class Erode
-
- createCachedCalculationForDerived(CalculationPartResolver<FeatureInputSingleObject>) - Method in class Shell
-
- createCalculationContext(Optional<String>, ExecutionTimeRecorder, InputOutputContext) - Method in class FeatureExporter
-
- createCalculationContext(ExecutionTimeRecorder, InputOutputContext) - Method in class SharedStateSegmentInstance
-
- createCalculator(CreateCalculatorHelper, ImageInitialization, BoundReplaceStrategy<FeatureInputStack, ? extends ReplaceStrategy<FeatureInputStack>>) - Method in class MergedPairsFeatures
-
- createChannel(int, boolean) - Method in class DisplayStack
-
Create
Channel
for a particular
index
after applying conversion.
- createChannel() - Method in class CheckMarkWithMask
-
- createChannel(Extent, ChannelFixture.IntensityFunction, VoxelDataType) - Method in class ChannelFixture
-
- createChannelDeriver(ChannelSource) - Method in class AggregateChannelTask
-
- createChannelDeriver(ChannelSource) - Method in class GroupedStackBase
-
A function to derive the
individual type used for aggregation from a
Channel
.
- createChannelDeriver(ChannelSource) - Method in class ExportImageHistograms
-
- createChannelsForSeries(int, Logger) - Method in class NamedChannelsInput
-
Creates a
NamedChannelsMap
representing the channels for a particular series in this
input.
- createChecked(boolean, CheckedSupplier<T, E>) - Static method in class OptionalFactory
-
- createCollection(Channel, ObjectCollection, CalculateLevel, int, MessageLogger) - Static method in class LevelResultCollectionFactory
-
- createColor(ColoredMarks, RegionMembershipWithFlags) - Static method in class OverlayCollectionMarkFactory
-
- createColors(int) - Method in class AssignmentColorPool
-
Creates a list of colors to describe the assignment.
- createComparer(Path, String) - Method in class ComparisonPlan
-
Creates the
ImageComparer
to use to compare between images loaded in a
temporary-directory and saved-images.
- createComparer(Path, String) - Static method in class SavedFiles
-
Creates a comparer between a directory and saved-files in a directory in the resources.
- createComparisonStacks(AnnotationWithMarks, DisplayStack, Path, ColorScheme, Path, OperationContext, boolean) - Method in class MultipleComparer
-
Creates a
Stack
illustrating the comparison between
annotation
and each
source in
sources
.
- createContextForWriting(Optional<ImageFileFormat>, ExecutionTimeRecorder) - Method in class OutputManager
-
- createConverter() - Method in class ConvertChannelTo
-
Creates the converter.
- createConverter() - Method in class ConvertChannelToWithHistogram
-
Creates the converter.
- createConverter() - Method in class ScaleByDictionary
-
- createConverter() - Method in class ScaleByMinMaxValue
-
- createConverter() - Method in class ScaleByTypeToByte
-
- createConverter() - Method in class ToByte
-
- createConverter() - Method in class ToByteUpperLowerQuantileIntensity
-
- createConverterFor(VoxelDataType) - Method in class IntensityQuantiles
-
- createConverterFor(VoxelDataType) - Method in class StackDisplayer
-
Determines what kind of converter to use for a particular channel, to map it to an unsigned
8-bit channel.
- createCountKernelMask(ObjectMask) - Method in class TouchingVoxels
-
- createDelegate(Feature<T>) - Method in class PermuteDivideByParam
-
- createDelegate(Feature<T>) - Method in class PermuteFeatureSequenceInteger
-
- createDelegate(Feature<T>) - Method in class PermuteFirstSecondOrder
-
- createDescending() - Static method in class HistogramFixture
-
- createDescriptor(Extent) - Method in class HOGParameters
-
Creates an empty
HOGDescriptor
to describe an image of a particular size.
- createDesignMatrix(List<Point3f>) - Method in class LinearLeastSquaresViaNormalEquationBase
-
- createDictionary() - Method in class EnergyScheme
-
returns the associated
Dictionary
or an empty set, if no dictionary is associated with the energy-scheme.
- createDim() - Method in class PointsFitterToMark
-
- createDimensions() - Method in class WithDimensionsBase
-
- createDims() - Method in class WithOptionalDimensionsBase
-
Returns the dimensions or null if none are provided
- createDistanceMapForVoxels(BinaryVoxels<UnsignedByteBuffer>, Optional<Resolution>, float) - Method in class DistanceTransform3D
-
- createDuplicate(ReadableTuple3i, Extent) - Static method in class BoundingBox
-
Creates a bounding-box from a corner and an extent - duplicating cornerMin
.
- createDuplicate(ReadableTuple3i, ReadableTuple3i) - Static method in class BoundingBox
-
Creates from two int
points (a minimum corner and a maximum corner) - reusing cornerMinInclusive
internally.
- createDuplicatePxlMarkMemoList() - Method in class VoxelizedMarksWithEnergy
-
- CreateEllipse - Class in org.anchoranalysis.plugin.mpp.bean.provider.single
-
- CreateEllipse() - Constructor for class CreateEllipse
-
- createEmpty(Extent, VoxelDataType) - Method in class VoxelsFactory
-
Creates empty voxels to match a particular size.
- createEmptyInitialised(Dimensions) - Method in class ChannelFactorySingleType
-
Create a
Channel
initialized with zero-valued voxel-buffers.
- createEmptyInitialisedToSupportMaxValue(Dimensions, long) - Method in class ChannelFactory
-
Creates an empty initialized channel with discrete type with as minimal as needed data-type
to support a maximum value.
- createEmptyMat(Extent, int) - Static method in class ConvertToMat
-
Creates a Mat
which contains only zero-values.
- createEmptyOff(Extent) - Static method in class BinaryVoxelsFactory
-
Creates binary-voxels using unsigned 8-bit byte type and with all voxels set to off
(0).
- createEmptyOff(Extent, VoxelDataType) - Static method in class BinaryVoxelsFactory
-
Creates an empty binary-voxels of a particular data-type with all voxels initialized to
off.
- createEmptyOn(Extent) - Static method in class BinaryVoxelsFactory
-
Creates binary-voxels using unsigned 8-bit byte type and with all voxels set to on
(255).
- createEmptyStackFor(Dimensions) - Static method in class ObjectsAsRGBGenerator
-
- createEmptyUninitialised(Dimensions) - Method in class ChannelFactorySingleType
-
Create a
Channel
without initialization with voxel-buffers.
- CreateException - Exception in org.anchoranalysis.core.exception
-
A generic exception that be thrown when the creation of a new object fails.
- CreateException(String) - Constructor for exception CreateException
-
Creates with a message, but without a cause.
- CreateException(Throwable) - Constructor for exception CreateException
-
Creates with a cause, but without a message.
- CreateException(String, HasFriendlyErrorMessage) - Constructor for exception CreateException
-
Creates with a message, and a cause with a user-friendly error message.
- CreateException(String, AnchorCombinableException) - Constructor for exception CreateException
-
Creates with a message, and a combinable-exception as a cause.
- createExperimentExecutor(CommandLine) - Method in class LauncherConfig
-
- createExperimentOutputter(Optional<String>, MultiLevelOutputEnabled, Optional<MultiLevelRecordedOutputs>, OutputWriteContext, PathPrefixerContext, Optional<Consumer<Path>>, Optional<Logger>) - Method in class OutputManager
-
Creates an outputter for the experiment in general.
- createExperimentState() - Method in class SegmentIntoMarks
-
- createExperimentState() - Method in class SegmentWithMarkedPointProcess
-
- createExporter(LabelHeaders, List<NamedBean<FeatureListProvider<U>>>, FeatureOutputNames, Optional<InputGrouper>, FeatureExporterContext) - Method in class FeatureSource
-
Creates the
FeatureExporter
to be used for calculating and exporting feature-results.
- createExporter(LabelHeaders, List<NamedBean<FeatureListProvider<S>>>, FeatureOutputNames, Optional<InputGrouper>, FeatureExporterContext) - Method in class SingleRowPerInput
-
- createExporter(LabelHeaders, List<NamedBean<FeatureListProvider<FeatureInputSingleObject>>>, FeatureOutputNames, Optional<InputGrouper>, FeatureExporterContext) - Method in class FromObjects
-
- createFeatureInput(Mark, RegionMap, EnergyStack) - Method in class FeatureValueCheckMark
-
- createFeatureInput(Mark, RegionMap, EnergyStack) - Method in class FeatureValueIndividualEnergyGreaterThan
-
- createFeatureInput(Mark, RegionMap, EnergyStack) - Method in class FeatureValueMarkGreaterEqualThan
-
- createFeatureList(String, TestLoader) - Static method in class FeaturesFromXmlFixture
-
- createFeatureNames() - Method in interface FeatureTableCalculator
-
Creates A list of names for each feature (columns of the table)
- createFeatureNames() - Method in class PairsTableCalculator
-
- createFeatureNames() - Method in class SingleTableCalculator
-
- createFeatures(List<NamedBean<FeatureListProvider<FeatureInputSingleObject>>>, NamedFeatureStoreFactory, boolean) - Method in class CombineObjectsForFeatures
-
Creates features that will be applied on the objects.
- createFeatures(List<NamedBean<FeatureListProvider<FeatureInputSingleObject>>>, NamedFeatureStoreFactory, boolean) - Method in class EachObjectIndependently
-
- createFeatures(NamedFeatureStore<FeatureInputSingleObject>) - Method in class EachObjectIndependently
-
- createFeatures(List<NamedBean<FeatureListProvider<FeatureInputSingleObject>>>, NamedFeatureStoreFactory, boolean) - Method in class PairNeighbors
-
- createFeatureSession() - Method in class FeatureEvaluator
-
Creates session for evaluating feature
optionally adding an energy-stack.
- createFeatureSession(UnaryOperator<FeatureList<T>>, SharedObjects) - Method in class FeatureListEvaluator
-
Creates session for evaluating features
.
- createFilenameForWriting(String, String) - Method in class AlwaysAllowed
-
- createFilenameForWriting(String, String) - Method in class CheckIfAllowed
-
- createFilenameForWriting(String, String) - Method in interface Writer
-
The path to write a particular output to.
- createFilenameForWriting(String, String) - Method in class WriterRouterErrors
-
The path to write a particular output to.
- createFileOutputFor(String, FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Static method in class CSVReporterUtilities
-
- createFitResultFromMatrixAandCenter(DoubleMatrix2D, DoubleMatrix2D, boolean) - Static method in class EllipsoidFitHelper
-
- createFlat(boolean, Supplier<Optional<T>>) - Static method in class OptionalFactory
-
Creates an
Optional
from a boolean flag and a supplier that returns an
Optional
.
- createFloat(Extent, IntFunction<FloatBuffer>) - Static method in class VoxelsArithmeticFactory
-
- createFloat(Voxels<FloatBuffer>, int) - Static method in class VoxelsAssignerFactory
-
- createFloat(Voxels<FloatBuffer>) - Static method in class VoxelsExtracterFactory
-
- createFloat(Extent) - Static method in class MaxIntensityProjection
-
Creates a buffer for a maximum-intensity projection for float voxels.
- createFloat(Extent) - Static method in class MinIntensityProjection
-
Creates a buffer for a minimum-intensity projection for float voxels.
- createFloat(Extent) - Static method in class MeanIntensityProjection
-
Creates a buffer for a mean-intensity projection for float voxels.
- createFloat(Extent) - Static method in class StandardDeviationIntensityProjection
-
Creates a buffer for a standard-deviation projection for float voxels.
- createForDirectoryPermissive(Path, DirectoryCreationParameters, Optional<Logger>) - Static method in class OutputterChecked
-
Creates, defaulting to a permissive output-manager in a particular directory.
- createForSingle(AnchorBean<?>, String) - Static method in class PermutationAssignerFactory
-
Creates an assigner for one or more properties, as identified by propertyPath
.
- createForSubdirectory(String) - Method in class TestLoader
-
Creates a new test-loader for a subdirectory of the current test.
- createForVoxelBuffer(VoxelBuffer<T>, Extent) - Method in interface VoxelsFactoryTypeBound
-
Create a new
Voxels
that has been
initialized with a single-slice's memory
buffers.
- createFrom(BufferedImage) - Static method in class CreateStackFromBufferedImage
-
- createFrom(Mask, int, boolean, boolean) - Static method in class FindContour
-
Creates an contour from a
Mask
at the boundary of depth
1
pixel.
- createFrom(ObjectMask, int, boolean, boolean) - Static method in class FindContour
-
- createFrom(VoxelsUntyped, Optional<ObjectMask>) - Static method in class HistogramFromObjectsFactory
-
Creates a
Histogram
of voxel intensity values in
voxels
, all or only those in
object
.
- createFrom(Channel, ObjectMask) - Static method in class HistogramFromObjectsFactory
-
Creates a
Histogram
of voxel intensity values in
channel
corresponding to
object
.
- createFrom(Channel, ObjectCollection) - Static method in class HistogramFromObjectsFactory
-
Creates a
Histogram
of voxel intensity values in
channel
corresponding to
objects
.
- createFrom(Channel, Optional<Mask>) - Static method in class HistogramFromObjectsFactory
-
Creates a
Histogram
of
all voxel intensity values in
channel
, or only
those in
mask
if it is dfined.
- createFrom(Channel, Mask) - Static method in class HistogramFromObjectsFactory
-
Creates a
Histogram
of
all voxel intensity values in
channel
corresponding to
Mask
.
- createFrom(int, ObjectMask) - Method in interface DecodeLabels.CreateElementFromScaledObject
-
Create from an index and it's scaled-object.
- createFrom(int, ObjectMask) - Method in interface AccessObjectMask
-
Creates an element of type T
from an object-representation and index.
- createFrom(int, ObjectMask) - Method in class AccessObjectMaskSimple
-
- createFrom(SliceBufferIndex<T>, VoxelDataType) - Method in class VoxelsFactory
-
- createFrom(VoxelBuffer<?>) - Static method in class HistogramFactory
-
- createFrom(VoxelsUntyped) - Static method in class HistogramFactory
-
- createFrom(OutputManager) - Static method in class OutputterCheckedFixture
-
- createFrom(OutputManager, OutputEnabledRules) - Static method in class OutputterCheckedFixture
-
- createFromChannel(Channel) - Method in class ChannelProviderUnary
-
Creates a
Channel
given the entity provided by the delegate.
- createFromChannel(Channel) - Method in class AnisotropicDiffusion
-
- createFromChannel(Channel) - Method in class MinimumFilter
-
- createFromChannel(Channel) - Method in class Invert
-
- createFromChannel(Channel) - Method in class AssignFromDictionary
-
- createFromChannel(Channel) - Method in class AssignFromIntersectingObjects
-
- createFromChannel(Channel) - Method in class Convert
-
- createFromChannel(Channel) - Method in class ConvertWithHistogram
-
- createFromChannel(Channel) - Method in class Duplicate
-
- createFromChannel(Channel) - Method in class GradientBaseAddSum
-
- createFromChannel(Channel) - Method in class Sobel
-
- createFromChannel(Channel) - Method in class IfParamEquals
-
- createFromChannel(Channel) - Method in class Blur
-
- createFromChannel(Channel) - Method in class IfVoxelZero
-
- createFromChannel(Channel) - Method in class Median
-
- createFromChannel(Channel, ObjectCollection) - Method in class NormalizeDifferenceToMedian
-
- createFromChannel(Channel, ObjectCollection) - Method in class NormalizeObjectIntensity
-
- createFromChannel(Channel) - Method in class QuantileStretch
-
- createFromChannel(Channel) - Method in class ScaleXY
-
- createFromChannel(Channel) - Method in class UnaryWithMaskBase
-
- createFromChannel(Channel) - Method in class LevelPerObjectBase
-
- createFromChannel(Channel, ObjectCollection) - Method in class IdentifyObjects
-
- createFromChannel(Channel, ObjectCollection) - Method in class ScoreObjects
-
- createFromChannel(Channel) - Method in class ExtractCenterSlice
-
- createFromChannel(Channel) - Method in class ExtractSliceRange
-
- createFromChannel(Channel) - Method in class MaximumIntensityProjection
-
- createFromChannel(Channel) - Method in class MeanIntensityProjection
-
- createFromChannel(Channel) - Method in class UnaryWithObjectsBase
-
- createFromChannel(Channel, ObjectCollection) - Method in class UnaryWithObjectsBase
-
- createFromChannel(Channel) - Method in class UnaryWithValueBase
-
- createFromChannel(Channel) - Method in class SegmentChannel
-
- createFromChannel(Channel) - Method in class SegmentWithSeeds
-
- createFromChannel(Channel) - Method in class WithChannelBase
-
- createFromChannel(Channel, int) - Method in class BackgroundSubtractor
-
- createFromChannel(Channel) - Method in class EdgeFilterIJ
-
- createFromChannel(Channel) - Method in class GaussianBlur2D
-
- createFromChannel(Channel) - Method in class MedianFilter3D
-
- createFromChannel(Channel, int) - Method in class WithFilterBase
-
- createFromChannel(Channel) - Method in class WithRadiusBase
-
- createFromChannel(Channel, int) - Method in class WithRadiusBase
-
- createFromChannelWithConstant(Channel, double) - Method in class ArithmeticWithConstantBase
-
- createFromChannelWithConstant(Channel, double) - Method in class ArithmeticWithConstantConditionallyWriteBase
-
- createFromChannelWithConstant(Channel, double) - Method in class UnaryWithValueBase
-
- createFromDimensions(Dimensions) - Method in class DistanceTransformForEachObject3D
-
- createFromDimensions(Dimensions) - Method in class CreateNew
-
- createFromDimensions(Dimensions) - Method in class FromDimensionsBase
-
- createFromDimensions(Dimensions) - Method in class RepeatSlice
-
- createFromDimensions(Dimensions) - Method in class AllValuesOff
-
- createFromDimensions(Dimensions) - Method in class AllValuesOn
-
- createFromDimensions(Dimensions) - Method in class FromObjects
-
- createFromDimensions(Dimensions) - Method in class FromDimensionsBase
-
- createFromDimensions(Dimensions) - Method in class Box
-
- createFromExisting(InitializationContext, Optional<Define>, Optional<SharedObjects>, Optional<Dictionary>) - Static method in class MarksInitializationFactory
-
- createFromExplicitDirectory(String) - Static method in class TestLoader
-
Creates a new test-data loader using an explicit file path as root.
- createFromExplicitDirectory(Path) - Static method in class TestLoader
-
Creates a new test-data loader using an explicit file path as root.
- createFromGenerator(TransformingGenerator<BoundingBox, Stack>, int, ColorIndex) - Static method in class DrawObjectOnStackGenerator
-
Creates an extracted-object generator that draws an outline - with default color green and
flattened in Z.
- createFromGuess3D(Mask, int, boolean, boolean) - Static method in class FindContour
-
- createFromHistogram(Histogram) - Method in class HistogramProviderUnary
-
Creates a
Histogram
given the entity provided by the delegate.
- createFromHistogram(Histogram) - Method in class CutBelowThreshold
-
- createFromHistogram(Histogram) - Method in class GreaterThanThreshold
-
- createFromList(List<T>, Function<T, BoundingBox>) - Static method in class BoundedList
-
Creates for a list, minimally fitting a bounding-box around all elements
- createFromMarks(MarkCollection, KernelCalculationContext, Logger) - Static method in class VoxelizedMarksWithEnergyFactory
-
- createFromMask(Mask) - Method in class MaskProviderUnary
-
Creates a
Mask
given the entity provided by the delegate.
- createFromMask(Mask) - Method in class DistanceTransform3D
-
- createFromMask(Mask) - Method in class FromMask
-
- createFromMask(Mask) - Method in class FromMaskBase
-
- createFromMask(Mask) - Method in class CombineBase
-
- createFromMask(Mask) - Method in class Duplicate
-
- createFromMask(Mask) - Method in class Invert
-
- createFromMask(Mask) - Method in class ExteriorContour
-
- createFromMask(Mask) - Method in class FitBoxToOnVoxels
-
- createFromMask(Mask) - Method in class MorphologicalOperatorBase
-
- createFromMask(Mask) - Method in class IfPredicateBase
-
- createFromMask(Mask) - Method in class ScaleXY
-
- createFromMask(Mask) - Method in class FlattenZ
-
- createFromMask(Mask) - Method in class RepeatSlice
-
- createFromMask(Mask) - Method in class FillHoles
-
- createFromMask(Mask) - Method in class MorphologicalOperation
-
- createFromMask(Mask, Mask) - Method in class ConvexHull2D
-
- createFromMask(Mask, Mask) - Method in class ConvexHull3D
-
- createFromMask(Mask) - Method in class ConvexHullBase
-
- createFromMask(Mask, Mask) - Method in class ConvexHullBase
-
- createFromMaskedChannel(Channel, Mask) - Method in class SubtractMean
-
- createFromMaskedChannel(Channel, Mask) - Method in class AssignFromChannel
-
- createFromMaskedChannel(Channel, Mask) - Method in class AssignValue
-
- createFromMaskedChannel(Channel, Mask) - Method in class UnaryWithMaskBase
-
- createFromMaskedChannel(Channel, Mask) - Method in class ZeroOutsideMask
-
- createFromMavenWorkingDirectory() - Static method in class TestLoader
-
Creates a new test-data loader finding PATH_RESOURCES
using the Maven working
directory.
- createFromMavenWorkingDirectory(String) - Static method in class TestLoader
-
Creates a new test-data loader finding PATH_RESOURCES/PLUS_SOMETHING
using the Maven
working directory.
- createFromNotObjects(ObjectCollection, Dimensions, BinaryValuesInt) - Static method in class MaskFromObjects
-
- createFromObjects(ObjectCollection) - Method in class ObjectCollectionProviderUnary
-
- createFromObjects(ObjectCollection, Dimensions, BinaryValuesInt) - Static method in class MaskFromObjects
-
- createFromObjects(ObjectCollection) - Method in class AtIndex
-
- createFromObjects(ObjectCollection) - Method in class DecomposeIntoConnectedComponents
-
- createFromObjects(ObjectCollection) - Method in class RejectIfNotConnected
-
- createFromObjects(ObjectCollection) - Method in class Duplicate
-
- createFromObjects(ObjectCollection) - Method in class ObjectWithMaximumFeature
-
- createFromObjects(ObjectCollection) - Method in class ObjectWithMaximumFeatureFromEachMatchedCollection
-
- createFromObjects(ObjectCollection) - Method in class SortByFeature
-
- createFromObjects(ObjectCollection, Optional<List<ObjectMask>>, Optional<Dimensions>) - Method in class Filter
-
- createFromObjects(ObjectCollection, Optional<List<ObjectMask>>, Optional<Dimensions>) - Method in class FilterByGroup
-
- createFromObjects(ObjectCollection) - Method in class IntersectsWithContainer
-
- createFromObjects(ObjectCollection) - Method in class Match
-
- createFromObjects(ObjectCollection) - Method in class NotInContainer
-
- createFromObjects(ObjectCollection) - Method in class ObjectCollectionProviderFilterBase
-
- createFromObjects(ObjectCollection, Optional<List<ObjectMask>>, Optional<Dimensions>) - Method in class ObjectCollectionProviderFilterBase
-
- createFromObjects(ObjectCollection) - Method in class RemoveTouchingBorder
-
- createFromObjects(ObjectCollection) - Method in class AndObjectsWithMasks
-
- createFromObjects(ObjectCollection) - Method in class MergeGreedyToIncreaseObjectFeature
-
- createFromObjects(ObjectCollection) - Method in class MergeWithFeature
-
- createFromObjects(ObjectCollection) - Method in class ObjectCollectionProviderMorphological
-
- createFromObjects(ObjectCollection) - Method in class Scale
-
- createFromObjects(ObjectCollection, Channel) - Method in class BinarySegmentByObject
-
- createFromObjects(ObjectCollection, Channel) - Method in class SegmentChannelByObject
-
- createFromObjects(ObjectCollection) - Method in class ExtendInZ
-
- createFromObjects(ObjectCollection) - Method in class ExtendInZWithinContainer
-
- createFromObjects(ObjectCollection) - Method in class FlattenZ
-
- createFromObjects(ObjectCollection) - Method in class SliceAt
-
- createFromObjects(ObjectCollection) - Method in class RemoveIntersectingVoxels
-
- createFromObjects(ObjectCollection) - Method in class SplitByObjects
-
- createFromObjects(ObjectCollection) - Method in class SplitIntoSquares
-
- createFromObjects(ObjectCollection) - Method in class UnaryWithChannelBase
-
- createFromObjects(ObjectCollection, Channel) - Method in class UnaryWithChannelBase
-
- createFromObjects(ObjectCollection) - Method in class DrawLineAlongConvexHull
-
- createFromObjects(ObjectCollection) - Method in class FillHoles
-
- createFromObjects(ObjectCollection) - Method in class MergeSpatialClusters
-
- createFromObjects(ObjectCollection) - Method in class SplitContourAtSaddlePoints
-
- createFromOutputter(String, OutputterChecked) - Static method in class CSVWriter
-
Creates and starts a CSVWriter if it's allowed, otherwise returns
Optional.empty()
.
- createFromOutputterWithHeaders(String, OutputterChecked, Supplier<List<String>>, ErrorReporter) - Static method in class CSVWriter
-
- createFromPath(Path, OperationContext) - Static method in class ObjectCollectionReader
-
Reads an object-collection from a path (or path prefix) trying different methods to read the
objects.
- createFromSource(Channel) - Method in class AutoLocalThreshold
-
- createFromSource(Channel) - Method in class FromChannel
-
- createFromSource(Channel) - Method in class FromChannelBase
-
- createFromSource(Channel) - Method in class SegmentChannel
-
- createFromSource(Channel) - Method in class Threshold
-
- createFromStack(Stack) - Method in class StackProviderUnary
-
Creates a
Stack
given the entity provided by the delegate.
- createFromStack(ScaleableBackground, int, ColorIndex) - Static method in class DrawObjectOnStackGenerator
-
Creates the generator with a stack as the background - and with default color green and
flattened across the Z-dimension.
- createFromStack(Optional<ScaleableBackground>, int, ColorIndex) - Static method in class DrawObjectOnStackGenerator
-
Creates the generator with maybe a stack as the background, or else an empty background - and
with default color green and flattened in Z.
- createFromStack(Stack) - Method in class MontageSlices
-
- createFromStack(Stack) - Method in class ColorConverterBase
-
- createFromString(String) - Static method in class AxisConverter
-
Maps a string of x, y, z (case ignored) to a corresponding axis type.
- createFromTupleDuplicate(ReadableTuple3i) - Static method in class Extent
-
Creates from a
ReadableTuple3i
representing the sizes in each dimension, where the
tuple
is not used internally.
- createFromTupleReuse(ReadableTuple3i) - Static method in class Extent
-
Creates from a
ReadableTuple3i
representing the sizes in each dimension, where the
tuple
is used internally.
- createFromTwoMasks(Mask, Mask) - Method in class And
-
- createFromTwoMasks(Mask, Mask) - Method in class CombineBase
-
Creates masks from some combination of two masks
- createFromTwoMasks(Mask, Mask) - Method in class IfHighLow
-
- createFromTwoMasks(Mask, Mask) - Method in class Or
-
- createFromTwoMasks(Mask, Mask) - Method in class Xor
-
- createGrayscaleByte(Voxels<UnsignedByteBuffer>) - Static method in class BufferedImageFromVoxels
-
- createGrayscaleShort(Voxels<UnsignedShortBuffer>) - Static method in class BufferedImageFromVoxels
-
- createGroupMap(ConsistentChannelChecker, Optional<Stream<String>>, Optional<InputOutputContext>, OperationContext) - Method in class AggregateChannelTask
-
- createGroupMap(ConsistentChannelChecker, Optional<Stream<String>>, Optional<InputOutputContext>, OperationContext) - Method in class GroupedStackBase
-
Creates a map for the storing an aggregate-data-object for each group.
- createGroupMap(ConsistentChannelChecker, Optional<Stream<String>>, Optional<InputOutputContext>, OperationContext) - Method in class ExportImageHistograms
-
- createHashMapToId() - Method in class MarkCollection
-
- createHeaders(String[], Optional<String>, boolean) - Static method in class LabelHeadersForCSV
-
Creates the label-headers (the headers for columns not associated with features).
- createIdArr() - Method in class MarkCollection
-
- createIdHashMap() - Method in class MarkCollection
-
- createImageDim() - Method in class ReportFeatureForMarks
-
- createImageFormat(String) - Static method in class FileFormatFactory
-
- createInitialization(InitializationContext, ExportSharedObjects) - Method in class DefineOutputter
-
- createInitialization(InitializationContext, Optional<SharedObjects>, Optional<Dictionary>) - Method in class DefineOutputter
-
- createInitializationContext() - Method in class InputBound
-
- createInitialized(Extent) - Static method in class FromByte
-
Create a buffer of a particular size, that has been initialized.
- createInitialized(Extent) - Static method in class FromFloat
-
Create a buffer of a particular size, that has been initialized.
- createInitialized(Extent) - Static method in class FromInt
-
Create a buffer of a particular size, that has been initialized.
- createInitialized(Extent) - Static method in class FromShort
-
Create a buffer of a particular size, that has been initialized.
- createInitialized(Extent) - Method in interface VoxelsFactoryTypeBound
-
Create a new
Voxels
that has been
initialized with memory buffers.
- createInputGrouper(Optional<IndexRangeNegative>) - Method in class FromDerivePath
-
Creates an
InputGrouper
that can be used to derive a group-key from a particular
input.
- createInputGrouper(Optional<IndexRangeNegative>) - Method in class Grouper
-
Creates an
InputGrouper
that can be used to derive a group-key from a particular
input.
- createInputGrouper(Optional<IndexRangeNegative>) - Method in class WithoutGrouping
-
- createInputGrouper(Optional<IndexRangeNegative>) - Method in class IfGroupIndexRange
-
- createInputsFromFiles(FilesProvider, InputManagerParameters, Function<NamedFile, T>) - Method in class NamedFilesBase
-
Creates a list of inputs from a
FilesProvider
which together with the
namer
can create the inputs.
- createInverted() - Method in class BinaryValuesInt
-
Inverts the values so off becomes on, and vice-versa.
- createKernel() - Method in class DilationContext
-
Creates a kernel for performing the dilation.
- createKernelFactoryNames() - Method in class KernelProposer
-
- createLabelledChannel(BoundedList<T>, Optional<Map<Integer, T>>) - Method in class LabelObjects
-
Creates a channel that contains a unique integer (label) for each element's
object-representation.
- createList(int) - Method in class ColorScheme
-
Creates a sequence of related colors.
- createList(int) - Method in class ColorSchemeUnary
-
- createList(int) - Method in class FromList
-
- createList(int) - Method in class FromSingle
-
- createList(int) - Method in class HSB
-
- createList(int) - Method in class VeryBright
-
- createListBeans(String, HierarchicalConfiguration, Object) - Static method in class BeanListCreator
-
A list of instantiated bean objects from an XML configuration.
- createListChildFeatures() - Method in class Feature
-
Returns a list of Features that exist as bean-properties of this feature, either directly or
in lists.
- createListMembershipWithFlags() - Method in class RegionMap
-
- createLoader(String) - Static method in class SavedFiles
-
Creates a loader for reading from a particular set of saved-files in a directory in the
resources.
- createMapToIndex() - Method in class FeatureNameList
-
Creates a map from the feature-names to their indices in the list.
- createMarkEllipsoidLeastSquares(ObjectMask, Dimensions, boolean, double) - Static method in class EllipsoidFactory
-
Creates a MarkEllipsoid using least-squares fitting to the points on the outline of an
object-mask
- createMarkEllipsoidLeastSquares(CheckedSupplier<List<Point3i>, CreateException>, Dimensions, boolean, double) - Static method in class EllipsoidFactory
-
- createMarkFromPoint(Point3i, int, boolean) - Static method in class MarkConicFactory
-
- createMarkFromPoint(Point3d, int, boolean) - Static method in class MarkConicFactory
-
- CreateMarkFromPoints - Class in org.anchoranalysis.mpp.bean.points
-
- CreateMarkFromPoints() - Constructor for class CreateMarkFromPoints
-
- createMarkFromPoints3f(List<Point3f>) - Static method in class PointListFactory
-
- createMarkFromPoints3i(List<Point3i>) - Static method in class PointListFactory
-
- createMaskOff(Dimensions) - Static method in class MaskFactory
-
Creates a binary-mask for specific dimensions with all voxels set to off.
- createMaskOff(Dimensions, BinaryValuesInt) - Static method in class MaskFactory
-
Creates a binary-mask for specific dimensions with all voxels set to off.
- createMaskOn(Dimensions) - Static method in class MaskFactory
-
Creates a binary-mask for specific dimensions with all voxels set to on.
- createMaskOn(Dimensions, BinaryValuesInt) - Static method in class MaskFactory
-
Creates a binary-mask for specific dimensions with all voxels set to on.
- createMatcherFile(Path, Optional<InputContextParameters>) - Method in class FilePathMatcher
-
Create a predicate to be used for matching against path.
- createMatcherFile(Path, Optional<InputContextParameters>) - Method in class MatchExtensions
-
- createMatcherFile(Path, Optional<InputContextParameters>) - Method in class MatchGlob
-
- createMatcherFile(Path, Optional<InputContextParameters>) - Method in class MatchRegularExpression
-
- createMerged(ColoredMarks) - Method in class ColoredMarks
-
- createMerged(MarkCollection) - Method in class MarkCollection
-
- createMessageForDescription(String) - Method in exception BeanMisconfiguredXMLException
-
- createMessageForDescription(String) - Method in exception LocalisedBeanException
-
- createMessageForDescription(String) - Method in exception AnchorCombinableException
-
Creates a message for the exception from the description.
- createMessageForDescription(String) - Method in exception NamedProviderGetException
-
- createMinusOne() - Method in class Extent
-
Creates a new
Extent
with each dimension decreased by one.
- createMockFeatureWithCalculation() - Static method in class MockFeatureWithCalculationFixture
-
Creates a mock-feature (using a mock-FeatureCalculation under the hood) which counts the
number of pixels in an object
- createMockFeatureWithCalculation(ToDoubleFunction<T>) - Static method in class MockFeatureWithCalculationFixture
-
Creates a mock-feature (using a mock-FeatureCalculation under the hood) with a result
calculated using a lambda
- CreateModelFailedException - Exception in org.anchoranalysis.inference.concurrency
-
When creating a model to be used for inference fails.
- CreateModelFailedException(Throwable) - Constructor for exception CreateModelFailedException
-
Creates with a cause only.
- CreateModelForPool<T extends InferenceModel> - Interface in org.anchoranalysis.inference.concurrency
-
Creates a model to use in the pool.
- createModelPool(ConcurrencyPlan, Logger) - Method in class SegmentStackIntoObjectsPooled
-
Creates the model pool (to be used by multiple threads).
- createModelPool(ConcurrencyPlan, Logger) - Method in class SuppressNonMaximum
-
- createModelPool(ConcurrencyPlan, Logger) - Method in class SegmentObjectsFromONNXModel
-
- createModelPool(ConcurrencyPlan, Logger) - Method in class SegmentObjectsFromTensorFlowModel
-
- createNamedFeatureList(List<NamedBean<FeatureListProvider<T>>>) - Method in class NamedFeatureStoreFactory
-
- createNamedFeatureProviders(String, TestLoader) - Static method in class FeaturesFromXmlFixture
-
- createNecessaryDirectories(Path) - Static method in class DirectoryCreator
-
Creates necessary directories to make a path to a file valid.
- CreateNew - Class in org.anchoranalysis.plugin.image.bean.channel.provider
-
Creates a new channel with all values initialized to a constant (by default zero)
- CreateNew() - Constructor for class CreateNew
-
- CreateNew - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection
-
- CreateNew() - Constructor for class CreateNew
-
- CreateNew - Class in org.anchoranalysis.plugin.mpp.bean.provider.collection
-
Creates a new empty collection of marks
- CreateNew() - Constructor for class CreateNew
-
- createNewDocument() - Static method in class XMLParser
-
Creates a new XML document.
- createObject(Dimensions, BinaryValuesByte) - Method in class OverlayMark
-
- createObject(Dimensions, BinaryValuesByte) - Method in class OverlayObjectMask
-
- createObject(Dimensions, BinaryValuesByte) - Method in class Overlay
-
Derives an object-mask representation of the overlay to be drawn with overlayWriter
.
- createObjects() - Method in class PointsFitterToMark
-
- createObjectsImage(Assignment<ObjectMask>, boolean, AssignmentColorPool) - Method in class DrawColoredObjects
-
Creates an image with the objects colored, as indicated in the class description.
- createOneToMany(Generator<T>, CheckedFunction<S, Stream<T>, ?>) - Static method in class GeneratorBridge
-
Creates a bridge that maps ONE-TO-MANY from source to destination (i.e.
- createOneToOne(Generator<T>, CheckedFunction<S, T, ?>) - Static method in class GeneratorBridge
-
Creates a bridge that maps ONE-TO-ONE from source to destination (i.e.
- createOrReuse(Throwable) - Static method in exception InitializeException
-
- createOrReuse(T) - Method in class AlwaysNew
-
- createOrReuse(FeatureList<T>, FeatureInitialization, SharedFeatures, Logger) - Method in class BoundReplaceStrategy
-
- createOrReuse(T) - Method in class CacheAndReuseStrategy
-
- createOrReuse(T) - Method in interface ReplaceStrategy
-
- createOrReuse(T) - Method in class ReuseSingletonStrategy
-
- createOutPathString() - Method in class AppendCsv
-
- createOutPathString() - Method in class AppendDictionary
-
- createOutPathString() - Method in class AppendFilePath
-
- createOutPathString() - Method in class AppendHistogram
-
- createOutPathString() - Method in class AppendMarks
-
- createOutPathString() - Method in class AppendObjects
-
- createOutPathString() - Method in class AppendStack
-
- createOutPathString() - Method in class AppendStackDirect
-
- createOutPathString() - Method in class FilePathAppendBase
-
- createOutputManager(Optional<Path>, Optional<OutputEnabledRules>) - Static method in class OutputManagerFixture
-
- createPair(CreateCalculatorHelper, ImageInitialization, CacheTransferSourceCollection) - Method in class MergedPairsFeatures
-
- createPairsUnique() - Method in class RandomCollectionWithAddCriteria
-
- createPairsUnique() - Method in class EnergySavedPairs
-
- createParam(String, boolean) - Method in class PermuteFeatureSequenceInteger
-
- createParameters() - Method in class TouchingVoxels
-
- createParameters(boolean, boolean) - Method in class SurfaceNumberVoxelFaces
-
- createParameters(boolean, boolean) - Method in class SurfaceNumberVoxels
-
- createParameters(boolean, boolean) - Method in class SurfaceNumberVoxelsBase
-
- createPathDeriver(String, String) - Method in class FilePathAppendBase
-
Creates a (rooted) file-path generator for a rootName and a regEx which matches three groups
The first group should correspond to top-level folder for the project The second group should
correspond to the unique name of the dataset.
- createPayloadCalculator() - Method in class MergePairs
-
- createPayloadCalculator() - Method in class MergeToIncreaseObjectFeature
-
- createPayloadCalculator() - Method in class MergeWithFeature
-
Determines the payload for any given or potential vertex
- createPermutedCopies(List<T>, PermuteProperty<S>, PermutationAssigner) - Method in class PermutedCopyCreator
-
Applies a permutation to a copy of each element in a list of beans, updating the custom name
of each bean to reflect the permutation.
- createPermutedFeaturesFor(Feature<T>) - Method in class PermuteFeature
-
- createPermutedFeaturesFor(Feature<T>) - Method in class PermuteFeatureBase
-
- createPermutedFeaturesFor(Feature<T>) - Method in class PermuteFeatureSequenceInteger
-
- createPolicy() - Method in class ConvertBase
-
- createPrioritizer() - Method in class MergePairs
-
- createPrioritizer() - Method in class MergeToIncreaseObjectFeature
-
- createPrioritizer() - Method in class MergeWithFeature
-
Determines the priority (and selection criteria) used to allow merges between neighbors
- createPriority(ObjectVertex, ObjectVertex, Logger) - Method in interface Prioritizer
-
- createRadiiArray() - Method in class ConicBase
-
- createRadiiArray() - Method in class Ellipse
-
- createRadiiArray() - Method in class Ellipsoid
-
- createRadiiArrayResolved(Optional<Resolution>) - Method in class ConicBase
-
- createRadiiArrayResolved(Optional<Resolution>) - Method in class Ellipse
-
- createRadiiArrayResolved(Optional<Resolution>) - Method in class Ellipsoid
-
- createReducedFeature(Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>) - Method in class FeatureListProviderAggregatePair
-
- createReuse(ReadableTuple3i, Extent) - Static method in class BoundingBox
-
Creates a bounding-box from a corner and an extent - reusing cornerMin
internally.
- createReuse(ReadableTuple3i, ReadableTuple3i) - Static method in class BoundingBox
-
Creates from two int
points (a minimum corner and a maximum corner) - reusing cornerMinInclusive
internally.
- createReuse(Point3d, Point3d) - Static method in class BoundingBox
-
Creates from two double
points (a minimum corner and a maximum corner).
- createRGB(Voxels<UnsignedByteBuffer>, Voxels<UnsignedByteBuffer>, Voxels<UnsignedByteBuffer>, Extent) - Static method in class BufferedImageFromStack
-
Creates a
BufferedImage
from three
Voxels<UnsignedByteBuffer>
representing
respectively, red, green, blue color components.
- createRGBStack(Channel, Channel, Channel, VoxelDataType) - Static method in class ThreeChannels
-
- createRoot() - Static method in class ProposerFailureDescription
-
- createRow(String[]) - Method in class ColumnDefinition
-
- createSameSize(ChannelProvider, String, Channel) - Static method in class DimensionsChecker
-
Creates a new channel from a provider, making sure it's the same size as an an existing
channel.
- createSameSize(MaskProvider, String, Channel) - Static method in class DimensionsChecker
-
Creates a new channel from a provider, making sure it's the same size as an an existing
channel
- createSecondLevelFromSet(StringSet) - Method in class AddToDefaults
-
- createSecondLevelFromSet(StringSet) - Method in class IgnoreUnderscorePrefixUnless
-
- createSecondLevelFromSet(StringSet) - Method in class NoneExcept
-
- createSecondLevelFromSet(StringSet) - Method in class OutputEnableRulesSpecify
-
- createSecondLevelFromSet(StringSet) - Method in class PermissiveExcept
-
- createSegmenter() - Method in class InstanceSegmentationTestBase
-
Creates the segmentation implementation to be tested.
- createSequence(VoxelDataType) - Method in class MultiBufferSized
-
- createSession() - Method in class ObjectCollectionProviderWithFeature
-
- createSet() - Method in class MarkCollection
-
- createSetter(AnchorBean<?>) - Method in class PermuteProperty
-
- createSharedStateJob(InputOutputContext) - Method in class ConvertImageFormat
-
Sets a new output-sequence for the series.
- createSharedStateJob(InputOutputContext) - Method in class RasterTask
-
Creates a shared-state for the duration of a particular input-job
- createSingle(CreateCalculatorHelper, ImageInitialization, BoundReplaceStrategy<FeatureInputSingleObject, CacheAndReuseStrategy<FeatureInputSingleObject>>) - Method in class MergedPairsFeatures
-
- createSingle(T, Function<T, BoundingBox>) - Static method in class BoundedList
-
Creates for a single element using its current bounding-box.
- CreateStackFromBufferedImage - Class in org.anchoranalysis.image.core.bufferedimage
-
- createStackSequenceForSeries(int, Logger) - Method in interface StackSequenceInput
-
Creates a supplier of a
TimeSeries
of stacks for a particular series number.
- createStackSequenceForSeries(int, Logger) - Method in class ConvertNamedChannelsInputToStack
-
- createStatisticsFor(VoxelizedMarkMemo, Dimensions) - Method in class MarkRegion
-
- createStatisticsFor(VoxelizedMark, Mark, Dimensions) - Method in class CenterSliceBase
-
- createStatisticsFor(VoxelizedMark, Mark, Dimensions) - Method in class GreatestAreaSlice
-
- createStatisticsFor(VoxelizedMarkMemo, Dimensions) - Method in class IndexedRegionBase
-
- createStatisticsFor(VoxelizedMark, Mark, Dimensions) - Method in class IndexedRegionBase
-
- createStatisticsFor(VoxelizedMark, Mark, Dimensions) - Method in class MaxNonZero
-
- createStatisticsFor(VoxelizedMark, Mark, Dimensions) - Method in class SelectSlicesWithIndexBase
-
- createStatisticsFor(VoxelizedMark, Mark, Dimensions) - Method in class Specific
-
- createStatisticsFor(VoxelizedMarkMemo, Dimensions) - Method in class Thresholded
-
- createStatisticsForBBox(VoxelizedMark, Dimensions, BoundingBox, int) - Method in class CenterSlice
-
- createStatisticsForBBox(VoxelizedMark, Dimensions, BoundingBox, int) - Method in class CenterSliceBase
-
- createStatisticsForBBox(VoxelizedMark, Dimensions, BoundingBox, int) - Method in class CenterSliceWindow
-
- createSubdirectory(String, boolean) - Method in class AlwaysAllowed
-
- createSubdirectory(String, boolean) - Method in class CheckIfAllowed
-
- createSubdirectory(String, boolean) - Method in interface Writer
-
Maybe creates a subdirectory for writing to.
- createSubdirectory(String, boolean) - Method in class WriterRouterErrors
-
Maybe creates a subdirectory for writing to.
- createSubset(Collection<Integer>) - Method in class ObjectCollection
-
A subset of the collection identified by particular indices.
- createToColorUnselectedObjects(Interpolator) - Static method in class OutlinePreserveRelativeSize
-
Alternative constructor that switches on the coloring of unselected objects by default.
- createTransformerFactory() - Static method in class XMLParser
-
Creates a
TransformerFactory
that ignores any DTDs in the document and disables
external entities (to prevent XXE attacks).
- createUninitialised(Dimensions, VoxelDataType) - Method in class ChannelFactory
-
Create a
Channel
without initialization with voxel-buffers.
- createUninitialized(Extent) - Static method in class FromByte
-
Create a buffer of a particular size, that has not been initialized.
- createUninitialized(Extent) - Static method in class FromFloat
-
Create a buffer of a particular size, that has not been initialized.
- createUninitialized(Extent) - Static method in class FromInt
-
Create a buffer of a particular size, that has not been initialized.
- createUninitialized(Extent) - Static method in class FromShort
-
Create a buffer of a particular size, that has not been initialized.
- createUninitialized(Extent) - Method in interface VoxelsFactoryTypeBound
-
Create a new
Voxels
that has
not yet been initialized with memory buffers.
- createUnsignedByte(Extent, IntFunction<UnsignedByteBuffer>) - Static method in class VoxelsArithmeticFactory
-
- createUnsignedByte(Voxels<UnsignedByteBuffer>, int) - Static method in class VoxelsAssignerFactory
-
- createUnsignedByte(BinaryVoxels<UnsignedByteBuffer>) - Method in class ObjectsFromConnectedComponentsFactory
-
Finds the connected-components in unsigned byte voxels.
- createUnsignedByte(Voxels<UnsignedByteBuffer>) - Static method in class VoxelsExtracterFactory
-
- createUnsignedByte(Extent) - Static method in class MaxIntensityProjection
-
Creates a buffer for a maximum-intensity projection for unsigned byte voxels.
- createUnsignedByte(Extent) - Static method in class MinIntensityProjection
-
Creates a buffer for a minimum-intensity projection for unsigned byte voxels.
- createUnsignedByte(Extent) - Static method in class MeanIntensityProjection
-
Creates a buffer for a mean-intensity projection for unsigned byte voxels.
- createUnsignedByte(Extent) - Static method in class StandardDeviationIntensityProjection
-
Creates a buffer for a standard-deviation projection for unsigned byte voxels.
- createUnsignedInt(Extent, IntFunction<UnsignedIntBuffer>) - Static method in class VoxelsArithmeticFactory
-
- createUnsignedInt(Voxels<UnsignedIntBuffer>, int) - Static method in class VoxelsAssignerFactory
-
- createUnsignedInt(BinaryVoxels<UnsignedIntBuffer>) - Method in class ObjectsFromConnectedComponentsFactory
-
Finds the connected-components in unsigned int voxels.
- createUnsignedInt(Voxels<UnsignedIntBuffer>) - Static method in class VoxelsExtracterFactory
-
- createUnsignedInt(Extent) - Static method in class MaxIntensityProjection
-
Creates a buffer for a maximum-intensity projection for unsigned int voxels.
- createUnsignedInt(Extent) - Static method in class MinIntensityProjection
-
Creates a buffer for a minimum-intensity projection for unsigned int voxels.
- createUnsignedInt(Extent) - Static method in class MeanIntensityProjection
-
Creates a buffer for a mean-intensity projection for unsigned int voxels.
- createUnsignedInt(Extent) - Static method in class StandardDeviationIntensityProjection
-
Creates a buffer for a standard-deviation projection for unsigned int voxels.
- createUnsignedShort(Extent, IntFunction<UnsignedShortBuffer>) - Static method in class VoxelsArithmeticFactory
-
- createUnsignedShort(Voxels<UnsignedShortBuffer>, int) - Static method in class VoxelsAssignerFactory
-
- createUnsignedShort(Voxels<UnsignedShortBuffer>) - Static method in class VoxelsExtracterFactory
-
- createUnsignedShort(Extent) - Static method in class MaxIntensityProjection
-
Creates a buffer for a maximum-intensity projection for unsigned short voxels.
- createUnsignedShort(Extent) - Static method in class MinIntensityProjection
-
Creates a buffer for a minimum-intensity projection for unsigned short voxels.
- createUnsignedShort(Extent) - Static method in class MeanIntensityProjection
-
Creates a buffer for a mean-intensity projection for unsigned short voxels.
- createUnsignedShort(Extent) - Static method in class StandardDeviationIntensityProjection
-
Creates a buffer for a standard-deviation projection for unsigned short voxels.
- createVector() - Method in class AxisAlignedUnitVector
-
- createVector() - Method in class DirectionVectorBean
-
Creates a vector in a particular direction.
- createVector() - Method in class SpecifyVector
-
- createVoxelsResizer() - Method in class ImgLib2Lanczos
-
- createVoxelsResizer() - Method in class ImgLib2Linear
-
- createVoxelsResizer() - Method in class Interpolator
-
Create a
VoxelsResizer
that can be used for resizing voxel-buffers.
- createVoxelsResizer() - Method in class None
-
- createVoxelsResizer() - Method in class ImageJ
-
- createVoxelsResizer() - Method in class OpenCV
-
- createWithConsoleFallback(OutputterChecked, ExecutionArguments, boolean) - Method in class LoggingDestination
-
Creates a logger for this destination - and if anything goes wrong reporting fallback into
the console.
- createWithEmptyBackground(int, ColorIndex) - Static method in class DrawObjectOnStackGenerator
-
Creates the generator with an empty background - and with default color green and flattened
in Z-dimension.
- createWithEmptyList() - Static method in class SpecificPathList
-
Factory method for creating the class with an empty list of paths.
- createWithLeftUnassigned(ObjectCollection) - Static method in class OverlappingObjects
-
Creates with only left unassigned objects.
- createWithLogFallback(OutputterChecked, MessageLogger, ExecutionArguments, boolean) - Method in class LoggingDestination
-
Creates a logger for this destination - and if anything goes wrong reporting fallback into a
log.
- createWithoutColor(MarkCollection, RegionMembershipWithFlags) - Static method in class OverlayCollectionMarkFactory
-
- createWithoutStacks(InitializationContext) - Static method in class InitializationFactory
-
- createWithPrefix(DirectoryWithPrefix, MultiLevelOutputEnabled, OutputWriteContext, Optional<MultiLevelRecordedOutputs>, DirectoryCreationParameters, Optional<Logger>) - Static method in class OutputterChecked
-
Creates a bound output-manager from an existing
OutputManager
with a prefix.
- createWithRight(ObjectCollection) - Static method in class OverlappingObjects
-
Creates with only right unassigned objects.
- createWithStacks(ProvidesStackInput, InitializationContext) - Static method in class InitializationFactory
-
- createWithXY(double) - Static method in class Resolution
-
Creates with only XY resolution, identical in both dimensions.
- createWithXYAndZ(double, double) - Static method in class Resolution
-
Creates with XY resolution and Z resolution.
- createWriter(FeatureCSVMetadata) - Method in class LabelledResultsCSVWriter
-
- createWriter() - Method in class BioformatsWriter
-
Creates or gets an instance of IFormatWriter
which dictates the file format to use
for writing.
- createWriter() - Method in class OMETiff
-
- createWriter() - Method in class OMEXML
-
- createWriter() - Method in class Tiff
-
- createWriter() - Method in class StackWriterTestBase
-
- cropRemoveLargerValues(long) - Method in class Histogram
-
- cropRemoveSmallerValues(long) - Method in class Histogram
-
Creates a
Histogram
reusing the bins in the current histogram, but with an upper
limit on the total count.
- crossProduct(Vector3d) - Method in class Vector3d
-
- csvAggregated(FeatureNameList) - Method in class FeatureOutputMetadata
-
Specific metadata for writing an aggregated CSV file.
- CSVComparer - Class in org.anchoranalysis.test.image.csv
-
- CSVComparer(String, boolean, int, boolean, boolean) - Constructor for class CSVComparer
-
- CSVGenerator<T> - Class in org.anchoranalysis.io.generator.tabular
-
- CSVGenerator() - Constructor for class CSVGenerator
-
- csvNonAggregated() - Method in class FeatureOutputMetadata
-
Specific metadata for writing a non-aggregated CSV file.
- CSVReader - Class in org.anchoranalysis.io.input.csv
-
Reads a CSV File from the file-system.
- CSVReader(String, boolean) - Constructor for class CSVReader
-
Create, expecting unquoted strings.
- CSVReader(String, boolean, boolean) - Constructor for class CSVReader
-
- CSVReader.OpenedCSVFile - Class in org.anchoranalysis.io.input.csv
-
A CSV file that has been opened for reading from the file-system.
- CSVReaderByLine - Class in org.anchoranalysis.io.input.csv
-
Reads a CSV file line-by-line.
- CSVReaderException - Exception in org.anchoranalysis.io.input.csv
-
When an error occurs reading a CSV file.
- CSVReaderException(String) - Constructor for exception CSVReaderException
-
Create with a message only.
- CSVReaderException(Throwable) - Constructor for exception CSVReaderException
-
Create with a cause only.
- CSVReporterAggregated - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
-
Outputs statistics on current energy / kernel acceptance etc.
- CSVReporterAggregated() - Constructor for class CSVReporterAggregated
-
- CSVReporterBest - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
-
Outputs a CSV with statistics on the configuration/energy only the best
configuration state changes.
- CSVReporterBest() - Constructor for class CSVReporterBest
-
- CSVReporterUtilities - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
-
- CSVRow - Class in org.anchoranalysis.plugin.mpp.experiment.objects.csv
-
A row of the CSV File
- CSVRow(ColumnDefinition) - Constructor for class CSVRow
-
- CSVWriter - Class in org.anchoranalysis.io.generator.tabular
-
- csvWriter(FeatureCSVMetadata) - Method in class FeatureExporterContext
-
- currentStateDescription() - Method in class ConcurrentJobMonitor
-
A human-understandable string describing the aggregate state.
- currentTemperature() - Method in class AnnealScheme
-
- currentTemperature() - Method in class Geometry
-
- currentTemperature() - Method in class NoAnnealing
-
- customizeExperimentExecutor(ExperimentExecutor, CommandLine) - Method in class LauncherConfig
-
- CutBelowThreshold - Class in org.anchoranalysis.plugin.image.bean.histogram.provider
-
This cuts a Histogram below a threshold BUT TRANSFERS ALL THE COUNT greater than equal to the
threshold into the bin just below the threshold value
- CutBelowThreshold() - Constructor for class CutBelowThreshold
-
- CutOffCorners - Class in org.anchoranalysis.test.image.object
-
The bounding box is filled apart from cuboids cut out of the corners
- CutOffCorners(int, int, Extent) - Constructor for class CutOffCorners
-
- CutOffCornersObjectFixture - Class in org.anchoranalysis.test.image.object
-
Creates one or more objects that are otherwise rectangles with on values, but with corner
voxels as off.
- CutOffCornersObjectFixture() - Constructor for class CutOffCornersObjectFixture
-
Create without any check on dimensions.
- CutOffCornersObjectFixture(Dimensions) - Constructor for class CutOffCornersObjectFixture
-
Create with any check on dimensions.
- CVFindContours - Class in org.anchoranalysis.plugin.opencv
-
- CVInit - Class in org.anchoranalysis.plugin.opencv
-
Provides for initialization of the JavaCPP bridge to OpenCV.
- GaussianBlur2D - Class in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter
-
- GaussianBlur2D() - Constructor for class GaussianBlur2D
-
- GaussianCumulative<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.statistics
-
- GaussianCumulative() - Constructor for class GaussianCumulative
-
- GaussianSampler - Class in org.anchoranalysis.plugin.mpp.bean.proposer.scalar
-
Samples from a Gaussian distribution whose parameters are determined by a
Dictionary
.
- GaussianSampler() - Constructor for class GaussianSampler
-
- generalWriteException(Class<T>, Path, Exception) - Static method in class WriterErrorMessageHelper
-
- generateBackgroundRegion(ObjectCollectionWithProperties, Either<Dimensions, DisplayStack>) - Method in class DrawCroppedObjectsGenerator
-
- generateBackgroundRegion(ObjectCollectionWithProperties, Either<Dimensions, DisplayStack>) - Method in class DrawObjectsGenerator
-
- generateBackgroundRegion(ObjectCollectionWithProperties, Either<Dimensions, DisplayStack>) - Method in class ObjectsAsRGBGenerator
-
Creates a
RGBStack
containing the background, without objects being drawn upon it.
- generateEdge(VoxelizedMarkMemo, VoxelizedMarkMemo, EnergyStack, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in interface AddCriteria
-
- generateEdge(VoxelizedMarkMemo, VoxelizedMarkMemo, EnergyStack, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class AddCriteriaEnergyPair
-
- generateEdge(VoxelizedMarkMemo, VoxelizedMarkMemo, EnergyStack, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class AddCriteriaNever
-
- generateEdge(VoxelizedMarkMemo, VoxelizedMarkMemo, EnergyStack, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class AddCriteriaPair
-
- generateIntersectingObjects(int, int, boolean) - Static method in class IntersectingCircleObjectsFixture
-
Generates a number of circles that intersect and don't intersect
- generateIterableElement(Reporting<VoxelizedMarksWithEnergy>) - Method in class PeriodicSubdirectoryReporter
-
- generateIterableElement(Reporting<VoxelizedMarksWithEnergy>) - Method in class KernelIterDescriptionSerializerPeriodicReporter
-
- generateIterableElement(Reporting<VoxelizedMarksWithEnergy>) - Method in class ObjectSerializerPeriodicReporter
-
- generateIterableElement(Reporting<VoxelizedMarksWithEnergy>) - Method in class TextFileMarksReporter
-
- generateIterableElement(Reporting<VoxelizedMarksWithEnergy>) - Method in class VoxelizedMarksPeriodicReporter
-
- generateMasks(ObjectCollectionWithProperties) - Method in class DrawCroppedObjectsGenerator
-
- generateMasks(ObjectCollectionWithProperties) - Method in class DrawObjectsGenerator
-
- generateMasks(ObjectCollectionWithProperties) - Method in class ObjectsAsRGBGenerator
-
- generateNormal(double, double) - Method in interface RandomNumberGenerator
-
Generates a Gaussian (Normal) random variable with particular parameterization.
- generateNormal(double, double) - Method in class RandomNumberGeneratorMersenne
-
- generatePoisson(double) - Method in interface RandomNumberGenerator
-
Generates a Poisson random variable with particular parameterization.
- generatePoisson(double) - Method in class RandomNumberGeneratorMersenne
-
- GenerateToMatchObjects - Class in org.anchoranalysis.plugin.image.bean.color.provider
-
Generates colors to match the size of an object-collection.
- GenerateToMatchObjects() - Constructor for class GenerateToMatchObjects
-
- GenerateUniqueParameterization - Interface in org.anchoranalysis.bean
-
Objects that must implement well-defined equals()
and hashCode()
methods and also
generate a name uniquely identifying the class and all parameterization.
- generator() - Static method in class ObjectCollectionWriter
-
- Generator<T> - Interface in org.anchoranalysis.io.generator
-
A class that writes a particular type of object(s) to the filesystem.
- GeneratorBridge<S,T> - Class in org.anchoranalysis.io.generator
-
Exposes a Generator<T>
as if it was an Generator<S>
.
- GeneratorOutputter - Class in org.anchoranalysis.image.io.stack.output.generator
-
Settings and methods for writing to the filesystem from a generator.
- Geometry - Class in org.anchoranalysis.plugin.mpp.segment.bean.annealing
-
- Geometry() - Constructor for class Geometry
-
- Geometry(double, double) - Constructor for class Geometry
-
- get() - Method in interface Provider
-
Gets or creates an object of type T
.
- get() - Method in class DictionaryProviderReference
-
- get() - Method in class CachedSupplier
-
- get(K) - Method in class LRUCache
-
Get a value, calculating if necessary, and caching the result.
- get(K) - Method in class MapCreate
-
Gets an existing element from the map, returning null if it is absent.
- get(int) - Method in interface ColorIndex
-
The color for a particular index.
- get(int) - Method in class ColorIndexModulo
-
- get(int) - Method in class ColorList
-
- get(int) - Method in class RGBColor
-
Gets a component from an index value.
- get(int) - Method in class SingleColor
-
- get() - Method in interface CheckedSupplier
-
Applies a supplier like with Supplier.get()
.
- get() - Method in interface StoreSupplier
-
Gets the object being supplied to the store.
- get() - Method in class Define
-
- get() - Method in class DefinedNamed
-
- get() - Method in class DefineSingle
-
- get(int) - Method in class FeatureList
-
Returns the element at the specified position in this list.
- get() - Method in class PrependName
-
- get() - Method in class FeatureProviderDefine
-
- get() - Method in class FeatureProviderReference
-
- get() - Method in interface FeatureCalculationInput
-
The underlying feature-input.
- get(int) - Method in class LabelledResultsVector
-
The result of a feature-calculation stored at a particular index
.
- get(int) - Method in class FeatureNameList
-
Gets a name corresponding to a particular position.
- get(int) - Method in class ResultsVector
-
The result of a feature-calculation stored at a particular index
.
- get(int) - Method in class ResultsVectorList
-
- get() - Method in interface CacheSupplier
-
Gets the cache.
- get() - Method in class SessionInputSequential
-
- get(int) - Method in class NamedFeatureStore
-
Gets a feature at a particular position.
- get(String) - Method in class NamedFeatureStore
-
Gets a feature corresponding to a particular name.
- get(int) - Method in class StackArrangement
-
Gets the
BoundingBox
corresponding to a particular index.
- get() - Method in class ChannelProviderBinary
-
- get() - Method in class ChannelProviderTernary
-
- get() - Method in class ChannelProviderUnary
-
- get() - Method in class HistogramProviderUnary
-
- get() - Method in class MaskProviderUnary
-
- get() - Method in class ObjectCollectionProviderUnary
-
- get() - Method in class Arrange
-
- get() - Method in class StackProviderUnary
-
- get(int) - Method in class ObjectCollectionWithProperties
-
Get an item at a particular index.
- get() - Method in interface NamedStacksSupplier
-
- get() - Method in class TileWithLabels
-
- get() - Method in class WriteText
-
- get(String) - Method in class ChannelMap
-
Gets the index corresponding to a particular channel-name.
- get(VoxelDataType) - Method in class VoxelDataTypeFactoryMultiplexer
-
Multiplexes one of the factories according to data-type
- get(int) - Method in class ObjectCollection
-
Get an
ObjectMask
at a particular position in the collection.
- get() - Method in class WithPriority
-
Gets the underlying element stored in the structure.
- get(int) - Method in interface DestinationChannelForIndex
-
- get() - Method in class ReadFromFile
-
- get() - Method in class FilePathProviderReference
-
- get() - Method in class FromFiles
-
- get() - Method in interface PathSupplier
-
- get(Optional<String>) - Method in class InputOutputContextSubdirectoryCache
-
Gets (from the cache if it's already there) a context for a subdirectory of given-name
- get() - Method in interface ElementSupplier
-
Gets/creates the element to be written.
- get() - Method in interface ElementWriterSupplier
-
- get(int) - Method in class RunningSumCollection
-
An individual item in the collection.
- get(int) - Method in class ImageMoments
-
Get an eigenvalue and corresponding eigenvector for a particular axis.
- get(int) - Method in class MarksWithTotalEnergy
-
- get(int) - Method in class EnergySavedInd
-
- get(String) - Method in class EnergySchemeSet
-
- get(int) - Method in class MemoList
-
- get(int) - Method in class UpdatableMarksList
-
- get(int) - Method in class IndexByChannel
-
- get(String) - Method in interface MultiInputSubMap
-
Returns null if non-existent
- get(String) - Method in class OperationMap
-
- get(String) - Method in class StackWithMap
-
- get(int) - Method in class MarkCollection
-
- get(int) - Method in class AggIDCounter
-
- get(int) - Method in class WeightedKernelList
-
- get(int) - Method in class OverlayCollection
-
Access a particular element in the collection by index.
- get(String) - Method in class GroupedAnnotationLabels
-
- get() - Method in class FromDimensionsBase
-
- get() - Method in class FromInput
-
- get() - Method in class FromStack
-
- get() - Method in class FromMaskBase
-
- get() - Method in class Reference
-
- get() - Method in class ScoreVoxels
-
- get() - Method in class Concatenate
-
- get() - Method in class GenerateToMatchObjects
-
- get() - Method in class FromChannel
-
- get() - Method in class GuessDimensions
-
- get() - Method in class SpecifyDimensions
-
- get() - Method in class FromChannel
-
- get() - Method in class Reference
-
- get() - Method in class FromStackChannel
-
- get() - Method in class FromChannelBase
-
- get() - Method in class FromDimensionsBase
-
- get() - Method in class Reference
-
- get() - Method in class Concatenate
-
- get() - Method in class ConnectedComponentsFromMask
-
- get() - Method in class Empty
-
- get() - Method in class IfParamEqual
-
- get() - Method in class FromMask
-
- get() - Method in class MergeTwoCollectionsItemwise
-
- get() - Method in class Permute
-
- get() - Method in class Reference
-
- get() - Method in class ReferenceOrElse
-
- get() - Method in class SegmentStack
-
- get() - Method in class WithChannelBase
-
- get() - Method in class ColoredBase
-
- get() - Method in class ThreeChannels
-
- get() - Method in class Concatenate
-
- get() - Method in class FromChannelOrMask
-
- get() - Method in class FromInput
-
- get() - Method in class Reference
-
- get() - Method in class IntensityMoments
-
- get() - Method in class DeriveFromPair
-
- get() - Method in class FeatureListProviderAggregatePair
-
- get() - Method in class PermuteFeatureBase
-
- get(int) - Method in class ListWithThumbnails
-
- get() - Method in class PriorityQueueIndexRangeDownhill
-
- get(T) - Method in class FileLabelMap
-
- get() - Method in class FeatureListProviderLDAClassifier
-
- get() - Method in class FeatureListProviderSVMClassifier
-
- get() - Method in class MarkBoundsDefine
-
- get() - Method in class MarkBoundsReference
-
- get() - Method in class FromMarks
-
- get() - Method in class CreateNew
-
- get() - Method in class FromSingleMark
-
- get() - Method in class PointsFromObjects
-
- get() - Method in class Reference
-
- get() - Method in class ReferenceOrEmpty
-
- get() - Method in class ScaleXY
-
- get() - Method in class CreateEllipse
-
- get() - Method in class RequireFeatureRelationThreshold
-
- get() - Method in class RetrieveSingleMarkOnly
-
- get(int) - Method in class ContiguousVoxelPath
-
- get(String) - Method in class IndexedCSVRows
-
- get(String) - Method in class MapGroupToRow
-
- get() - Method in class HOGDescriptor
-
- get() - Method in interface FeatureResultSupplier
-
- get() - Method in class FitPointsFromObjects
-
- get(int) - Method in class BoundedList
-
Gets a particular element.
- getAboveMaxValue() - Method in class RangeCompareBase
-
Constant to return if outside the range (above the maximum allowed)
- getAcceptAll() - Method in class Aggregator
-
- getAcquisitionTime() - Method in class ImageMetadata
-
A timestamp, if available, of when the image was first physically created by the
camera/device.
- getAcqusitionTime() - Method in class ImageTimestampsAttributes
-
A timestamp, if available, of when the image was first physically created by the
camera/device.
- getAdd() - Method in class VisualizeOnBackground
-
- getAddCriteria() - Method in class RandomCollectionWithAddCriteria
-
- getAdditionalBackgrounds() - Method in class MarkProposerStrategy
-
Additional background-stacks that are possible to use while annotating.
- getAdditionalChannels() - Method in class MultiInputManagerQuick
-
Additional channels other than the main one, which are located in the main raster file
- getAdditionalChannels() - Method in class NamedChannelsQuick
-
Additional channels other than the main one, which are located in the main raster file
- getAdditionalPropertyPaths() - Method in class PermuteProperty
-
Additional property paths that are also changed, together with propertyPath
.
- getAddSum() - Method in class GradientBaseAddSum
-
Added to all gradients (so we can store negative gradients)
- getAdjacentChannels() - Method in class NamedChannelsQuick
-
Channels that are located in a separate raster file adjacent to the main raster file
- getAfterPreoperation() - Method in class OverlappingObject
-
After pre-operation but before scaling
- getAggInterval() - Method in class ReporterInterval
-
- getAggIntervalLog10() - Method in class ReporterInterval
-
How many iterations before printing a new report? Encoded in log10.
- getAggregateReceiver() - Method in class ReporterAggregate
-
- getAggregateReceiver() - Method in class ConsoleAggregatedReporter
-
- getAggregateReceiver() - Method in class CSVReporterAggregated
-
- getAggregateReceiver() - Method in class Log4JReporter
-
- getAggregateReceiver() - Method in class MemoryUsageReporter
-
- getAggregateReceiver() - Method in class OptimizationStepLogReporter
-
- getAggregateReceiver() - Method in class TextFile
-
- getAggregateTriggerBank() - Method in class FeedbackBeginParameters
-
- getAggregator() - Method in class AggregateChannelTask
-
- getAlign() - Method in class Grow
-
How to align the box after it is grown, as much as possible.
- getAlign() - Method in class Overlay
-
Indicates how to align the image across the three axes.
- getAlign() - Method in class ScaleImageCommonSize
-
How a smaller image (after scaling) is aligned to the larger image (with the common size).
- getAligner() - Method in class Tile
-
How to align a smaller image inside a larger cell.
- getAligner() - Method in class Montage
-
When varyImageSize==false
and varyImageLocation==false
, how to align a
smaller image inside a larger cell.
- getAlignerLabel() - Method in class Montage
-
When label==false
and varyImageLocation==false
, how to align the label with
its associated image.
- getAlignX() - Method in class Align
-
Indicates how to align the image across the X-axis (i.e.
- getAlignY() - Method in class Align
-
Indicates how to align the image across the Y-axis (i.e.
- getAlignZ() - Method in class Align
-
Indicates how to align the image across the Z-axis: one of top, bottom, center,
repeat
.
- getAll() - Method in class MarksWithEnergyBreakdown
-
Certain features are stored for every object, so that we can reference them in our
calculations for the 'all' component
- getAllCacheNames() - Method in class CacheTransferSourceCollection
-
The names of all child-caches that are made available.
- getAllKernelFactories() - Method in class KernelProposer
-
- getAllowsChildren() - Method in class ErrorNodeImpl
-
- getAngle() - Method in class OrientationAxisAngle
-
Angle part of axis-angle orientation (anti-clock in radians).
- getAngleDegrees() - Method in class Orientation2D
-
The angle of the rotation in the 2D plane anti-clockwise, in degrees.
- getAnnealScheme() - Method in class SimulatedAnnealing
-
- getAnnotations() - Method in class FromAnnotations
-
- getAnnotatorStrategy() - Method in class AnnotationInputManager
-
The strategy to be used for annotating.
- getAppendChannels() - Method in class NamedChannelsQuick
-
Channels that are located in a separate raster file somewhere else in the project's structure
- getAppendCSV() - Method in class FromCSVInputManager
-
- getAppendCsv() - Method in class MatchedAppendCsv
-
- getAppendDictionary() - Method in class MultiInputManager
-
- getAppendFilePath() - Method in class MultiInputManager
-
- getAppendHistogram() - Method in class MultiInputManager
-
- getAppendMarks() - Method in class MultiInputManager
-
- getAppendMarksFromAnnotation() - Method in class MultiInputManager
-
- getAppendMarksFromAnnotationAcceptedOnly() - Method in class MultiInputManager
-
- getAppendMarksFromAnnotationRejectedOnly() - Method in class MultiInputManager
-
- getAppendObjects() - Method in class MultiInputManager
-
- getAppendStack() - Method in class MultiInputManager
-
- getArbitraryElement() - Method in interface NamedProvider
-
Gets one element of the provider (arbitrarily).
- getArrange() - Method in class Arrange
-
Determines how the stacks in list
are arranged.
- getArrange() - Method in class Cell
-
How to arrange any
RGBStack
s in this particular cell.
- getAsBoolean() - Method in interface CheckedBooleanSupplier
-
Applies a supplier like with BooleanSupplier.getAsBoolean()
.
- getAsDouble(String) - Method in class Dictionary
-
Retrieves a value from the dictionary, and converts to a double
.
- getAspectRatio() - Method in class ExtentToArrange
-
The aspect-ratio: width of extent
divided by height.
- getAssigner() - Method in class CompareAnnotations
-
- getAssignmentCSV() - Method in class ComparisonSharedState
-
- getAssignMode() - Method in class SimulatedAnnealing
-
- getAssociatedMark() - Method in class ErrorNodeImpl
-
- getAsStack() - Method in class ChannelProvider
-
- getAsStack() - Method in class MaskProvider
-
- getAsStack() - Method in class StackProvider
-
- getAsStack() - Method in interface ProviderAsStack
-
Retrieves or creates a
Stack
representation of an entity.
- getAsString(String) - Method in class Dictionary
-
Retrieves a value from the dictionary as a
String
.
- getAttributes() - Method in class ImageTimestampsAttributes
-
Timestamps and other metadata associated with an image file-path, but not with the file's
contents.
- getAttributes() - Method in class StackWriteOptions
-
The attributes of the particular stack to write.
- getAxis() - Method in class AxisAlignedUnitVector
-
Which axis the unit-vector will align with.
- getAxis() - Method in class CenterOfGravity
-
- getAxis() - Method in class GradientForAxis
-
Which axis? X=0, Y=1, Z=2
- getAxis() - Method in class ForSpecificAxis
-
- getAxis() - Method in class ArbitraryInsidePoint
-
- getAxis() - Method in class BoundingBoxAlongAxisBase
-
- getAxis() - Method in class GradientMeanForAxis
-
- getAxis() - Method in class PrincipalAxisOrientation
-
Which axis to read from (x,y,z)
- getAxis() - Method in class BoundingBoxExtent
-
- getAxis() - Method in class OrientationAxisAngle
-
Axis part of axis-angle orientation (should be normalized).
- getBackground() - Method in class AnnotatorStrategy
-
The visual background to use while annotating.
- getBackground() - Method in class SegmentedBackground
-
The background image to use for segmentation, when visualizing segmentations.
- getBackground() - Method in class ObjectsAsRGBGenerator
-
A background image or dimensions to define an empty background.
- getBackground() - Method in class DualStack
-
The background
- getBackground() - Method in class CompareAnnotations
-
The name of the stack to use as background to the annotations.
- getBackground() - Method in class ColoredBase
-
The background.
- getBackgroundChannelIndex() - Method in class OutlinePreserveRelativeSize
-
Uses only this channel (identified by an index in the stack) as the background, -1 disables.
- getBackgroundChannelProvider() - Method in class MorphologicalOperatorBase
-
- getBackgroundID() - Method in class VisualizeOnBackground
-
- getBackgroundIntensity() - Method in class ScaleImageCommonSize
-
The background intensity to use in each channel when the scaled image does not cover the
entire canvas.
- getBackgroundStackMap() - Method in class AnnotationBackground
-
If non-null, maps underlying stack-name to a background.
- getBackgroundStackName() - Method in class SegmentIntoMarks
-
- getBaseName() - Method in class FilenameSplitExtension
-
The part of the filename without an extension.
- getBeanExtension() - Method in class QuickMultiDatasetExperiment
-
- getBeanExtension() - Method in class QuickMultiDatasetStructuredExperiment
-
- getBeanName() - Method in class AnchorBean
-
A short-name identifying a bean (by default the name of the class associated with the bean).
- getBelowMinValue() - Method in class RangeCompareBase
-
Constant to return if outside the range (below the minimum allowed)
- getBest() - Method in class DualState
-
- getBest() - Method in class OptimizationStep
-
- getBestState() - Method in class Reporting
-
- getBinaryInputChannelID() - Method in class AddDistanceTransform
-
The ID of the binary input mask that determines the region of the Watershed.
- getBinarySgmn() - Method in class BinarySegmentByObject
-
- getBirthRepeats() - Method in class KernelReplace
-
- getBitDepthPerChannel() - Method in class ImageMetadata
-
The number of bits in memory to describe each voxel's intensity, per channel.
- getBitsPerPixel() - Method in class ForceBitsPerPixel
-
- getBlockSize() - Method in class HOGParameters
-
The block-size as per OpenCV implementation (identical default-size).
- getBlockStride() - Method in class HOGParameters
-
The block-stride as per OpenCV implementation (identical default-size).
- getBlue() - Method in class RGBColorBean
-
The blue component value of the RGB color.
- getBlue() - Method in class RGBColor
-
The blue component value of the RGB color.
- getBlue() - Method in class ThreeChannels
-
- getBorderWidth() - Method in class MontageSlices
-
Adds a border around each part of the montage
- getBoundRadius() - Method in class MarkWithPositionAndSingleRadius
-
- getBounds() - Method in class RandomOrientation
-
- getBox() - Method in class BoundingBoxEnclosed
-
- getBridgeMatcher() - Method in class Bridge
-
Used to match each input-object to an intermediary-object
- getBundleSize() - Method in class ObjectSerializerPeriodicReporter
-
- getBundleSize() - Method in class VoxelizedMarksChangeReporter
-
- getCache() - Method in interface FeatureCalculationInput
-
- getCache() - Method in class CacheAndReuseStrategy
-
- getCache() - Method in class SessionInputSequential
-
- getCacheNames() - Method in class CacheTransferSource
-
The names of the child-caches that can be used as sources.
- getCacheSize() - Method in class RelationWithMatches
-
Size of feature evaluation cache for featureEvaluatorMatch
- getCalculateLevel() - Method in class CalculateLevelUnary
-
- getCalculateLevel() - Method in class ThresholderGlobal
-
- getCalculateLevel() - Method in class LevelPerObjectBase
-
Method to calculate the level for a particular object.
- getCalculateLevel() - Method in class GreaterThanThreshold
-
Calculates the level for the threshold
- getCalculateLevel() - Method in class LevelFromHistogram
-
- getCalculateLevel() - Method in class ThresholdHistogram
-
- getCalculateLevel() - Method in class CalculateLevelBase
-
- getCalculateLevelElse() - Method in class CalculateLevelRelativeToThreshold
-
- getCalculator() - Method in class NamedFeatureCalculatorMulti
-
- getCallUponDirectoryCreation() - Method in class InputArguments
-
When defined, this
Consumer
is called when an output directory is first created.
- getCallUponDirectoryCreation() - Method in class DirectoryCreationParameters
-
When defined, this consumer
is called when the directory is first created, as it is
created lazily only when first needed.
- getCellDefault() - Method in class Tile
-
Used to define an individual cell, when no specific entry is found in cells
for a
particular cell.
- getCells() - Method in class Tile
-
Defines the corresponding
StackArranger
for an individual cell in table.
- getCellSize() - Method in class HOGParameters
-
The cell-size as per OpenCV implementation (identical default-size).
- getCenter() - Method in class SlidingBuffer
-
The buffer for the currently selected slice.
- getCenterPoint() - Method in class FitResult
-
- getCenterPointX() - Method in class EllipseStandardFormConverter
-
- getCenterPointY() - Method in class EllipseStandardFormConverter
-
- getChangedMarkIDArr() - Method in class KernelDecision
-
- getChangedMarkIDs() - Method in class Reporting
-
- getChannel(int) - Method in class EnergyStack
-
Returns the channel at a particular position in the stack.
- getChannel(int) - Method in class EnergyStackWithoutParameters
-
Returns the channel at a particular position in the stack.
- getChannel() - Method in class ChannelProviderUnary
-
- getChannel(int) - Method in class RGBStack
-
Returns the channel at a particular position in the stack.
- getChannel(int) - Method in class Stack
-
Returns the channel at a particular position in the stack.
- getChannel(int) - Method in class StackNotUniformSized
-
Returns the channel at a particular position in the stack.
- getChannel(String, int, Logger) - Method in interface ChannelGetter
-
Retrieve the
Channel
corresponding to
channelName
at a particular time-frame.
- getChannel(String, int, Logger) - Method in class NamedChannelsConcatenate
-
- getChannel(String, int, Logger) - Method in class OpenedNamedChannels
-
- getChannel() - Method in class FromChannel
-
- getChannel() - Method in class FromChannel
-
- getChannel() - Method in class FromChannelBase
-
- getChannel() - Method in class IntensityGreaterEqualThan
-
- getChannel() - Method in class UnaryWithChannelBase
-
- getChannel() - Method in class WithChannelBase
-
- getChannel() - Method in class FromChannelOrMask
-
A channel that is provided to the stack.
- getChannel() - Method in class NamedChannel
-
- getChannel(String, Logger) - Method in class ChannelGetterForTimepoint
-
- getChannel1() - Method in class ChannelProviderBinary
-
- getChannel1() - Method in class ChannelProviderTernary
-
- getChannel2() - Method in class ChannelProviderBinary
-
- getChannel2() - Method in class ChannelProviderTernary
-
- getChannel3() - Method in class ChannelProviderTernary
-
- getChannelAssignFrom() - Method in class AssignFromChannel
-
- getChannelChecker() - Method in class GroupedSharedState
-
Checks that
Channel
s have a consistent voxel-data type.
- getChannelConversionStyle() - Method in class ConvertImageFormat
-
To convert as RGB or independently or in another way.
- getChannelConverter() - Method in class Convert
-
- getChannelConverter() - Method in class ConvertImageFormat
-
Optionally, how to convert from one bit-depth to another (scaling, clamping etc.)
- getChannelElse() - Method in class IfParamEquals
-
- getChannelFirst() - Method in class Difference
-
Index of first channel
- getChannelGroupID() - Method in class RegularExpression
-
- getChannelID() - Method in class AddEdgeFilters
-
The ID of the channel that provides the input to the filter.
- getChannelIfVoxelZero() - Method in class IfVoxelZero
-
If a pixel is zero in the input-channel, the output is formed from the corresponding pixel in
this channel instead
- getChannelIndex() - Method in class FromStack
-
- getChannelIndex() - Method in class FromStackChannel
-
- getChannelIndex() - Method in class One
-
The index of the channel to retrieve from stackName
.
- getChannelIndex() - Method in class FileDetails
-
- getChannelIndex() - Method in class MultiInputManagerQuick
-
If either stackAsChannel==true or we have specified additionalChannels this indicated which
channel to use from the stack
- getChannelLookup() - Method in class NormalizeDifferenceToMedian
-
- getChannelMap() - Method in class NamedChannels
-
- getChannelMask() - Method in class ExportImageHistograms
-
If defined, this is the name of channel used as a mask over the values which are fed into the
histogram
- getChannelName() - Method in class SingleChannel
-
- getChannelName() - Method in class ConvertNamedChannelsToStack
-
By default all channels are converted into a stack.
- getChannelNames() - Method in class ConsistentChannelNamesChecker
-
The names of
Channel
s that are consistent across all images.
- getChannelNamesChecker() - Method in class GroupedSharedState
-
Checks that each image provides a consistent set of channels, and that they have the same
RGB-state.
- getChannelNum() - Method in class SortedSetChannel
-
- getChannelOptional(String, int, Logger) - Method in class NamedChannelsConcatenate
-
- getChannelOptional(String, int, Logger) - Method in interface NamedChannelsMap
-
Gets a channel if it exists, returning empty if it doesn't.
- getChannelOptional(String, int, Logger) - Method in class OpenedNamedChannels
-
- getChannelSecond() - Method in class Difference
-
Index of second channel
- getChannelsExtra() - Method in class ScoreVoxels
-
- getChannelsPerByteArray() - Method in class ForceChannelsPerByteArray
-
- getChannelThreshold() - Method in class ThresholdAgainstChannel
-
- getChannelVoxelType() - Method in class ChannelSpecification
-
Default data-type for all channels in the stack if not otherwise specified.
- getCheck() - Method in class Not
-
- getChecked() - Method in class Outputter
-
- getCheckMark() - Method in class FromObjects
-
- getCheckMark() - Method in class Check
-
- getCheckMark() - Method in class Check
-
- getCheckParsedFilePathBag() - Method in class GroupFiles
-
Imposes a condition on each parsed-file-path-bag which must be-fulfilled if a file is to be
included.
- getChildAt(int) - Method in class ErrorNodeImpl
-
- getChildCount() - Method in class ErrorNodeImpl
-
- getClassifierProvider() - Method in class BinaryClassifierImageLabeller
-
- getClassLabels() - Method in class ImageInferenceContext
-
If available, labels of classes loaded from a text file at classLabelsPath
.
- getClassLabelsPath() - Method in class SegmentStackIntoObjectsScaleDecode
-
Relative-path to the class-labels file, a text file where each line specifies a class label
in order, relative to the models/ directory in the Anchor distribution.
- getCode(int) - Method in class EncodedIntBuffer
-
- getCollection() - Method in class KernelDeath.MarkAnd
-
- getColor() - Method in class FromSingle
-
The single color to repeat.
- getColor(int) - Method in class ColoredOverlayCollection
-
Access a particular color in the collection by index.
- getColor() - Method in class AnnotationLabel
-
An optional color associated with the label when displayed via GUI
- getColor() - Method in class ColoredMask
-
- getColor() - Method in class ColoredObject
-
The RGB color.
- getColorIDGetter() - Method in class ObjectDrawAttributes
-
Gets a color ID associated with the object
- getColorIndex() - Method in class ObjectDrawAttributes
-
Colors for a given index
- getColorList() - Method in class ColoredMarks
-
- getColors() - Method in class ColorSchemeUnary
-
The delegate that creates the color-list before subsequent processing.
- getColors() - Method in class FromList
-
The list of colors to specify.
- getColors() - Method in class ColoredOverlayCollection
-
The list of colors, each element corresponding to overlays
.
- getColors() - Method in class ColoredBaseWithGenerator
-
Colors to use for drawing objects
- getColorScheme() - Method in class GenerateToMatchObjects
-
- getColorsUnpaired() - Method in class CompareAnnotations
-
- getColorUnselectedObjects() - Method in class OutlinePreserveRelativeSize
-
Optionally outline the other (unselected for the thumbnail) objects in this particular color.
- getColumn() - Method in class Cell
-
The column in the table that the cell refers to (zero-indexed).
- getColumnDefinition() - Method in class ExportObjectsFromCSV
-
Column definition for the CSV files
- getColumnGroup() - Method in class ColumnDefinition
-
Name of CSV column used to group results (the same values, are outputted together)
- getColumnID() - Method in class ColumnDefinition
-
Name of CSV column with the file identifier
- getColumns() - Method in class MontageSlices
-
How many columns to use in the montage, or 0 to guess an approximately square output
- getColumnUniquePixel() - Method in class ColumnDefinition
-
Name of CSV column with X coordinate of point for the first Object
- getCombine() - Method in class FromObjects
-
- getCombined() - Method in interface VoxelPartition
-
- getCombined() - Method in class VoxelPartitionHistogram
-
- getCommand() - Method in class MorphologicalOperation
-
One of: open, close, fill, erode, dilate, skel, outline
- getCommandName() - Method in class HelpConfig
-
What the application command is described as in the help message e.g. anchor or
anchorGUI
- getComparerLeft() - Method in class AnnotationComparisonInputManager
-
- getComparerMultiplex(boolean) - Method in class AnnotationComparisonInput
-
- getComparerRight() - Method in class AnnotationComparisonInputManager
-
- getComparers() - Method in class AnnotationComparisonInput
-
- getCondition() - Method in class IfParamEquals
-
- getCondition() - Method in class IfKeyValueCondition
-
- getConfidence() - Method in class ObjectForReduction
-
The associated confidence.
- getConfidence() - Method in class LabelledWithConfidence
-
The confidence associated with element
.
- getConfidence() - Method in class WithConfidence
-
The confidence associated with element
.
- getConnPoint() - Method in class ContiguousVoxelPath
-
- getConstant() - Method in class MaxWithConstant
-
- getContains() - Method in class DescriptiveNameContainsImageLabeller
-
- getContains() - Method in class FilterDescriptiveName
-
A descriptive-name must contain (case-sensitive) this string.
- getContext() - Method in class SharedObjects
-
Logger and other common configuration
- getContext() - Method in class ParametersExperiment
-
- getContext() - Method in class OutputterChecked
-
General settings for writing outputs.
- getContext() - Method in class FeatureCalculationContext
-
- getContext() - Method in class FeatureExporterContext
-
Context for reading from or writing outputs to the file-system.
- getContextExperiment() - Method in class InputBound
-
The input-output context associated with the current experiment.
- getContextJob() - Method in class InputBound
-
The input-output context associated with the current job.
- getContextParameters() - Method in class InputArguments
-
Context parameters that an influence determining inputs.
- getConversion() - Method in class ConvertedInput
-
The converted input.
- getConvert() - Method in class ConvertWithHistogram
-
- getConverters() - Method in class DisplayStack
-
A list of optional converters that will be applied to the respective channel in stack
if they exist.
- getCopyFilesNaming() - Method in class CopyFilesNamingOne
-
- getCost(int, int) - Method in class CostMatrix
-
Gets the cost from an element from the first-list to an element from the second-list.
- getCost() - Method in class MergeStrategy
-
A cost of how undesirable (the higher the more undesirable) this merge is.
- getCosts() - Method in class AssignOverlappingObjects
-
A matrix linking the overlap between each
ObjectMask
to each other, respectively as
rows and columns.
- getCount() - Method in class RecordedExecutionTimes.RecordedOperation
-
How many times the operation occurred.
- getCount() - Method in class Counter
-
The count, as per current state.
- getCount() - Method in class RunningSum
-
The running count.
- getCount(int) - Method in class Histogram
-
The count corresponding to a particular value.
- getCount() - Method in class VarianceCalculatorDouble
-
The running count of values.
- getCount() - Method in class VarianceCalculatorLong
-
The running count of values.
- getCountThreshold() - Method in class SummarizerSplitMoreThan
-
If there are more than countThreshold
elements, use summarizerGreaterThan
,
else summarizerElse
.
- getCreateMark() - Method in class PointsFitter
-
- getCreationTime() - Method in class ImageFileAttributes
-
The creation timestamp on the file the image was loaded from.
- getCsvFeaturesAggregated() - Method in class FeatureOutputNames
-
The CSV of aggregated feature-results, if enabled.
- getCsvFeaturesGroup() - Method in class FeatureOutputNames
-
The CSV individually written for each group, if enabled.
- getCsvFeaturesNonAggregated() - Method in class FeatureOutputNames
-
The CSV of non-aggregated feature-results.
- getCsvFilePath() - Method in class FilterCSVColumn
-
- getCsvFilePath() - Method in class FromCSVInput
-
- getCurrent() - Method in class DualState
-
- getCurrent() - Method in class OptimizationStep
-
- getCurrentTemp() - Method in class Geometry
-
- getCustomName() - Method in class Feature
-
An optional additional name that be associated with the feature (defaults to an empty
string).
- getDatasetName() - Method in class ExperimentResultsExperimentStructure
-
The name of the experiment including version suffix
- getDatasets() - Method in class QuickMultiDatasetExperiment
-
- getDatasets() - Method in class QuickMultiDatasetStructuredExperiment
-
- getDatasetSpecific() - Method in class QuickMultiDatasetExperiment
-
- getDatasetSpecific() - Method in class QuickMultiDatasetStructuredExperiment
-
- getDatasetSuffix() - Method in class FilePathAppendBase
-
A suffix appended to the dataset name extracted from the reg exp
- getDatasetVersion() - Method in class ExperimentResultsExperimentStructure
-
A version-suffix appended to the dataset name extracted from the reg exp
- getDebugModeParameters() - Method in class InputManagerParameters
-
Parameters for debug-mode (only defined if we are in debug mode).
- getDebugModeParameters() - Method in class InputContextParameters
-
Parameters for debug-mode (only defined if we are in debug mode).
- getDecode() - Method in class SegmentStackIntoObjectsScaleDecode
-
Decodes inference output into segmented objects.
- getDefault() - Static method in class BinaryValuesByte
-
Default values to use, if not otherwise specified.
- getDefault() - Static method in class BinaryValuesInt
-
Default values to use, if not otherwise specified.
- getDefaultBeanClass() - Method in class AnchorDefaultBeanFactory
-
Returns null as
Optional
is not supported by
BeanFactory
interface.
- getDefaultColors() - Method in class OutputWriteSettings
-
The default color-scheme used for outputs, if no other scheme is specified.
- getDefaultExtension() - Method in interface FileFormat
-
The default extension to write associated with a particular format.
- getDefaultExtension() - Method in enum ImageFileFormat
-
- getDefaultExtension() - Method in enum NonImageFileFormat
-
- getDefaultInstances() - Method in class AnchorDefaultBeanFactory
-
Default bean-classes to use for particular family types of beans.
- getDefaultInstances() - Static method in class RegisterBeanFactories
-
Default instances of different family-types of beans.
- getDefaultStackReaderForMetadata() - Method in class ConvertNamedChannels
-
Supplies to the imageMetadataReader
to use, if no other reader is specified.
- getDefine() - Method in class MarkEvaluator
-
- getDefine() - Method in class DefineOutputter
-
- getDefine() - Method in class Develop
-
Defines entities (chanels, stacks etc.) that are derived from inputs and other entities.
- getDefine() - Method in class ExportReportFeatures
-
- getDefine() - Method in class FromObjects
-
- getDefine() - Method in class ExportObjectsAsCroppedImages
-
- getDefine() - Method in class SegmentWithMarkedPointProcess
-
Adds definitions of stacks/objects etc.
- getDelegate() - Method in class RasterGeneratorDelegateToRaster
-
The delegate.
- getDelegate() - Method in class UnsignedByteBuffer
-
The underlying storage buffer, to which calls are delegated with our without conversion.
- getDelegate() - Method in class UnsignedIntBuffer
-
The underlying storage buffer, to which calls are delegated with our without conversion.
- getDelegate() - Method in class UnsignedShortBuffer
-
The underlying storage buffer, to which calls are delegated with our without conversion.
- getDelegate() - Method in class InputFromManagerDelegate
-
The delegate.
- getDelegate() - Method in class BoundMinMax
-
- getDelegate() - Method in class CalculateInputFromDelegate
-
- getDelimiter() - Method in class SubsetRangeIfRequested
-
Character used to split the name into groups.
- getDelimiter() - Method in class LastDirectoryAsPrefix
-
- getDelta() - Method in class Mser
-
- getDeltat() - Method in class AnisotropicDiffusion
-
the integration constant for the numerical integration scheme.
- getDepth() - Method in class ImposeResolution
-
Physical pixel size of a voxel in z-dimension.
- getDerivePath() - Method in class DualMarksAnnotationAsObjects
-
- getDerivePath() - Method in class MarksAsObjects
-
- getDerivePath() - Method in class MaskAsObject
-
Where to find the
Mask
to compare, as a function of the source file-path.
- getDerivePath() - Method in class Objects
-
Where to find the objects to compare, as a function of the source file-path.
- getDerivePath() - Method in class CollapseFileName
-
Called as a delegate to provide a
source
Path
.
- getDerivePath() - Method in class RemoveTrailingDirectory
-
- getDescription() - Method in exception AnchorCombinableException
-
The (uncombined) description associated with the exception.
- getDescription() - Method in class KernelDecision
-
- getDescription() - Method in class KernelWithIdentifier
-
- getDestination() - Method in class MarkPair
-
- getDestination() - Method in class PairVoxelizedMarkMemo
-
- getDestination() - Method in class DualVoxelizedMarks
-
- getDestination() - Method in class ToVoxelized
-
- getDestinationDirectory() - Method in class CopyContext
-
Destination directory for copying.
- getDictionaries() - Method in class DictionaryInitialization
-
- getDictionary() - Method in class FeatureInitialization
-
A dictionary of key-value pairs.
- getDictionary() - Method in class FeatureRelatedInitialization
-
- getDictionary() - Method in class FeatureEvaluator
-
Parameters to optionally associated with stackEnergy
, and meaningless if stackEnergy
is not specified.
- getDictionary() - Method in class EnergySchemeCreatorByElement
-
- getDictionary() - Method in class ScaleByDictionary
-
- getDictionary() - Method in class AssignFromDictionary
-
The dictionary from which an assignment will occur.
- getDictionary() - Method in class ScoreVoxels
-
- getDictionary() - Method in class DictionaryCondition
-
The dictionary to provide a value to check.
- getDictionary() - Method in class IfParamEqual
-
- getDictionary() - Method in class ParamFromCollection
-
- getDictionary() - Method in class FeatureListProviderLDAClassifier
-
- getDictionary() - Method in class FeatureValueCheckMark
-
- getDictionary() - Method in class DefineOutputterWithEnergy
-
- getDictionary() - Method in class GaussianSampler
-
The dictionary that parameterizes the Gaussian-distribution that is sampled from.
- getDictionary() - Method in class Develop
-
If non-empty, the identifier for a dictionary that is treated as part of the energy-stack.
- getDictionary() - Method in class SegmentMarksFromImage
-
If non-empty, a dictionary that is passed to the segmentation procedure.
- getDictionaryOptional() - Method in interface FeatureInputDictionary
-
The associated dictionary, if it exists.
- getDictionaryOptional() - Method in class FeatureInputEnergy
-
- getDictionaryOptional() - Method in class FeatureInputMark
-
- getDictionaryRequired() - Method in interface FeatureInputDictionary
-
The associated dictionary, or an exception if it doesn't exist.
- getDimensions() - Method in class ImageMetadata
-
The dimensions of the image.
- getDimensions() - Method in class ImageInferenceContext
-
The size of the image for which we wish to segment, before and after any scaling for model
inference.
- getDimensions() - Method in class ReportFeatureForMarks
-
- getDimensions() - Method in class FromDimensionsBase
-
- getDimensions() - Method in class FromDimensionsBase
-
- getDimensions() - Method in class RepeatSlice
-
Dimensions to create new mask
- getDimensions() - Method in class MergeBase
-
- getDimensions() - Method in class WithDimensionsBase
-
- getDimensions() - Method in class WithOptionalDimensionsBase
-
- getDimensions() - Method in class ToDimensions
-
The dimensions the source image/entity is desired to be scaled to.
- getDimensions() - Method in class FromMarks
-
- getDimensions() - Method in class RequireFeatureRelationThreshold
-
- getDimensions() - Method in class PointsFitterToMark
-
- getDimensionsOptional() - Method in class FeatureInputMark
-
- getDimensionsRequired() - Method in class FeatureInputMark
-
- getDimensionsSourceFallback() - Method in class ToDimensions
-
- getDirection() - Method in class ConvertToPhysicalDistance
-
Direction of the distance being converted, defaults to a unit vector along the X-axis
- getDirection() - Method in class FeatureMarkDirection
-
- getDirectionVector() - Method in class LineSegment
-
- getDirectionVector() - Method in class FromUnitValueDistance
-
- getDirectory() - Method in class PathDifference
-
The directory component of the difference, if it exists.
- getDirectory() - Method in class FilesProviderWithDirectoryString
-
A directory in which to look for files.
- getDirectory() - Method in class FileWithDirectoryInput
-
A directory that must be a containing directory (at some hierarchical level) of file
associated with this input.
- getDirectory() - Method in class GlobExtractor.GlobWithDirectory
-
The directory part of the string, or null if it doesn't exist
- getDirectory() - Method in class DualPathPredicates
-
Only accepts any containing directories where the predicate returns true
- getDirectory() - Method in class OutputterTarget
-
- getDirectory() - Method in class DirectoryWithPrefix
-
- getDirectory() - Method in class HomeSubdirectory
-
A relative-path (to the user home directory) which is used as an output directory
- getDirectory() - Method in class WriteIntoDirectory
-
The directory in which stacks are written
- getDirectoryAsPath(InputContextParameters) - Method in class FilesProviderWithDirectory
-
The associated directory with the list of files.
- getDirectoryAsPath(InputContextParameters) - Method in class FilesProviderWithDirectoryString
-
- getDirectoryAsPath(InputContextParameters) - Method in class FilesProviderWithDirectoryUnary
-
- getDirectoryAsPath(InputContextParameters) - Method in class SingleFile
-
- getDirectoryAsPathEnsureAbsolute(InputContextParameters) - Method in class FilesProviderWithDirectory
-
- getDirectoryDataset() - Method in class QuickMultiDatasetExperiment
-
- getDirectoryDistance() - Method in class QuickMultiDatasetStructuredExperiment
-
How many directories to recurse back from the current file to the Experiments/ directory
- getDirectoryOutput() - Method in class QuickExperiment
-
- getDirectoryPathToCopyMissingImagesTo() - Method in class ComparisonPlan
-
- getDisplayer() - Method in class SegmentStackIntoObjectsScaleDecode
-
How to convert an image to be displayed to the user.
- getDisplayer() - Method in class SegmentedBackground
-
How to convert the background in an image suitable to be displayed.
- getDisplayer() - Method in class CompareAnnotations
-
How to convert an image to be displayed to the user.
- getDisplayer() - Method in class ColoredBase
-
How to convert an image to be displayed to the user.
- getDisplayer() - Method in class OutlinePreserveRelativeSize
-
How to convert an image so that it can be displayed.
- getDisplayer() - Method in class ScaleToSize
-
How to convert an image to be displayed to the user.
- getDisplayer() - Method in class Montage
-
How to convert an image to be displayed to the user.
- getDisplayer() - Method in class ExportObjectsAsCroppedImages
-
How to convert an image to be displayed to the user.
- getDisplayer() - Method in class ExportObjectsFromCSV
-
How to convert an image to be displayed to the user.
- getDisplayer() - Method in class SegmentMarksFromImage
-
How to convert an image to be displayed to the user.
- getDisplayer() - Method in class SegmentWithMarkedPointProcess
-
How to convert an image to be displayed to the user.
- getDistance() - Method in class LevelPerObjectNeighbors
-
How many neighbors to include by distance (distance==1 implies all directly touching
neighbors, distance==2 implies those touching the directly touching etc.)
- getDistance() - Method in class DistanceIndex
-
- getDistance() - Method in class DistanceIndexTwice
-
- getDistanceMapProvider() - Method in class MergeSpatialClusters
-
A distance map which can also be used for making decisions on merging
- getDistanceMax() - Method in class CalculateLevel
-
- getDistanceTransformMultiplyBy() - Method in class AddDistanceTransform
-
Multiplies the distance transform by this factor to make it more meaningful in a short.
- getDistanceTransformSmoothSigmaMeters() - Method in class AddDistanceTransform
-
If non-zero, a Gaussian blur is applied to the distance transform using the sigma in meters
below.
- getDistanceX() - Method in class ReflectInAxesWithinDistance
-
- getDistanceY() - Method in class ReflectInAxesWithinDistance
-
- getDistanceZ() - Method in class ReflectInAxesWithinDistance
-
- getDistanceZEndIfEmpty() - Method in class XYOrientationExtendToZ
-
- getDivideByZeroValue() - Method in class Divide
-
- getDivisor() - Method in class PermutePropertySequenceDouble
-
What to divide the integer-sequence by.
- getDscr() - Method in class ResolvedBound
-
- getDualStack() - Method in class OptimizationContext
-
- getEigenvalue() - Method in class EigenvalueAndVector
-
The eigenvalue.
- getEigenvector() - Method in class EigenvalueAndVector
-
The eigenvector corresponding to eigenvalue
.
- getElemAllAsFeatureList() - Method in class EnergyScheme
-
- getElemAllCreator() - Method in class EnergySchemeCreatorByElement
-
- getElemByCliqueSize(int) - Method in class EnergyScheme
-
- getElement() - Method in class ObjectForReduction
-
The underlying
ObjectMask
with whom a confidence and label is associated.
- getElement() - Method in class LabelledWithConfidence
-
The underlying element with whom a confidence and label is associated.
- getElement() - Method in class WithConfidence
-
The underlying element with whom a confidence is associated.
- getElemIndAsFeatureList() - Method in class EnergyScheme
-
- getElemIndCreator() - Method in class EnergySchemeCreatorByElement
-
- getElemPairAsFeatureList() - Method in class EnergyScheme
-
- getElemPairCreator() - Method in class EnergySchemeCreatorByElement
-
- getEllipsoidCalculator() - Method in class Ellipsoid
-
- getEllipsoidSum(double, double, double, DoubleMatrix2D) - Static method in class Ellipsoid
-
- getElseName() - Method in class FileNamerContext
-
A fallback name, if a failure occurs when naming.
- getEmptyValue() - Method in class CenterOfGravity
-
- getEmptyValue() - Method in class Intersection
-
- getEmptyValue() - Method in class ArbitraryInsidePoint
-
- getEmptyValue() - Method in class IntensityMeanMaxSlice
-
- getEmptyValue() - Method in class IntensityMeanShellBase
-
- getEmptyValue() - Method in class DerivedObject
-
- getEnclosing() - Method in class BoundingBoxEnclosed
-
An enclosing box (equal to or larger than box
covering all screen-space used for this
entity, including padding.
- getEnd() - Method in class SequenceInteger
-
An index beyond which we cannot iterate (inclusive).
- getEndIndex() - Method in class IndexRangeNegative
-
The index if the last element to use in the subsetting range, inclusive.
- getEndPoint() - Method in class LineSegment
-
- getEnergy() - Method in class Aggregator
-
- getEnergyChannelIndex() - Method in class Identity
-
- getEnergyChannelIndex() - Method in class RejectIfIntensityLessThan
-
- getEnergyChannelIndex() - Method in class SingleChannel
-
- getEnergyChannelIndex() - Method in class QuantileAcrossConnectedComponents
-
- getEnergyChannelIndexCheck() - Method in class IdentityImposeValueRelationToHistogram
-
- getEnergyChannelIndexFail() - Method in class IdentityImposeValueRelationToHistogram
-
- getEnergyIndex() - Method in class NumberNeighboringVoxels
-
Index of which channel in the energy-stack to select
- getEnergyIndex() - Method in class SpecificEnergyChannelBase
-
Index of which channel in the energy-stack to select
- getEnergyIndex() - Method in class FeatureEnergyChannel
-
Index of channel to use in the energy-stack (0 is the first channel, 1 is second etc.)
- getEnergyIndex() - Method in class OutsideRange
-
- getEnergyIndex() - Method in class Intensity
-
The channel that that forms the histogram.
- getEnergyIndex() - Method in class AsObjectMask
-
The channel that that forms an object-mask with the bounding-box set to entire channel's
dimensions
- getEnergyIndex() - Method in class OverlapMaskBase
-
- getEnergyIndexGradient() - Method in class TextureScore
-
- getEnergyIndexMask() - Method in class IntensityMeanShellBase
-
A channel of the energyStack that is used as an additional mask using default byte values for
on and off.
- getEnergyIndexMask() - Method in class Intensity
-
Optionally, index of another channel that masks the histogram.
- getEnergyIndexX() - Method in class IntensityGradientBase
-
- getEnergyIndexY() - Method in class IntensityGradientBase
-
- getEnergyIndexZ() - Method in class IntensityGradientBase
-
- getEnergyScheme() - Method in class MarksWithEnergyBreakdown
-
- getEnergyScheme() - Method in class MarksWithTotalEnergy
-
Associated Energy Scheme, which should include the EnergySavedPairs
- getEnergyScheme() - Method in class VoxelizedMarksWithEnergy
-
- getEnergyScheme() - Method in class EnergySchemeWithSharedFeatures
-
- getEnergyScheme() - Method in class KernelCalculationContext
-
- getEnergyScheme() - Method in class OptimizationContext
-
- getEnergySchemeCreator() - Method in class MarkEvaluator
-
- getEnergySchemeCreator() - Method in class SegmentWithMarkedPointProcess
-
Creates an energy scheme that assigns an energy score to each collection of marks.
- getEnergyStack() - Method in class FeatureInitialization
-
An energy-stack, which may form an input to the feature for calculation.
- getEnergyStack() - Method in class ProposerContext
-
- getEnergyStack() - Method in class DualStack
-
The energy-stack
- getEnergyStack() - Method in class FeatureCalculatorFromProvider
-
- getEnergyStack() - Method in class InitializationWithEnergyStack
-
- getEnergyStackOptional() - Method in class FeatureInputEnergy
-
The associated energy-stack.
- getEnergyStackRequired() - Method in class FeatureInputEnergy
-
The associated energy-stack or throws an exception if it isn't present.
- getEnergyTotal() - Method in class EnergyPair
-
- getEnergyTotal() - Method in class MarksWithEnergyBreakdown
-
- getEnergyTotal() - Method in class MarksWithTotalEnergy
-
The pre-annealed total energy
- getEnergyTotal() - Method in class VoxelizedMarksWithEnergy
-
- getEnergyTotal() - Method in class EnergySavedAll
-
- getEnergyTotal() - Method in class EnergySavedInd
-
- getEnergyTotal() - Method in class EnergySavedPairs
-
Pairwise energy total
- getEquals() - Method in class FilterDescriptiveName
-
A descriptive-name must be exactly equal to (case-sensitive) this string.
- getError(int) - Method in class ResultsVector
-
Gets an error state at a particular position.
- getErrorMessage() - Method in class ErrorNodeImpl
-
- getErrorNode() - Method in class ProposerContext
-
- getErrorReporter() - Method in interface InputOutputContext
-
The associated error reporter.
- getErrorReporter() - Method in class Outputter
-
- getErrorReporter() - Method in class GraphLogger
-
- getErrorTree() - Method in class ProposerFailureDescription
-
- getExactDepth() - Method in class DirectoryDepth
-
- getException() - Method in exception CheckedStream.ConvertedToRuntimeException
-
- getException(String) - Method in interface NamedProvider
-
Retrieves the item if it exists, or throws an exception if it doesn't exist.
- getException(String) - Method in class LazyEvaluationStore
-
- getException(String) - Method in class SharedFeaturesSubset
-
Gets a feature by name, throwing an exception if it doesn't exist.
- getException(String) - Method in class ChannelMap
-
- getExecutionArguments() - Method in class InputOutputContextStateful
-
User-supplied arguments that can further specify an experiment's execution.
- getExecutionArguments() - Method in class ParametersExperiment
-
User-supplied arguments that can further specify an experiment's execution.
- getExecutionDuration() - Method in class JobStateMonitor
-
How long the job took to execute in milliseconds.
- getExecutionTime() - Method in class KernelDecision
-
- getExecutionTime() - Method in class Reporting
-
- getExecutionTimeRecorder() - Method in class OperationContext
-
Allows for the execution time of certain operations to be recorded.
- getExecutionTimeRecorder() - Method in class ExperimentFeedbackContext
-
Allows execution-time for particular operations to be recorded.
- getExecutionTimeRecorder() - Method in class InputOutputContextStateful
-
- getExecutionTimeRecorder() - Method in class ParametersExperiment
-
Allows execution-time for particular operations to be recorded.
- getExecutionTimeRecorder() - Method in class ImageInferenceContext
-
Allows execution-time for particular operations to be recorded.
- getExecutionTimeRecorder() - Method in class InputManagerParameters
-
Allows for the execution time of certain operations to be recorded.
- getExecutionTimeRecorder() - Method in interface InputOutputContext
-
Allows execution-times to be recorded for particular operations.
- getExecutionTimeRecorder() - Method in class OutputWriteContext
-
Records the execution time of particular operations.
- getExecutionTimeRecorder() - Method in class ElementOutputter
-
Records the execution time of particular operations.
- getExecutionTimeRecorder() - Method in class FeatureCalculationContext
-
Records the execution-time of particular operations.
- getExperiment() - Method in class ExperimentResultsExperimentStructure
-
- getExperiment() - Method in class ExperimentStructure
-
- getExperimentDescription() - Method in class OptimizationContext
-
- getExperimentIdentifier() - Method in class OutputExperiment
-
A name for the experiment.
- getExperimentIdentifier() - Method in class ParametersExperiment
-
- getExperimentType() - Method in class FilePathAppendBase
-
A folder identifying the type of experiment (where the outputs are all put in the same
directory
- getExperimentType() - Method in class QuickMultiDatasetStructuredExperiment
-
The value of $1 (see comment above) in naming-structure.
- getExperimentType() - Method in class RootedExperiment
-
A directory identifying the type of experiment.
- getExpression() - Method in class RegExSimple
-
A Java-style regular expression containing groups.
- getExpression() - Method in class MatchRegularExpression
-
The regular-expression, Java-style as described in
Pattern
.
- getExpression() - Method in class RegularExpression
-
- getExtension() - Method in class FilenameSplitExtension
-
The extension of the filename.
- getExtension() - Method in class OneOrThreeChannelsWriter
-
Which extension to use to write the image (without any leading period).
- getExtension() - Method in class AppendStack
-
- getExtension() - Method in class AppendStackDirect
-
- getExtensions() - Method in class MatchExtensions
-
A set of file-extensions (without the period), one of which must match the end of a path.
- getExtensions() - Method in class BranchExtension
-
Any extensions to match (case insensitive) excluding any leading period.
- getExtent() - Method in class ExtentToArrange
-
- getExtent() - Method in class KernelPointCursor
-
The size of the image the kernel iterates over.
- getExtent() - Method in class SizeMapping
-
The size.
- getExtractScoreSize() - Method in class DirectAssignMode
-
- getExtractScoreSize() - Method in class UniformProposal
-
- getExtractScoreSizeReport() - Method in class TransformationAssignMode
-
- getExtractScoreSizeState() - Method in class TransformationAssignMode
-
- getExtractWeight() - Method in class KernelInitialMarksFromPartition
-
- getFactor() - Method in class ScoreObjects
-
- getFactor() - Method in class Scale
-
- getFactorHigh() - Method in class Identity
-
- getFactorLow() - Method in class Identity
-
- getFactorStandardDeviation() - Method in class GaussianSampler
-
Multiples the standard deviation of the distribution found in keyStandardDeviation
.
- getFallback() - Method in class SpecificPathList
-
If no paths can be found either from listPaths or the input-context, then the fallback is
called if exists, otherwise an error is thrown
- getFallback() - Method in class ToSuggested
-
- getFallback() - Method in class ExtractToRGB
-
If a channel doesn't match an RGB pattern, this conversion-style can be used instead.
- getFallback() - Method in class RGBIfNamesMatch
-
If a channel doesn't match an RGB pattern, this conversion-style can be used instead.
- getFallback() - Method in class InferFromHeader
-
Fallback to use if EXIF information is non-existing or absent.
- getFallbackName() - Method in class ExperimentIdentifierAuto
-
If there's no task-name, then this constant is used as a fallback name.
- getFeature() - Method in class FeatureProviderDefine
-
The feature to provide.
- getFeature() - Method in class FeatureEvaluator
-
The single feature that will be calculated (possibly repeatedly) in the session.
- getFeature() - Method in class OutputFeatureTable
-
A list of features to calculate in an evaluation context.
- getFeature() - Method in class ScoreObjects
-
Feature that calculates the score for an object.
- getFeature() - Method in class PermuteFeatureBase
-
- getFeature() - Method in class AddCriteriaFeatureRelationThreshold
-
- getFeature() - Method in class FeatureValueCheckMark
-
- getFeature() - Method in class RequireFeatureRelationThreshold
-
- getFeatureCondition() - Method in class IfCondition
-
- getFeatureCondition() - Method in class IfConditionWithinRange
-
Calculates value for the condition - which is checked if it lies within a certain range
- getFeatureElse() - Method in class IfCondition
-
- getFeatureEvaluator() - Method in class MultipleComparer
-
Calculates the cost used when making assignments.
- getFeatureEvaluator() - Method in class ReportFeatureEvaluator
-
- getFeatureEvaluator() - Method in class FeatureCostAssigner
-
- getFeatureEvaluator() - Method in class DiscardOutliers
-
- getFeatureEvaluator() - Method in class RelationWithMatches
-
- getFeatureEvaluator() - Method in class ThresholdedFeature
-
- getFeatureEvaluator() - Method in class ObjectCollectionProviderWithFeature
-
- getFeatureEvaluator() - Method in class MergeGreedyToIncreaseObjectFeature
-
- getFeatureEvaluator() - Method in class MergeToIncreaseObjectFeature
-
- getFeatureEvaluatorMatch() - Method in class RelationWithMatches
-
- getFeatureEvaluatorMerge() - Method in class MergePairs
-
- getFeatureEvaluatorThreshold() - Method in class MergePairs
-
Allows merge only if the feature-value satisfies a relation to this threshold
- getFeatureLists() - Method in class FeatureRelatedInitialization
-
- getFeatureNameIndex() - Method in class FeatureInputResults
-
A mapping from the name of the feature that produced a result, to its index position in
results
.
- getFeatureNames() - Method in class FeatureCalculationContext
-
The name of each feature being calculated, in identical order, as that is placed in the
exported CSV.
- getFeatureNames() - Method in class FeatureExporter
-
The names of the features to be exported.
- getFeatureProvider() - Method in class FeatureEvaluator
-
The single feature that will be calculated (possibly repeatedly) in the session
- getFeatures() - Method in class FeatureListEvaluator
-
A list of providers, combined together to form a list of features, to be calculated in a
session
- getFeatures() - Method in class ExportFeatures
-
The features to be exported (after possibly some manipulation or augmentation).
- getFeatures() - Method in class SegmentInstanceWithModel
-
Features to calculate for objects in the features output.
- getFeaturesAggregate() - Method in class ExportFeatures
-
- getFeaturesImage() - Method in class PairNeighbors
-
Additional features that only depend on the image, so do not need to be replicated for every
object.
- getFeatureSource() - Method in class FeatureCalculationContext
-
The features that are calculated, encapsulated in some object.
- getFeaturesPair() - Method in class PairNeighbors
-
Additional features that are processed on the pair of images (i.e.
- getFeatureTables() - Method in class Develop
-
Specifies a feature-table that can also be outputted.
- getFeedbackReceiver() - Method in class FeedbackReceiverRequireArguments
-
- getFeedbackReceiver() - Method in class SegmentWithMarkedPointProcess
-
Processes feedback from the segmentation algorithm for outputting / debugging.
- getFile() - Method in class NamedFile
-
The file.
- getFile() - Method in class SingleFileInputBase
-
The associated single file.
- getFileAttributes() - Method in class ImageMetadata
-
Attributes associated with the file on the filesystem.
- getFileFilter() - Method in class ExperimentResultsExperimentStructure
-
Files to search for
- getFileId() - Method in class AppendCsv
-
Unique identifier for the stack, object-mask-collection etc.
- getFileId() - Method in class FilePathBaseAppendToManagerWithFileID
-
Unique identifier for the stack, object-mask-collection etc.
- getFileInput() - Method in class GroupFiles
-
- getFileInput() - Method in class NamedChannels
-
- getFileInput() - Method in class Stacks
-
- getFileInput() - Method in class QuickExperiment
-
A string indicating the input file(s)
- getFilename() - Method in class PathDifference
-
The file-name component of the difference, if it exists.
- getFilePath() - Method in class SortedSetSlice
-
- getFilePath() - Method in class FromSerializedMarks
-
- getFilePath() - Method in class FromSerializedObject
-
- getFilePathParser() - Method in class MultiFileReader
-
- getFilePathProviderSVM() - Method in class FeatureListProviderSVMClassifier
-
- getFilePaths() - Method in class FilePathInitialization
-
Named-store of file-paths.
- getFilePaths() - Method in class FeatureRelatedInitialization
-
A named-set of file-paths.
- getFiles() - Method in class ReadFromFile
-
Provides a single file containing a dictionary.
- getFiles() - Method in class FilesProviderUnary
-
- getFiles() - Method in class FilesProviderWithDirectoryUnary
-
- getFiles() - Method in class FromFiles
-
A provider that should return exactly one
File
whose path is employed.
- getFiles() - Method in class Rooted
-
- getFiles() - Method in class NamedFiles
-
The files to use as inputs.
- getFiles() - Method in class NamedFilesWithDirectory
-
The files to use as inputs.
- getFiles() - Method in class QuickBase
-
A path to the main channel of each file
- getFilter() - Method in class IfObjectFilter
-
- getFilter() - Method in class ObjectCollectionProviderFilterBase
-
- getFilter() - Method in class Filter
-
- getFilter() - Method in class ImageLabellerStringMap
-
- getFilterFilesCsv() - Method in class QuickBase
-
If set, a CSV is read with two columns: the names of images and a
- getFilterInitialization(Path) - Method in class SharedStateFilteredImageOutput
-
- getFindOutlinePixelAngle() - Method in class TraversePointsOnContour
-
- getFirst() - Method in class CostMatrix
-
The first set of elements.
- getFirst() - Method in class FeatureInputPairObjects
-
- getFirst() - Method in class OutputEnableRulesSpecify
-
Output-names in the first-level.
- getFirst() - Method in class Compose
-
First transformation from S
to U
- getFirstArgument() - Method in class HelpConfig
-
What the application argument is described as in the help message
e.g. experimentFile.xml
- getFirstBinaryValues() - Method in class ObjectCollection
-
- getFirstBinaryValuesByte() - Method in class ObjectCollection
-
- getFixedSizeScaler() - Method in class Montage
-
How to calculate the size of each image, when varyImageSize==false
.
- getFloat() - Static method in class VoxelsFactory
-
A factory that creates voxels of type float.
- getFontColor() - Method in class TextStyle
-
Font-color of drawn text
- getFontName() - Method in class TextStyle
-
Font-name of drawn text
- getFontSize() - Method in class TextStyle
-
Font-size of drawn text
- getForAllSlices(int) - Method in class IndexByRegion
-
- getFormats() - Method in class InferFromHeader
-
The formats whose headers will be searched, to find sufficient metadata to populate
ImageMetadata
.
- getFormatVoxelwiseCompare() - Method in class ComparisonPlan
-
The file-format to use for the voxel-wise comparison (if it's activated).
- getForSlice(int, int) - Method in class IndexByRegion
-
- getFrame(int) - Method in class TimeSeries
-
Gets a frame in the time-series.
- getFriendlyName() - Method in class Feature
-
A user-friendly human-readable name for the
Feature
.
- getFrom() - Method in class TypedEdge
-
The vertex the edge joins from.
- getGaussianSigmaMeters() - Method in class AddEdgeFilters
-
- getGenerator() - Method in class BoundOutputter
-
The generator to be (repeatedly) used to write elements in the sequence.
- getGlob() - Method in class MatchGlob
-
The string describing a glob e.g.
- getGlob() - Method in class GlobExtractor.GlobWithDirectory
-
- getGradient() - Method in class ScoreVoxels
-
- getGrayscaleReconstruction() - Method in class MinimaImpositionGrayscaleReconstruction
-
- getGreen() - Method in class RGBColorBean
-
The green component value of the RGB color.
- getGreen() - Method in class RGBColor
-
The green component value of the RGB color.
- getGreen() - Method in class ThreeChannels
-
- getGroup() - Method in class RowLabels
-
An identifier for a higher-level group which the row belongs to (foreign key)
- getGroup() - Method in class AnnotationLabel
-
Specifies a group for the label (similar labels that are displayed together)
- getGroup() - Method in class ExportFeatures
-
Includes an additional group column in CSVs, and creates group-specific feature files.
- getGroup() - Method in class GroupedStackBase
-
How to partition the inputs into groups.
- getGroup() - Method in class IfGroupIndexRange
-
Fallback to use when no group-index-range is specified.
- getGroup() - Method in class CSVRow
-
- getGroup() - Method in class AppendHistogram
-
- getGrouper() - Method in class FeatureExporter
-
When defined, assigns each input to a group.
- getGrouper() - Method in class GroupedSharedState
-
How to group the inputs.
- getGroupGeneratorName() - Method in class FeatureCalculationContext
-
- getGroupHeaders() - Method in class LabelHeaders
-
Headers describing the non-feature columns outputted in the CSV related to identifying the
group of a row
- getGroupIndexRange() - Method in class TaskArguments
-
An index-range to use for grouping, by subsetting components from each input's identifier.
- getGroupMap() - Method in class GroupedSharedState
-
- getHeaders() - Method in class FeatureCSVMetadata
-
Headers for the CSV file.
- getHeaders() - Method in class CSVReader.OpenedCSVFile
-
The header-names of the CSV file if available.
- getHeight() - Method in class SizeXY
-
Size in Y dimension.
- getHeight() - Method in class ImposeResolution
-
Physical pixel size of a voxel in y-dimension.
- getHistogram() - Method in class HistogramProviderUnary
-
- getHistogram() - Method in class FeatureInputHistogram
-
- getHistogram() - Method in class ConvertWithHistogram
-
If set, a histogram used in conversion to describe input intensities (across perhaps multiple
images).
- getHistogram() - Method in class SegmentChannel
-
An optional histogram of voxel intensity values which can be used by segment
- getHistogram() - Method in class LevelResult
-
- getHistogram() - Method in class FromHistogram
-
If non-null, a histogram is extracted from this provider rather than the histogram from the
inputted CSV.
- getHistogramChannelIndex() - Method in class CalculateLevelBase
-
- getHistogramIndex() - Method in class IdentityImposeValueRelationToHistogram
-
- getHistogramsExtra() - Method in class ScoreVoxels
-
- getId() - Method in class DictionaryProviderReference
-
- getId() - Method in class Reference
-
The identifier that uniquely determines the other feature to reference.
- getId() - Method in class FeatureProviderReference
-
The name of the feature to reference.
- getId() - Method in class FeatureResultsStatistic
-
The name of the feature, whose results will provide the statistic.
- getId() - Method in class BinarySegmentationReference
-
- getId() - Method in class FilePathProviderReference
-
- getId() - Method in class KernelDecision
-
- getId() - Method in class Reference
-
- getId() - Method in class FromChannel
-
- getId() - Method in class Reference
-
- getId() - Method in class Reference
-
- getId() - Method in class Reference
-
- getId() - Method in class ReferenceOrElse
-
- getId() - Method in class Reference
-
- getId() - Method in class FeatureIntersectingObjects
-
ID for the particular object-collection
- getId() - Method in class ExportFeatures
-
Translates an input file name to a unique ID.
- getId() - Method in class MarkBoundsReference
-
- getId() - Method in class MarkProposerReference
-
- getId() - Method in class MarkMergeProposerReference
-
- getId() - Method in class MarkSplitProposerReference
-
- getId() - Method in class Reference
-
- getId() - Method in class ReferenceOrEmpty
-
- getId() - Method in class CreateEllipse
-
- getId() - Method in class CSVRow
-
- getId() - Method in class Reference
-
- getIdentifier(T, int) - Method in interface IdentifierGetter
-
Gets the unique identifier.
- getIdentifier(T, int) - Method in class IdentifyFromIteration
-
- getIdentifier() - Method in class NamedFile
-
Unique identifier associated with the file.
- getIdentifier() - Method in class Mark
-
- getIdentifier() - Method in class OverlayMark
-
- getIdentifier() - Method in class KernelWithIdentifier
-
- getIdentifierSubrange() - Method in class InputContextParameters
-
If defined, this indicates and specifies only a subset of the naming-elements to use.
- getIdentifierSuffix() - Method in class QuickMultiDatasetExperiment
-
- getIdentifierSuffix() - Method in class QuickMultiDatasetStructuredExperiment
-
- getIdGenerator() - Method in class ExportObjectsFromCSV
-
- getIdGetter() - Method in class ObjectDrawAttributes
-
Gets a unique ID associated with the object
- getIfPresent(K) - Method in class LRUCache
-
Gets an value, if present, but doesn't create any new entry if it's absent.
- getIgnoreContains() - Method in class AnnotationBackground
-
If non-empty, to not display any stacks in backgroundStackMap
whose name contains
this string.
- getImage() - Method in class MergedPairsFeatures
-
- getImage() - Method in class PointsInitialization
-
- getImage() - Method in class InitializationWithEnergyStack
-
- getImageDimensions() - Method in class ImageFileShape
-
- getImageLabeller() - Method in class ImageAssignLabel
-
Maps a label to an image
- getImageMetadataReader() - Method in class Montage
-
- getImageMetadataReader() - Method in class ScaleImageCommonSize
-
- getImageMetadataReader() - Method in class ConvertNamedChannels
-
- getImgChannelMapCreator() - Method in class GroupFiles
-
- getIncrement() - Method in class SequenceInteger
-
Size of step to use when incrementing.
- getIndex() - Method in interface AssociatedIndex
-
The associated index.
- getIndex() - Method in class Indexable
-
- getIndex() - Method in class ExtentToArrange
-
Index position.
- getIndex() - Method in class ObjectForReduction
-
The index of the element in the original list for reduction, or NEWLY_ADDED
if newly
added.
- getIndex() - Method in class IndexedChannel
-
The index (starting at zero) of this
Channel
relative to others.
- getIndex() - Method in class KernelPointCursor
-
The index in the buffer that the kernel currently is focussed on.
- getIndex(TreeNode) - Method in class ErrorNodeImpl
-
- getIndex() - Method in class KernelDecision
-
- getIndex() - Method in class AtIndex
-
- getIndex() - Method in class SliceAt
-
Index in z-dimension of slice to extract
- getIndex() - Method in class SpecificAxisBase
-
Specifies which principal-axis to use for calculations (0=largest eigenvalue,
1=second-largest eigenvalue etc.)
- getIndex() - Method in class IndexedRegionBase
-
- getIndex() - Method in class DistanceIndex
-
- getIndex() - Method in class OrderedRadius
-
- getIndex() - Method in class AsObject
-
- getIndex() - Method in class HOGFeature
-
Which index to return from the HOG descriptor.
- getIndexDay() - Method in class TimestampPattern
-
The index of the group in regularExpression
that encodes the day, starting
from 0 for the first group.
- getIndexedRowsOrCreate(Path, ColumnDefinition) - Method in class FromCSVSharedState
-
- getIndexEnd() - Method in class NameElementRange
-
The index of the last element (inclusive) for the range.
- getIndexEnd() - Method in class ExtractSliceRange
-
Slice index to end extracting from (inclusive).
- getIndexForMemo(VoxelizedMarkMemo) - Method in class EnergyMemoList
-
- getIndexHighest() - Method in class DistanceIndexTwice
-
Highest-level index.
- getIndexHours() - Method in class TimestampPattern
-
The index of the group in regularExpression
that encodes the hours, starting
from 0 for the first group.
- getIndexLowest() - Method in class DistanceIndexTwice
-
Lowest-level index.
- getIndexMinutes() - Method in class TimestampPattern
-
The index of the group in regularExpression
that encodes the minutes, starting
from 0 for the first group.
- getIndexMonth() - Method in class TimestampPattern
-
The index of the group in regularExpression
that encodes the month, starting
from 0 for the first group.
- getIndexNonZero() - Method in class SelectSlicesWithIndexBase
-
- getIndexSeconds() - Method in class TimestampPattern
-
The index of the group in regularExpression
that encodes the seconds, starting
from 0 for the first group.
- getIndexStart() - Method in class NameElementRange
-
The index of the first element (inclusive) for the range.
- getIndexStart() - Method in class ExtractSliceRange
-
Slice index to start extracting from (inclusive).
- getIndexYear() - Method in class TimestampPattern
-
The index of the group in regularExpression
that encodes the year, starting
from 0 for the first group.
- getIndividual() - Method in class MarksWithEnergyBreakdown
-
- getInitContext() - Method in class FeedbackBeginParameters
-
- getInitialization() - Method in class InitializableBean
-
The parameters used for initialization.
- getInitialization() - Method in class ImageLabellerStringMapInitialization
-
- getInitializationType() - Method in class BeanInitializer
-
Type of parameters to be propagated, corresponding to P
.
- getInitialKernel() - Method in class KernelProposer
-
- getInitialPoint() - Method in class ContiguousVoxelPath
-
- getInnerCoreDistance() - Method in class Ellipsoid
-
- getInput() - Method in class AnnotationInputManager
-
The inputs to be annotated.
- getInput() - Method in class InputOutputExperiment
-
The input-manager to specify where/which/how necessary inputs for the experiment occur.
- getInput() - Method in class InputBound
-
The input is bound.
- getInput() - Method in class ParametersUnbound
-
- getInput() - Method in class InputManagerUnary
-
The delegate input-manager which will be circumstantially called by the current
input-manager.
- getInput() - Method in class ExperimentExecutor
-
- getInput() - Method in class MultiInputManager
-
- getInput() - Method in class AnnotationComparisonInputManager
-
- getInput() - Method in class AnnotationComparisonInput
-
- getInput() - Method in class NamedChannelsAppend
-
- getInput() - Method in class ConvertNamedChannelsToStack
-
- getInput() - Method in class FromCSVInputManager
-
- getInputContext() - Method in class InputManagerParameters
-
Additional parameters that offer context for many beans that provide input-functions.
- getInputDebug() - Method in class BranchIfDebug
-
If defined, this provides an input to the manager when in debug-mode, rather than than
otherwise inputs
.
- getInputDirectory() - Method in class FileNamerContext
-
A directory associated with the inputs, which if defined, is guaranteed to be a parent of
them all.
- getInputDirectory() - Method in class InputContextParameters
-
If defined, a directory which can be used by beans to find input.
- getInputFilterExtensions() - Method in class InputContextParameters
-
A trie of extensions that can be used filter inputs.
- getInputFilterGlob() - Method in class InputContextParameters
-
A glob that can be used by beans to filter input.
- getInputIfPresent(T) - Method in class CacheTransferSource
-
Gets corresponding
FeatureCalculationInput
for an
input
, if present, but
doesn't create any new entry if it's absent.
- getInputName() - Method in class MultiInputManager
-
- getInputName() - Method in class SegmentObjectsFromONNXModel
-
The name of the input in the ONNX model.
- getInputName() - Method in class QuickExperiment
-
- getInputName() - Method in class MultiInputManagerQuick
-
- getInputOutput() - Method in class InitializationContext
-
The input-output context.
- getInputOutputContext() - Method in class OptimizationContext
-
- getInputPaths() - Method in class InputContextParameters
-
A list of paths referring to specific inputs.
- getInputPointShift() - Method in class ConicFitterBase
-
- getInputScale() - Method in class MultiScaleObject
-
Gets the
ObjectMask
at the scale associated with the input-image.
- getInstance() - Static method in class VoxelsResizerFactory
-
- getInstanceFor(Class<? extends T>) - Method in class BeanInstanceMap
-
Gets an instance from the map for a particular family-type.
- getInt(int) - Method in class VoxelBuffer
-
Gets an element from the buffer at a particular position, converting, if necessary, to an
int
.
- getInt(int) - Method in class ProcessVoxelNeighborAbsoluteWithSlidingBuffer
-
Get a value from the buffer at a particular absolute position.
- getInt(int, int) - Method in class ProcessVoxelNeighborAbsoluteWithSlidingBuffer
-
Get a value from the buffer at a particular relative position.
- getIntensity() - Method in class ScoreVoxels
-
- getIntensityHistogram() - Method in class BinarySegmentationParameters
-
A histogram of the intensity values of the voxels that are being segmented.
- getInterpolator() - Method in class Arrange
-
The interpolator to use for scaling images, if needed.
- getInterpolator() - Method in class SegmentStackIntoObjectsScaleDecode
-
The interpolator to use for scaling images.
- getInterpolator() - Method in class ScaleXY
-
The interpolator to use for scaling images.
- getInterpolator() - Method in class AtScale
-
The interpolator to use.
- getInterpolator() - Method in class OutlinePreserveRelativeSize
-
Interpolator used when scaling the background
- getInterpolator() - Method in class ScaleToSize
-
- getInterpolator() - Method in class CombineObjectsForFeatures
-
Interpolator used to resize images in thumbnail generation.
- getInterpolator() - Method in class Montage
-
How to resize images.
- getInterpolator() - Method in class GroupedStackBase
-
The interpolator to use for scaling images.
- getInterpolator() - Method in class ScaleImage
-
The interpolator to use for scaling images.
- getInterpolator() - Method in class SegmentInstanceWithModel
-
The interpolator to use for scaling images.
- getInterpolator() - Method in class DecodeMaskRCNN
-
The interpolator to use for scaling images.
- getInterpolator() - Method in class HOGParameters
-
The interpolator to use for scaling images.
- getItem() - Method in class NamedBean
-
The item that is to be named, the underlying bean.
- getItem() - Method in class DefineSingle
-
The sole feature that forms the list.
- getItem() - Method in class PrependName
-
Provides the features and names before any prepending.
- getItem() - Method in class FeatureUnary
-
- getItem() - Method in class FeatureDeriveFromPair
-
- getItem() - Method in class ReportFeatureWrapError
-
- getItem() - Method in class ThresholdHistogram
-
- getItem() - Method in class DeriveFromPair
-
- getItem() - Method in class FeatureListProviderAggregatePair
-
For each feature in the list, a corresponding aggregate feature is created in the
output list.
- getItem() - Method in class Intensity
-
Feature to apply to the histogram
- getItem() - Method in class DerivedObject
-
- getItem() - Method in class FeatureIntersectingObjectsSingleElement
-
- getItem() - Method in class PairedWithMask
-
- getItem() - Method in class RejectIfIntensityLessThan
-
- getItem() - Method in class FeatureSingleObjectFromShared
-
- getItem() - Method in class Intensity
-
Feature to apply to the histogram.
- getItem() - Method in class AsObjectMask
-
- getItem() - Method in class QuantileAcrossConnectedComponents
-
- getItem() - Method in class Rooted
-
- getItem() - Method in class CoefficientOfVarianceFromAll
-
- getItem() - Method in class MeanFromAll
-
- getItem() - Method in class Intensity
-
Feature to apply to the histogram
- getItem() - Method in class FeaturePairMemoOne
-
- getItem1() - Method in class FeatureBinary
-
Provides the first value for the binary-function.
- getItem2() - Method in class FeatureBinary
-
Provides the second value for the binary-function.
- getItemMean() - Method in class StatisticalBase
-
- getItemProportionate() - Method in class FeatureAsIndividualProportionate
-
- getItemStdDev() - Method in class StatisticalBase
-
- getIteration() - Method in class Reporting
-
- getIterations() - Method in class AnisotropicDiffusion
-
How many iterations to perform diffusion.
- getIterations() - Method in class MorphologicalOperatorBase
-
- getIterations() - Method in class ObjectCollectionProviderMorphological
-
- getIterations() - Method in class Repeat
-
The maximum number of iterations.
- getIterations() - Method in class Intersection
-
The number of dilations and erosions to apply to determine if two objects intersect
- getIterations() - Method in class IntensityMeanShellBase
-
The number of dilations and erosions to apply and whether to do in the Z dimension.
- getIterations() - Method in class Erode
-
- getIterations() - Method in class NumberRemovedVoxelsAfterClosing
-
- getIterations() - Method in class Shell
-
The number of dilations and erosions to apply and whether to do in the Z dimension
- getIterations() - Method in class MorphologicalOperation
-
iterations for erode, dilate, open, close
- getIterations() - Method in class UniformProposal
-
- getIterations() - Method in class NumberIterationsBase
-
The number of iterations for which the number-of-marks must remain constant.
- getIterationsDilation() - Method in class MorphologicalIterations
-
Number of times to perform morphological dilation
- getIterationsErosion() - Method in class MorphologicalIterations
-
Number of times to perform morphological erosion
- getJobDescription() - Method in class SubmittedJob
-
A unique description for the job.
- getJobState() - Method in class SubmittedJob
-
The current execution-state of the job.
- getKappa() - Method in class AnisotropicDiffusion
-
A parameter kappa associated with the diffusion functions.
- getKeep() - Method in class MergeCandidate
-
- getKeepProcessorsFree() - Method in class DebugDependentProcessor
-
How many processors to avoid using for the tasks.
- getKeepProcessorsFree() - Method in class ParallelProcessor
-
How many processors to avoid using for the tasks.
- getKernel() - Method in class KernelWithIdentifier
-
- getKernel() - Method in class WeightedKernel
-
- getKernel() - Method in class OptimizationStep
-
- getKernel() - Method in class Reporting
-
- getKernel() - Method in class KernelProposerOptionSingle
-
- getKernelAccepted() - Method in class Aggregator
-
- getKernelApplication() - Method in class DilationContext
-
How the kernel is applied to the scene.
- getKernelCalcContext() - Method in class TransformationContext
-
- getKernelFactoryList() - Method in class FeedbackBeginParameters
-
- getKernelHalfWidth() - Method in class Median
-
Kernel will be a square kernel of size (2*kernelHalfWidth+1)x(2*kernelHalfWidth+1)
- getKernelNegative() - Method in class KernelProposerOptionDual
-
- getKernelNoProposalDescription() - Method in class Reporting
-
- getKernelPositive() - Method in class KernelProposerOptionDual
-
- getKernelProposed() - Method in class Aggregator
-
- getKernelProposer() - Method in class SegmentWithMarkedPointProcess
-
Proposes kernel-changes during iterations of hte marked-point-processes.
- getKernelStateBridge() - Method in class TransformationAssignMode
-
- getKey() - Method in exception GetOperationFailedException
-
The key that was used in the operation that created this exception.
- getKey() - Method in class AssignFromDictionary
-
The key of the value in the dictionary that will be assigned.
- getKey() - Method in class DictionaryCondition
-
The key in the dictionary whose value is checked.
- getKey() - Method in class IfParamEqual
-
- getKey() - Method in class ParamFromCollection
-
The name of the key in the dictionary, whose corresponding value will be returned.
- getKey() - Method in class FilePathParser
-
- getKey() - Method in class RegularExpression
-
- getKey() - Method in class FromDictionary
-
- getKeyGroupID() - Method in class RegularExpression
-
- getKeyLower() - Method in class ScaleByDictionary
-
- getKeyMean() - Method in class GaussianSampler
-
The name of the key in the dictionary with the mean of the distribution.
- getKeyPrefix() - Method in class FromDictionary
-
Prefix prepended to key
- getKeyStandardDeviation() - Method in class GaussianSampler
-
The name of the key in the dictionary with the standard-deviation.
- getKeySuffix() - Method in class FromDictionary
-
- getKeyUpper() - Method in class ScaleByDictionary
-
- getLabel() - Method in class ImageLabelAnnotation
-
The label that applies to the image.
- getLabel() - Method in class ObjectForReduction
-
The label associated with the element.
- getLabel() - Method in class LabelledWithConfidence
-
The label associated with the element.
- getLabel() - Method in class StackProviderWithLabel
-
The label associated with stack
.
- getLabelled() - Method in class ObjectForReduction
-
The underlying labelled
ObjectMask
for input to a reduction algorithm.
- getLabelMap() - Method in class ImageCSVLabellerInitialization
-
- getLabels() - Method in class LabelledResultsVector
-
The labels.
- getLabels() - Method in class ImageLabelStrategy
-
- getLabels() - Method in class LabelledResultsVectorWithThumbnail
-
The labels.
- getLastDivider() - Method in class Aggregator
-
- getLastPoints1() - Method in class MarkMergeProposer
-
- getLastPoints2() - Method in class MarkMergeProposer
-
- getLeft() - Method in class ObjectsToCompare
-
Objects on left-side of the comparison
- getLeftUnassigned() - Method in class OverlappingObjects
-
The unassigned objects in the left set.
- getLevel() - Method in class Constant
-
- getLevel() - Method in class LevelResult
-
- getLimitUpper() - Method in class InputContextParameters
-
If defined, an upper limit that is imposed on the number of inputs.
- getLine() - Method in class CSVRow
-
- getList() - Method in class Concatenate
-
- getList() - Method in class RegExList
-
The list of
RegEx
es that are successively tried to be matched.
- getList() - Method in class StringMap
-
A list of mappings between a single-items in the respective sets.
- getList() - Method in class ToMultiple
-
The list of loggers to log to
- getList() - Method in class Define
-
The list that specifies features.
- getList() - Method in class DefinedNamed
-
- getList() - Method in class FeatureList
-
The list of features.
- getList() - Method in class FeatureFromList
-
The features whose results will be somehow combined, to form the result of this class.
- getList() - Method in class Arrange
-
The stacks that are passed in respect order into arrange
.
- getList() - Method in class TileWithLabels
-
- getList() - Method in class RegionMap
-
- getList() - Method in class AddCriteriaOr
-
- getList() - Method in class FeedbackReceiverList
-
- getList() - Method in class TerminationConditionListOr
-
- getList() - Method in class Concatenate
-
- getList() - Method in class CalculateLevelListBase
-
- getList() - Method in class ObjectFilterCombine
-
A list of other filters from which the sub-classes implement filtering behaviour.
- getList() - Method in class Concatenate
-
- getList() - Method in class Sequence
-
A list of binary-segmentations that are applied successively (the output of the predecessor
becomes the input of the sucecssor)
- getList() - Method in class Concatenate
-
- getList() - Method in class SpecificAndRename
-
- getList() - Method in class FromEntries
-
- getList() - Method in class Combine
-
- getList() - Method in class Concatenate
-
- getList() - Method in class SummarizerAggregate
-
- getList() - Method in class AndList
-
- getList() - Method in class VisitSchedulerAnd
-
- getList() - Method in class VisitSchedulerUniformSample
-
- getList() - Method in class MarkProposerFromList
-
- getListAdditionalChannelProviders() - Method in class ScoreObjects
-
- getListAppend() - Method in class NamedChannelsAppend
-
- getListAppend() - Method in class MultiInputManagerQuick
-
Additional entities that are appended to the multi-input
- getListFeatures() - Method in class BinaryClassifierImageLabeller
-
- getListFromManager(MultiInputManager) - Method in class AppendDictionary
-
- getListFromManager(MultiInputManager) - Method in class AppendFilePath
-
- getListFromManager(MultiInputManager) - Method in class AppendHistogram
-
- getListFromManager(MultiInputManager) - Method in class AppendMarks
-
- getListFromManager(MultiInputManager) - Method in class AppendObjects
-
- getListFromManager(MultiInputManager) - Method in class AppendStack
-
- getListFromManager(MultiInputManager) - Method in class AppendStackDirect
-
- getListFromManager(MultiInputManager) - Method in class FilePathBaseAppendToManager
-
- getListImageFeatures() - Method in class EnergySchemeCreatorByElement
-
- getListImageFeatures() - Method in class EnergyScheme
-
- getListPaths() - Method in class SpecificPathList
-
If specified, this forms the list of paths which is provided as input.
- getListReportFeatures() - Method in class ExportReportFeatures
-
- getListStackProvider() - Method in class ExportObjectsAsCroppedImages
-
The channels we extract the object-masks from - all assumed to be of same dimension
- getListStackProviderMIP() - Method in class ExportObjectsAsCroppedImages
-
The channels we extract the object-masks from - all assumed to be of same dimension
- getLoader() - Method in class TestLoaderImage
-
Delegate loader (for non image-related loading)
- getLoader1() - Method in class DualComparer
-
- getLoader2() - Method in class DualComparer
-
- getLocal(int) - Method in interface BufferRetriever
-
Get a buffer at a particular index in the z-dimension.
- getLocal(int) - Method in class LocalSlices
-
- getLocalPath() - Method in class AnchorBean
-
A local path on the filesystem associated with this bean (from serialization) if defined.
- getLog() - Method in class OnlyIf
-
The logger to use if conditions are fulfilled
- getLogExperiment() - Method in class OutputExperiment
-
Where log messages that do not pertain to a specific job (input) appear.
- getLogExperimentPath() - Method in class QuickMultiDatasetExperiment
-
Relative path to a logger for the experiment in gneeral
- getLogger() - Method in class InitializableBean
-
The logger.
- getLogger() - Method in class CommonContext
-
The logger.
- getLogger() - Method in class OperationContext
-
Where to write informative messages to, and and any non-fatal errors (fatal errors are throw
as exceptions).
- getLogger() - Method in class InitializationContext
-
The associated logger.
- getLogger() - Method in class InputBound
-
The
Logger
associated with this input, as it is being processed as a job.
- getLogger() - Method in class InputOutputContextStateful
-
- getLogger() - Method in class ImageInferenceContext
-
Where to log information messages during inference.
- getLogger() - Method in class InputManagerParameters
-
Where to write informative messages to, and and any non-fatal errors (fatal errors are throw
as exceptions).
- getLogger() - Method in class FileNamerContext
-
Logs information messages.
- getLogger() - Method in interface InputOutputContext
-
The associated logger.
- getLogger() - Method in class ReporterAggregate
-
- getLogger() - Method in class FeedbackEndParameters
-
- getLogger() - Method in class OptimizationContext
-
- getLogger() - Method in class TransformationContext
-
- getLogger() - Method in class FeatureCalculationContext
-
- getLoggerExperiment() - Method in class ExperimentFeedbackContext
-
The logger associated with the experiment.
- getLoggerExperiment() - Method in class ParametersExperiment
-
The message-logger used for experiment-wide messages.
- getLoggerTaskCreator() - Method in class ParametersExperiment
-
This is a means to create new log-reporters for each task.
- getLogReporterJob() - Method in class InputBound
-
- getLogTask() - Method in class InputOutputExperiment
-
Where log messages that do pertain to a specific job (input) appear.
- getLogTaskPath() - Method in class QuickMultiDatasetExperiment
-
Relative path to a logger for a specific task
- getMainChannelIndex() - Method in class NamedChannelsQuick
-
Index of the mainChannel
- getMainChannelName() - Method in class NamedChannelsQuick
-
The name of the channel provided by the rasters in file Provider
- getMainObjectName() - Method in class MultiInput
-
- getMainObjectName() - Method in class StackWithMap
-
- getMajorAxisAngle() - Method in class EllipseStandardFormConverter
-
- getMajorAxisSlope() - Method in class EllipseStandardFormConverter
-
- getMap() - Method in class OperationMap
-
- getMap() - Method in class ImageLabellerStringMap
-
- getMap() - Method in class ImageLabellerStringMapInitialization
-
- getMapping() - Method in class AnonymizeSharedState
-
- getMark() - Method in class FeatureInputMark
-
- getMark() - Method in class VoxelizedMarkMemo
-
The associated mark
- getMark() - Method in class OverlayMark
-
- getMark() - Method in class KernelDeath.MarkAnd
-
- getMark() - Method in class ObjectWithEllipse
-
- getMarkBounds() - Method in class MarkBoundsDefine
-
- getMarkBounds() - Method in class SegmentThresholdAboveMinBound
-
- getMarkEvaluator() - Method in class MarkProposerStrategy
-
A mark-evaluator that is added to the GUI to support this annotation
- getMarkFactory() - Method in class MarkEvaluator
-
- getMarkFactory() - Method in class KernelCalculationContext
-
- getMarkFactory() - Method in class MarkFactoryContext
-
- getMarkFactory() - Method in class OptimizationContext
-
- getMarkFactory() - Method in class SegmentWithMarkedPointProcess
-
Creates a new mark, before perhaps further manipulations by a kernel.
- getMarkFactory() - Method in class FitPointsFromObjects
-
- getMarkFromMarksProposer() - Method in class KernelSplit
-
- getMarkProposer() - Method in class MarkProposerStrategy
-
- getMarkProposer() - Method in class FromMarkProposer
-
- getMarkProposer() - Method in class MergeMarkEllipse
-
- getMarkProposer() - Method in class KernelBirthAndKill
-
- getMarkProposer() - Method in class KernelExchange
-
- getMarkProposer() - Method in class KernelBirthVoxelized
-
- getMarkProposerAdditionalBirth() - Method in class KernelBirthAndKill
-
- getMarkProvider() - Method in class CreateMarkFromPoints
-
- getMarkProvider() - Method in class ReportFeatureOnMark
-
- getMarkProvider() - Method in class FromSingleMark
-
- getMarkProvider() - Method in class RequireFeatureRelationThreshold
-
- getMarkRmv() - Method in class KernelDeath
-
- getMarks() - Method in class RandomCollectionWithAddCriteria
-
- getMarks() - Method in class FeatureInputMarkCollection
-
- getMarks() - Method in class IndexableMarksWithEnergy
-
- getMarks() - Method in class MarksWithEnergyBreakdown
-
- getMarks() - Method in class MarksWithTotalEnergy
-
The marks
- getMarks() - Method in class VoxelizedMarksWithEnergy
-
- getMarks() - Method in class ReportFeatureOnMarks
-
- getMarks() - Method in class MarksWithDisplayStack
-
- getMarks() - Method in class ColoredMarks
-
- getMarks() - Method in class MarkCollection
-
The underlying
List
that stores the
Mark
s in the collection.
- getMarks() - Method in class FromMarks
-
- getMarks() - Method in class ScaleXY
-
- getMarks() - Method in class RetrieveSingleMarkOnly
-
- getMarks() - Method in class ColoredMarks
-
- getMarks() - Method in class MarksFromPartition
-
- getMarksAfter() - Method in class Reporting
-
- getMarksAfterOptional() - Method in class Reporting
-
- getMarksColored() - Method in class ColoredMarksWithDisplayStack
-
- getMarksProposer() - Method in class KernelInitialMarksFromPartition
-
- getMarksProposer() - Method in class KernelInitialMarksProposed
-
- getMarksProposer() - Method in class KernelInitialMarksVoxelized
-
- getMarksReject() - Method in class DualMarksAnnotation
-
Marks covering area that should be rejected, can be null
- getMarksWithTotalEnergy() - Method in class MarksWithEnergyBreakdown
-
- getMask() - Method in class MaskProviderUnary
-
The delegate Provider<Mask>
that is called.
- getMask() - Method in class FromMaskBase
-
- getMask() - Method in class UnaryWithMaskBase
-
- getMask() - Method in class ScoreVoxels
-
- getMask() - Method in class FromChannel
-
- getMask() - Method in class SegmentChannel
-
An optional mask which restricts the algorithm to only parts of the channel where the mask
has an on voxel
- getMask() - Method in class ConnectedComponentsFromMask
-
- getMask() - Method in class AndObjectsWithMasks
-
- getMask() - Method in class FromMask
-
- getMask() - Method in class SegmentChannel
-
- getMask() - Method in class ColoredMask
-
- getMask() - Method in class FromChannelOrMask
-
A mask that is provided to the stack.
- getMask() - Method in class PairedWithMask
-
- getMask() - Method in class MaskAsSingleObject
-
- getMask() - Method in class FillHoles
-
- getMask() - Method in class CheckMarkWithMask
-
- getMask() - Method in class FindPointOnContourWalk
-
- getMask() - Method in class XYOrientationExtendToZ
-
- getMaskContour() - Method in class TraverseOuterContourOnImage
-
- getMaskElse() - Method in class IfPredicateBase
-
Returned instead of mask
if the predicate is not satisfied
- getMaskFilled() - Method in class TraverseOuterContourOnImage
-
- getMaskFilled() - Method in class XYOrientationExtendToZ
-
- getMaskIndex() - Method in class SurfaceSizeMaskNonZero
-
- getMaskValue() - Method in class ExportImageHistograms
-
What voxel value to read as "On" in the mask above.
- getMaskValue() - Method in class OverlapMaskBase
-
- getMatch() - Method in class FilterCSVColumn
-
- getMatch() - Method in class MatchedAppendCsv
-
- getMatcher() - Method in class SearchDirectory
-
- getMatcher() - Method in class MatchExtensions
-
A secondary matcher, which is required additionally match (as well as the extension).
- getMatcher() - Method in class RelationWithMatches
-
- getMatcher() - Method in class ObjectWithMaximumFeatureFromEachMatchedCollection
-
- getMatcher() - Method in class Match
-
- getMatches() - Method in class MatchedObject
-
The matches associated with the source-object
- getMatrix() - Method in class CostMatrix
-
A two-dimensional array mapping the costs from first
to second
.
- getMatrix() - Method in class RotationMatrix
-
The underlying matrix used internally in the rotation-matrix.
- getMax() - Method in class MinMaxRange
-
The maximum value.
- getMax() - Method in class BoundMinMax
-
- getMax() - Method in class ResolvedBound
-
- getMax() - Method in class PointListBase
-
- getMax() - Method in class ScaleByMinMaxValue
-
- getMax() - Method in class ClampHistogramMax
-
- getMax() - Method in class UnitsWithinRange
-
Maximum-boundary for acceptable range
- getMax() - Method in class OutsideRange
-
- getMax() - Method in class MaxOverlapRatio
-
- getMax() - Method in class InvertedMax
-
- getMax() - Method in class CompareWithRangeFeature
-
Calculates maximally-allowed range boundary
- getMax() - Method in class RangeCompareFromScalars
-
Boundary value indicating maximally-allowed range value
- getMaxCost() - Method in class MultipleComparer
-
The maximum cost (as calculated by featureEvaluator
) to accept when creating an
assignment between objects.
- getMaxCost() - Method in class FeatureCostAssigner
-
- getMaxDirectoryDepth() - Method in class SearchDirectory
-
If non-negative the max depth of directories.
- getMaxDirectoryDepth() - Method in class ExperimentResultsExperimentStructure
-
- getMaxDistance() - Method in class MergeWithOptionalDistanceConstraint
-
An optional maximum distance
- getMaxDistance() - Method in class CostOverlapWithinMidpointDistance
-
- getMaxDistance() - Method in class FindPointOnContourWalk
-
- getMaxDistanceBetweenMinima() - Method in class AddDistanceTransform
-
- getMaxDistanceCOG() - Method in class MergeSpatialClusters
-
The maximum distance allowed between center-of-gravities of objects
- getMaxDistanceDeltaContour() - Method in class AddDistanceTransform
-
The maximum distance allowed between two seeds in terms of their values in the distance map
- getMaxDistanceDeltaContour() - Method in class MergeSpatialClusters
-
The maximum distance allowed between the 'distance from contour' values provided from the
distanceMap for each point.
- getMaxDistanceProposer() - Method in class VisitSchedulerMaxDistanceAlongContour
-
- getMaxDistanceZ() - Method in class XYOrientationExtendToZ
-
- getMaximumIndex() - Method in interface IndexRange
-
The maximum index in the range.
- getMaximumNumberChannels() - Method in class IntensityMoments
-
An upper limit on the number of channels in the energy-stack for which we create features.
- getMaxInstant() - Method in class ClusterIdentifier
-
Maximum timestamp in cluster.
- getMaxIter() - Method in class Repeat
-
- getMaxIter() - Method in class Repeat
-
- getMaxIter() - Method in class Repeat
-
- getMaxIter() - Method in class RadiiProposerRepeat
-
- getMaxNumberItems() - Method in class Limit
-
- getMaxNumberItems() - Method in class Limit
-
- getMaxNumberProcessors() - Method in class TaskArguments
-
Suggests a maximum number of processors (CPUs) for a task.
- getMaxNumberProcessors() - Method in class DebugDependentProcessor
-
An upper limit on the number of the processors that can be simultaneously used in parallel,
if they are available.
- getMaxNumberProcessors() - Method in class ParallelProcessor
-
Theoretical maximum number of (CPU) processors to use in parallel.
- getMaxNumberProcessors() - Method in class QuickMultiDatasetExperiment
-
An upper limit on the number of the processors that can be simultaneously used in parallel,
if they are available.
- getMaxNumberProcessors() - Method in class QuickMultiDatasetStructuredExperiment
-
- getMaxNumItems() - Method in class LimitWithDirectory
-
- getMaxPathWidth() - Method in class ExtractIdentifierAndPath
-
The maximum width permitted for an identifier, so that it is printed as one line.
- getMaxResolved(Optional<Resolution>, boolean) - Method in class BoundDegrees
-
- getMaxResolved(Optional<Resolution>, boolean) - Method in class BoundPhysicalExtent
-
- getMaxResolved(Optional<Resolution>, boolean) - Method in class BoundUnitless
-
- getMaxResolved(Optional<Resolution>, boolean) - Method in class MarkBounds
-
- getMaxSize() - Method in class Mser
-
- getMaxSplitGroups() - Method in class CompareAnnotations
-
- getMaxTime() - Method in class ClusterIdentifier
-
Gets the latest date-time in the cluster.
- getMaxValue() - Method in class Histogram
-
Maximum possible value in the histogram (inclusive).
- getMaxVar() - Method in class Mser
-
- getMaxVolume() - Method in class FillHoles
-
- getMaxX() - Method in class Box
-
Maximum X coordinate inclusive.
- getMaxY() - Method in class Box
-
Maximum Y coordinate inclusive.
- getMaxZ() - Method in class Box
-
Maximum Z coordinate inclusive.
- getMean() - Method in class MeanScale
-
The mean.
- getMean(int) - Method in class ImageMoments
-
Get the mean-value for a particular axis.
- getMedianRadiusMeters() - Method in class AddEdgeFilters
-
- getMemoForIndex(int) - Method in class VoxelizedMarksWithEnergy
-
- getMemoForIndex(int) - Method in class EnergyMemoList
-
- getMemoForIndex(int) - Method in class MemoList
-
- getMemoForIndex(int) - Method in interface MemoForIndex
-
- getMemoForMark(Mark) - Method in class VoxelizedMarksWithEnergy
-
- getMemoForMark(MarkCollection, Mark) - Method in class EnergyMemoList
-
- getMerge() - Method in class MergeCandidate
-
- getMerged() - Method in class FeatureInputPairObjects
-
Returns a merged version of the two-objects available (or null if not available)
- getMergedOptional() - Method in class FeatureInputPairObjects
-
- getMergedPosTolerance() - Method in class MergeMarkEllipse
-
- getMergeMarkProposer() - Method in class KernelMerge
-
- getMessage() - Method in exception GetOperationFailedException
-
A message describing the failure.
- getMessage() - Method in class ReportFeatureWrapError
-
- getMessageLogger() - Method in class InputOutputContextStateful
-
- getMessageNoInputs() - Method in class InputOutputExperiment
-
A message written to the logger if no inputs exist for the experiment, and it thus ends
early.
- getMessageReporter() - Method in interface InputOutputContext
-
The associated message reporter.
- getMessages() - Method in class ConvertedInput
-
Any messages written to the log during conversion.
- getMetadata() - Method in class FeatureInputImageMetadata
-
The image metadata.
- getMethod() - Method in class AutoLocalThreshold
-
- getMethod() - Method in class ThresholderAutoIJ
-
One of the following strings to identify ImageJ's thresholding algorithms (or an empty string
for the default).
- getMethod() - Method in class CopyFiles
-
How the copying occurs from source to destination file.
- getMin() - Method in class MinMaxRange
-
The minimum value.
- getMin() - Method in class BoundMinMax
-
- getMin() - Method in class ResolvedBound
-
- getMin() - Method in class PointListBase
-
- getMin() - Method in class ScaleByMinMaxValue
-
- getMin() - Method in class UnitsWithinRange
-
Minimum-boundary for acceptable range
- getMin() - Method in class OutsideRange
-
- getMin(Function<FileDetails, Optional<Integer>>) - Method in class ParsedFilePathBag
-
- getMin() - Method in class RadiiMinRatio
-
- getMin() - Method in class CompareWithRangeFeature
-
Calculates minimally-allowed range boundary
- getMin() - Method in class RangeCompareFromScalars
-
Boundary value indicating minimally-allowed range value
- getMinConfidence() - Method in class ThresholdConfidence
-
The minimum confidence of an element for its object-mask to be initially included for
consideration (before merging).
- getMinConfidence() - Method in class DecodeMaskRCNN
-
Only proposals outputted from the model with a score greater or equal to this threshold are
considered.
- getMinConfidence() - Method in class DecodeEAST
-
Proposed bounding boxes below this confidence interval are removed from consideration.
- getMinDiff() - Method in class MeanIntensityDifference
-
- getMinDifference() - Method in class Difference
-
A minimum difference, below which 0.0 is returned
- getMinDifference() - Method in class DifferenceCalculateLevelStandardDeviation
-
- getMinDiversity() - Method in class Mser
-
- getMinimaImposition() - Method in class ImposeMinima
-
- getMinimumBoundingBoxVolume() - Method in class FloodFillEachIntensityLevel
-
Only objects whose bounding-box volume is greater or equal to this threshold are included.
- getMinimumIndex() - Method in interface IndexRange
-
The minimum index in the range.
- getMinimumPerCluster() - Method in class ClusterByTimestamp
-
The minimum number of files that must exist for a cluster.
- getMinInstant() - Method in class ClusterIdentifier
-
Minimum timestamp in cluster.
- getMinIntensity() - Method in class RejectIfIntensityLessThan
-
- getMinIntensity() - Method in class ThresholderSimpleFillHoles2D
-
Intensity for thresholding
- getMinIntensityValue() - Method in class MorphologicalOperatorBase
-
- getMinMaskValue() - Method in class DecodeMaskRCNN
-
Only voxels with a value greater or equal to this threshold are considered as part of the
mask.
- getMinNumberObjects() - Method in class DiscardOutliers
-
- getMinNumberPoints() - Method in class SplitContourAtSaddlePoints
-
If a contour has less than this number of points, we don't split it, and return it as-is
- getMinNumberVoxels() - Method in class SplitIntoSquares
-
Only includes squares that have at least this number of voxels.
- getMinNumberVoxels() - Method in class ConnectedComponentsFromBinarySegmentation
-
- getMinNumberVoxels() - Method in class ThresholdConfidence
-
The minimum number of voxels that must exist in a connected-component to be included.
- getMinNumPoints() - Method in class CreateMarkFromPoints
-
- getMinNumPoints() - Method in class PointsFitterToMark
-
If an object has fewer points than before being fitted, we ignore
- getMinNumSlices() - Method in class XYOrientationExtendToZ
-
- getMinNumZSlices() - Method in class AtLeastZSlices
-
- getMinorAxisAngle() - Method in class EllipseStandardFormConverter
-
- getMinorAxisSlope() - Method in class EllipseStandardFormConverter
-
- getMinOverlap() - Method in class CostOverlapWithinMidpointDistance
-
- getMinRadius() - Method in class LinearLeastSquaresEllipseFitter
-
- getMinRadius() - Method in class LinearLeastSquaresEllipsoidFitter
-
- getMinRatio() - Method in class DiscardOutliers
-
- getMinResolution() - Method in class MinimumXYResolution
-
- getMinResolved(Optional<Resolution>, boolean) - Method in class BoundDegrees
-
- getMinResolved(Optional<Resolution>, boolean) - Method in class BoundPhysicalExtent
-
- getMinResolved(Optional<Resolution>, boolean) - Method in class BoundUnitless
-
- getMinResolved(Optional<Resolution>, boolean) - Method in class MarkBounds
-
- getMinSize() - Method in class Mser
-
- getMinTime() - Method in class ClusterIdentifier
-
Gets the earliest date-time in the cluster.
- getMinusOne() - Method in class SlidingBuffer
-
The voxel-buffer for the slice with the currently selected slice's index -1
or null
if it's the first slice.
- getMinVal() - Method in class FeatureValueCheckMark
-
- getMinVolume() - Method in class ConnectedComponentsFromMask
-
- getMinVolume() - Method in class VolumeMin
-
- getMinVolumeConnectedComponent() - Method in class AddDistanceTransform
-
- getMinX() - Method in class Box
-
Minimum X coordinate inclusive.
- getMinY() - Method in class Box
-
Minimum Y coordinate inclusive.
- getMinZ() - Method in class Box
-
Minimum Z coordinate inclusive.
- getModel() - Method in class ConcurrentModel
-
The underlying model.
- getModelBinaryPath() - Method in class SegmentObjectsFromTensorFlowModel
-
Relative-path to the TensorFlow model file, likely with .pb
extension, relative
to the models/ directory in the Anchor distribution.
- getModelDirectory() - Method in class CommonContext
-
Directory where machine-learning models can be found.
- getModelDirectory() - Method in class InputArguments
-
A directory indicating where models can be located.
- getModelDirectory() - Method in class InputOutputContextStateful
-
- getModelDirectory() - Method in interface InputOutputContext
-
An input-directory in which models are stored.
- getModelDirectory() - Method in class FeatureCalculationContext
-
- getModelPath() - Method in class SegmentObjectsFromONNXModel
-
Relative-path to the model file in ONNX form, relative to the models/ directory in the
Anchor distribution.
- getModelPool() - Method in class SharedStateSegmentInstance
-
- getModelScale() - Method in class MultiScaleObject
-
Gets the
ObjectMask
at the scale associated with the segmentation.
- getModelTextGraphPath() - Method in class SegmentObjectsFromTensorFlowModel
-
Relative-path to the TensorFlow model file, likely with .pb.txt
extension,
relative to the models/ directory in the Anchor distribution.
- getModificationTime() - Method in class ImageFileAttributes
-
The last modified timestamp on the file the image was loaded from.
- getMultipleComparer() - Method in class MarkProposerStrategy
-
- getMultipleOf() - Method in class FitTo
-
The eventual width and height of the image must be a multiple of this number.
- getMultiplyBy() - Method in class DistanceTransform3D
-
- getName() - Method in class FromXMLList
-
The name of the file in the current working directory WITHOUT THE .xml EXTENSION
- getName() - Method in class NamedBean
-
The name associated with item
.
- getName() - Method in class RootPath
-
The name of the root-path, which need not be unique in itself.
- getName() - Method in interface NameValue
-
The associated name.
- getName() - Method in class SimpleNameValue
-
- getName() - Method in class ExperimentIdentifierConstant
-
- getName() - Method in class IndexedChannel
-
The name of the
Channel
this entry represents.
- getName() - Method in class OptionalNameValue
-
An optional-name.
- getName() - Method in class NamedPath
-
A unique name associated with the path
- getName() - Method in class Circle
-
- getName() - Method in class Ellipse
-
- getName() - Method in class Ellipsoid
-
- getName() - Method in class Sphere
-
- getName() - Method in class Mark
-
- getName() - Method in class LineSegment
-
- getName() - Method in class PointList
-
- getName() - Method in class Polygon
-
- getName() - Method in class PolygonCurve
-
- getName() - Method in class RotatableBoundingBox
-
- getName() - Method in class Kernel
-
- getName() - Method in class WeightedKernel
-
- getName() - Method in class NamedChannel
-
- getName() - Method in class AdjacentFile
-
A name to describe the adjacent file
- getName() - Method in class FilePathAppendBase
-
The name of the appended entity
- getNameLeft() - Method in class AnnotationComparisonInputManager
-
- getNamer() - Method in class GroupFiles
-
- getNamer() - Method in class RemoveExtension
-
- getNamer() - Method in class SubsetRangeIfRequested
-
The namer that is called to provide names that are subsetted.
- getNamer() - Method in class NamedFilesBase
-
- getNamer() - Method in class QuickBase
-
Assigns each input a unique compact name.
- getNameRight() - Method in class AnnotationComparisonInputManager
-
- getNames() - Method in class StatisticsToExport
-
- getNames() - Method in class NamedFeatureCalculatorMulti
-
- getNames() - Method in class AnnotationComparisonInput
-
- getNameSubrange() - Method in class FileNamerContext
-
If defined, this indicates and specifies only a subset of the naming-elements to use.
- getNaming() - Method in class CopyFiles
-
How an output name (and path) is selected for an input file.
- getNamingSharedState() - Method in class RecordingCounter
-
- getNavigateHigherDirectories() - Method in class MultiFileReader
-
Search x number directories higher than file.
- getNoProposalReason() - Method in class KernelDecision
-
- getNumber() - Method in class JobDescription
-
- getNumberBins() - Method in class HOGParameters
-
The number of bins in each histogram for a cell.
- getNumberChannels() - Method in class EnergyStack
-
The number of channels in the stack.
- getNumberChannels() - Method in class EnergyStackWithoutParameters
-
The number of channels in the stack.
- getNumberChannels() - Method in class DisplayStack
-
The number of channels in the stack.
- getNumberChannels() - Method in class ImageMetadata
-
The number of channels in the image.
- getNumberChannels() - Method in class Stack
-
The number of channels in the stack.
- getNumberChannels() - Method in class StackNotUniformSized
-
The number of channels in the
Stack
.
- getNumberChannels() - Method in class ScaleableBackground
-
Number of channels in the background.
- getNumberChannels() - Method in class ForceNumberChannels
-
- getNumberChannels() - Method in class ImageFileShape
-
- getNumberChannels() - Method in class ChannelSpecification
-
How many channels in the stack?
- getNumberChannelsPerArray() - Method in class ImageFileEncoding
-
The total number of channels found in any one buffer.
- getNumberColumns() - Method in class Tile
-
The number of columns to use in the table produced when tiling.
- getNumberConverter() - Method in class AnonymizeSharedState
-
- getNumberDecimalPlaces() - Method in class FeatureCostAssigner
-
- getNumberDigits() - Method in class IncrementingNumber
-
Number of digits in the number, with leading zeros as necessary.
- getNumberDilations() - Method in class LevelPerObjectIndependently
-
- getNumberDimensions() - Method in class RotationMatrix
-
The number of dimensions in the rotation-matrix.
- getNumberFrames() - Method in class ImageMetadata
-
The number of frames (separate images representing different points in a time-series) in the
image.
- getNumberFrames() - Method in class ForceNumberFrames
-
- getNumberFrames() - Method in class ImageFileShape
-
- getNumberGPUProcessors() - Method in class ParallelProcessor
-
How many GPU processors to use when this is possible as a substitute for a CPU processor
- getNumberKernels() - Method in class KernelProposer
-
- getNumberLevelsGrouping() - Method in class CompareAnnotations
-
- getNumberLoopPoints() - Method in class SplitContourAtSaddlePoints
-
- getNumberParentOperations() - Method in class RecordedExecutionTimes.RecordedOperation
-
The number of parent operations.
- getNumberParentOperations() - Method in class RunningSumParented
-
The number of parent operations.
- getNumberRows() - Method in class Fill
-
The number of rows to use the montage, when sufficient images are available.
- getNumberRows() - Method in class Tile
-
The number of rows to use in the table produced when tiling.
- getNumberSeries() - Method in class ImageMetadata
-
The number of separate images stored in the file.
- getNumberSlices() - Method in class ImageFileShape
-
- getNumberSubdirectories() - Method in class LastDirectories
-
How many directories to include in the name.
- getNumColumns() - Method in class TileWithLabels
-
- getNumMarks() - Method in class FromMarkProposer
-
- getObject() - Method in class Found
-
The found object.
- getObject() - Method in class FeatureInputSingleObject
-
- getObject() - Method in class OverlayObjectMask
-
- getObject() - Method in class LevelResult
-
- getObject() - Method in class ColoredObject
-
The object-mask.
- getObject() - Method in class ObjectVertex
-
- getObject() - Method in class ObjectWithEllipse
-
- getObject1() - Method in class FeatureInputPairMemo
-
- getObject2() - Method in class FeatureInputPairMemo
-
- getObjectMatcher() - Method in class Bridge
-
Used to match each intermediary-object to a final-object
- getObjects() - Method in class ObjectCollectionProviderUnary
-
The delegate Provider<ObjectCollection>
that is called.
- getObjects() - Method in class FeatureInputObjectCollection
-
- getObjects() - Method in class SegmentedObjects
-
The segmented-objects, at two different scales.
- getObjects() - Method in class OutputFeatureTable
-
The objects for which features are calculated.
- getObjects() - Method in class ReportFeatureOnObjectsBase
-
- getObjects() - Method in class DistanceTransformForEachObject3D
-
- getObjects() - Method in class LevelPerObjectBase
-
The objects for whom a level is calculated
- getObjects() - Method in class UnaryWithObjectsBase
-
- getObjects() - Method in class GenerateToMatchObjects
-
- getObjects() - Method in class FromObjects
-
- getObjects() - Method in class IntersectsWith
-
- getObjects() - Method in class Always
-
- getObjects() - Method in class Intersection
-
- getObjects() - Method in class Permute
-
- getObjects() - Method in class ColoredObjects
-
Objects to draw on a background
- getObjects() - Method in class ObjectAggregationBase
-
- getObjects() - Method in class FromObjects
-
- getObjects() - Method in class ObjectAsPoints
-
- getObjects() - Method in class IncludeRandomObjects
-
- getObjects() - Method in class PointsFromObjects
-
- getObjects() - Method in class FromObjects
-
- getObjects() - Method in class ExportObjectsBase
-
- getObjects() - Method in class PointsFitterToMark
-
- getObjects1() - Method in class MergeTwoCollectionsItemwise
-
First collection with items to be merged
- getObjects2() - Method in class MergeTwoCollectionsItemwise
-
Second collection with items to be merged
- getObjectsBlue() - Method in class ThreeColoredObjects
-
- getObjectsContainer() - Method in class WithContainerBase
-
- getObjectsElse() - Method in class ReferenceOrElse
-
- getObjectsGreater() - Method in class GreaterIntersectionWith
-
- getObjectsGreen() - Method in class ThreeColoredObjects
-
- getObjectsGrouped() - Method in class FilterByGroup
-
- getObjectsLesser() - Method in class GreaterIntersectionWith
-
- getObjectsRed() - Method in class ThreeColoredObjects
-
- getObjectsSeeds() - Method in class SegmentChannel
-
- getObjectsSeeds() - Method in class SegmentWithSeeds
-
- getObjectsSource() - Method in class AssignFromIntersectingObjects
-
- getObjectsSource() - Method in class SegmentWithSeeds
-
- getObjectsSplitBy() - Method in class SplitByObjects
-
- getObjectsTarget() - Method in class AssignFromIntersectingObjects
-
- getOff() - Method in class BinaryValuesByte
-
The byte representation of the value for off.
- getOff() - Method in class BinaryValuesInt
-
The integer representation of the value for off.
- getOffset() - Method in class ClusterIdentifier
-
The offset to assume the time-stamp belongs in.
- getOn() - Method in class BinaryValuesByte
-
The byte representation of the value for on.
- getOn() - Method in class BinaryValuesInt
-
The integer representation of the value for on.
- getOperationContext() - Method in class InputManagerParameters
-
Allows for logging and recording the execution-time of particular operations.
- getOperationContext() - Method in class ProposerContext
-
- getOperationContext() - Method in class MarkFactoryContext
-
Context for reading a stack from the file-system.
- getOperationContext() - Method in class FeatureCalculationContext
-
- GetOperationFailedException - Exception in org.anchoranalysis.core.index
-
When a get operation fails for a particular key.
- GetOperationFailedException(Exception) - Constructor for exception GetOperationFailedException
-
Creates with only a cause, omitting a key and a message.
- GetOperationFailedException(int, String) - Constructor for exception GetOperationFailedException
-
Creates with a message, but no cause - with an integer key.
- GetOperationFailedException(String, String) - Constructor for exception GetOperationFailedException
-
Creates with a message, but no cause - with
a String
key.
- GetOperationFailedException(int, Throwable) - Constructor for exception GetOperationFailedException
-
Creates with a cause, but no message - with an integer key.
- GetOperationFailedException(String, Throwable) - Constructor for exception GetOperationFailedException
-
Creates with a cause, but no message - with
a String
key.
- getOperationIdentifier() - Method in class RecordedExecutionTimes.RecordedOperation
-
An (unique) identifier for the operation.
- getOptimization() - Method in class SegmentWithMarkedPointProcess
-
The optimization-scheme that determines which configurations are accepted/rejected from one
iteration to the next.
- getOptional(String) - Method in interface NamedProvider
-
Retrieves the item if it exists, or returns
Optional.empty()
if it doesn't exist.
- getOptional(String) - Method in class NamedProviderBridge
-
- getOptional(String) - Method in class NamedProviderCombine
-
- getOptional(String) - Method in class NameValueMap
-
- getOptional(String) - Method in class EagerEvaluationStore
-
- getOptional(String) - Method in class LazyEvaluationStore
-
- getOptional(String) - Method in class SharedFeatures
-
- getOptional(String) - Method in class NamedStacks
-
- getOptional(String) - Method in class ExtractFrameStore
-
- getOptionList() - Method in class KernelProposer
-
- getOptions() - Method in class BioformatsReader
-
Options that influence how stack is read.
- getOptions() - Method in class ReadOptionsDelegate
-
- getOrCalculate(T) - Method in class ResolvedPart
-
Executes the operation and returns a result, either by doing the calculation, or retrieving a
cached-result from previously.
- getOrCalculate(T, U) - Method in class ResolvedPartMap
-
Executes the operation and returns a result, either by doing the calculation, or retrieving a
cached-result from a previous execution.
- getOrCalculate(T) - Method in class CalculationPart
-
Executes the operation and returns a result, either by doing the calculation, or retrieving a
cached-result from previously.
- getOrCalculate(T, U) - Method in class CalculationPartMap
-
Executes the operation and returns a result, either by doing the calculation, or retrieving a
cached-result from a previous execution.
- getOrCreate(Class<?>) - Method in class SharedObjects
-
Gets an existing store, or creates a new one
- getOrientation() - Method in class Ellipse
-
- getOrientation() - Method in class Ellipsoid
-
- getOrientationProposer() - Method in class OrientationAndRadiiProposer
-
- getOrientationXYProposer() - Method in class XYOrientationExtendToZ
-
- getOriginal() - Method in class OverlappingObject
-
Original unscaled element before any operations
- getOrLog(String, Logger) - Method in interface Findable
-
Gets an object or otherwise logs a message describing what went wrong.
- getOrLog(String, Logger) - Method in class Found
-
- getOrLog(String, Logger) - Method in class NotFound
-
- getOrNull(U) - Method in class CalculationPartMap
-
Gets an existing result for the current input from the cache.
- getOtherwise() - Method in class IfRelativeToDirectory
-
The namer to use if the relative-to-directory option is not selected.
- getOutlineColor() - Method in class SegmentInstanceWithModel
-
The color of the outline.
- getOutlinePixelsRetriever() - Method in class TraversePointsOnContour
-
- getOutlinePixelsRetrieverReverse() - Method in class TraversePointsOnContour
-
- getOutlineWidth() - Method in class Outline
-
The size of the outline, in terms of the number of voxels.
- getOutlineWidth() - Method in class CompareAnnotations
-
How many pixels should the outline be around objects.
- getOutlineWidth() - Method in class AtScale
-
- getOutlineWidth() - Method in class ColoredBase
-
The width of the outline (only relevant if outline==true
.
- getOutlineWidth() - Method in class OutlinePreserveRelativeSize
-
The width of the outline.
- getOutlineWidth() - Method in class SegmentInstanceWithModel
-
The width of the outline.
- getOutlineWidth() - Method in class VisualizeOnBackground
-
- getOutlineWidth() - Method in class ExportObjectsAsCroppedImages
-
- getOutPath() - Method in class InsertRegExGroups
-
Constructs a path as an output, replacing $1, $2 etc.
- getOutput() - Method in class OutputExperiment
-
The output-manager that specifies how/where/which elements occur duing outputting.
- getOutput() - Method in class ExperimentExecutor
-
- getOutput() - Method in class QuickMultiDatasetExperiment
-
- getOutputDirectory() - Method in class Outputter
-
- getOutputDirectory() - Method in class OutputterChecked
-
- getOutputDirectory() - Method in class OutputPrefixerSettings
-
A directory indicating where inputs can be located
- getOutputEnabledDelta() - Method in class OutputArguments
-
Additions/subtractions of outputs for the experiment supplied by the user.
- getOutputName() - Method in class ToTextFileBase
-
The name to use (without extension) for the text-file log
- getOutputName() - Method in class FeatureCSVMetadata
-
The output name for the features CSV.
- getOutputName() - Method in class OutputNameStyle
-
An identifier used in rules to determine if an output is enabled or not.
- getOutputName() - Method in class PeriodicSubdirectoryReporter
-
- getOutputName() - Method in class AggregateChannelTask
-
How to name the aggregated channel in the output.
- getOutputName() - Method in class MinimalExecutionTimeStatsReporter
-
- getOutputName() - Method in class VoxelizedMarksChangeReporter
-
- getOutputNameStyle() - Method in class OutputPattern
-
- getOutputNameStyle() - Method in class FromOutputName
-
- getOutputPattern() - Method in class BoundOutputter
-
- getOutputRGBOutline() - Method in class ExportObjectsAsCroppedImages
-
- getOutputRGBOutlineFlattened() - Method in class ExportObjectsAsCroppedImages
-
- getOutputsDisabled() - Method in class SpecificDisabled
-
The names of the outputs that are disbled.
- getOutputsEnabled() - Method in class SpecificEnabled
-
The names of the outputs that are enabled.
- getOutputsEnabled() - Method in class OutputManager
-
Which outputs are enabled or not enabled.
- getOutputsEnabled() - Method in class OutputterChecked
-
Which outputs are enabled or not enabled.
- getOutputsEnabled() - Method in class ElementOutputter
-
Which outputs are enabled or not enabled.
- getOutputStackProvider() - Method in class ImageAssignLabel
-
If it's set, a stack is generated that is outputted into subdirectory corresponding to the
groupIdentifier.
- getOutputter() - Method in class InitializationContext
-
An outputter that writes to the particular output-directory.
- getOutputter() - Method in class InputBound
-
The
Outputter
associated with this input, as it is being processed as a job.
- getOutputter() - Method in class InputOutputContextStateful
-
- getOutputter() - Method in class ParametersExperiment
-
An outputter that writes to the particular output-directory.
- getOutputter() - Method in class BoundOutputter
-
The outputter to be used for the sequence.
- getOutputter() - Method in interface InputOutputContext
-
An outputter that writes to the particular output-directory.
- getOutputter() - Method in class ElementOutputter
-
The outputter for writing the element.
- getOutputter() - Method in class OptimizationContext
-
- getOutputterFor(String) - Method in class SharedStateFilteredImageOutput
-
groupIdentifierFor should always called at least once before getOutputManagerFor
- getOutputWriteSettings() - Method in class OutputManager
-
General settings (default file extensions, colors etc.) for outtping files.
- getOutputWriteSettings() - Method in class QuickExperiment
-
- getOutside() - Method in class UnitsWithinRange
-
Returned as a constant if a value lies otside the range
- getOutsideKernelPolicy() - Method in class KernelApplicationParameters
-
How to handle voxels that appear in a neighborhood that lies outside the scene boundaries.
- getOverlapRatioThreshold() - Method in class KernelBirthAndKill
-
- getOverlay(int) - Method in class ColoredOverlayCollection
-
Access a particular
Overlay
in the collection by index.
- getOverlays() - Method in class ColoredOverlayCollection
-
The collection of overlays, each element corresponding to colors
.
- getPadding() - Method in class ExportObjectsBase
-
Padding placed on each side of the outputted image (if it's within the image)
- getPaddingXY() - Method in class Padding
-
Padding placed on each side of the outputted image (if it's within the image) in XY
directions
- getPaddingZ() - Method in class Padding
-
Padding placed on each side of the outputted image (if it's within the image) in Z direction
- getPair() - Method in class MergedPairsFeatures
-
- getPair() - Method in class EnergyPair
-
- getPair() - Method in class MarksWithEnergyBreakdown
-
Every combination of interactions between marks and the associated energy
- getPairAddCriteria() - Method in class EnergySchemeCreatorByElement
-
- getPairAddCriteria() - Method in class EnergyScheme
-
- getPairCollection() - Method in class KernelMerge
-
- getPairsFor(Mark) - Method in class RandomCollectionWithAddCriteria
-
- getPairTypeClass() - Method in class RandomCollectionWithAddCriteria
-
- getParameters() - Method in class EnergyStack
-
The associated parameters.
- getParameters() - Method in class HOGDescriptor
-
Parameters used for calculating HOG
- getParameters() - Method in class HOGFeature
-
Parameters used for calculating HOG.
- getParametersExperiment() - Method in class ParametersUnbound
-
- getParamPrefix() - Method in class PermuteFeatureSequenceInteger
-
- getParent() - Method in class ErrorNodeImpl
-
- getParentDirectoryCreator() - Method in class OutputterTarget
-
- getParentOutputter() - Method in class PeriodicSubdirectoryReporter
-
- getPartition() - Method in class MarksFromPartition
-
- getPath() - Method in class AnnotationWithStrategy
-
Path to annotation.
- getPath() - Method in class NotFound
-
The path an object was not found at.
- getPath() - Method in class RootPath
-
A path on a file-system to the directory, that defines the root.
- getPath() - Method in class SingleFile
-
The path of the single-file.
- getPath() - Method in class NamedFile
-
- getPath() - Method in class NamedPath
-
The path
- getPath() - Method in class SizeMapping
-
The path.
- getPath() - Method in class RootedFilePath
-
- getPath() - Method in class StaticFilePath
-
- getPath() - Method in class FileDetails
-
- getPathAnnotation() - Method in class SinglePathStrategy
-
Derives the path to the corresponding annotation files, given a path to the image to be
annotated.
- getPathDefaultMarks() - Method in class MarkProposerStrategy
-
- getPathDictionary() - Method in class MarkProposerStrategy
-
- getPathLabel() - Method in class ImageCSVLabeller
-
Path to a CSV label file (comma-separated, with header, no quotes)
- getPathParser() - Method in class GroupFiles
-
- getPaths() - Method in class FileSetFromStringSet
-
- getPaths() - Method in class FilterForExistingFiles
-
All files need to be present
- getPayload() - Method in class TypedEdge
-
The edge.
- getPayload() - Method in class ObjectVertex
-
- getPenaltyValue() - Method in class MaxOverlapRatio
-
- getPeriodTriggerBank() - Method in class FeedbackBeginParameters
-
- getPermutation() - Method in class PermuteFeature
-
A permutation to apply.
- getPermutations() - Method in class PermuteFeature
-
A list of permutations to apply.
- getPermuteProperty() - Method in class Permute
-
- getPermuteProperty() - Method in class PermuteFeatureSequenceInteger
-
- getPixelsForPlane(int) - Method in class EncodedVoxels
-
- getPlusOne() - Method in class SlidingBuffer
-
The voxel-buffer for the slice with the currently selected slice's index +1
or null
if it's the final slice.
- getPoint() - Method in class KernelPointCursor
-
The point around which the cursor may iterate.
- getPointFitters() - Method in class PointsInitialization
-
- getPoints() - Method in class PointListBase
-
- getPoints() - Method in class Contour
-
An ordered list of points in the contour.
- getPointsFitter() - Method in class CreateMarkFromPoints
-
- getPointsFitter() - Method in class MarkProposerStrategy
-
- getPointsFitter() - Method in class FitPoints
-
- getPointsFitter() - Method in class FitPointsFromObjects
-
- getPointsFitter() - Method in class PointsFitterToMark
-
- getPointsFitter() - Method in class ReflectInAxesWithinDistance
-
- getPointsFromOrientationProposer() - Method in class MergeLists
-
- getPointsFromOrientationXYProposer() - Method in class XYOrientationExtendToZ
-
- getPointsProposer() - Method in class FitPoints
-
- getPosition() - Method in class MarkWithPosition
-
- getPositionProposer() - Method in class Position
-
- getPositionProposer() - Method in class Repeat
-
- getPostcondition() - Method in class DilationContext
-
If defined, a condition which must be satisfied after an iteration occurs, otherwise
no more iterations occur.
- getPower() - Method in class MeanRaisedToPower
-
- getPrefix() - Method in class DefineAdderWithPrefixBean
-
A prefix that is placed before the name of every bean created.
- getPrefix() - Method in class PrependName
-
The string to prepend to the custom-name of each feature.
- getPrefix() - Method in class PathPrefixerAvoidResolve
-
A string prefixed to each output-path.
- getPrefix() - Method in class OutputterTarget
-
- getPrefix() - Method in class Outputter
-
- getPrefix() - Method in class OutputterChecked
-
- getPrefix() - Method in class DeriveFromPair
-
- getPrefix() - Method in class FeatureListProviderAggregatePair
-
The string to prepend.
- getPrefix() - Method in class ExperimentStructure
-
- getPrefixer() - Method in class OutputArguments
-
Where outputs are written, and how identifiers are styled.
- getPrefixer() - Method in class ParametersExperiment
-
Determines prefixes used in the paths for outputted files.
- getPrefixer() - Method in class OutputManager
-
Determines a prefix to use when outputting a file based upon an input-path.
- getPrefixer() - Method in class PathPrefixerContext
-
Settings for where and how outputs should be prefixed.
- getPrefixer() - Method in class LastDirectoryAsPrefix
-
- getPrefixer() - Method in class Rooted
-
- getPrefixerElse() - Method in class IfIncrementingNumberRequested
-
Called if the requested condition is not true.
- getPrefixerIf() - Method in class IfIncrementingNumberRequested
-
Called if the requested condition is true.
- getPrefixToRemove() - Method in class DirectoryStructure
-
- getPrependColor() - Method in class Prepend
-
The color to prepend.
- getPriority() - Method in class PrioritisedVertex
-
- getProbNeg() - Method in class KernelPosNeg
-
- getProbPos() - Method in class KernelPosNeg
-
- getProperties() - Method in class ObjectWithProperties
-
A mapping between keys and corresponding values.
- getProperty(String) - Method in class ObjectWithProperties
-
Retrieves the value of a property corresponding to a particular name.
- getPropertyInitializer() - Method in class InitializableBean
-
Assigns a parameter, if possible, to a bean - as used by bean initializer
.
- getPropertyPath() - Method in class PermuteProperty
-
Either a direct property of a bean or a nested-property with the children separated by
full-stops.
- getProposal() - Method in class OptimizationStep
-
- getProposal() - Method in class Reporting
-
- getProposalSecondary() - Method in class Reporting
-
An optional additional marks-Energy that provides an additional explanation of proposed
- getProposer() - Method in class MarkFromCollectionProposerUnary
-
- getProposer() - Method in class MarkProposerUnary
-
- getProvider() - Method in class FromProvider
-
- getPxlPartMemo() - Method in class FeatureInputAllMemo
-
- getPxlPartMemo() - Method in class FeatureInputSingleMemo
-
- getPyramid() - Method in class ImageMetadata
-
Metadata to describe an image pyramid, if it exists.
- getQuantile() - Method in class Quantile
-
The quantile.
- getQuantile() - Method in class QuantileStretch
-
- getQuantile() - Method in class Quantile
-
- getQuantile() - Method in class DiscardOutliers
-
- getQuantile() - Method in class Quantile
-
- getQuantile() - Method in class QuantileAcrossObjects
-
- getQuantile() - Method in class QuantileAcrossConnectedComponents
-
- getQuantileHigh() - Method in class Range
-
- getQuantileLow() - Method in class Range
-
- getQuantileLower() - Method in class IntensityQuantiles
-
The lower quantile to use as the lower-limit for the intensity range to display.
- getQuantileLower() - Method in class ToByteUpperLowerQuantileIntensity
-
- getQuantileUpper() - Method in class IntensityQuantiles
-
The lower quantile to use as the upper-limit for the intensity range to display.
- getQuantileUpper() - Method in class ToByteUpperLowerQuantileIntensity
-
- getRadii() - Method in class Ellipse
-
- getRadii() - Method in class Ellipsoid
-
- getRadiiProposer() - Method in class OrientationAndRadiiProposer
-
- getRadiiProposer() - Method in class RadiiProposerRepeat
-
- getRadius() - Method in class MarkWithPositionAndSingleRadius
-
- getRadius() - Method in class AutoLocalThreshold
-
- getRadius() - Method in class WithRadiusBase
-
- getRadiusBound() - Method in class UniformRandomRadiiProposer
-
- getRadiusX() - Method in class FitResult
-
- getRadiusY() - Method in class FitResult
-
- getRadiusZ() - Method in class FitResult
-
- getRandomNumberGenerator() - Method in class ProposerContext
-
- getRangeC() - Method in class SizeExtents
-
- getRangeT() - Method in class SizeExtents
-
- getRangeZ() - Method in class SizeExtents
-
- getRate() - Method in class Geometry
-
- getRatioHeightForLabel() - Method in class Montage
-
When label==true
, this determines the height of the label.
- getRatioRowsToColumns() - Method in class Montage
-
An ideal approximate ratio of the number of rows to the number of columns.
- getRaw() - Method in class UnsignedByteBuffer
-
Gets an unsigned-byte (represented as a byte) at the current buffer position.
- getRaw(int) - Method in class UnsignedByteBuffer
-
Gets an unsigned-byte (represented as a byte) at a particular buffer position.
- getRaw() - Method in class UnsignedIntBuffer
-
Gets an unsigned-int (represented as an int) at the current buffer position.
- getRaw(int) - Method in class UnsignedIntBuffer
-
Gets an unsigned-int (represented as a int) at a particular buffer position.
- getRaw() - Method in class UnsignedShortBuffer
-
Gets an unsigned-short (represented as a short) at the current buffer position.
- getRaw(int) - Method in class UnsignedShortBuffer
-
Gets an unsigned-short (represented as a short) at a particular buffer position.
- getReader() - Method in class RotateImageToMatchEXIFOrientation
-
Reads the image that is subsequently flattened.
- getReaderMatching() - Method in class BranchExtension
-
The reader to use if the extension matches.
- getReaderNotMatching() - Method in class BranchExtension
-
The reader to use if the extension does not match.
- getReason() - Method in class NotFound
-
The reason an object could not be found.
- getReceive() - Method in class CombineBase
-
- getRecordedOutputs() - Method in class RecordedOutputsWithRules
-
If defined, records output-names that are written / not-written during the experiment.
- getRed() - Method in class RGBColorBean
-
The red component value of the RGB color.
- getRed() - Method in class RGBColor
-
The red component value of the RGB color.
- getRed() - Method in class ThreeChannels
-
- getReduce() - Method in class SuppressNonMaximum
-
The algorithm for reducing the number of object-masks.
- getReduce() - Method in class FeatureListProviderAggregatePair
-
Method for reducing all pairs into a single value e.g.
- getReferencePoissonIntensity() - Method in class MarkWithIdentifierFactory
-
- getReferences() - Method in class ReferencingFeatureListProvider
-
The names of other feature-lists, whose features may be referenced by this feature.
- getReferencesFeatureListCreator() - Method in class PermuteFeature
-
Makes sure a particular feature list creator is evaluated
- getReferencesList() - Method in class FeatureProviderReference
-
The name of the list in which the feature referenced by id
resides.
- getRegex() - Method in class RegularExpressionBase
-
- getRegEx() - Method in class RegExMatcher
-
- getRegEx() - Method in class PathRegEx
-
Regular expression to use to match path with at least one group in it.
- getRegEx() - Method in class RemoveMatching
-
If a path matches a regular expression it is removed.
- getRegEx() - Method in class Exclude
-
A regular-expression to be matched against the identifiers of inputs.
- getRegEx() - Method in class InsertRegExGroups
-
The regular-expression to use for matching groups.
- getRegEx() - Method in class JoinRegExGroups
-
- getRegex() - Method in class Replace
-
Regular expression to match against string
- getRegex() - Method in class QuickBase
-
A regular-expression applied to the image file-path that matches three groups.
- getRegEx() - Method in class ExperimentStructure
-
- getRegexAdjacent() - Method in class NamedChannelsQuick
-
This needs to be set if there is at least one adjacentChannel.
- getRegExDirectory() - Method in class MultiFileReader
-
If non-empty a regular-expression is applied to directories.
- getRegExFile() - Method in class MultiFileReader
-
If non-empty a regular-expression is applied to files.
- getRegion() - Method in class Thresholded
-
- getRegion() - Method in class Intensity
-
- getRegionID() - Method in class RegionMembershipWithFlags
-
- getRegionID() - Method in class VolumeMin
-
- getRegionID() - Method in class FromMarks
-
- getRegionID() - Method in class IndexedRegionBase
-
- getRegionID() - Method in class ColoredMarks
-
- getRegionID() - Method in class FeatureMarkRegion
-
- getRegionID() - Method in class FeatureSingleMemoRegion
-
- getRegionID() - Method in class FeaturePairMemoSingleRegion
-
- getRegionID() - Method in class KernelBirthAndKill
-
- getRegionMap() - Method in class EnergySchemeCreatorByElement
-
- getRegionMap() - Method in class EnergyScheme
-
- getRegionMap() - Method in class EnergySchemeWithSharedFeatures
-
- getRegionMap() - Method in class EnergyMemoList
-
- getRegionMap() - Method in class VoxelizedMarkMemo
-
- getRegionMap() - Method in class ProposerContext
-
- getRegionMap() - Method in class FromMarks
-
- getRegionMap() - Method in class AsObject
-
- getRegionMap() - Method in class SurfaceSizeMaskNonZero
-
- getRegionMembership() - Method in class RegionMembershipWithFlags
-
- getRegularExpression() - Method in class TimestampPattern
-
The regular-expression that checks a match and specifies groups for the encoded date-time.
- getRejectionReason() - Method in class DualMarksAnnotation
-
A reason for rejection, if the annotation was rejected by the annotator.
- getRelation() - Method in class RelationToConstant
-
The relation to the threshold, where the threshold forms the second operand.
- getRelation() - Method in class ObjectFilterRelation
-
- getRelation() - Method in class MergePairs
-
Relation to threshold
- getRelation() - Method in class IdentityImposeValueRelationToHistogram
-
- getRelation() - Method in class RejectIfConditionXYResolution
-
A predicate defined by the relationship of the XY-resolution to a constant threshold.
- getRelation() - Method in class AddCriteriaFeatureRelationThreshold
-
- getRelation() - Method in class RequireFeatureRelationThreshold
-
- getRemainder() - Method in class SplitPath
-
The second component, what remains in the path.
- getRepeats() - Method in class KernelBirth
-
Total number of births
- getRepeatZProvider() - Method in class WriteText
-
Repeats the generated (2D) string in z, so it's the same z-size as intensityProvider
- getReplacement() - Method in class SubstituteRegularExpression
-
- getReplacement() - Method in class Replace
-
What to replace in the path
- getReplacement() - Method in class AdjacentFile
-
The replacement string used to determine the file
- getRequireArguments() - Method in class OnlyIf
-
The conditions that must be fulfilled
- getRequireArguments() - Method in class FeedbackReceiverRequireArguments
-
- getResizer() - Method in class ImageInferenceContext
-
How to resize images or voxel-buffers.
- getResizeTo() - Method in class GroupedStackBase
-
If set, each channel is scaled to a specific size before aggregation (useful for combining
different sized images).
- getResizeTo() - Method in class HOGDescriptor
-
The input-image is rescaled to this width/height before calculating HOG descriptors
- getResizeTo() - Method in class HOGFeature
-
The input is rescaled to this width/height before calculating HOG descriptors.
- getResolution() - Method in class BinarySegmentationParameters
-
A
Resolution
associated with the image being segmented.
- getResolutionCount() - Method in class ImagePyramidMetadata
-
The number of distinct resolution-levels that exist in the pyramid.
- getResolutionOptional() - Method in class FeatureInputDimensions
-
- getResolutionOptional() - Method in class FeatureInputEnergy
-
- getResolutionOptional() - Method in interface FeatureInputWithResolution
-
The resolution of the associated image, if it is available.
- getResolutionOptional() - Method in class FeatureInputHistogram
-
- getResolutionOptional() - Method in class FeatureInputMarkCollection
-
- getResolutionOptional() - Method in class FeatureInputMark
-
- getResolutionRequired() - Method in interface FeatureInputWithResolution
-
The resolution of the associated image, or an exception if it is not available.
- getRestrictTo() - Method in class Invert
-
If set, the inversion only occurs on a particular region of the mask, as determined by this
mask
- getResult(int) - Method in class ResultsVector
-
Gets a result value at a particular position.
- getResults() - Method in class FeatureInputResults
-
The results of a prior feature-calculation, corresponding to a list of features.
- getResults() - Method in class LabelledResultsVector
-
The results.
- getResults() - Method in class FeatureCalculationContext
-
The stored results and thumbnail writer.
- getResults() - Method in class FeatureExporter
-
Saved store feature calculation results, and writes associated thumbnails.
- getResults() - Method in class LabelledResultsVectorWithThumbnail
-
The results.
- getResultsVector() - Method in class ResultsVectorWithThumbnail
-
- getRGB() - Method in class RGBColorBean
-
- getRGB() - Method in class RGBColor
-
- getRgb() - Method in class StackWriteAttributes
-
Whether it's an RGB or RGBA image when it has three/four channels respectively.
- getRight() - Method in class ObjectsToCompare
-
Objects on right-side of the comparison
- getRightUnassigned() - Method in class OverlappingObjects
-
The unassigned objects in the right set.
- getRoot() - Method in class SplitPath
-
The first component, the root of the path.
- getRoot() - Method in class ProposerFailureDescription
-
- getRoot() - Method in class TestLoader
-
Path to where the test-data is stored.
- getRoot1() - Method in class QuadraticEquationSolver.QuadraticRoots
-
The first root.
- getRoot2() - Method in class QuadraticEquationSolver.QuadraticRoots
-
The second root.
- getRootName() - Method in class Rooted
-
The name of the root-path to associate with this fileset.
- getRootName() - Method in class RootedFilePath
-
- getRootName() - Method in class Rooted
-
- getRootName() - Method in class Rooted
-
- getRootName() - Method in class QuickBase
-
If non-empty then a rooted filesystem is used with this root
- getRootName() - Method in class RootedExperiment
-
Root-name assuming multi-rooted structure.
- getRootNameForStructure() - Method in class ExperimentResultsExperimentStructure
-
If rootInStructure==true, the rootName is placed in the folder structure.
- getRotationAngle() - Method in class BoundRotation2D
-
- getRotationMatrix() - Method in class Orientation
-
Derives a
RotationMatrix
that can be applied to rotate an entity
anti-clockwise to the current orientation.
- getRotationMatrix() - Method in class OrientationRotationMatrix
-
The rotation-matrix.
- getRotationX() - Method in class BoundRotation3D
-
- getRotationY() - Method in class BoundRotation3D
-
- getRotationZ() - Method in class BoundRotation3D
-
- getRotMatrix() - Method in class FitResult
-
The rotation matrix, which must be considered immutable to be used here.
- getRow() - Method in class Cell
-
The row in the table that the cell refers to (zero-indexed).
- getRunningSum() - Method in class RunningSumParented
-
- getSampleEvery() - Method in class SampleWithDirectory
-
- getScalarProposer() - Method in class MaxWithConstant
-
- getScalarProposer() - Method in class Scale
-
- getScale() - Method in class MeanScale
-
The scale, typically the standard-deviation.
- getScale() - Method in class MontageSlices
-
Whether to increase or reduce the size of the images
- getScaleCalculator() - Method in class ScaleXY
-
- getScaleCalculator() - Method in class ScaleXY
-
Determines how much to scale by.
- getScaleCalculator() - Method in class Scale
-
- getScaleCalculator() - Method in class AtScale
-
- getScaleCalculator() - Method in class Invert
-
- getScaleCalculator() - Method in class ScaleImage
-
Calculates what scale-factor to apply on the image.
- getScaleCalculator() - Method in class ScaleXY
-
- getScaleFactor() - Method in class ImageInferenceContext
-
The inverse of the scaling-factor applied to reduce unscaledDimensions
to the
input-matrix used for inference.
- getScaleFactor() - Method in class GradientBase
-
- getScaleInput() - Method in class SegmentStackIntoObjectsScaleDecode
-
Any scaling to be applied to the input-image before being input to the model for inference.
- getScaleLower() - Method in class ScaleByDictionary
-
- getScaleLower() - Method in class ToByteUpperLowerQuantileIntensity
-
Sets the min by multiplying the quantileLower by this constant.
- getScaleRadii() - Method in class ConicFitterBase
-
- getScaleRoundingError() - Method in class ExtentToArrange
-
Stores the difference that occurs between a discretized scaled width and what it should
ideally be.
- getScaleUpper() - Method in class ScaleByDictionary
-
- getScaleUpper() - Method in class ToByteUpperLowerQuantileIntensity
-
Sets the max by multiplying the quantileUpper by this constant.
- getScore() - Method in class ScoreVoxels
-
- getScoreExtracter() - Method in class AcceptanceProbabilityCalculator
-
- getScoreProvider() - Method in class ExtractSlice
-
- getScoreThreshold() - Method in class RemoveOverlappingObjects
-
Bounding boxes with scores above this threshold are removed.
- getSearchObjects() - Method in class FeatureIntersectingObjects
-
- getSecond() - Method in class CostMatrix
-
The second set of elements.
- getSecond() - Method in class FeatureInputPairObjects
-
- getSecond() - Method in class OutputEnableRulesSpecify
-
Output-names in the second-level (for all first level output-names).
- getSecond() - Method in class Compose
-
Second transformation from U
to T
- getSecondary() - Method in class StateReporterToPixelized
-
- getSegment() - Method in class BinarySegmentationUnary
-
- getSegment() - Method in class SegmentChannelIntoObjectsUnary
-
- getSegment() - Method in class SuppressNonMaximum
-
The segmentation algorithm that is applied as an input to non-maximum suppression.
- getSegment() - Method in class SegmentChannel
-
Segmentation algorithm
- getSegment() - Method in class SegmentChannel
-
- getSegment() - Method in class SegmentChannelByObject
-
- getSegment() - Method in class SegmentStack
-
The segmentation procedure.
- getSegment() - Method in class SegmentWithSeeds
-
- getSegment() - Method in class ConnectedComponentsFromBinarySegmentation
-
- getSegment() - Method in class SegmentInstanceWithModel
-
The segmentation algorithm.
- getSegment() - Method in class SegmentMarksFromImage
-
How to perform the segmentation.
- getSegmentStack() - Method in class SegmentOnMaximumIntensityAndExpandInZ
-
- getSelect() - Method in class DeriveFromPair
-
Either "merged" or "first" or "second" indicating which feature to delegate from
- getSelectChannels() - Method in class GroupedStackBase
-
Selects which channels are included, optionally renaming.
- getSemiMajorAxis() - Method in class EllipseStandardFormConverter
-
- getSemiMinorAxis() - Method in class EllipseStandardFormConverter
-
- getSeperator() - Method in class CombineCSV
-
- getSequence() - Method in class PermutePropertySequence
-
A sequence of integers, with each element assigned assigned directly during the permutation,
or after further manipulation.
- getSequence() - Method in class ChangeableOutputSequence
-
- getSeriesIndex() - Method in class FromStackReader
-
The series to open to the read the metadata (zero-indexed).
- getSettings() - Method in class Outputter
-
- getSettings() - Method in class OutputterChecked
-
General settings for outputting.
- getSettings() - Method in class OutputWriteContext
-
User-define settings for outputting in output-manager.
- getSettings() - Method in class ElementOutputter
-
General settings for outputting.
- getSharedFeatures() - Method in class FeatureRelatedInitialization
-
Shared features available for reference during calculation.
- getSharedFeatures() - Method in class EnergySchemeSet
-
- getSharedFeatures() - Method in class EnergySchemeWithSharedFeatures
-
- getSharedObjects() - Method in class FeatureInitialization
-
Shared-objects, which can be referenced by the feature to influence calculation.
- getSharedState() - Method in class InputBound
-
The state shared between inputs.
- getSharedState() - Method in class ParametersUnbound
-
- getSharedState() - Method in class CopyContext
-
State shared across all inputs when copying.
- getSharedState() - Method in class SharedStateRememberConverted
-
The shared state.
- getShell() - Method in class MarkEllipseFactory
-
- getShell() - Method in class MarkEllipsoidFactory
-
- getShell() - Method in class Ellipse
-
The size of the shell, expressed as a ratio of the radius.
- getShell() - Method in class Ellipsoid
-
- getShell() - Method in class FromObjects
-
- getShell() - Method in class CreateEllipse
-
- getShell() - Method in class ConicFitterBase
-
- getShortName() - Method in class JobDescription
-
- getShowOngoingJobsLessThan() - Method in class ParallelProcessor
-
When the number of ongoing jobs is less than this threshold, they are shown in event logs.
- getSigma() - Method in class BlurStrategy
-
- getSigma() - Method in class GaussianBlur2D
-
- getSimplePairCollectionID() - Method in class KernelMerge
-
- getSingle() - Method in class MergedPairsFeatures
-
- getSize() - Method in class TaskArguments
-
Suggests dimensions or a scaling-factor to resize an image to.
- getSize() - Method in class WriteText
-
Explicit size of the image the string is draw on.
- getSize() - Method in class Kernel
-
The size of the kernel-matrix in one dimension, either X or Y.
- getSize() - Method in class Aggregator
-
- getSize() - Method in class OutlinePreserveRelativeSize
-
Size of all created thumbnails
- getSize() - Method in class ScaleToSize
-
- getSize() - Method in class IntegerRange
-
- getSizeXY() - Method in class SpecifyDimensions
-
Length of X and Y dimensions.
- getSizeZ() - Method in class SpecifyDimensions
-
Length of Z dimension.
- getSkipFirstTrim() - Method in class RemoveTrailingDirectory
-
- getSkipFirstTrim() - Method in class FilePathAppendBase
-
- getSkipNumberSubdirectories() - Method in class LastDirectories
-
Initially skip this number of directories before including them in the description.
- getSlice(int) - Method in interface VoxelPartition
-
- getSlice(int) - Method in class VoxelPartitionHistogram
-
- getSlice() - Method in class RepeatSlice
-
- getSliceFirst() - Method in class MontageSlices
-
First slice.
- getSliceID() - Method in class SelectSlicesBase
-
Index of slice to use, or -1 to use all slices
- getSliceIndex() - Method in class RepeatSlice
-
Which slice to use from mask
- getSliceIndex() - Method in class FileDetails
-
- getSliceLast() - Method in class MontageSlices
-
Last slice.
- getSmoothingFactor() - Method in class SplitContourAtSaddlePoints
-
- getSource() - Method in class StringMapItem
-
The origin of the mapping.
- getSource() - Method in class MatchedObject
-
The source object (which is matched against others)
- getSource() - Method in class MarkPair
-
- getSource() - Method in class PairVoxelizedMarkMemo
-
- getSource() - Method in class ExportFeatures
-
Source of feature-values to be exported.
- getSource() - Method in class DualVoxelizedMarks
-
- getSource() - Method in class ToVoxelized
-
- getSourceDirectory() - Method in class CopyContext
-
Source directory of copying.
- getSources() - Method in class MultipleComparer
-
The other entities to compare with the annotation.
- getSplitIdentifierRegex() - Method in class CompareAnnotations
-
If non-empty, the string (a regular-expression) is used to split the file's identifier into
groups.
- getSplitProposer() - Method in class KernelSplit
-
- getSquareSize() - Method in class SplitIntoSquares
-
- getStack() - Method in class StackProviderUnary
-
The delegate Provider<Stack>
that is called.
- getStack() - Method in class DisplayStack
-
The underlying stack that will be displayed, possibly after conversion.
- getStack() - Method in class StackProviderWithLabel
-
Provides the stack.
- getStack() - Method in class ColoredMarksWithDisplayStack
-
- getStack() - Method in class MarksWithDisplayStack
-
- getStack() - Method in class FromStack
-
Provides a stack.
- getStack() - Method in class SegmentStack
-
The stack to segment
- getStack() - Method in class MontageSharedState
-
The stack into which individual images are written.
- getStack() - Method in class ExportObjectsFromCSV
-
The stack that is the background for our objects
- getStackEnergy() - Method in class FeatureEvaluator
-
Optionally specifies an energy-stack to be associated with every calculation input.
- getStackEnergy() - Method in class FromImage
-
Optionally defines a energy-stack for feature calculation (if not set, the energy-stack is
considered to be the input stacks).
- getStackEnergy() - Method in class BinaryClassifierImageLabeller
-
- getStackEnergy() - Method in class ExtractSlice
-
- getStackEnergy() - Method in class DefineOutputterWithEnergy
-
- getStackID() - Method in class IfStackExists
-
- getStackName() - Method in class One
-
If defined, processing only occurs the stack with this specific name and index.
- getStackNameDefault() - Method in class AnnotationBackground
-
The name of the default stack from backgroundStackMap
to display as background when
annotating.
- getStackProviderID() - Method in class FromStack
-
Specifies the ID of an existing stack.
- getStackProviderID() - Method in class FromStackChannel
-
- getStackReader() - Method in class AnnotatorStrategy
-
How to read raster
Stack
s from the file-system.
- getStackReader() - Method in class FromStackReader
-
- getStackReader() - Method in class InputManagerWithStackReader
-
How to read an image from the file-system.
- getStackReader() - Method in class MaskAsObject
-
How to read the
Mask
from the file-system.
- getStackReader() - Method in class AnnotationComparisonInput
-
- getStackReader() - Method in class Montage
-
Fallback for imageMetadataReader
to read image files without a directy metadata
reader.
- getStackReader() - Method in class ScaleImageCommonSize
-
Fallback for imageMetadataReader
to read image files without a direct metadata
reader.
- getStackReader() - Method in class FlattenAsChannel
-
Reads the image that is subsequently flattened.
- getStackReader() - Method in class ImposeResolution
-
Reads an image before a resolution is imposed.
- getStackReader() - Method in class MultiFileReader
-
- getStackReader() - Method in class ReadVoxelExtentXml
-
Reads an image before a resolution is imposed.
- getStackReader() - Method in class RejectIfConditionXYResolution
-
Reads an image before a resolution is imposed.
- getStackReaderAdjacent() - Method in class NamedChannelsQuick
-
The raster-reader to use for opening any adjacent-channels
- getStackReaderAppend() - Method in class QuickBase
-
The raster-reader for reading any appended files
- getStackStore() - Method in class ChannelSource
-
- getStart() - Method in class SequenceInteger
-
The index to begin iteration from.
- getStartIndex() - Method in class IndexRangeNegative
-
The index if the first element to use in the subsetting range, zero-indexed.
- getStartingIntensity() - Method in class FloodFillEachIntensityLevel
-
The first intensity-value to consider as a valid object (e.g.
- getStartPoint() - Method in class LineSegment
-
- getState() - Method in class FeedbackEndParameters
-
- getStateReporter() - Method in class TransformationAssignMode
-
- getStrategy() - Method in class AnnotationWithStrategy
-
The strategy on how annotation occurs.
- getStrategy() - Method in class BoundReplaceStrategy
-
The strategy that has been bound (if it exists).
- getStrategy() - Method in class Blur
-
- getStyle() - Method in class WriteText
-
- getStyle() - Method in class ExportFeatures
-
Visual style for how feature export occurs.
- getStyle() - Method in class SegmentInstanceWithModel
-
Visual style for how feature export occurs.
- getSubdirectory() - Method in class AppendDictionary
-
- getSubdirectory() - Method in class ExperimentResultsExperimentStructure
-
If non-empty than an additional subdirectory is appended as a suffix
${DATASET_NAME}_${DATASET_SUFFIX}/${SUBDIRECTORY}/
- getSubdirectoryName() - Method in class OutputPattern
-
The name of a subdirectory in the current context to write to, or if empty, files are written
into the current directory context.
- getSubtractConstant() - Method in class IntensityGradientBase
-
- getSubtractMean() - Method in class SegmentStackIntoObjectsScaleDecode
-
A constant intensity for each respective channel to be subtracted before performing
inference.
- getSubtractRadii() - Method in class ConicFitterBase
-
- getSuggestedFormatToWrite() - Method in class StackWriteOptions
-
A suggestion on what file-format to write.
- getSuggestedFormatToWrite() - Method in class OutputWriteContext
-
A suggestion on what file-format to write.
- getSuggestedFormatToWrite() - Method in class ElementOutputter
-
- getSuggestedImageOutputFormat() - Method in class OutputPrefixerSettings
-
A file format suggested for writing images to the file system.
- getSuggestedSize() - Method in class InitializationContext
-
A suggested input on how to resize an image, if one is provided.
- getSum() - Method in class RunningSum
-
The running sum.
- getSummarizer() - Method in class SummarizerInputFromManager
-
- getSummarizer() - Method in class SummarizeBase
-
- getSummarizerElse() - Method in class SummarizerSplitMoreThan
-
Used for summary if count(elements) <= countThreshold
- getSummarizerGreaterThan() - Method in class SummarizerSplitMoreThan
-
Used for summary if count(elements) > countThreshold
- getTarget() - Method in class StringMapItem
-
The destination of the mapping.
- getTargetClass() - Method in class ExtractDerivedParameter
-
The class of the target type T
.
- getTargetSize() - Method in class FitTo
-
The target size.
- getTask() - Method in class JobProcessor
-
The task to be applied to inputs.
- getTask() - Method in class ExperimentExecutor
-
- getTask() - Method in class ConvertNamedChannels
-
The underlying task that will be called, perhaps with a different input-type.
- getTask() - Method in class QuickExperiment
-
- getTask() - Method in class QuickMultiDatasetExperiment
-
- getTask() - Method in class QuickMultiDatasetStructuredExperiment
-
- getTaskArguments() - Method in class InputBound
-
The arguments for the task that is being processed.
- getTaskName() - Method in class TaskArguments
-
A name to describe the ongoing task.
- getTaskProcessor() - Method in class InputOutputExperiment
-
What task is associated with the experiment, and how it is processed.
- getTemperature() - Method in class Aggregator
-
- getTemperature() - Method in class Reporting
-
- getTemplateMark() - Method in class MarkWithIdentifierFactory
-
- getTemporary() - Method in class EncodedVoxels
-
- getTermination() - Method in class SimulatedAnnealing
-
- getText() - Method in class WriteText
-
Text to draw on an image.
- getThreshold() - Method in class RelationToConstant
-
The constant threshold.
- getThreshold() - Method in class CutBelowThreshold
-
- getThreshold() - Method in class CalculateLevelRelativeToThreshold
-
- getThreshold() - Method in class IntensityGreaterEqualThan
-
- getThreshold() - Method in class ThresholdedFeature
-
- getThreshold() - Method in class ThresholdedVolume
-
- getThreshold() - Method in class Count
-
- getThreshold() - Method in class RatioThreshold
-
- getThreshold() - Method in class FeatureIntersectingObjectsThreshold
-
Only considers values greater or equal to the threshold
- getThreshold() - Method in class AddCriteriaFeatureRelationThreshold
-
- getThreshold() - Method in class RequireFeatureRelationThreshold
-
- getThreshold() - Method in class GreatestAreaSlice
-
- getThreshold() - Method in class Thresholded
-
- getThreshold() - Method in class IfCondition
-
- getThresholder() - Method in class BinarySegmentationThreshold
-
Performs the global thresholding.
- getThresholder() - Method in class Threshold
-
The thresholder that will convert a channel into a binary-channel
- getThresholdHours() - Method in class ClusterByTimestamp
-
Files whose creation-time differs <=
this parameter are joined into the same cluster.
- getThresholdNumberObjectsGlobal() - Method in class ThresholdConfidence
-
When the number of objects is greater or equal than this, they are reduced globally, without
separation.
- getThumbnail() - Method in class CombineObjectsForFeatures
-
Generates a thumbnail representation of one or more combined objects, as form a single input.
- getThumbnail() - Method in class FromImage
-
Method to generate a thumbnail for images.
- getThumbnail() - Method in class ResultsVectorWithThumbnail
-
- getThumbnailBatch() - Method in class ListWithThumbnails
-
- getTimeAnnotationLastUpdated() - Method in class DualMarksAnnotation
-
Number of seconds since the UNIX epoch
- getTimeIndex() - Method in class ConvertNamedChannelsToStack
-
- getTimeIndex() - Method in class FileDetails
-
- getTimeIndexGroupID() - Method in class RegularExpression
-
- getTimes() - Method in class Repeat
-
How many times to duplicate the list.
- getTimestampPatterns() - Method in class ClusterByTimestamp
-
The patterns which can be used to extract a date-time from a filename.
- getTimeZoneOffset() - Method in class ClusterByTimestamp
-
If >= 0
, sets a specific time-offset in hours.
- getTitle() - Method in class ReportFeatureEvaluator
-
- getTo() - Method in class TypedEdge
-
The vertex the edge joins to.
- getTolerance() - Method in class UnchangedScore
-
An exponent of 10 which determines a tolerance, less than which a score will be deemed
unchanged compared to another.
- getTotal() - Method in class EnergyTotal
-
- getTotalCount() - Method in class Histogram
-
The total count across values in the histogram.
- getTotalNumberJobs() - Method in class ConcurrentJobMonitor
-
The total number of submitted jobs to be executed.
- getTransformer() - Method in class RemovePartitionAndThen
-
- getTransformer() - Method in class VoxelizeWithTransform
-
- getTransformer() - Method in class KernelStateBridgePixelize
-
- getTransformerKernelToState() - Method in class KernelStateBridgeTransformer
-
- getTransformerMarks() - Method in class AddDualTransformer
-
- getTransformerPrimary() - Method in class StateReporterTransformer
-
- getTransformerSecondary() - Method in class StateReporterTransformer
-
- getTransformerStateToKernel() - Method in class KernelStateBridgeTransformer
-
- getTriggerTerminationCondition() - Method in class OptimizationContext
-
- getTrimTrailingDirectory() - Method in class RemoveTrailingDirectory
-
- getTrimTrailingDirectory() - Method in class FilePathAppendBase
-
- getUnconvertedVoxelAt(int, Point3i) - Method in class DisplayStack
-
Retrieve the intensity of a voxel at a particular point, before any conversion is applied.
- getUniqueLabel() - Method in class AnnotationLabel
-
Label that uniquely identifies the ID (for machine purposes)
- getUnit() - Method in class BoundingBoxExtent
-
- getUnit() - Method in class FeatureSingleMemoRegion
-
- getUnitConverterOptional() - Method in class FeatureInputEnergy
-
Converts voxelized measurements to/from physical units.
- getUnitType() - Method in class DistancePhysical
-
A string indicating type of units to use, as per
SpatialUnits
.
- getUnitType() - Method in class AreaPhysical
-
How much each value represents e.g.
- getUnitType() - Method in class VolumePhysical
-
How much each value represents e.g.
- getUnitType() - Method in class FeatureConvertUnits
-
- getUnitType() - Method in class UnitConverter
-
- getUnitTypeFrom() - Method in class ConvertUnits
-
- getUnitTypeTo() - Method in class ConvertUnits
-
- getUnitValueDistance() - Method in class FromUnitValueDistance
-
- getUnsigned() - Method in class UnsignedBufferAsInt
-
Gets an unsigned-byte (represented as a int) at the current buffer position.
- getUnsigned(int) - Method in class UnsignedBufferAsInt
-
Gets an unsigned-byte (represented as a int) at a particular buffer position.
- getUnsigned() - Method in class UnsignedByteBuffer
-
- getUnsigned(int) - Method in class UnsignedByteBuffer
-
- getUnsigned() - Method in class UnsignedIntBuffer
-
Gets an unsigned-int (represented as a long) at the current buffer position.
- getUnsigned(int) - Method in class UnsignedIntBuffer
-
Gets an unsigned-int (represented as a long) at a particular buffer position.
- getUnsigned() - Method in class UnsignedShortBuffer
-
- getUnsigned(int) - Method in class UnsignedShortBuffer
-
- getUnsignedByte() - Static method in class VoxelsFactory
-
A factory that creates voxels of type unsigned byte.
- getUnsignedInt() - Static method in class VoxelsFactory
-
A factory that creates voxels of type unsigned int.
- getUnsignedShort() - Static method in class VoxelsFactory
-
A factory that creates voxels of type unsigned short.
- getUserFriendlyLabel() - Method in class AnnotationLabel
-
Descriptive user-friendly label displayed via GUI
- getValue() - Method in class NamedBean
-
- getValue() - Method in interface NameValue
-
The associated value.
- getValue() - Method in class SimpleNameValue
-
- getValue() - Method in class TypedValue
-
The value.
- getValue() - Method in class Constant
-
The constant value.
- getValue() - Method in class DistancePhysical
-
The value in units of type unitType
.
- getValue() - Method in class DistanceVoxels
-
The distance in units of voxels.
- getValue() - Method in class AreaPhysical
-
The volume in units of meters, with the unit described by unitType
.
- getValue() - Method in class AreaPixels
-
The volume in pixels.
- getValue() - Method in class VolumePhysical
-
The volume in units of meters, with the unit described by unitType
.
- getValue() - Method in class VolumeVoxels
-
The volume in voxels.
- getValue() - Method in class OptionalNameValue
-
The value.
- getValue() - Method in class AssignValue
-
- getValue() - Method in class CreateNew
-
- getValue() - Method in class UnaryWithValueBase
-
- getValue() - Method in class DictionaryCondition
-
The value the key should have in the dictionary, in order for the condition to be fulfilled.
- getValue() - Method in class EmptyHistogramConstant
-
- getValue() - Method in class IfParamEqual
-
- getValue() - Method in class ConstantScaleFactor
-
The constant floating-point value to scale each dimension by.
- getValue() - Method in class CountEqual
-
- getValue() - Method in class IdentityImposeValueRelationToHistogram
-
- getValue() - Method in class NormalizeByConstant
-
- getValue() - Method in class Constant
-
- getValue() - Method in class Constant
-
- getValue() - Method in class WithValueBase
-
- getValueIfEmpty() - Method in class FeatureHistogramStatistic
-
The value to return iff exceptionifEmpty
is false.
- getValueIfTooFewVoxels() - Method in class ImageMomentsBase
-
A value to return if there are too few voxels (less than MIN_NUM_VOXELS
to calculate
moments
- getValueNoObject() - Method in class ScoreObjects
-
- getValueNoObjects() - Method in class FeatureIntersectingObjects
-
- getValues() - Method in class StatisticsToExport
-
- getValues() - Method in class PermutePropertyDoubleSet
-
The respect double values to assign during the permutation.
- getValues() - Method in class PermutePropertyStringSet
-
The respect string values to assign during the permutation.
- getVaryingSizeWidth() - Method in class Montage
-
If no specific width or scaling-factor is suggested, this determines the default width that
the combined-montage should have, when varyImageSize==true
.
- getVaryingSizeWidthRatio() - Method in class Montage
-
If no specific width or scaling-factor is suggested, this determines the default percentage
of the existing size, the combined-montage should have, when varyImageSize==true
.
- getVersion() - Method in class ExperimentIdentifierConstant
-
- getVertex() - Method in class PrioritisedVertex
-
- getVisitScheduler() - Method in class TraverseOuterContourOnImage
-
- getVoxelDataType() - Method in class ConsistentChannelChecker
-
The voxel-data-type that is consistent across all channels.
- getVoxelDataType() - Method in class Channel
-
The underlying data-type of the voxels in the channel, represented by a
VoxelDataType
instance.
- getVoxelDataType() - Method in class VoxelsUntyped
-
The underlying data-type of the voxels, represented by a
VoxelDataType
instance.
- getVoxels() - Method in class SlidingBuffer
-
The voxels from which buffers corresponding to slices are extracted.
- getVoxelsConverter() - Method in class IntensityRange
-
- getVoxelsConverter() - Method in class MaxIntensity
-
- getVoxelsConverter() - Method in interface ChannelConverterAttached
-
Converts voxels to have type voxel-type T
.
- getVoxelsConverter() - Method in class MaxIntensityFromHistogram
-
- getVoxelsConverter() - Method in class QuantileIntensityFromHistogram
-
- getVoxelsConverter() - Method in class UpperLowerQuantileIntensityFromHistogram
-
- getVoxelsConverter() - Method in class ChannelConverter
-
A converter used to change the
Voxels
to
targetDataType
.
- getWeight() - Method in class WeightedKernel
-
- getWeight() - Method in class KernelProposerOptionSingle
-
- getWeightBackground() - Method in class OtsuWeighted
-
- getWeightedKernelFactory(int) - Method in class KernelProposer
-
- getWeightForeground() - Method in class OtsuWeighted
-
- getWeightItem1Greater() - Method in class Range
-
- getWeightItem2Greater() - Method in class Range
-
- getWeightNegative() - Method in class KernelProposerOption
-
- getWeightNegative() - Method in class KernelProposerOptionDual
-
- getWeightNegative() - Method in class KernelProposerOptionSingle
-
- getWeightPositive() - Method in class KernelProposerOption
-
- getWeightPositive() - Method in class KernelProposerOptionDual
-
- getWeightPositive() - Method in class KernelProposerOptionSingle
-
- getWeightWidthDescription() - Method in class ImageLabelStrategy
-
- getWhenBinaryChannel() - Method in class BranchChannels
-
Writer employed if a stack is a single-channeled binary image.
- getWhenDetailed() - Method in class SwitchDetailedLogging
-
Logger to use when detailed-logging is on
- getWhenEqual() - Method in class IfParamEqual
-
- getWhenFalse() - Method in class IfElse
-
The
DrawObject
that is used when
condition==false
.
- getWhenNot() - Method in class SwitchDetailedLogging
-
Logger to use when detailed-logging is off
- getWhenNotEightBit() - Method in class BranchChannels
-
Writer employed if a stack contains channels that are not 8-bit.
- getWhenNotEqual() - Method in class IfParamEqual
-
- getWhenRelative() - Method in class IfRelativeToDirectory
-
The namer to use if the relative-to-directory option is selected.
- getWhenRGB() - Method in class BranchChannels
-
Writer employed if a stack is a three-channeled RGB image.
- getWhenRGBAlpha() - Method in class BranchChannels
-
Writer employed if a stack is a four-channeled RGBA image.
- getWhenSingleChannel() - Method in class BranchChannels
-
Writer employed if a stack is a single-channeled image, not guaranteed to be binary.
- getWhenThreeChannels() - Method in class BranchChannels
-
Writer employed if a stack is a three-channeled non-RGB image.
- getWhenTrue() - Method in class IfElse
-
- getWidth() - Method in class Fill
-
The width of the combined image in pixels.
- getWidth() - Method in class SizeXY
-
Size in X dimension.
- getWidth() - Method in class Difference
-
Width (what the difference is divided by)
- getWidth() - Method in class ImposeResolution
-
Physical pixel size of a voxel in x-dimension.
- getWidthFactor() - Method in class DifferenceCalculateLevelStandardDeviation
-
- getWidthRatio() - Method in class Fill
-
What fraction of the natural width of the elements should be used to determine the final
width.
- getWindowSize() - Method in class CenterSliceWindow
-
- getWindowSize() - Method in class HOGParameters
-
The window-size as per OpenCV implementation.
- getWithConfidence() - Method in class LabelledWithConfidence
-
The element with associated confidence.
- getWithin() - Method in class UnitsWithinRange
-
Returned as a constant if a value lies within the range
- getWithinValue() - Method in class CompareWithRange
-
Constant to return if value lies within the range
- getWithinValue() - Method in class CompareWithRangeFeature
-
Constant to return if value lies within the range
- getWriter() - Method in class Flatten
-
- getWriter() - Method in class TextFileOutput
-
- getWriter() - Method in class BranchChannels
-
Default writer, if a more specific writer is not specified for a condition.
- getWriter() - Method in class WriteResolutionXml
-
- getWriterAlways2D() - Method in class BranchStack
-
Writer to use if it is guaranteed that the image will always be 2D.
- getWriterElse() - Method in class BranchStack
-
Otherwise the writer to use.
- getWriterIfNoSuggestion() - Method in class BranchSuggestedFormat
-
The writer to use if there is no suggested file-format.
- getWriterInstance(Class<? extends T>) - Method in class OutputWriteSettings
-
Gets a writer-instance for a particular writerParentClass
.
- getWriters() - Method in class OutputWriteSettings
-
Specifies a writer bean instance for a particular type of writer (identified by the writer
bean class)
- getWriters() - Method in class OutputterChecked
-
The writers associated with this output-manager.
- getWritersIfSuggested() - Method in class BranchSuggestedFormat
-
A list of writers to select if a given format is used
- getX() - Method in class SpecifyVector
-
Component of the vector along the x-axis.
- getXmlAggregatedGroup() - Method in class FeatureOutputNames
-
The name of the XML file outputted with aggregated values for each group, if enabled.
- getXMLConfiguration() - Method in class Experiment
-
The configuration of experiment serialized into XML form.
- getY() - Method in class SpecifyVector
-
Component of the vector along the y-axis.
- getZ() - Method in class SpecifyVector
-
Component of the vector along the z-axis.
- getZSliceGroupID() - Method in class RegularExpression
-
- getZSliceNum() - Method in class SortedSetSlice
-
- GlobalRegionIdentifiers - Class in org.anchoranalysis.mpp.mark
-
- GlobExtractor - Class in org.anchoranalysis.io.input.path
-
Extracts a glob from a string describing it, and a direcory which gives it context.
- GlobExtractor.GlobWithDirectory - Class in org.anchoranalysis.io.input.path
-
A string describing a glob, associated with a directory onto which it will be applied.
- GlobWithDirectory(Optional<String>, String) - Constructor for class GlobExtractor.GlobWithDirectory
-
- GradientBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider.gradient
-
Base class to calculate the gradient of the voxels in a
Channel
.
- GradientBase() - Constructor for class GradientBase
-
- GradientBaseAddSum - Class in org.anchoranalysis.plugin.image.bean.channel.provider.gradient
-
Like
GradientBase
but allows an arbitrary constant to be added to voxels storing the
gradient.
- GradientBaseAddSum() - Constructor for class GradientBaseAddSum
-
- gradientCalculation() - Method in class IntensityGradientBase
-
- GradientForAxis - Class in org.anchoranalysis.plugin.image.bean.channel.provider.gradient
-
Extracts the gradient in the direction of a particular axis (identified by an index)
- GradientForAxis() - Constructor for class GradientForAxis
-
- GradientMagnitude - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient
-
Calculates the mean of the intensity-gradient defined by multiple Energy channels in a particular
direction
- GradientMagnitude() - Constructor for class GradientMagnitude
-
- GradientMeanForAxis - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient
-
Calculates the mean of the intensity-gradient defined by multiple Energy channels in a particular
direction
- GradientMeanForAxis() - Constructor for class GradientMeanForAxis
-
- GradientXY - Class in org.anchoranalysis.plugin.image.bean.channel.provider.gradient
-
Calculates a
Channel
's gradient along the x and y axes.
- GradientXY() - Constructor for class GradientXY
-
- GraphLogger - Class in org.anchoranalysis.plugin.image.object.merge
-
- GraphLogger(DescribeGraph, Logger) - Constructor for class GraphLogger
-
- GraphWithoutPayload<V> - Class in org.anchoranalysis.core.graph
-
A graph, either directed or undirected, where edges contain no payload.
- GraphWithoutPayload(boolean) - Constructor for class GraphWithoutPayload
-
Creates the graph.
- GraphWithPayload<V,P> - Class in org.anchoranalysis.core.graph
-
A graph, either directed or undirected, with edges containing a payload of type E
.
- GraphWithPayload(boolean) - Constructor for class GraphWithPayload
-
Creates the graph.
- GrayscaleReconstruction2DIJ - Class in org.anchoranalysis.plugin.fiji.bean.channel.grayscalereconstruction
-
- GrayscaleReconstruction2DIJ() - Constructor for class GrayscaleReconstruction2DIJ
-
- GrayscaleReconstructionByErosion - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction
-
- GrayscaleReconstructionByErosion() - Constructor for class GrayscaleReconstructionByErosion
-
- GrayscaleReconstructionRobinson - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction
-
- GrayscaleReconstructionRobinson() - Constructor for class GrayscaleReconstructionRobinson
-
- GreaterIntersectionWith - Class in org.anchoranalysis.plugin.image.bean.object.filter.independent
-
Only accepts an object if it has greater (or EQUAL) intersection with objectsGreater
than
objectsLesser
- GreaterIntersectionWith() - Constructor for class GreaterIntersectionWith
-
- GreaterThan - Class in org.anchoranalysis.math.relation
-
Returns true iff valueFirst
is greater than valueSecond
.
- GreaterThan() - Constructor for class GreaterThan
-
- GreaterThanBean - Class in org.anchoranalysis.bean.shared.relation
-
A relation double1 > double2
.
- GreaterThanBean() - Constructor for class GreaterThanBean
-
- GreaterThanEqualTo - Class in org.anchoranalysis.math.relation
-
Returns true iff valueFirst
is greater than or equal to valueSecond
.
- GreaterThanEqualTo() - Constructor for class GreaterThanEqualTo
-
- GreaterThanEqualToBean - Class in org.anchoranalysis.bean.shared.relation
-
A relation double1 >= double2
.
- GreaterThanEqualToBean() - Constructor for class GreaterThanEqualToBean
-
- GreaterThanThreshold - Class in org.anchoranalysis.plugin.image.bean.histogram.provider
-
Thresholds a histogram using a CalculateLevel keeping only the values greater equal than the
threshold
- GreaterThanThreshold() - Constructor for class GreaterThanThreshold
-
- GreatestAreaSlice - Class in org.anchoranalysis.plugin.mpp.bean.region
-
- GreatestAreaSlice() - Constructor for class GreatestAreaSlice
-
- greedyMatch() - Method in class HungarianAlgorithm
-
Find a valid matching by greedily selecting among zero-cost matchings.
- GREEN - Static variable in class RGBChannelNames
-
Name for the green channel.
- green() - Method in class RGBStack
-
The green channel.
- GroupedAnnotationLabels - Class in org.anchoranalysis.plugin.annotation.bean.label
-
A set of annotation labels partitoned into their unique groups
- GroupedAnnotationLabels(Collection<AnnotationLabel>) - Constructor for class GroupedAnnotationLabels
-
- groupedLabels() - Method in class ImageLabelStrategy
-
- GroupedResults - Class in org.anchoranalysis.feature.io.results.group
-
Stores feature-calculation results, indexing by their group.
- GroupedResults() - Constructor for class GroupedResults
-
- GroupedSharedState<S,T> - Class in org.anchoranalysis.plugin.image.task.grouped
-
Commonality between shared state for grouped export tasks.
- GroupedSharedState(Optional<InputGrouper>, Function<ConsistentChannelChecker, GroupMapByName<S, T>>) - Constructor for class GroupedSharedState
-
- GroupedStackBase<S,T> - Class in org.anchoranalysis.plugin.image.task.bean.grouped
-
Base class for stacks (usually each channel from an image) that are somehow grouped-together.
- GroupedStackBase() - Constructor for class GroupedStackBase
-
- Grouper - Class in org.anchoranalysis.io.input.bean.grouper
-
Determines how partition inputs into groups.
- Grouper() - Constructor for class Grouper
-
- GroupFiles - Class in org.anchoranalysis.plugin.io.bean.file.group
-
- GroupFiles() - Constructor for class GroupFiles
-
- groupForKey(String) - Method in class AnnotationComparisonAssigner
-
- groupForKey(String) - Method in class FeatureCostAssigner
-
- groupForKey(String) - Method in class MaskIntersectionAssigner
-
- GroupingRoot - Annotation Type in org.anchoranalysis.bean.annotation
-
Indicates that a set of definitions of classes can be collectively grouped using this class.
- GroupMapByName<S,T> - Class in org.anchoranalysis.plugin.image.task.grouped
-
Adds items to aggregate structures identified uniquely by a name, and allows these items to be
later outputted.
- GroupMapByName(String, Optional<Stream<String>>, Optional<InputOutputContext>, Supplier<T>, CheckedBiConsumer<S, T, OperationFailedException>) - Constructor for class GroupMapByName
-
Creates a group-map.
- groupNameSet() - Method in class IndexedCSVRows
-
- groupsForImage(SplitString) - Method in class ComparisonSharedState
-
- Grow - Class in org.anchoranalysis.image.bean.spatial.arrange.align
-
Grow the bounding-box to fill larger
as much as possible.
- Grow(boolean) - Constructor for class Grow
-
Create to preserve the aspect-ratio or not.
- Grow() - Constructor for class Grow
-
- Grow(boolean, Align) - Constructor for class Grow
-
- growBuffer(Point3i, Point3i, Optional<Extent>, VoxelsFactoryTypeBound<T>) - Method in class BoundedVoxels
-
Grows the voxel buffer in the positive and negative directions by a certain amount.
- growBuffer(Point3i, Point3i, Optional<Extent>) - Method in class ObjectMask
-
Grows the object-mask's voxel buffers in the positive and negative directions by a certain
amount.
- growBy(Tuple3i, Extent) - Method in class BoundingBox
-
Grow the bounding-box by toAdd
amount in each dimension in both positive and negative
directions.
- growBy(int) - Method in class Extent
-
Creates a new
Extent
with
toAdd
size
added to each dimension.
- growBy(ReadableTuple3i) - Method in class Extent
-
Creates a new
Extent
with
toAdd
size
added to each respective
dimension.
- growToZ(int, VoxelsFactoryTypeBound<T>) - Method in class BoundedVoxels
-
Grows a single z-sliced
BoundedVoxels
by duplicating the slice across the z-dimension
sizeZ
number of times.
- growToZ(int) - Method in class ObjectMask
-
Grows a single z-sliced
ObjectMask
by duplicating the slice across the z-dimension
sizeZ
number of times.
- growWidth(int) - Method in class ExtentToArrange
-
Changes the width of the underlying
Extent
by adding
growBy
pixels.
- guaranteedImageAttributes() - Method in class AssignmentGenerator
-
- guaranteedImageAttributes() - Method in class ChannelGenerator
-
- guaranteedImageAttributes() - Method in class ObjectsAsGrayscaleGenerator
-
- guaranteedImageAttributes() - Method in class ObjectAsMaskGenerator
-
- guaranteedImageAttributes() - Method in class ObjectsAsRGBGenerator
-
- guaranteedImageAttributes() - Method in class DrawObjectOnStackGenerator
-
- guaranteedImageAttributes() - Method in class ExtractBoundingBoxAreaFromStackGenerator
-
- guaranteedImageAttributes() - Method in class DisplayStackGenerator
-
- guaranteedImageAttributes() - Method in class FlattenStackGenerator
-
- guaranteedImageAttributes() - Method in class RasterGenerator
-
Guarantees on the attributes of all images created by the generator.
- guaranteedImageAttributes() - Method in class RasterGeneratorDelegateToDisplayStack
-
- guaranteedImageAttributes() - Method in class RasterGeneratorDelegateToRaster
-
- guaranteedImageAttributes() - Method in class StackGenerator
-
- guaranteedImageAttributes() - Method in class MarksAsUniqueValueGenerator
-
- guaranteedImageAttributes() - Method in class MarksGeneratorBase
-
- GuessDimensions - Class in org.anchoranalysis.plugin.image.bean.dimensions.provider
-
Guesses dimensions from an input-image if it exists.
- GuessDimensions() - Constructor for class GuessDimensions
-
- idAndIncrement() - Method in class MarkWithIdentifierFactory
-
- identiferFor(ChannelSpecification, boolean, String, boolean) - Static method in class IdentifierHelper
-
Builds an identifier for particular properties.
- identifier(Optional<String>) - Method in class ExperimentIdentifier
-
Creates an identifier for the experiment.
- identifier(Optional<String>) - Method in class ExperimentIdentifierAuto
-
- identifier(Optional<String>) - Method in class ExperimentIdentifierConstant
-
- identifier() - Method in class SingleFileInputBase
-
- identifier() - Method in interface InputFromManager
-
A unique name associated with the input.
- identifier() - Method in class InputFromManagerDelegate
-
- identifier() - Method in class MultiInput
-
- identifier() - Method in class Mark
-
- identifierAsPath() - Method in interface InputFromManager
-
- IdentifierGetter<T> - Interface in org.anchoranalysis.core.identifier.getter
-
Gets a unique identifier for a particular element at a particular iteration point.
- IdentifierHelper - Class in org.anchoranalysis.test.image.stackwriter
-
Builds an identifier (a filename without extension) for a saved-raster corresponding to certain
properties.
- IdentifyFromIteration<T> - Class in org.anchoranalysis.core.identifier.getter
-
Identify an element uniquely only by its iteration timepoint.
- IdentifyFromIteration() - Constructor for class IdentifyFromIteration
-
- IdentifyObjects - Class in org.anchoranalysis.plugin.image.bean.channel.provider.score
-
Assigns a unique id number to each object.
- IdentifyObjects() - Constructor for class IdentifyObjects
-
- Identity - Class in org.anchoranalysis.io.input.bean.path
-
Returns the same
Path
as the argument passed in.
- Identity() - Constructor for class Identity
-
- Identity - Class in org.anchoranalysis.plugin.image.feature.bean.score
-
- Identity() - Constructor for class Identity
-
- IdentityImposeValueRelationToHistogram - Class in org.anchoranalysis.plugin.image.feature.bean.score
-
- IdentityImposeValueRelationToHistogram() - Constructor for class IdentityImposeValueRelationToHistogram
-
- idFor(ObjectWithProperties, int) - Method in class ObjectDrawAttributes
-
ID for a particular object
- IfCondition<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.conditional
-
The result of featureCondition is compared to a threshold, and then either the underlying feature
is calculated (positive case), or featureElse is (negative case)
- IfCondition() - Constructor for class IfCondition
-
- IfConditionWithinRange<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.range
-
Calculates a value if a condition lies within a certain range, otherwise returns constants
- IfConditionWithinRange() - Constructor for class IfConditionWithinRange
-
- IfElse - Class in org.anchoranalysis.image.io.bean.object.draw
-
Branches to two different
DrawObject
depending on a predicate.
- IfElse(IfElse.Predicate, DrawObject, DrawObject) - Constructor for class IfElse
-
Creates for a particular condition.
- IfElse() - Constructor for class IfElse
-
- IfElse.Predicate - Interface in org.anchoranalysis.image.io.bean.object.draw
-
Interface for the condition that is tested, to determine which
DrawObject
to use.
- IfGreaterThan - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold
-
Calculates a level from the first delegate and if greater than a threshold, recalculates from a
second delegate.
- IfGreaterThan() - Constructor for class IfGreaterThan
-
- IfGroupIndexRange - Class in org.anchoranalysis.plugin.io.bean.grouper
-
- IfGroupIndexRange() - Constructor for class IfGroupIndexRange
-
- IfHighLow - Class in org.anchoranalysis.plugin.image.bean.mask.provider.combine
-
Outputs the logical operation iff first==HIGH and second==LOW then LOW
voxelwise on both
masks, modifying {mask} with the result.
- IfHighLow() - Constructor for class IfHighLow
-
- IfIncrementingNumberRequested - Class in org.anchoranalysis.plugin.io.bean.file.path.prefixer
-
Multiplexes between two
PathPrefixer
s depending on whether an
incrementing number
sequence was output was requested.
- IfIncrementingNumberRequested() - Constructor for class IfIncrementingNumberRequested
-
- IfKeyValueCondition - Class in org.anchoranalysis.plugin.image.bean.mask.provider.predicate
-
The current mask
is returned if a condition on key-values is satisfied otherwise maskElse
is returned.
- IfKeyValueCondition() - Constructor for class IfKeyValueCondition
-
- IfLessThan - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold
-
Calculates a level from the first delegate and if less than a threshold, recalculates from a
second delegate.
- IfLessThan() - Constructor for class IfLessThan
-
- IfNotEmpty - Class in org.anchoranalysis.plugin.image.bean.mask.provider.predicate
-
The current mask
is returned if it's non-empty (at least one on voxel) otherwise
maskElse
is returned.
- IfNotEmpty() - Constructor for class IfNotEmpty
-
- IfObjectFilter - Class in org.anchoranalysis.plugin.image.bean.mask.provider.predicate
-
The current mask
is returned if the mask (treated as an object) passed an object-filter,
otherwise maskElse
is returned.
- IfObjectFilter() - Constructor for class IfObjectFilter
-
- ifOptionWithoutArgument(String, Consumer<T>) - Method in class AddOptionsFromCommandLine
-
Executes consumer
if an option exists without any argument.
- IfOutsideRange<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.range
-
Clamps a value if it lies outside the range - instead returning particular constants if below or
above an acceptable range
- IfOutsideRange() - Constructor for class IfOutsideRange
-
- IfParamEqual - Class in org.anchoranalysis.plugin.image.bean.object.provider
-
Multiplexes between two object-collection-providers depending on whether a parameter value equals
a particular string
- IfParamEqual() - Constructor for class IfParamEqual
-
- IfParamEquals - Class in org.anchoranalysis.plugin.image.bean.channel.provider
-
- IfParamEquals() - Constructor for class IfParamEquals
-
- IfPredicateBase - Class in org.anchoranalysis.plugin.image.bean.mask.provider.predicate
-
Base class which multiplexes between the current mask and an alternative depending if a condition
is met.
- IfPredicateBase() - Constructor for class IfPredicateBase
-
- ifPresent(Optional<S>, CheckedConsumer<S, E>) - Static method in class OptionalUtilities
-
- ifPresentMultiple(String, CheckedConsumer<String[], ExperimentExecutionException>) - Method in class CommandLineExtracter
-
Executes a
Consumer
if an option is present - allowing that option to occur
multiple times.
- ifPresentMultiple(String, CheckedConsumer<String[], ExperimentExecutionException>) - Method in class AddOptionsFromCommandLine
-
Executes consumer
if one or more options exists with a single
argument.
- ifPresentSingle(String, CheckedConsumer<String, ExperimentExecutionException>) - Method in class CommandLineExtracter
-
Executes a
Consumer
if an option is present - allowing that option to occur only
once.
- ifPresentSingle(String, CheckedConsumer<String, ExperimentExecutionException>) - Method in class AddOptionsFromCommandLine
-
Executes consumer
if maximally one option exists with a single
argument - without passing associated
.
- ifPresentSingleAssociated(String, CheckedBiConsumer<T, String, ExperimentExecutionException>) - Method in class AddOptionsFromCommandLine
-
Executes consumer
if maximally one option exists with a single
argument - passing associated
.
- IfRelativeToDirectory - Class in org.anchoranalysis.plugin.io.bean.file.namer
-
Multiplexes between two namers depending on if the relative-to-directory option is
selected.
- IfRelativeToDirectory() - Constructor for class IfRelativeToDirectory
-
- IfStackExists - Class in org.anchoranalysis.plugin.image.bean.mask.provider.predicate
-
The current mask
is a particular stack exists (at least one on voxel) otherwise
maskElse
is returned.
- IfStackExists() - Constructor for class IfStackExists
-
- IfVoxelZero - Class in org.anchoranalysis.plugin.image.bean.channel.provider.intensity
-
Creates a new channel which is a merged version of two input channels according to rules.
- IfVoxelZero() - Constructor for class IfVoxelZero
-
- IgnoreUnderscorePrefix - Class in org.anchoranalysis.io.output.bean.enabled
-
All outputs are allowed unless the name's first character is an underscore.
- IgnoreUnderscorePrefix() - Constructor for class IgnoreUnderscorePrefix
-
- IgnoreUnderscorePrefixUnless - Class in org.anchoranalysis.io.output.bean.rules
-
Like
IgnoreUnderscorePrefix
for all first and level-outputs unless a particular outputs
are explicitly specified.
- IgnoreUnderscorePrefixUnless(StringSet) - Constructor for class IgnoreUnderscorePrefixUnless
-
Create with first-level output names
- IgnoreUnderscorePrefixUnless() - Constructor for class IgnoreUnderscorePrefixUnless
-
- image() - Method in class MarksInitialization
-
- ImageAssignLabel<T> - Class in org.anchoranalysis.plugin.image.task.bean.labeller
-
Assigns a label to each image and copies into subdirectories for each label, and creates a
labelling CSV.
- ImageAssignLabel() - Constructor for class ImageAssignLabel
-
- ImageBean<T> - Class in org.anchoranalysis.image.bean
-
- ImageBean() - Constructor for class ImageBean
-
Create with default initializer and assigner.
- ImageComparer - Interface in org.anchoranalysis.test.image.rasterwriter.comparison
-
Base class for a method comparing two image files.
- ImageCounter<T> - Interface in org.anchoranalysis.plugin.annotation.counter
-
Counts images on aggregate, some with associated annotations, others without.
- ImageCounterList<T extends Assignment<ObjectMask>> - Class in org.anchoranalysis.plugin.annotation.counter
-
Allows operations to be applied to several
ImageCounter
s collectively.
- ImageCounterList() - Constructor for class ImageCounterList
-
- ImageCounterWithStatistics<T> - Interface in org.anchoranalysis.plugin.annotation.counter
-
- ImageCSVLabeller - Class in org.anchoranalysis.plugin.image.task.bean.labeller
-
- ImageCSVLabeller() - Constructor for class ImageCSVLabeller
-
- ImageCSVLabellerInitialization - Class in org.anchoranalysis.plugin.image.task.labeller
-
- ImageCSVLabellerInitialization(FileLabelMap<String>) - Constructor for class ImageCSVLabellerInitialization
-
- ImageFileAttributes - Class in org.anchoranalysis.image.core.stack
-
Timestamps and other metadata associated with an image file-path, but not with the file's
contents.
- ImageFileAttributes(Path, ZonedDateTime, ZonedDateTime) - Constructor for class ImageFileAttributes
-
- ImageFileEncoding - Class in org.anchoranalysis.io.bioformats.copyconvert
-
How values are encoded into an image-file.
- ImageFileEncoding(boolean, boolean, int) - Constructor for class ImageFileEncoding
-
- ImageFileFormat - Enum in org.anchoranalysis.core.format
-
A type of image format that are read/written to the filesystem, together with the extensions it
may use.
- ImageFileShape - Class in org.anchoranalysis.io.bioformats.copyconvert
-
How to shape the image (across various dimensions) after the copying
- ImageFileShape(Dimensions, int, int) - Constructor for class ImageFileShape
-
- ImageInferenceContext - Class in org.anchoranalysis.image.inference
-
Attributes describing the situation in which inference on images is occurring.
- ImageInferenceContext(DualScale<Dimensions>, ScaleFactor, Optional<List<String>>, VoxelsResizer, ExecutionTimeRecorder, Logger) - Constructor for class ImageInferenceContext
-
- ImageInferenceModel<T> - Interface in org.anchoranalysis.image.inference
-
A model used for inference that accepts an image as an input.
- ImageInitialization - Class in org.anchoranalysis.image.bean.nonbean.init
-
- ImageInitialization(SharedObjects) - Constructor for class ImageInitialization
-
Create with shared-objects.
- ImageInitialization(SharedObjects, Optional<ImageSizeSuggestion>) - Constructor for class ImageInitialization
-
Create with shared-objects and a resizing suggestion.
- ImageInitializationFactory - Class in org.anchoranalysis.image.io
-
- ImageIOException - Exception in org.anchoranalysis.image.io
-
When an error occurs reading or writing an image to/from the file-system.
- ImageIOException(Throwable) - Constructor for exception ImageIOException
-
Create with a cause only.
- ImageIOException(String) - Constructor for exception ImageIOException
-
Create with a message only.
- ImageIOException(String, Throwable) - Constructor for exception ImageIOException
-
Create with a message and cause.
- ImageIOWriter - Class in org.anchoranalysis.plugin.io.bean.stack.writer
-
- ImageIOWriter() - Constructor for class ImageIOWriter
-
- ImageJ - Class in org.anchoranalysis.io.imagej.bean.interpolator
-
- ImageJ() - Constructor for class ImageJ
-
- ImageJConversionException - Exception in org.anchoranalysis.io.imagej.convert
-
When conversion to ImageJ data/type is not possible, or an error occurs during conversion.
- ImageJConversionException(String) - Constructor for exception ImageJConversionException
-
Creates with a message.
- ImageJConversionException(Exception) - Constructor for exception ImageJConversionException
-
Creates with a message.
- ImageJRasterWriter - Class in org.anchoranalysis.io.imagej.bean.stack.writer
-
Base class for writing a raster using ImageJ.
- ImageJRasterWriter() - Constructor for class ImageJRasterWriter
-
- ImageLabelAnnotation - Class in org.anchoranalysis.annotation.image
-
A single label that is associated with an image.
- ImageLabelAnnotation(String) - Constructor for class ImageLabelAnnotation
-
- ImageLabelAnnotationReader - Class in org.anchoranalysis.annotation.io.image
-
- ImageLabelAnnotationReader() - Constructor for class ImageLabelAnnotationReader
-
- ImageLabelAnnotationWriter - Class in org.anchoranalysis.annotation.io.image
-
- ImageLabelAnnotationWriter() - Constructor for class ImageLabelAnnotationWriter
-
- ImageLabeller<T> - Class in org.anchoranalysis.plugin.image.task.bean.labeller
-
Associates a label with an image.
- ImageLabeller() - Constructor for class ImageLabeller
-
- ImageLabellerStringMap<T> - Class in org.anchoranalysis.plugin.image.task.bean.labeller
-
Maps one set of labels to another
- ImageLabellerStringMap() - Constructor for class ImageLabellerStringMap
-
- ImageLabellerStringMapInitialization<T> - Class in org.anchoranalysis.plugin.image.task.labeller
-
- ImageLabellerStringMapInitialization(Map<String, String>, T) - Constructor for class ImageLabellerStringMapInitialization
-
- ImageLabelStrategy - Class in org.anchoranalysis.plugin.annotation.bean.strategy
-
Assigns a single label per image, as a whole.
- ImageLabelStrategy() - Constructor for class ImageLabelStrategy
-
- ImageMetadata - Class in org.anchoranalysis.image.core.stack
-
Information about an image, but not about the intensity or content of image voxels.
- ImageMetadata(Dimensions, int, int, int, boolean, int, ImageFileAttributes, Optional<ZonedDateTime>, Optional<ImagePyramidMetadata>) - Constructor for class ImageMetadata
-
- ImageMetadataInput - Class in org.anchoranalysis.image.io.stack.input
-
An input that provides a
ImageMetadata
but only lazily when first called.
- ImageMetadataInput(NamedFile, CheckedSupplier<ImageMetadata, ImageIOException>) - Constructor for class ImageMetadataInput
-
Create for a particular file and metadata.
- ImageMetadataReader - Class in org.anchoranalysis.image.io.bean.stack.metadata.reader
-
- ImageMetadataReader() - Constructor for class ImageMetadataReader
-
- ImageMoments - Class in org.anchoranalysis.math.statistics.moment
-
The first moment (mean) and eigenvalues of the second moments (covariance) from a matrix of
points.
- ImageMoments(DoubleMatrix2D, boolean, boolean) - Constructor for class ImageMoments
-
Calculates the second-moments from the covariance of a matrix of points.
- ImageMomentsBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.moments
-
A base class for features that are calculated using image-moments.
- ImageMomentsBase() - Constructor for class ImageMomentsBase
-
- ImagePyramidMetadata - Class in org.anchoranalysis.image.core.stack
-
- ImagePyramidMetadata(int) - Constructor for class ImagePyramidMetadata
-
- ImageSize - Class in org.anchoranalysis.plugin.io.bean.summarizer.image
-
Summarizes the size of images.
- ImageSize() - Constructor for class ImageSize
-
- ImageSizePrereader - Class in org.anchoranalysis.plugin.image.task.stack
-
Reads the size of each image initially, before normal (parallel) task execution.
- ImageSizePrereader(ImageMetadataReader, StackReader, OperationContext) - Constructor for class ImageSizePrereader
-
- imageSizesFor(List<StackSequenceInput>) - Method in class ImageSizePrereader
-
- ImageSizeSuggestion - Interface in org.anchoranalysis.image.core.dimensions.size.suggestion
-
A suggestion on a size for an image.
- ImageSizeSuggestionFactory - Class in org.anchoranalysis.image.core.dimensions.size.suggestion
-
- ImageTimestampsAttributes - Class in org.anchoranalysis.image.io.stack.input
-
- ImageTimestampsAttributes(ImageFileAttributes, Optional<ZonedDateTime>) - Constructor for class ImageTimestampsAttributes
-
- ImageTimestampsAttributesFactory - Class in org.anchoranalysis.io.bioformats.metadata
-
- ImgLib2Lanczos - Class in org.anchoranalysis.image.bean.interpolator
-
- ImgLib2Lanczos() - Constructor for class ImgLib2Lanczos
-
- ImgLib2Linear - Class in org.anchoranalysis.image.bean.interpolator
-
- ImgLib2Linear() - Constructor for class ImgLib2Linear
-
- immutableAdd(Point2i, Point2i) - Static method in class Point2i
-
Adds two points immutably.
- immutableAdd(Tuple3d, Tuple3d) - Static method in class Point3d
-
Adds two tuples immutably.
- immutableAdd(Point3d, int, int, int) - Static method in class Point3d
-
Adds values to a point immutably.
- immutableAdd(ReadableTuple3i, ReadableTuple3i) - Static method in class Point3i
-
Adds two tuples immutably.
- immutableAdd(ReadableTuple3i, ReadableTuple3i, ReadableTuple3i) - Static method in class Point3i
-
Adds three tuples immutably.
- immutableAdd(ReadableTuple3i, int, int, int) - Static method in class Point3i
-
Adds values to a tuple immutably.
- immutableScale(Tuple3d, int) - Static method in class Point3d
-
Scales a tuple immutably.
- immutableScale(ReadableTuple3i, int) - Static method in class Point3i
-
Multiplies each component by factor
without changing any values in an existing point.
- immutableSubtract(Tuple3d, Tuple3d) - Static method in class Point3d
-
- immutableSubtract(Tuple3i, Tuple3d) - Static method in class Point3d
-
- immutableSubtract(ReadableTuple3i, ReadableTuple3i) - Static method in class Point3i
-
Subtracts two tuples immutably.
- ImposeMinima - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel
-
Imposes minima in seed locations on the input-channel before performing the segmentation
- ImposeMinima() - Constructor for class ImposeMinima
-
- imposeMinima(Channel, ObjectCollection, Optional<ObjectMask>) - Method in class MinimaImposition
-
- imposeMinima(Channel, ObjectCollection, Optional<ObjectMask>) - Method in class MinimaImpositionGrayscaleReconstruction
-
- imposeMinimumRadius(double) - Method in class FitResult
-
- ImposeResolution - Class in org.anchoranalysis.plugin.io.bean.stack.reader
-
Adds an explicit
Resolution
to an image after it has been read.
- ImposeResolution() - Constructor for class ImposeResolution
-
- IncludeBeanFactory - Class in org.anchoranalysis.bean.xml.factory
-
Defines an
AnchorBean
in a separate file on the file-system.
- IncludeBeanFactory() - Constructor for class IncludeBeanFactory
-
- includeFirst() - Method in class MergedPairsInclude
-
- includeFirstOrSecond() - Method in class MergedPairsInclude
-
- includeGroupInExperiment(boolean) - Method in class FeatureSource
-
Iff true, group columns are added to the CSV exports, and other group exports may occur in
sub-directories.
- includeGroupInExperiment(boolean) - Method in class FromHistogram
-
- includeGroupInExperiment(boolean) - Method in class FromImage
-
- includeGroupInExperiment(boolean) - Method in class FromImageMetadata
-
- includeGroupInExperiment(boolean) - Method in class FromObjects
-
If either a group-generator is defined or there's more than one provider, then groups should
be included.
- IncludeListBeanFactory<T> - Class in org.anchoranalysis.bean.xml.factory
-
Like
ListBeanFactory
but also includes elements in other lists defined in the
include
tag.
- IncludeListBeanFactory() - Constructor for class IncludeListBeanFactory
-
Default constructor.
- includeMarks(VoxelizedMarkMemo, VoxelizedMarkMemo, Dimensions, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class AddCriteriaOr
-
- includeMarks(VoxelizedMarkMemo, VoxelizedMarkMemo, Dimensions, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class AddCriteriaPair
-
- includeMarks(VoxelizedMarkMemo, VoxelizedMarkMemo, Dimensions, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class ArbitraryPointCommon
-
- includeMarks(VoxelizedMarkMemo, VoxelizedMarkMemo, Dimensions, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class BoundingBoxIntersection
-
- includeMarks(VoxelizedMarkMemo, VoxelizedMarkMemo, Dimensions, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class AddCriteriaFeatureRelationThreshold
-
- IncludeMarksFailureException - Exception in org.anchoranalysis.mpp.feature.addcriteria
-
- IncludeMarksFailureException(String) - Constructor for exception IncludeMarksFailureException
-
- IncludeMarksFailureException(Exception) - Constructor for exception IncludeMarksFailureException
-
- includeMerged() - Method in class MergedPairsInclude
-
- IncludeRandomObjects - Class in org.anchoranalysis.plugin.mpp.bean.proposer.points
-
1.
- IncludeRandomObjects() - Constructor for class IncludeRandomObjects
-
- includeSecond() - Method in class MergedPairsInclude
-
- IncorrectImageSizeException - Exception in org.anchoranalysis.image.core.dimensions
-
When an image has incompatible image-size with expectations.
- IncorrectImageSizeException(String) - Constructor for exception IncorrectImageSizeException
-
Create with a message.
- IncorrectVoxelTypeException - Exception in org.anchoranalysis.image.voxel.datatype
-
- IncorrectVoxelTypeException(String) - Constructor for exception IncorrectVoxelTypeException
-
Create with only a message.
- IncorrectVoxelTypeException(Throwable) - Constructor for exception IncorrectVoxelTypeException
-
Create with only a cause.
- incr(int) - Method in class AggIDCounter
-
- incr(Reporting<S>) - Method in class PeriodTriggerBank
-
- IncreaseFeatureCondition - Class in org.anchoranalysis.plugin.image.object.merge.condition
-
- IncreaseFeatureCondition(FeatureEvaluator<FeatureInputSingleObject>) - Constructor for class IncreaseFeatureCondition
-
- increment(K) - Method in class MapCreateCountdown
-
Increments the entry associated with key
, creating a counter for it if none already
exists.
- increment() - Method in class Counter
-
Increases the counter by one.
- increment(double) - Method in class RunningSum
-
Adds a new item to the sum, and increments the count by 1.
- increment(double, long) - Method in class RunningSum
-
Increments both the sum and count by particular values.
- increment(RunningSum) - Method in class RunningSum
-
Increments (adds) an existing
RunningSum
to the current.
- increment(Point2i) - Method in class RunningSumPoint
-
Increments the running-sum by a
Point2i
.
- increment(Point2d) - Method in class RunningSumPoint
-
Increments the running-sum by a
Point2d
.
- increment(Point3i) - Method in class RunningSumPoint
-
Increments the running-sum by a
Point3i
.
- increment(Point3d) - Method in class RunningSumPoint
-
Increments the running-sum by a
Point3d
.
- increment(Tuple3d) - Method in class Tuple3d
-
Increments each component's value by the corresponding value in a
Tuple3d
.
- incrementBy(int) - Method in class Counter
-
Increases the counter by a specific value.
- incrementCount(T) - Method in class SummarizerImageMetadata
-
- incrementCount(T) - Method in class FrequencyMap
-
- incrementCounter() - Method in class RecordingCounter
-
Increments the counter.
- incrementEnergy(double) - Method in class Aggregator
-
- incrementIndexOnly() - Method in class KernelPointCursor
-
Increments the current index state by one, without changing the current point state.
- incrementingByOne(String, OutputterChecked) - Method in class OutputSequenceStackFactory
-
Creates an sequence of stacks in a subdirectory with a number in the outputted file name that
increments each time by one.
- incrementingByOne(OutputPatternIntegerSuffix) - Method in class OutputSequenceFactory
-
Writes elements to directory
, with an incrementing integer in the filename.
- incrementingByOneCurrentDirectory(String, String, int) - Method in class OutputSequenceFactory
-
Writes elements to the current directory, with an incrementing integer in the filename.
- incrementingByOneStream(OutputPatternIntegerSuffix, Stream<T>) - Method in class OutputSequenceFactory
-
Writes file for each element in a stream with an incrementing integer sequence in the
outputted file-name.
- IncrementingNumber - Class in org.anchoranalysis.io.output.bean.path.prefixer
-
Outputs an incrementing number for each output that occurs.
- IncrementingNumber(String) - Constructor for class IncrementingNumber
-
- IncrementingNumber() - Constructor for class IncrementingNumber
-
- incrementKernelAcceptance(int) - Method in class Aggregator
-
- incrementKernelProp(int) - Method in class Aggregator
-
- incrementReturn() - Method in class Counter
-
Increases the counter by one, returning the previous value.
- incrementSize(double) - Method in class Aggregator
-
- incrementTemperature(double) - Method in class Aggregator
-
- incrementValue(int) - Method in class Histogram
-
Increments the count for a particular value by one.
- incrementValueBy(int, int) - Method in class Histogram
-
Increments the count for a particular value.
- incrementValueBy(int, long) - Method in class Histogram
-
- incrementX() - Method in class KernelPointCursor
-
Increments the point and associated index by one in the X dimension.
- incrementX() - Method in class Point2i
-
Increments the X component's value by one.
- incrementX(int) - Method in class Point2i
-
Increments the X component's value by a shift.
- incrementX(double) - Method in class Tuple3d
-
Increments the X component's value by a shift.
- incrementX() - Method in class Tuple3i
-
Increments the X component's value by one.
- incrementX(int) - Method in class Tuple3i
-
Increments the X component's value by a shift.
- incrementXTwice() - Method in class KernelPointCursor
-
Increments the point and associated index by two in the X dimension.
- incrementY() - Method in class KernelPointCursor
-
Increments the point and associated index by one in the Y dimension.
- incrementY() - Method in class Point2i
-
Increments the Y component's value by one.
- incrementY(int) - Method in class Point2i
-
Increments the Y component's value by a shift.
- incrementY(double) - Method in class Tuple3d
-
Increments the Y component's value by a shift.
- incrementY() - Method in class Tuple3i
-
Increments the Y component's value by one.
- incrementY(int) - Method in class Tuple3i
-
Increments the Y component's value by a shift.
- incrementYTwice() - Method in class KernelPointCursor
-
Increments the point and associated index by two in the Y dimension.
- incrementZ() - Method in class KernelPointCursor
-
Increments the point by one in the Z dimension.
- incrementZ(double) - Method in class Tuple3d
-
Increments the Z component's value by a shift.
- incrementZ() - Method in class Tuple3i
-
Increments the Z component's value by one.
- incrementZ(int) - Method in class Tuple3i
-
Increments the Z component's value by a shift.
- incrementZTwice() - Method in class KernelPointCursor
-
Increments the point by two in the Z dimension.
- IndependentChannels - Class in org.anchoranalysis.plugin.image.task.bean.format.convertstyle
-
Converts each channel independently and creates a single-channeled stack from the conversion.
- IndependentChannels() - Constructor for class IndependentChannels
-
- index(int, int, Extent) - Method in enum OrientationChange
-
Determines the index in a output-array to put an element after applying the
orientation-change.
- index(int, int, int, Extent) - Method in enum OrientationChange
-
Like {#link determineOutputIndex(int,int,Extent)} but also accepts an index.
- index(int) - Method in class IntegerRange
-
Maps an original integer to it's index from (0..size]
- Indexable - Class in org.anchoranalysis.core.index
-
Holds a single-index which is hashable and comparable.
- Indexable(int) - Constructor for class Indexable
-
- IndexableMarksWithEnergy - Class in org.anchoranalysis.mpp.feature.energy
-
- IndexableMarksWithEnergy(int, MarksWithEnergyBreakdown) - Constructor for class IndexableMarksWithEnergy
-
- IndexableOutputNameStyle - Class in org.anchoranalysis.io.output.namestyle
-
An output-name with an index somehow appended or prepended in a particular style.
- IndexableOutputNameStyle() - Constructor for class IndexableOutputNameStyle
-
- IndexableOutputNameStyle(String) - Constructor for class IndexableOutputNameStyle
-
- IndexableOutputNameStyle(IndexableOutputNameStyle) - Constructor for class IndexableOutputNameStyle
-
Copy constructor
- IndexByChannel<T> - Class in org.anchoranalysis.mpp.index
-
- IndexByChannel() - Constructor for class IndexByChannel
-
- IndexByRegion<T> - Class in org.anchoranalysis.mpp.index
-
- IndexByRegion(VoxelPartitionFactory<T>, int, int) - Constructor for class IndexByRegion
-
- indexDistanceMaxToClosestPoint(Point3i, List<ContiguousVoxelPath>, int) - Static method in class FindMinimumDistance
-
The index of whichever of the ContiguousPixelPaths has the nearest point
- IndexedChannel - Class in org.anchoranalysis.image.io.bean.channel
-
A particular
Channel
to be read from a file, identified by its position (index) in the
file.
- IndexedChannel(String, int) - Constructor for class IndexedChannel
-
- IndexedCSVRows - Class in org.anchoranalysis.plugin.mpp.experiment.objects.csv
-
Stores the rows from the CSV file.
- IndexedCSVRows(ReadByLine, ColumnDefinition) - Constructor for class IndexedCSVRows
-
Creates an index of the rows of the CSV file according to a particular columnDefinition
- IndexedRegionBase - Class in org.anchoranalysis.plugin.mpp.bean.region
-
- IndexedRegionBase() - Constructor for class IndexedRegionBase
-
- indexedWithInteger(OutputPatternIntegerSuffix) - Method in class OutputSequenceFactory
-
- indexIncr(String) - Method in class SequenceMemory
-
- indexInitialPoint() - Method in class ContiguousVoxelPath
-
- indexOf(String) - Method in class FeatureNameMapToIndex
-
The index for a particular featureName
- indexOf(Mark) - Method in class VoxelizedMarksWithEnergy
-
- indexOf(Object) - Method in class UpdatableMarksList
-
- indexOf(Mark) - Method in class MarkCollection
-
- IndexRange - Interface in org.anchoranalysis.core.index.range
-
A range of discrete integers with a minimum and a maximum.
- IndexRangeNegative - Class in org.anchoranalysis.core.index.range
-
Specifying a sub-range of indices, tolerating also negative indices.
- IndexRangeNegative(int, int) - Constructor for class IndexRangeNegative
-
Create with a start and end index.
- IndexRangeNegativeFactory - Class in org.anchoranalysis.core.index.range
-
- IndexRangeSeek - Interface in org.anchoranalysis.core.index.range
-
A range of discrete integers, where one can always find the succeeding or preceding index.
- indexUniquePixel - Variable in class ColumnDefinition
-
- InferenceModel - Interface in org.anchoranalysis.inference
-
A model used for inference.
- InferFromHeader - Class in org.anchoranalysis.plugin.io.bean.metadata.reader
-
Tries to construct the
ImageMetadata
from EXIF and other metadata, if available, or
otherwise falls back to another reader.
- InferFromHeader() - Constructor for class InferFromHeader
-
- InferFromHeader(ImageMetadataReader, List<HeaderFormat>) - Constructor for class InferFromHeader
-
- informLatestState(T) - Method in class Kernel
-
Called every time a proposal is accepted, so a kernel can potentially keep track of the state
of the current image
- informLatestState(T) - Method in class KernelIndependent
-
- initBeforeCalc(KernelCalculationContext) - Method in class Kernel
-
- initBeforeCalc(KernelCalculationContext) - Method in class KernelIndependent
-
- initBeforeCalc(KernelCalculationContext) - Method in class KernelProposer
-
- initHeaders(String[]) - Method in class ColumnDefinition
-
- initHeaders(String[]) - Method in class Pairwise
-
- initHeaders(String[]) - Method in class Single
-
- InitializableBean<B,P extends BeanInitialization> - Class in org.anchoranalysis.bean.initializable
-
A bean that must be initialized with some parameters before being used.
- InitializableBean(BeanInitializer<P>, InitializationParameterAssigner) - Constructor for class InitializableBean
-
- InitializationContext - Class in org.anchoranalysis.experiment.io
-
Context for creating initialization-parameters.
- InitializationContext(InputOutputContext) - Constructor for class InitializationContext
-
- InitializationContext(InputOutputContext, Optional<ImageSizeSuggestion>) - Constructor for class InitializationContext
-
- InitializationFactory - Class in org.anchoranalysis.image.feature.calculator
-
- InitializationFactory - Class in org.anchoranalysis.plugin.image.task.stack
-
- InitializationParameterAssigner - Interface in org.anchoranalysis.bean.initializable.property
-
Assigns a parameter to a bean, if the bean accepts it.
- InitializationWithEnergyStack - Class in org.anchoranalysis.plugin.image.task.feature
-
- InitializationWithEnergyStack(EnergyStack, InitializationContext) - Constructor for class InitializationWithEnergyStack
-
- InitializationWithEnergyStack(ImageInitialization, EnergyStack) - Constructor for class InitializationWithEnergyStack
-
- initialize(P, Logger) - Method in class InitializableBean
-
Initializes the bean with the necessary parameters.
- initialize(FeatureInitialization, Logger) - Method in interface FeatureCalculationCache
-
Initializes the cache.
- initialize(List<Histogram>, Optional<Dictionary>) - Method in class VoxelScore
-
Initializes the voxels-score.
- initialize(BeanInstanceMap) - Method in class OutputWriteSettings
-
- initialize() - Method in class MarksWithEnergyBreakdown
-
- initialize(VoxelPartitionFactory<T>, int, int, int) - Method in class IndexByChannel
-
- initialize(MarksInitialization, Logger) - Method in class ReportFeatureEvaluator
-
- initialize(Generator<T>) - Method in class PeriodicSubdirectoryReporter
-
We setup the sequence-writer.
- initialize() - Method in class KernelProposer
-
- initialize() - Method in class TerminationCondition
-
- initialize() - Method in class TerminationConditionListOr
-
- initialize() - Method in class TriggerTerminationCondition
-
- initialize(List<Histogram>, Optional<Dictionary>) - Method in class CalculateLevelBase
-
- initialize(List<Histogram>, Optional<Dictionary>) - Method in class FromDictionaryBase
-
- initialize(List<Histogram>, Optional<Dictionary>) - Method in class IdentityImposeValueRelationToHistogram
-
- initialize(List<Histogram>, Optional<Dictionary>) - Method in class NormalizeByMax
-
- initialize(Logger) - Method in interface AfterCondition
-
- initialize(Logger) - Method in class IncreaseFeatureCondition
-
- initialize(Path) - Method in class BinaryOutcomeImageLabeller
-
- initialize(Path) - Method in class ImageCSVLabeller
-
- initialize(Path) - Method in class ImageLabeller
-
Should be called once before calling any other methods
- initialize(Path) - Method in class ImageLabellerStringMap
-
- initialize(KernelBirth<T>, KernelDeath<T>) - Method in class KernelReplace
-
Must be called before makeProposal
- initialize() - Method in class NumberIterations
-
- initialize() - Method in class UnchangedBase
-
- initialize() - Method in class UnchangedScore
-
- initialize() - Method in class UnchangedSize
-
- InitializeException - Exception in org.anchoranalysis.core.exception
-
An exception that occurs when initializing something, and it doesn't succeed
- InitializeException(String) - Constructor for exception InitializeException
-
Creates with a message, but without a cause.
- InitializeException(Throwable) - Constructor for exception InitializeException
-
Creates with a cause, but without a message.
- InitializeException(String, Throwable) - Constructor for exception InitializeException
-
Creates with message and cause.
- initializePhase(int) - Method in class HungarianAlgorithm
-
Initialize the next phase of the algorithm by clearing the committed workers and jobs sets
and by initializing the slack arrays to the values corresponding to the specified root
worker.
- initializeRecursive(P, Logger) - Method in class InitializableBean
-
Initializes this object, and all children objects, so long as they have P
once a Bean
doesn't have P
, the children are not evaluated.
- initializeRecursive(Logger) - Method in class NullParametersBean
-
Initialize this bean and any suitable child beans.
- initializeRecursive(FeatureInitialization, Logger) - Method in class FeatureList
-
Initializes all features in the list, and recursively any features they contain.
- initializeRecursive(FeatureInitialization, Logger) - Method in class SharedFeaturesSubset
-
Initialize all features in this instance, recursively also initializating any child-features.
- initializerForMarksBeans() - Static method in class MarksBean
-
Creates a property-initializes for MPP-Beans
- initialKernel() - Method in class KernelProposer
-
- initRecursiveWithInitializer(BeanInitializer<?>, Logger) - Method in class InitializableBean
-
Initializes the bean and recursively all contained beans (who have compatible initialization
requirements)
- initSource(int, int) - Method in interface ProcessChangedPointAbsoluteMasked
-
The value and offset for the source point (around which we process neighbors).
- initSource(Point3i, int, int) - Method in interface ProcessVoxelNeighbor
-
Specify the source-point (of which all the processed points are neighbors).
- initSource(int, int) - Method in interface ProcessVoxelNeighborAbsolute
-
The value and offset for the source point (around which we process neighbors).
- initSource(int, int) - Method in class ProcessVoxelNeighborAbsoluteWithSlidingBuffer
-
- initUpdatableMarks(MemoForIndex, EnergyStack, Logger, SharedFeatures) - Method in class RandomCollectionWithAddCriteria
-
- initUpdatableMarks(MemoForIndex, EnergyStack, Logger, SharedFeatures) - Method in class EnergySavedPairs
-
- initUpdatableMarks(MemoForIndex, EnergyStack, Logger, SharedFeatures) - Method in class UpdatableMarksList
-
- initUpdatableMarks(MemoForIndex, EnergyStack, Logger, SharedFeatures) - Method in interface UpdatableMarks
-
- initWithProposerSharedObjects(MarksInitialization, Logger) - Method in class KernelProposer
-
- input() - Method in class ExecutionArguments
-
Arguments to help determine the input to the experiment.
- INPUT_IMAGE - Static variable in class StackIdentifiers
-
The image used as the primary input for a task.
- InputArguments - Class in org.anchoranalysis.experiment.arguments
-
Arguments that can further specify an experiment's input in addition to its bean
specification.
- InputArguments() - Constructor for class InputArguments
-
- InputBound<T,S> - Class in org.anchoranalysis.experiment.task
-
Input for executing a task, associated with shared-state and other parameters.
- InputBound(T, S, boolean, InputOutputContextStateful, InputOutputContextStateful) - Constructor for class InputBound
-
- inputContextParameters() - Method in class ExecutionArguments
-
Additional parameters that offer context for many beans that provide input-functions.
- InputContextParameters - Class in org.anchoranalysis.io.input
-
Additional parameters that offer context for many beans that provide input-functions.
- InputContextParameters() - Constructor for class InputContextParameters
-
- InputFactory - Class in org.anchoranalysis.launcher.executor.selectparam.path
-
SelectParam<Path>
factory for inputs.
- InputFromManager - Interface in org.anchoranalysis.io.input
-
One particular input for processing.
- InputFromManagerDelegate<T extends InputFromManager> - Class in org.anchoranalysis.io.input
-
A base class for
InputFromManager
-implementing classes that delegate to another.
- InputFromManagerDelegate(T) - Constructor for class InputFromManagerDelegate
-
- InputGrouper - Interface in org.anchoranalysis.io.input.grouper
-
Derives a grouping key from an input.
- InputManager<T extends InputFromManager> - Class in org.anchoranalysis.io.input.bean
-
Base class for describing the inputs.
- InputManager() - Constructor for class InputManager
-
- InputManagerParameters - Class in org.anchoranalysis.io.input.bean
-
Parameters passed to an
InputManager
to generate input-objects.
- InputManagerParameters(Logger) - Constructor for class InputManagerParameters
-
Create with only a logger, and using sensible default values for the other fields.
- InputManagerParameters(OperationContext) - Constructor for class InputManagerParameters
-
Create with only a
OperationContext
, and using sensible default values for the other
fields.
- InputManagerParameters(InputContextParameters, OperationContext) - Constructor for class InputManagerParameters
-
- InputManagerUnary<T extends InputFromManager> - Class in org.anchoranalysis.io.input.bean
-
- InputManagerUnary() - Constructor for class InputManagerUnary
-
- InputManagerWithStackReader<T extends InputFromManager> - Class in org.anchoranalysis.image.io.bean.stack.reader
-
- InputManagerWithStackReader() - Constructor for class InputManagerWithStackReader
-
- inputName() - Method in class SegmentStackIntoObjectsScaleDecode
-
The name of the tensor in the model which the input-image is mapped to.
- inputName() - Method in class StackWithMap
-
- inputName() - Method in class SegmentObjectsFromONNXModel
-
- inputName() - Method in class SegmentObjectsFromTensorFlowModel
-
- inputOutput(ExecutionArguments, OutputterChecked) - Method in class ExperimentFeedbackContext
-
- InputOutputContext - Interface in org.anchoranalysis.io.output.outputter
-
A context for performing input generally and outputting to a particular output-directory.
- InputOutputContextFixture - Class in org.anchoranalysis.test.image
-
- InputOutputContextStateful - Class in org.anchoranalysis.experiment.task
-
- InputOutputContextStateful(ExecutionArguments, Outputter, ExecutionTimeRecorder, StatefulMessageLogger, ErrorReporter) - Constructor for class InputOutputContextStateful
-
Creates with initialization arguments.
- InputOutputContextSubdirectoryCache - Class in org.anchoranalysis.io.output.outputter
-
- InputOutputContextSubdirectoryCache(InputOutputContext, boolean) - Constructor for class InputOutputContextSubdirectoryCache
-
- InputOutputExperiment<T extends InputFromManager,S> - Class in org.anchoranalysis.experiment.bean.io
-
- InputOutputExperiment() - Constructor for class InputOutputExperiment
-
- InputReadFailedException - Exception in org.anchoranalysis.io.input
-
When an error occurs reading an input.
- InputReadFailedException(String) - Constructor for exception InputReadFailedException
-
Create with a message only.
- InputReadFailedException(Throwable) - Constructor for exception InputReadFailedException
-
Create with a cause only.
- InputReadFailedException(String, Throwable) - Constructor for exception InputReadFailedException
-
Create with a message and cause.
- inputs(InputManagerParameters) - Method in class AnnotationInputManager
-
- inputs(InputManagerParameters) - Method in class InputManager
-
Creates a list of inputs given particular parameters.
- inputs(InputManagerParameters) - Method in class InputManagerUnary
-
- inputs() - Method in class InputsWithDirectory
-
The inputs.
- inputs(InputManagerParameters) - Method in class MultiInputManager
-
- inputs(InputManagerParameters) - Method in class AnnotationComparisonInputManager
-
- inputs(InputManagerParameters) - Method in class GroupFiles
-
- inputs(InputManagerParameters) - Method in class NamedChannels
-
- inputs(InputManagerParameters) - Method in class NamedChannelsAppend
-
- inputs(InputManagerParameters) - Method in class Concatenate
-
- inputs(InputManagerParameters) - Method in class NamedFiles
-
- inputs(InputManagerParameters) - Method in class NamedFilesWithDirectory
-
- inputs(InputManagerParameters) - Method in class ConvertNamedChannelsToStack
-
- inputs(InputManagerParameters) - Method in class Stacks
-
- inputs(ImageInitialization, Logger) - Method in class ExportObjectsBase
-
- inputs(InputManagerParameters) - Method in class FromCSVInputManager
-
- inputs(InputManagerParameters) - Method in class MultiInputManagerQuick
-
- inputs(InputManagerParameters) - Method in class NamedChannelsQuick
-
- inputSelectParam(CommandLine) - Static method in class SelectParamFactory
-
Can point to either:
a path ending in .xml, assumed to BeanXML for an input manager
a directory, set as an the inputDirectory in the input-context
a string with a wild-card, assumed to be a glob, set into the input-context as a glob
a string with a period and without any forward or backwards slashes, set into the
input-context as an extension to match
- inputsFromDelegate(InputsWithDirectory<T>, InputManagerParameters) - Method in class InputManagerUnary
-
Calculates the inputs to return given the inputs from the delegate.
- inputsFromDelegate(InputsWithDirectory<T>, InputManagerParameters) - Method in class BranchIfDebug
-
- inputsFromDelegate(InputsWithDirectory<T>, InputManagerParameters) - Method in class Exclude
-
- inputsFromDelegate(InputsWithDirectory<T>, InputManagerParameters) - Method in class FilterCSVColumn
-
- inputsFromDelegate(InputsWithDirectory<T>, InputManagerParameters) - Method in class FilterDescriptiveName
-
- inputsFromDelegate(InputsWithDirectory<T>, InputManagerParameters) - Method in class FilterIfDebug
-
- inputsFromDelegate(InputsWithDirectory<T>, InputManagerParameters) - Method in class Limit
-
- inputsFromDelegate(InputsWithDirectory<T>, InputManagerParameters) - Method in class LimitIfRequested
-
- inputsFromDelegate(InputsWithDirectory<T>, InputManagerParameters) - Method in class Shuffle
-
- inputsFromDelegate(InputsWithDirectory<T>, InputManagerParameters) - Method in class ShuffleIfRequested
-
- inputsFromDelegate(InputsWithDirectory<T>, InputManagerParameters) - Method in class SortAlphabetically
-
- InputsWithDirectory<T extends InputFromManager> - Class in org.anchoranalysis.io.input
-
All inputs for an experiment, together with any parent directory which is specified as a parent
for these inputs.
- InputsWithDirectory(List<T>) - Constructor for class InputsWithDirectory
-
Creates without any parent directory.
- InputsWithDirectory(List<T>, Optional<Path>) - Constructor for class InputsWithDirectory
-
- inputType() - Method in class Feature
-
The class corresponding to feature input-type.
- inputType() - Method in class FeatureBinary
-
- inputType() - Method in class FeatureFromList
-
- inputType() - Method in class FeatureGeneric
-
- inputType() - Method in class FeatureUnary
-
- inputType() - Method in class FeatureResults
-
- inputType() - Method in class FeatureEnergy
-
- inputType() - Method in class FeatureHistogram
-
- inputType() - Method in class FeatureImageMetadata
-
- inputType() - Method in class FeatureStack
-
- inputType() - Method in class FeatureObjectCollection
-
- inputType() - Method in class FeaturePairObjects
-
- inputType() - Method in class FeatureSingleObject
-
- inputType() - Method in class AsSingle
-
- inputType() - Method in class FeatureAllMemo
-
- inputType() - Method in class FeaturePairMemo
-
- inputType() - Method in class FeatureSingleMemo
-
- inputType() - Method in class FeatureMarkCollection
-
- inputType() - Method in class FeatureMark
-
- inputType() - Method in class FromDimensionsBase
-
- inputType() - Method in class FeatureSingleObjectFromShared
-
- inputType() - Method in class AsMark
-
- inputType() - Method in class AsObject
-
- inputTypesExpected() - Method in class Task
-
Highest class(es) that will function as a valid input.
- InputTypesExpected - Class in org.anchoranalysis.experiment.task
-
A list of base (parent) classes for input-types that a task expects.
- InputTypesExpected(Class<? extends InputFromManager>) - Constructor for class InputTypesExpected
-
Creates with the class of the input-type.
- inputTypesExpected() - Method in class HelloWorld
-
- inputTypesExpected() - Method in class AggregateAnnotations
-
- inputTypesExpected() - Method in class CompareAnnotations
-
- inputTypesExpected() - Method in class Montage
-
- inputTypesExpected() - Method in class ExportFeatures
-
- inputTypesExpected() - Method in class FeatureSource
-
Highest class(es) that will function as a valid input.
- inputTypesExpected() - Method in class FromHistogram
-
- inputTypesExpected() - Method in class FromImage
-
- inputTypesExpected() - Method in class FromImageMetadata
-
- inputTypesExpected() - Method in class GroupedStackBase
-
- inputTypesExpected() - Method in class ImageAssignLabel
-
- inputTypesExpected() - Method in class RasterTask
-
- inputTypesExpected() - Method in class ScaleImage
-
- inputTypesExpected() - Method in class SegmentInstanceWithModel
-
- inputTypesExpected() - Method in class ExtractSlice
-
- inputTypesExpected() - Method in class CombineCSV
-
- inputTypesExpected() - Method in class CopyFiles
-
- inputTypesExpected() - Method in class SummarizeInputs
-
- inputTypesExpected() - Method in class ConvertNamedChannels
-
- inputTypesExpected() - Method in class Develop
-
- inputTypesExpected() - Method in class ExportReportFeatures
-
- inputTypesExpected() - Method in class FromObjects
-
- inputTypesExpected() - Method in class ExportObjectsAsCroppedImages
-
- inputTypesExpected() - Method in class ExportObjectsFromCSV
-
- inputTypesExpected() - Method in class SegmentMarksFromImage
-
- insertAfter(List<Point3i>) - Method in class ContiguousVoxelPath
-
Inserts points at end of existing path.
- insertBefore(List<Point3i>) - Method in class ContiguousVoxelPath
-
Inserts points before existing path.
- insertBeginning(String) - Method in class FeatureNameList
-
Inserts a new feature-name at the beginning of the list.
- insertBeginning(String[]) - Method in class FeatureNameList
-
Inserts new feature-names at the beginning of the list.
- InsertRegExGroups - Class in org.anchoranalysis.plugin.io.bean.path.derive
-
Generates an out string where $digit$ is replaced with the #digit group from a regex
- InsertRegExGroups() - Constructor for class InsertRegExGroups
-
- InsertRegExGroups(RegEx, String) - Constructor for class InsertRegExGroups
-
- instance() - Static method in class NullInitialization
-
- instance() - Static method in class ExecutionTimeRecorderIgnore
-
Singleton instance.
- INSTANCE - Static variable in class NoSharedState
-
A singleton instance.
- instance() - Static method in class FeatureInputNull
-
A singleton instance.
- instance() - Static method in class DefaultChildCacheFinder
-
- instance() - Static method in class ChannelFactory
-
- INSTANCE - Static variable in class FloatVoxelType
-
A singleton instance of the type.
- INSTANCE - Static variable in class SignedShortVoxelType
-
A singleton instance of the type.
- INSTANCE - Static variable in class UnsignedByteVoxelType
-
A singleton instance of the type.
- INSTANCE - Static variable in class UnsignedIntVoxelType
-
A singleton instance of the type.
- INSTANCE - Static variable in class UnsignedShortVoxelType
-
A singleton instance of the type.
- instance() - Static method in class VoxelsFactory
-
Singleton instance.
- instance() - Static method in class ConfigureBioformatsLogging
-
- INSTANCE - Static variable in class All
-
A singleton instance of
All
.
- INSTANCE - Static variable in class IgnoreUnderscorePrefix
-
- INSTANCE - Static variable in class None
-
A singleton instance of
None
.
- INSTANCE - Static variable in class Permissive
-
- instance() - Static method in class RegionMapSingleton
-
- instance() - Static method in class ErrorNodeNull
-
- instance() - Static method in class RootPathMap
-
- INSTANCE - Static variable in class ResolutionFixture
-
- InstanceSegmentationTestBase - Class in org.anchoranalysis.test.image.segment
-
- InstanceSegmentationTestBase() - Constructor for class InstanceSegmentationTestBase
-
- InsufficientPointsException - Exception in org.anchoranalysis.mpp.bean.points.fitter
-
- InsufficientPointsException() - Constructor for exception InsufficientPointsException
-
- InsufficientPointsException(String, Throwable) - Constructor for exception InsufficientPointsException
-
- InsufficientPointsException(String) - Constructor for exception InsufficientPointsException
-
- InsufficientPointsException(Throwable) - Constructor for exception InsufficientPointsException
-
- IntBinaryPredicate - Interface in org.anchoranalysis.core.functional.unchecked
-
- IntegerList - Class in org.anchoranalysis.bean.primitive
-
A bean defining a list of
Integer
s.
- IntegerList(Integer...) - Constructor for class IntegerList
-
Constructs with one or more values added to the list.
- IntegerListFactory - Class in org.anchoranalysis.bean.xml.factory.primitive
-
- IntegerListFactory() - Constructor for class IntegerListFactory
-
- IntegerRange - Class in org.anchoranalysis.plugin.io.multifile
-
- IntegerRange(int) - Constructor for class IntegerRange
-
- IntegerRange(int, int) - Constructor for class IntegerRange
-
- IntegerSet - Class in org.anchoranalysis.bean.primitive
-
- IntegerSet(Integer...) - Constructor for class IntegerSet
-
Constructs with one or more values added to the list.
- IntegerSet() - Constructor for class IntegerSet
-
- IntegerSetFactory - Class in org.anchoranalysis.bean.xml.factory.primitive
-
- IntegerSetFactory() - Constructor for class IntegerSetFactory
-
- IntegerSuffixOutputNameStyle - Class in org.anchoranalysis.io.output.namestyle
-
Outputs a file-name involving an integer of length numberDigits
with leading zeros.
- IntegerSuffixOutputNameStyle() - Constructor for class IntegerSuffixOutputNameStyle
-
- IntegerSuffixOutputNameStyle(String, int) - Constructor for class IntegerSuffixOutputNameStyle
-
- IntegerSuffixOutputNameStyle(String, String, int) - Constructor for class IntegerSuffixOutputNameStyle
-
- Intensity - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity
-
Calculates a statistic from the intensity values covered by a single object-mask in a channel.
- Intensity() - Constructor for class Intensity
-
- Intensity - Class in org.anchoranalysis.plugin.image.feature.bean.stack.intensity
-
The intensity of a particular channel of the stack, by default the mean-intensity.
- Intensity() - Constructor for class Intensity
-
- Intensity - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
-
- Intensity() - Constructor for class Intensity
-
- IntensityGradientBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient
-
- IntensityGradientBase() - Constructor for class IntensityGradientBase
-
- IntensityGreaterEqualThan - Class in org.anchoranalysis.plugin.image.bean.object.filter.independent
-
Only keep objects where at least one voxel (on a particular channel) has intensity greater or
equal to a threshold.
- IntensityGreaterEqualThan() - Constructor for class IntensityGreaterEqualThan
-
- intensityMax(Voxels<T>) - Static method in class IterateVoxelsAll
-
Finds the maximum intensity-value (as an int) among all voxels.
- IntensityMeanCalculator - Class in org.anchoranalysis.plugin.image.intensity
-
- IntensityMeanMaxSlice - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity
-
- IntensityMeanMaxSlice() - Constructor for class IntensityMeanMaxSlice
-
- IntensityMeanShell - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity
-
Constructs a 'shell' around an object by a number of dilation/erosion operations (not including
the original object-mask) and measures the mean intensity of this shell
- IntensityMeanShell() - Constructor for class IntensityMeanShell
-
- IntensityMeanShellBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity
-
Constructs a shell around an object-mask using a standard dilation and erosion process
- IntensityMeanShellBase() - Constructor for class IntensityMeanShellBase
-
- IntensityMeanShellMaxSlice - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity
-
Constructs a 'shell' around an object by a number of dilation/erosion operations (not including
the original object-mask) and measures the mean intensity of this shell
- IntensityMeanShellMaxSlice() - Constructor for class IntensityMeanShellMaxSlice
-
- intensityMin(Voxels<T>) - Static method in class IterateVoxelsAll
-
Finds the minimum intensity-value (as an int) among all voxels.
- intensityMinMax(Voxels<T>) - Static method in class IterateVoxelsAll
-
Finds the maximum intensity-value (as an int) among all voxels.
- IntensityMoments - Class in org.anchoranalysis.plugin.image.feature.bean.list
-
Calculate various moment-related statistics about the intensity of each channel of an image.
- IntensityMoments() - Constructor for class IntensityMoments
-
- IntensityQuantiles - Class in org.anchoranalysis.image.bean.displayer
-
Implementation of
StackDisplayer
that converts to unsigned-8bit by taking the upper and
lower quantiles of the intensity range.
- IntensityQuantiles() - Constructor for class IntensityQuantiles
-
- IntensityRange - Class in org.anchoranalysis.image.core.channel.convert.attached.channel
-
- IntensityRange() - Constructor for class IntensityRange
-
Default constructor.
- Interpolator - Class in org.anchoranalysis.image.bean.interpolator
-
Defines a particular type of interpolation method that can be used for resizing images.
- Interpolator() - Constructor for class Interpolator
-
- intersect(ObjectMask, Extent) - Method in class ObjectMask
-
Intersects this object-mask with another
- IntersectingCircleObjectsFixture - Class in org.anchoranalysis.test.feature.plugins.objects
-
- IntersectingObjects<T> - Class in org.anchoranalysis.image.voxel.object
-
A data-structure to efficiently determine which object-masks intersect in a collection.
- IntersectingObjects(Collection<T>, Function<T, ObjectMask>) - Constructor for class IntersectingObjects
-
Creates an r-tree for particular objects, as extracted from elements.
- Intersection - Class in org.anchoranalysis.plugin.image.bean.object.match
-
- Intersection() - Constructor for class Intersection
-
- Intersection - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair
-
Finds the intersection of two objects and calculates a feature on it
- Intersection() - Constructor for class Intersection
-
- intersection() - Method in class BoundingBox
-
For evaluating the intersection between this bounding-box and others.
- IntersectionOverUnion - Class in org.anchoranalysis.spatial.box
-
- intersectsWith(ObjectMask) - Method in class IntersectingObjects
-
All elements that intersect with a particular object.
- intersectsWith(BoundingBox) - Method in class IntersectingObjects
-
All elements that intersect with a particular bounding box.
- IntersectsWith - Class in org.anchoranalysis.plugin.image.bean.object.filter.independent
-
Keeps objects which intersects with ANY ONE of a collection of other objects.
- IntersectsWith() - Constructor for class IntersectsWith
-
- intersectsWith(BoundingBox) - Method in class BoundingBoxRTree
-
Which bounding-boxes intersect with another specific bounding box?
- intersectsWith(double, double) - Method in class IntervalRTree
-
Which bounding-boxes intersect with another specific bounding box?
- IntersectsWithContainer - Class in org.anchoranalysis.plugin.image.bean.object.provider.filter
-
Returns only the objects that intersect with at least one object in the container
- IntersectsWithContainer() - Constructor for class IntersectsWithContainer
-
- intersectsWithStream(ObjectMask) - Method in class IntersectingObjects
-
- intersectsWithStream(BoundingBox) - Method in class BoundingBoxRTree
-
- intersectsWithStream(double, double) - Method in class IntervalRTree
-
- intersectsWithStream(Rectangle) - Method in class RTree
-
A stream of the elements that a rectangle intersects with.
- intersectWith(Extent) - Method in class Extent
-
Intersects this extent with another (i.e.
- IntervalRTree<T> - Class in org.anchoranalysis.spatial.rtree
-
An R-Tree that contains items, each with an associated one-dimensional interval.
- IntervalRTree() - Constructor for class IntervalRTree
-
Creates an empty R-Tree.
- IntervalRTree(int) - Constructor for class IntervalRTree
-
Creates an empty R-Tree with a specified number of children.
- intFromDouble(Point3d, boolean) - Static method in class PointConverter
-
- intFromDoubleCeil(Point3d) - Static method in class PointConverter
-
- intFromDoubleFloor(Point2d) - Static method in class PointConverter
-
- intFromDoubleFloor(Point3d) - Static method in class PointConverter
-
- intFromFloat(Point3f, boolean) - Static method in class PointConverter
-
- IntToFloatFunction - Interface in org.anchoranalysis.core.functional.unchecked
-
Represents a function that accepts an int-valued argument and produces a float-valued result.
- INVALID_AXIS_INDEX - Static variable in class AxisConverter
-
Human-readable error message used when an invalid int
-value for axis
is
passed.
- INVALID_AXIS_STRING - Static variable in class AxisConverter
-
Human-readable error message used when an invalid
String
-value for
axis
is
passed.
- invalidate() - Method in interface FeatureCalculationCache
-
Invalidates existing caches so the next calculation occurs freshly.
- invalidate() - Method in interface ResettableCalculation
-
Resets the cached-calculation, so the next call to doOperationWithParameters() is guaranteed
to calculation the operation, and store the value in the cache.
- invalidate() - Method in class CalculationPart
-
- invalidate() - Method in class CalculationPartMap
-
Invalidates the cache, removing any items already stored.
- invalidateExcept(Set<ChildCacheName>) - Method in interface FeatureCalculationCache
-
Invalidates existing caches so the next calculations occur freshly - except some particular
child-caches who are not invalidated.
- InvalidPathArgumentException - Exception in org.anchoranalysis.launcher.executor.selectparam.path.convert
-
An exception throw if an invalid-path is inputted as an argument.
- InvalidPathArgumentException(String) - Constructor for exception InvalidPathArgumentException
-
- InvalidPathArgumentException(String, InvalidPathException) - Constructor for exception InvalidPathArgumentException
-
- invert(Mask) - Static method in class MaskInverter
-
Modifies a mask so that off voxels become on voxels and vice versa.
- invert() - Method in class BinaryVoxels
-
Changes the off state to be the on state and vice-versa.
- invert() - Method in class BinaryValuesByte
-
Inverts the values so off becomes on, and vice-versa.
- invert() - Method in class ObjectMask
-
Produces a new object-mask that uses the same voxel-buffer but switches the off and
on mapping.
- Invert - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
-
Subtracts each voxel from the maximum value for the channel's data type (e.g.
- Invert() - Constructor for class Invert
-
- Invert - Class in org.anchoranalysis.plugin.image.bean.mask.provider
-
Switches on voxels to off and vice-versa.
- Invert() - Constructor for class Invert
-
- Invert - Class in org.anchoranalysis.plugin.image.bean.scale
-
Invert the
ScaleFactor
calculated by the
scaleCalculator
delegate.
- Invert() - Constructor for class Invert
-
- Invert - Class in org.anchoranalysis.plugin.image.bean.segment.binary
-
Performs a segmentation and inverts and on and off bytes
- Invert() - Constructor for class Invert
-
- invert() - Method in class ScaleFactor
-
Build a new scale factor where each dimension is set to the reciprocal of its current value.
- InvertedMax<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic
-
Finds the repciprocal (multiplicate inverse), but imposes a maximum ceiling via a constant.
- InvertedMax() - Constructor for class InvertedMax
-
- invertObjectDuplicate(ObjectMask) - Static method in class MaskInverter
-
Creates a new object-mask where off voxels become on voxels and vice versa.
- isAcceptDirectoryErrors() - Method in class SearchDirectory
-
If true, continues when a directory-access-error occurs (logging it), otherwise throws an
exception.
- isAccepted() - Method in class DualMarksAnnotation
-
Whether the the annotation was marked as accepted by the annotator?
- isAccepted() - Method in class KernelDecision
-
- isAccepted() - Method in class Reporting
-
- isAcceptMissingResolution() - Method in class WithResolutionBase
-
Whether to throw an exception (if true) if image-resolution is missing, or return Double.Nan
(if false).
- isAcceptMissingResolution() - Method in class VoxelPhysicalSize
-
Whether to throw an exception (if true) if image-resolution is missing, or return Double.Nan
(if false).
- isAcceptNoResolution() - Method in class ReadVoxelExtentXml
-
If false, an exception is thrown if the resolution file is missing for a particular image.
- isAcceptOutsideScene() - Method in class CheckMarkWithMask
-
- isAddName() - Method in class CombineCSV
-
- isAddOne() - Method in class Quantile
-
- isAlways2D() - Method in class StackWriteAttributes
-
Whether the output is guaranteed to only ever 2D i.e.
- isAnyChannel3D() - Method in class Stack
-
Is at least one channel 3D?
- isAnyChannel3D() - Method in class StackNotUniformSized
-
Is at least one channel 3D?
- isApplyResolution() - Method in class DistanceTransform3D
-
Multiples the values by the x-resolution, if it exists.
- isApplyToPath() - Method in class MatchRegularExpression
-
If true, the filter is applied to the path, not just the filename (using forward slashes as
directory separators)
- isAsPercentage() - Method in class Quantile
-
If true, the quantile is interpreted as a percentage rather than a decimal.
- isAtLeastOnePositive() - Method in class MorphologicalIterations
-
Checks that at least one of iterationsDilation
and iterationsErosion
is more
than 0
- isAvoidBulletOnFirst() - Method in class SummarizerAggregate
-
Iff true no bullet is added for the very first-item in the list
- isAvoidDivideByZero() - Method in class Divide
-
- isAvoidOverlappingObjects() - Method in class PairNeighbors
-
If true, no overlapping objects are treated as pairs
- isBest() - Method in class Reporting
-
- isBest() - Method in class VoxelizedMarksChangeReporter
-
- isBigNeighborhood() - Method in class Dilate
-
- isBigNeighborhood() - Method in class ConnectedComponentsFromMask
-
If true uses 8 neighborhood rather than 4 neighborhood etc.
- isBigNeighborhood() - Method in class DecomposeIntoConnectedComponents
-
if true, uses 8 neighborhood instead of 4, and similarly in 3d
- isBigNeighborhood() - Method in class Dilate
-
- isBigNeighborhood() - Method in class TraverseOuterContourOnImage
-
- isBinary() - Method in class StackWriteAttributes
-
Whether all channels represent a binary image.
- isBinary() - Method in class ScaleImage
-
Iff true the image to be scaled is treated as a binary-mask, and interpolation during scaling
ensures only two binary-values are outputted.
- isBit0() - Method in class RegionMembership
-
- isBit1() - Method in class RegionMembership
-
- isBit2() - Method in class RegionMembership
-
- isBit3() - Method in class RegionMembership
-
- isBit4() - Method in class RegionMembership
-
- isBit5() - Method in class RegionMembership
-
- isBit6() - Method in class RegionMembership
-
- isBit7() - Method in class RegionMembership
-
- isBold() - Method in class TextStyle
-
Whether to bold the drawn text
- isBoundingBoxAtBorder(BoundingBox, Extent) - Method in class AtBorderBase
-
- isBoundingBoxAtBorder(BoundingBox, Extent) - Method in class AtBorderXY
-
- isBoundingBoxAtBorder(BoundingBox, Extent) - Method in class AtBorderZ
-
- isBufferOff(UnsignedByteBuffer) - Method in class KernelPointCursor
-
Is the value at the current index in this buffer corresponding to an off state?
- isBufferOn(UnsignedByteBuffer) - Method in class KernelPointCursor
-
Is the value at the current index in this buffer corresponding to an on state?
- isBySlices() - Method in class ConnectedComponentsFromMask
-
- isBytewiseCompare() - Method in class ComparisonPlan
-
- isCalledRegisterAllPackage() - Static method in class RegisterBeanFactories
-
- isCaseSensitive() - Method in class PatternSpan
-
Iff true, a case sensitive search is used to match patterns.
- isChangeExisting() - Method in class ConvertBase
-
If true, the existing channel can be changed.
- isClearOutsideMask() - Method in class ThresholdAgainstChannel
-
- isCollapseFilename() - Method in class FilePathAppendBase
-
- isCompatibleWith(Class<? extends FeatureInput>, Class<? extends FeatureInput>) - Static method in class FeatureInputType
-
Can these parameters be used with a particular feature?
- isCompatibleWith(Mark) - Method in interface CompatibleWithMark
-
- isCompatibleWith(Mark) - Method in class AndList
-
- isCompatibleWith(Mark) - Method in class CheckMarkWithMask
-
- isCompatibleWith(Mark) - Method in class FeatureValueCheckMark
-
- isCompatibleWith(Mark) - Method in class Not
-
- isCompatibleWith(Mark) - Method in class RadiiMinRatio
-
- isCompatibleWith(Mark) - Method in class VolumeMin
-
- isCompatibleWith(Mark) - Method in class CreateNew
-
- isCompatibleWith(Mark) - Method in class FromMarkProposer
-
- isCompatibleWith(Mark) - Method in class FromObjects
-
- isCompatibleWith(Mark) - Method in class FromProvider
-
- isCompatibleWith(Mark) - Method in class FromSerializedMarks
-
- isCompatibleWith(Mark) - Method in class Check
-
- isCompatibleWith(Mark) - Method in class Check
-
- isCompatibleWith(Mark) - Method in class MarkFromCollectionProposerUnary
-
- isCompatibleWith(Mark) - Method in class UniformRandom
-
- isCompatibleWith(Mark) - Method in class FromSerializedObject
-
- isCompatibleWith(Mark) - Method in class MarkProposerFromList
-
- isCompatibleWith(Mark) - Method in class MarkProposerReference
-
- isCompatibleWith(Mark) - Method in class MarkProposerUnary
-
- isCompatibleWith(Mark) - Method in class ObjectAsPoints
-
- isCompatibleWith(Mark) - Method in class OrientationAndRadiiProposer
-
- isCompatibleWith(Mark) - Method in class Position
-
- isCompatibleWith(Mark) - Method in class MarkMergeProposerReference
-
- isCompatibleWith(Mark) - Method in class MergeMarkEllipse
-
- isCompatibleWith(Mark) - Method in class RandomOrientation
-
- isCompatibleWith(Mark) - Method in class RandomXY
-
- isCompatibleWith(Mark) - Method in class IncludeRandomObjects
-
- isCompatibleWith(Mark) - Method in class XYOrientationExtendToZ
-
- isCompatibleWith(Mark) - Method in class RadiiProposerRepeat
-
- isCompatibleWith(Mark) - Method in class UniformRandomRadiiProposer
-
- isCompatibleWith(Mark) - Method in class MarkSplitProposerReference
-
- isCompatibleWith(Mark) - Method in class KernelBirthPartition
-
- isCompatibleWith(Mark) - Method in class KernelReplacePartition
-
- isCompatibleWith(Mark) - Method in class KernelBirthAndKill
-
- isCompatibleWith(Mark) - Method in class KernelDeath
-
- isCompatibleWith(Mark) - Method in class KernelExchange
-
- isCompatibleWith(Mark) - Method in class KernelInitialMarksFromPartition
-
- isCompatibleWith(Mark) - Method in class KernelInitialMarksProposed
-
- isCompatibleWith(Mark) - Method in class KernelInitialMarksVoxelized
-
- isCompatibleWith(Mark) - Method in class KernelMerge
-
- isCompatibleWith(Mark) - Method in class KernelSplit
-
- isCompatibleWith(Mark) - Method in class KernelBirthVoxelized
-
- isCompatibleWith(Mark) - Method in class ConstantWeight
-
- isCompatibleWith(Mark) - Method in class NumberPoints
-
- isCompatibleWith(Mark) - Method in class FitPoints
-
- isCompatibleWith(Mark) - Method in class LinearLeastSquaresEllipseFitter
-
- isCompatibleWith(Mark) - Method in class LinearLeastSquaresEllipsoidFitter
-
- isCompatibleWith(Mark) - Method in class Reference
-
- isCompatibleWith(Mark) - Method in class ReflectInAxesWithinDistance
-
- isCompleted() - Method in class JobStateMonitor
-
Is a job completed?
- isCompletedFailure() - Method in class JobStateMonitor
-
Has a job completed with a failure?
- isCompletedSuccessfully() - Method in class JobStateMonitor
-
Has a job completed with a successful outcome?
- isConditionTrue() - Method in class DictionaryCondition
-
- isConnectedComponentID(int) - Method in class EncodedIntBuffer
-
- isConnectedComponentIDCode(int) - Method in class EncodedVoxels
-
- isConnectedComponentIDCode(int) - Method in class WatershedEncoding
-
- isConsiderForMerge() - Method in class PrioritisedVertex
-
- isConvexHull() - Method in class FitPointsFromObjects
-
If true, Reduces the set of points by applying a convex-hull operation
- isCopyNonInputs() - Method in class InputArguments
-
When true, any files in the input directory that are unused as inputs, are copied to the
output directory.
- isCov() - Method in class ObjectRadiusStandardDeviation
-
- isCreateShort() - Method in class Arrange
-
If true, the created raster has unsigned short voxel data type.
- isCreateShort() - Method in class TileWithLabels
-
When true, the voxel-data-type of the created image is unsigned short, otherwise
unsigned byte.
- isCreateShort() - Method in class WriteText
-
When true, text
is drawn across all z-slices in the stack.
- isCreateShort() - Method in class DistanceTransform3D
-
- isCreateShort() - Method in class DistanceTransformForEachObject3D
-
- isCreateShort() - Method in class CreateNew
-
If True creates an unsigned short-image
- isCsvIgnoreZeros() - Method in class ExportImageHistograms
-
Iff true, bins with zero-counts are not written as a row in the CSV file.
- isDatasetNameSubdirectory() - Method in class ExperimentResultsExperimentStructure
-
If true the datasetName is appended as a subdirectory e.g.
- isDay() - Method in class ExperimentIdentifierAuto
-
If true, the current day (yyyy.MM.dd) is included in the output.
- isDebug() - Method in class RootPath
-
If true this root is preferred, when executing a job in debugging mode.
- isDebug() - Method in class ThresholdedFeature
-
- isDebugEnabled() - Method in class InputOutputContextStateful
-
- isDebugEnabled() - Method in interface InputOutputContext
-
Is debug-mode enabled?
- isDebugEnabled() - Method in class OptimizationContext
-
- isDebugMode() - Method in class PathPrefixerContext
-
Whether debug-mode is activated.
- isDebugModeActivated() - Method in class InputManagerParameters
-
Whether debug-mode has been activated.
- isDebugModeEnabled() - Method in class ExecutionArguments
-
Has debug mode been enabled when executing an experiment?
- isDefault() - Method in interface SelectParam
-
Is this the default option that occurs without any additional user effort?
- isDefault() - Method in class UseDefaultManager
-
- isDeleteExistingDirectory() - Method in class DirectoryCreationParameters
-
When true, this will delete any existing directory with the same path, and then create it
anew.
- isDetailedLogging() - Method in class ExperimentFeedbackContext
-
Iff true, additional log messages are written to describe each job in terms of its unique
name, output folder, average execution time etc.
- isDetailedLogging() - Method in class InputBound
-
Whether logging is more detailed (true) or less detailed (false).
- isDetailedLogging() - Method in class ParametersExperiment
-
Iff true, additional log messages are written to describe each job in terms of its unique
name, output folder, average execution time etc.
- isDifferentColorsForPairs() - Method in class AssignmentColorPool
-
If true, different colors are used for paired objects, otherwise always the same color is
used.
- isDirect() - Method in class UnsignedBuffer
-
Is this buffer direct or non-direct?
- isDirect() - Method in class VoxelBuffer
-
Is this buffer direct or non-direct?
- isDirect() - Method in class VoxelBufferUnsigned
-
- isDirectionChainCode(int) - Method in class EncodedVoxels
-
- isDirectionChainCode(int) - Method in class WatershedEncoding
-
- isDisableDebugMode() - Method in class RootedFilePath
-
- isDisableDebugMode() - Method in class Rooted
-
- isDo3D() - Method in class AnisotropicDiffusion
-
Whether to perform the diffusion in 3D direction, or rather only in the 2D plane.
- isDo3D() - Method in class ObjectCollectionProviderMorphological
-
- isDo3D() - Method in class MorphologicalIterations
-
Whether to perform the morphological dimensions in 3D or 2D
- isDo3D() - Method in class PairNeighbors
-
- isDo3D() - Method in class TouchingVoxels
-
- isDo3D() - Method in class Erode
-
- isDo3D() - Method in class NumberRemovedVoxelsAfterClosing
-
- isDo3D() - Method in class OutlineKernelBase
-
- isDo3D() - Method in class UniformRandomRadiiProposer
-
- isDuplicate() - Method in class Reference
-
If true the channel is duplicated after it is retrieved, to prevent overwriting existing data
This is a shortcut to avoid embedding beans in a ChannelProviderDuplicate
- isDuplicate() - Method in class Reference
-
If true the channel is duplicated after it is retrieved, to prevent overwriting exisiting
data This is a shortcut to avoid embedding beans in a ChannelProviderDuplicate
- isEightBitChannels() - Method in class StackWriteAttributes
-
Whether each channel is 8 bits.
- isEmpty() - Method in class DoubleList
-
- isEmpty() - Method in class DoubleSet
-
- isEmpty() - Method in class IntegerList
-
- isEmpty() - Method in class IntegerSet
-
- isEmpty() - Method in interface PrimitiveBeanCollection
-
Whether the collection is empty or not.
- isEmpty() - Method in class StringList
-
- isEmpty() - Method in class StringSet
-
- isEmpty() - Method in class MapCreate
-
Whether the map is empty or not.
- isEmpty() - Method in class StringSetTrie
-
Does the set contain no elements?
- isEmpty() - Method in interface NamedProvider
-
Are there any items in the provider?
- isEmpty() - Method in class RecordedExecutionTimes
-
Are there no recorded operations?
- isEmpty() - Method in class FeatureList
-
Returns true
if this list contains no elements.
- isEmpty() - Method in class ResultsVectorList
-
Returns true
if the list contains no elements.
- isEmpty() - Method in class ObjectCollectionWithProperties
-
Whether the number of objects is zero.
- isEmpty() - Method in class ReduceObjectsGraph
-
Do no elements exist?
- isEmpty() - Method in class SegmentedObjects
-
Whether no segmented objects exist.
- isEmpty() - Method in class TimeSeries
-
Whether the series contains no frames?
- isEmpty() - Method in class ObjectCollection
-
Whether the collection contains no objects.
- isEmpty() - Method in class InputsWithDirectory
-
Whether no inputs exist.
- isEmpty() - Method in class RecordedOutputs
-
If no output-names exist.
- isEmpty() - Method in class Histogram
-
If no value exists in the histogram with a count greater than zero.
- isEmpty() - Method in class UpdatableMarksList
-
- isEmpty() - Method in class MarkCollection
-
- isEmpty() - Method in class Extent
-
Does the extent contain zero voxels?
- isEmpty() - Method in class PointRange
-
Has a valid min and max defined?
- isEmpty() - Method in class RTree
-
Returns true if and only if the R-tree is empty of entries.
- isEnabled() - Method in class TextFileOutput
-
- isErodeAtBoundary() - Method in class ConvexHullBase
-
- isErrorDisconnectedObjects() - Method in class RemoveIntersectingVoxels
-
If true, throws an error if there is a disconnected object after the erosion
- isEvaluated() - Method in class CachedSupplierBase
-
Has the function already been evaluated?
- isExceptionIfEmpty() - Method in class FeatureHistogramStatistic
-
- isExcludeZero() - Method in class Intensity
-
Iff true, zero-valued voxels are excluded from the histogram
- isExcludeZero() - Method in class IntensityMeanMaxSlice
-
- isExcludeZero() - Method in class Intensity
-
If true, zeros are excluded from considering in the histogram
- isExecuting() - Method in class JobStateMonitor
-
Is a job currently executing?
- isExitBeforeOptimization() - Method in class SegmentWithMarkedPointProcess
-
Iff true the algorithm exits before optimization begins (useful for debugging).
- isExitWithMinima() - Method in class WatershedYeong
-
If true, exits early and just returns the minima, without any further segmentation
- isExpandLabelZ() - Method in class TileWithLabels
-
When true, the label is repeated across all z-slices in the stack.
- isExtendInZ() - Method in class ExportObjectsAsCroppedImages
-
Extends the objects in z-dimension (uses maximum intensity for the segmentation, but in all
slices)
- isFieldAnnotatedAsOptional(Field) - Static method in class FieldAccessor
-
- isFindMaxima() - Method in class ExtractSlice
-
If true, the maxima of the score is searched for.
- isFinished() - Method in class DualMarksAnnotation
-
- isFirst() - Method in class AsSingle
-
Iff true, first object is used, otherwise the second
- isFirstDefined() - Method in class OutputEnableRulesSpecify
-
- isFirstLineHeaders() - Method in class CombineCSV
-
- isFixRandomSeed() - Method in class SegmentWithMarkedPointProcess
-
Iff true uses a constant seed for the random-number-generator (useful for debugging).
- isFlatten() - Method in class MultipleComparer
-
If true, a maximum-intensity-projection is first applied to any 3D objects into a 2D plane,
before comparison.
- isFlatten() - Method in class CompareAnnotations
-
If true, a maximum-intensity-projection is first applied to any 3D objects into a 2D plane,
before comparison.
- isFlatten() - Method in class ExteriorContour
-
If true, any 3D mask is flattened in the z-dimension (maximum intensity projection) to make
it 2D
- isFlatten() - Method in class ColoredBase
-
If true, objects and the background are flattened in the z dimension (via maximum intensity
projection), so that a 2D image is produced.
- isForceChangeBytes() - Method in class Invert
-
If true, rather than modifying the binary-values (an index) bytes are modified in the buffer
to reflect the existing binary-values.
- isForceDetailedLogging() - Method in class OutputExperiment
-
Whether more detailed log-messages around each experiment occur.
- isForceEagerEvaluation() - Method in class NamedChannelsAppend
-
- isForceRGB() - Method in class Arrange
-
Iff true, ensures every stack is converted into 3 channels.
- isForwardDirectionOnly() - Method in class XYOrientationExtendToZ
-
- isGaussian() - Method in class AddEdgeFilters
-
If true, the Gaussian filter is included.
- isGpu() - Method in class ConcurrentModel
-
Whether model is using the GPU or not.
- isGPU() - Method in class WithPriority
-
- isHighestTwoRadiiOnly() - Method in class RadiiRatio
-
- isIgnoreAtThreshold() - Method in class OutlineKernelBase
-
- isIgnoreCase() - Method in class FilePathPattern
-
if true, case is ignored in the pattern matching.
- isIgnoreFileNotFoundAppend() - Method in class NamedChannelsAppend
-
- isIgnoreFittingFailure() - Method in class FitPointsFromObjects
-
If true, if too few points exist to make a mark, or otherwise a fitting errors, it is simply
not included (with only a log error) If false, an exception is thrown
- isIgnoreHidden() - Method in class SearchDirectory
-
If true, case is ignored in the pattern matching.
- isIgnoreHidden() - Method in class FilePathPattern
-
Iff true, any hidden-path is not considered, and simply ignored
- isIgnoreHigherSide() - Method in class GaussianCumulative
-
- isIgnoreLowerSide() - Method in class GaussianCumulative
-
- isIgnoreMissingChannel() - Method in class IndependentChannels
-
Iff true and we cannot find a channel in the file, we ignore it and carry on
- isIgnoreNaN() - Method in class Sum
-
If true, we ignore any NaN values.
- isIgnoreNoObjects() - Method in class SegmentInstanceWithModel
-
When true, then the outputs (outline, mask, image etc.) are not written for images that
produce no objects.
- isIgnoreOutside() - Method in class KernelApplicationParameters
-
When true, any parts of the neighborhood that lie outside the scene are not considered in
kernel neighborhoods.
- isIgnoreOutside() - Method in enum OutsideKernelPolicy
-
When true, any parts of the neighborhood that lie outside the scene are not considered in
kernel neighborhoods.
- isIgnoreZero() - Method in class RatioNonMode
-
- isIgnoreZeros() - Method in class HistogramCSVGenerator
-
Iff true bins in the histogram with a zero count are not written
- isIgnoreZIfNaN() - Method in class DistanceTransform3D
-
If the z-resolution is undefined, the z dimenion is ignored.
- isIncludeBatchDimension() - Method in class SegmentObjectsFromONNXModel
-
If true, a 4-dimensional tensor is created (with the first dimension describing a batch-size
of 1), instead of the usual 3-dimensional tensor describing channel, height, width.
- isIncludeDirectories() - Method in class DirectoryStructure
-
If false, the folders are ignored, and only the file-name is used in the output
- isIncludeFeatureNames() - Method in class EnergySchemeCreatorByElement
-
If true, the names of the imageFeatures are taken as a combination of the namedItem and the
actual features
- isIncludeFileName() - Method in class AppendDictionary
-
- isIncludeFirst() - Method in class PairNeighbors
-
Include features for the First-object of the pair
- isIncludeMerged() - Method in class PairNeighbors
-
Include features for the Merged-object of the pair
- isIncludeSecond() - Method in class PairNeighbors
-
Include features for the Second-object of the pair
- isIncludeShell() - Method in class MaxOverlapRatio
-
- isIncludeZ() - Method in class Outline
-
If true the outline is also applied in the z-dimension, otherwise this is ignored as possible
boundary
- isIncludeZ() - Method in class NotTouchingSceneBorder
-
- isInitialized() - Method in class InitializableBean
-
- isInputCompatibleWith(Class<? extends InputFromManager>) - Method in class JobProcessor
-
Is an input-type compatible with this particular task?
- isInputCompatibleWith(Class<? extends InputFromManager>) - Method in class Task
-
Is an input-object type compatible with this particular task?
- isInteger() - Method in class FloatVoxelType
-
- isInteger() - Method in class SignedVoxelType
-
- isInteger() - Method in class UnsignedVoxelType
-
- isInteger() - Method in class VoxelDataType
-
Whether the data-type represents an integer or floating-point?
- isInterleaveChannels() - Method in class SegmentObjectsFromONNXModel
-
If true, the channels are placed as the final position of the tensor (**after** width/height)
instead of **before** width/height.
- isInterleaved() - Method in class ImageFileEncoding
-
Whether the channels are interleaved
- isInverse() - Method in class IntersectsWithContainer
-
- isInverse() - Method in class IntensityMeanShellBase
-
Iff true, calculates instead on the inverse of the object-mask (what's left when the shell is
removed).
- isInverseMask() - Method in class IntensityMeanShellBase
-
If true, uses the inverse of the passed mask.
- isInvert() - Method in class MaskAsObject
-
- isInvert() - Method in class FromObjects
-
- isInvert() - Method in class FilterWithRegularExpression
-
Iff true, then a file is rejected if the regular-expression matches and vice-versa.
- isInvertDecisionValue() - Method in class FeatureListProviderSVMClassifier
-
- isKeepEntireImage() - Method in class ExportObjectsAsCroppedImages
-
If true, rather than writing out a bounding-box around the object-mask, the entire image is
written
- isKeepExtension() - Method in class CollapseFileName
-
When true, the extension is appended to the directory.
- isKeepExtremes() - Method in class Identity
-
- isKeepZ() - Method in class ImposeResolution
-
Keep the z-resolution if it is already defined
- isKeyRequired() - Method in class RegularExpression
-
- isLabel() - Method in class MontageSlices
-
If true a label is added beside every image showing the slice index
- isLeaf() - Method in class ErrorNodeImpl
-
- isLocalized() - Method in class FilesProviderWithDirectoryString
-
- isLogPath() - Method in class Rooted
-
if true, the pathIn and pathOut are logged.
- isMakeRGB() - Method in class ChannelSpecification
-
If true, the the RGB-flag is set on the created stack, if false it is not.
- isMarksSpan(MarkCollection) - Method in class RandomCollectionWithAddCriteria
-
- isMarksSpan() - Method in class VoxelizedMarksWithEnergy
-
- isMarksSpan(MarkCollection) - Method in class EnergySavedPairs
-
- isMax() - Method in class IdentityImposeValueRelationToHistogram
-
- isMedian() - Method in class AddEdgeFilters
-
If true, the median filter is included.
- isMemberFlag(byte, byte) - Method in class RegionMembership
-
- isMemberFlag(byte, byte) - Method in class RegionMembershipAnd
-
- isMemberFlag(byte, byte) - Method in class RegionMembershipOr
-
- isMemberFlag(byte) - Method in class RegionMembershipWithFlags
-
- isMemberFlagAnd(byte, byte) - Static method in class RegionMembershipUtilities
-
- isMemberFlagOr(byte, byte) - Static method in class RegionMembershipUtilities
-
- isMerge() - Method in class CutBelowThreshold
-
- isMinima(int) - Method in class EncodedIntBuffer
-
- isMinima(int) - Method in class EncodedVoxels
-
- isMip() - Method in class NumberVoxels
-
- isMip() - Method in class SurfaceNumberVoxelsBase
-
- isMip() - Method in class OverlapMIPBase
-
- isNoBlack() - Method in class ThresholderAutoIJ
-
- isNormalize() - Method in class Identity
-
- isNormalize() - Method in class BoundingBoxZOverlapRatio
-
- isNormalizeFeatures() - Method in class FeatureListProviderSVMClassifier
-
Normalize features
- isNoScale() - Method in class ScaleFactor
-
Does the scale-factor involve no scaling at all?
- isNumeric() - Method in class TypedValue
-
Whether the value is numeric or not.
- isNumeric() - Method in class ReportFeature
-
- isNumeric() - Method in class ReportFeatureOnMark
-
- isNumeric() - Method in class ReportFeatureOnMarks
-
- isNumeric() - Method in class ReportFeatureOnObjectsBase
-
- isNumeric() - Method in class ReportFeatureWrapError
-
- isOff(int, int, int) - Method in interface BinaryOnOffSetter
-
Does the voxel at this point have an off state?
- isOff(Point3i) - Method in interface BinaryOnOffSetter
-
Does the voxel at this point have an off state?
- isOff(byte) - Method in class BinaryValuesByte
-
Does a particular value correspond to the off state?
- isOmitExperimentIdentifier() - Method in class OutputArguments
-
Has a request occurred that the experiment-identifier is omitted?
- isOmitExperimentIdentifier() - Method in class OutputPrefixerSettings
-
When true, Requests that the experiment-identifier (name and index) is not included in the
output-directory path.
- isOn(int, int, int) - Method in interface BinaryOnOffSetter
-
Does the voxel at this point have an on state?
- isOn(Point3i) - Method in interface BinaryOnOffSetter
-
Does the voxel at this point have an on state?
- isOn(byte) - Method in class BinaryValuesByte
-
Does a particular value correspond to the on state?
- isOn() - Method in interface OutputSequence
-
- isOn() - Method in class OutputSequenceIncrementing
-
- isOn() - Method in class OutputSequenceIndexed
-
- isOpenInDesktop() - Method in class ExperimentExecutor
-
Whether to open the output directory in the desktop GUI after execution (if supported on the
O/S).
- isOperationAlreadyRecorded(String) - Method in class ExecutionTimeRecorder
-
Has a particular operation already been recorded?
- isOperationAlreadyRecorded(String) - Method in class ExecutionTimeRecorderIgnore
-
- isOutline() - Method in class ColoredBase
-
If true, an outline is drawn around the entries.
- isOutlineAtBoundary() - Method in class ExteriorContour
-
- isOutputEnabled() - Method in class CSVWriter
-
- isOutputEnabled(String) - Method in class All
-
- isOutputEnabled(String) - Method in class IgnoreUnderscorePrefix
-
- isOutputEnabled(String) - Method in class None
-
- isOutputEnabled(String) - Method in class SpecificDisabled
-
- isOutputEnabled(String) - Method in class SpecificEnabled
-
- isOutputEnabled(String) - Method in class MultiLevelBinary
-
- isOutputEnabled(String) - Method in class MultiLevelNot
-
- isOutputEnabled(String) - Method in class OutputEnabledMutable
-
- isOutputEnabled(String) - Method in class SingleLevelBinary
-
- isOutputEnabled(String) - Method in class SingleLevelInSet
-
- isOutputEnabled(String) - Method in class SingleLevelNot
-
- isOutputEnabled(String) - Method in interface SingleLevelOutputEnabled
-
Is a particular a particular output-enabled?
- isOutputIncrementingNumberSequence() - Method in class OutputPrefixerSettings
-
When true, requests outputting with an incrementing number sequence, rather than the usual
outputter (normally based upon input filenames).
- isOutputShort() - Method in class GradientBase
-
Iff true, outputs a short channel, otherwise byte channel
- isOutsideAtThreshold() - Method in class OutlineKernelBase
-
- isOutsideOffUnignored() - Method in class KernelApplicationParameters
-
True only when voxels outside the scene should not be ignored and considered as
off.
- isOutsideOffUnignored() - Method in class KernelPointCursor
-
True only when voxels outside the scene should not be ignored and considered as
off.
- isOutsideOn() - Method in class KernelApplicationParameters
-
- isOutsideOn() - Method in class KernelPointCursor
-
Whether to treat voxels that lie outside the scene as on (if true) or off (if
false).
- isOutsideOn() - Method in enum OutsideKernelPolicy
-
- isOutsideOnUnignored() - Method in class KernelApplicationParameters
-
True only when voxels outside the scene should not be ignored and considered as
on.
- isOverlappingObjects() - Method in class OutlinePreserveRelativeSize
-
Whether objects may overlap or not when unscaled.
- isParamPrefixAppendNumber() - Method in class PermuteFirstSecondOrder
-
If true the constant is appended to the param prefix (a dot and a number)
- isPhysical() - Method in class UnitConverter
-
- isPixelOn(int, int, int) - Method in class CutOffCorners
-
- isPixelOn(int, int, int) - Method in interface VoxelPattern
-
- isPlateau(int) - Method in class EncodedVoxels
-
- isPlayloadUsed() - Method in class MergePairs
-
- isPlayloadUsed() - Method in class MergeToIncreaseObjectFeature
-
- isPlayloadUsed() - Method in class MergeWithFeature
-
Is the payload considered in making decisions? (iff false, payload of nodes is irrelvant)
- isPointConvexTo(Point3i, Point3i, BinaryVoxels<UnsignedByteBuffer>) - Static method in class VisitSchedulerConvexAboutRoot
-
- isPointConvexTo(Point3i, Point3i, BinaryVoxels<UnsignedByteBuffer>, boolean) - Static method in class VisitSchedulerConvexAboutRoot
-
- isPointInside(Point3i) - Method in class Ellipse
-
- isPointInside(Point3i) - Method in class Ellipsoid
-
- isPointInside(Point3i) - Method in class MarkWithPositionAndSingleRadius
-
- isPointInside(Point3i) - Method in class Mark
-
- isPointInside(Point3i) - Method in class LineSegment
-
- isPointInside(Point3i) - Method in class PointList
-
- isPointInside(Point3i) - Method in class Polygon
-
- isPointInside(Point3i) - Method in class PolygonCurve
-
- isPointInside(Point3i) - Method in class RotatableBoundingBox
-
- isPointOnMask(Point3d, EnergyStack, Function<Point3d, Point3i>) - Method in class CheckMarkWithMask
-
- isPrefix() - Method in class FromXMLList
-
If true, a prefix is prepended to the name of each added bean.
- isPreserveAspectRatio() - Method in class Grow
-
Whether to preserve the aspect-ratio of the smaller image when growing.
- isPreserveAspectRatio() - Method in class FitTo
-
If true, the aspect-ratio is preserved between width and height.
- isPreserveAspectRatio() - Method in class ToDimensions
-
If true, the ratio between x and y is kept constant when scaling.
- isPreserveExtensionIfDuplicate() - Method in class RemoveExtension
-
Keeps the extension if the file-name (without the extension) becomes duplicated with another.
- isPreserveSubdirectories() - Method in class ClusterByTimestamp
-
If true, the entire relative-path is used when copying files into the cluster directory.
- isPrioritizeInputContext() - Method in class MatchExtensions
-
When true, any extensions available in the input-context are prioritized ahead of extensions
.
- isProposal() - Method in class VoxelizedMarksPeriodicReporter
-
- isProposed() - Method in class KernelDecision
-
- isRadiusInMeters() - Method in class WithRadiusBase
-
- isReadFromResources() - Method in class SegmentObjectsFromONNXModel
-
When true, rather than reading modelPath
from the file-system, it is read from Java
resources on the class-path.
- isRecordedAsEnabled(String) - Method in class RecordedOutputs
-
Is a particular output-name recorded as enabled?
- isRecurseSubfolders() - Method in class MultiFileReader
-
- isRecursive() - Method in class SearchDirectory
-
If true the search is applied recursively over sub-directories.
- isRecursive() - Method in class ExperimentResultsExperimentStructure
-
Whether to apply the search recursively or not
- isRejectIterationIfAllLow() - Method in class Erode
-
- isRejectIterationIfDisconnected() - Method in class Erode
-
- isRelativeForIdentifier() - Method in class InputContextParameters
-
If true, the entire filename or relative path (excluding extension) is used to determine a
unique identifier.
- isRelativeToDirectory() - Method in class FileNamerContext
-
If true, the namer should prefer to derive file-names relative to the directory, rather than
only the varying elements in the file-names.
- isRemoveExtension() - Method in class FilePathPattern
-
if true, the extension is removed from paths before finding the pattern.
- isRemoveExtensionInDescription() - Method in class LastDirectories
-
Whether to remove the file-extension from the filename.
- isRemoveNaNColumns() - Method in class ExportFeaturesStyle
-
When true, columns containing all
Double.NaN
values are removed before outputting.
- isRemoveNaNColumns() - Method in class FeatureExporterContext
-
When true, columns containing all
Double.NaN
values are removed before outputting.
- isRemoveTouchingBorderXY() - Method in class FeatureCostAssigner
-
- isReplaceMatchesWithSolids() - Method in class CompareAnnotations
-
- isReplaceWithMidpoint() - Method in class MergeGreedyToIncreaseObjectFeature
-
- isReportFitterErrors() - Method in class FitPoints
-
- isRequireAllFilesMatch() - Method in class GroupFiles
-
- isRequireBBoxNeighbors() - Method in class MergeWithFeature
-
Requires for any potential merge that the bounding-boxes of the two objects must intersect or
touch
- isRequireTouching() - Method in class MergeWithFeature
-
Requires the object-masks to touch.
- isResultUnusual(double) - Method in class ReplaceInfinity
-
- isResultUnusual(double) - Method in class ReplaceNaN
-
- isResultUnusual(double) - Method in class ReplaceUnusualValue
-
- isRewardHigherSide() - Method in class GaussianCumulative
-
Treat the higher side as if it's the the fill cdf
- isRewardLowerSide() - Method in class GaussianCumulative
-
- isRGB() - Method in class DisplayStack
-
Does the display-stack contain an RGB image?
- isRgb() - Method in class ImageMetadata
-
Whether the image is RGB or not.
- isRGB() - Method in class Stack
-
If true, and the stack has exactly three channels, this stack can be interpreted as a RGB
image.
- isRGB(Logger) - Method in class NamedChannelsConcatenate
-
- isRGB(Logger) - Method in interface NamedChannelsMap
-
Whether the channels describe an RGB image.
- isRGB(Logger) - Method in class OpenedNamedChannels
-
- isRGB(Logger) - Method in interface OpenedImageFile
-
Whether the image-file has RGB encoded voxels.
- isRGB() - Method in class ScaleableBackground
-
Does the display-stack contain an RGB image?
- isRGB(IFormatReader) - Method in class Default
-
- isRGB(IFormatReader) - Method in class ForceBitsPerPixel
-
- isRGB(IFormatReader) - Method in class ForceNumberChannels
-
- isRGB(IFormatReader) - Method in class ForceTimeSeriesToStack
-
- isRGB(IFormatReader) - Method in class ReadOptions
-
Is it an image with three channels (red, green and blue)?
- isRGB(IFormatReader) - Method in class ReadOptionsDelegate
-
- isRGB(IFormatReader) - Method in class SwitchChannelTime
-
- isRgb() - Method in class ImageFileEncoding
-
Whether the source bytes encoded as RGB (i.e.
- isRgb() - Method in class FromChannelOrMask
-
If true, the output contains three channels (the input and two duplicates) instead of one
- isRgb() - Method in class NamedChannels
-
Whether the channels originate from a
Stack
that is RGB, or not.
- isRGB(Logger) - Method in class OpenedMultiFile
-
- isRootInStructure() - Method in class ExperimentResultsExperimentStructure
-
If true the directory structure is
ROOT/experiments/${ROOT_NAME}/${DATASET_NAME}_${DATASET_SUFFIX} If false, the directory
structure is ROOT/experiments/${DATASET_NAME}_${DATASET_SUFFIX}
- isSecond() - Method in class ExperimentIdentifierAuto
-
Only relevant if time==true.
- isSecondary() - Method in class VoxelizedMarksPeriodicReporter
-
If proposal
is true, this toggles between the primary and secondary proposal
- isSelective() - Method in class OutputPattern
-
Whether the output should be checked to see if it is allowed or not.
- isSeparateEachLabel() - Method in class SuppressNonMaximum
-
If true, each label is reduced separately.
- isShowAgg() - Method in class MemoryUsageReporter
-
- isShowBest() - Method in class MemoryUsageReporter
-
- isShuffle() - Method in class InputContextParameters
-
If true, the order of the inputs are shuffled (randomized).
- isSigmaInMeters() - Method in class BlurStrategy
-
- isSilentlyDeleteExisting() - Method in class OutputManager
-
Whether to silently first delete any existing output at the intended path, or rather throw an
error.
- isSingleChannel() - Method in class StackWriteAttributes
-
The number of channels is guaranteed to be 1 in the output.
- isSkipAtBorder() - Method in class FillHoles
-
If true we do not fill any objects that touch the border
- isSkipComparisonForRGB() - Method in class ComparisonPlan
-
- isSkipFileName() - Method in class LastDirectories
-
Iff true the filename is not considered, only the subdirectories.
- isSkipFileName() - Method in class FilePathAppendBase
-
- isSkipMissingChannels() - Method in class NamedChannelsAppend
-
- isSlicesSeparately() - Method in class FitBoxToOnVoxels
-
- isSlicewise() - Method in class AggregateChannelTask
-
When true, a 3D image is added slice-by-slice to the aggregation, treating each slice as a
separate image.
- isSortIfNotRequested() - Method in class ShuffleIfRequested
-
When true, the inputs are sorted alphabetically, if a shuffle is not requested.
- isStackAsChannel() - Method in class MultiInputManagerQuick
-
If true, a raster-stack is treated as a single-channel, even if multiple exist (and no
additionalChannel is set)
- isStackBackground() - Method in class VisualizeOnBackground
-
- isStrongEdgeEnhancer() - Method in class AnisotropicDiffusion
-
If true uses, the strong-edge-enhancer diffusion function, otherwise the
wide-region-enhancer.
- isSubtractFromMaskOnly() - Method in class SubtractMean
-
- isSuppress3D() - Method in class MorphologicalOperatorBase
-
- isSuppress3D() - Method in class SurfaceNumberVoxelsBase
-
- isSuppress3D() - Method in class SegmentThresholdAboveMinBound
-
- isSuppressDirectories() - Method in class FromDescriptiveName
-
If true, any directory separators in the identifier in a descriptive-name are replaced by
underscores.
- isSuppressErrors() - Method in class ExportFeaturesStyle
-
When false, an image is reported as errored, if any exception is thrown during calculation.
- isSuppressErrors() - Method in class FeatureCalculationContext
-
When false, an image is reported as errored, if any exception is thrown during calculation.
- isSuppressErrors() - Method in class FeatureExporterContext
-
If false, an image is reported as errored, if any exception is thrown during calculation.
- isSuppressErrors() - Method in class FromObjects
-
When true, exceptions aren't thrown when feature-calculations fail, but rather a log error
message is written.
- isSuppressExceptions() - Method in class JobProcessor
-
When true, any exception thrown processing and input is caught and logged.
- isSuppressExceptions() - Method in class ParametersUnbound
-
- isSuppressExceptions() - Method in class QuickMultiDatasetExperiment
-
- isSuppressExceptions() - Method in class QuickMultiDatasetStructuredExperiment
-
- isSuppressOutlineZ() - Method in class ColoredBase
-
if true, the outline is suppressed in the z-dimension i.e.
- isSuppressRes() - Method in class RadiiRatio
-
- isSuppressRootOut() - Method in class Rooted
-
if true, the root is not added to the outFilePath, and the path is instead localized against
the location of the BeanXML.
- isSuppressSeries() - Method in class ConvertImageFormat
-
If true, the series index is not included in the outputted file-names.
- isSuppressSubfolders() - Method in class DefineOutputter
-
- isSuppressZ() - Method in class BoundingBoxIntersection
-
- isSuppressZ() - Method in class DistanceTransform3D
-
- isSuppressZ() - Method in class DistanceTransformForEachObject3D
-
- isSuppressZ() - Method in class MergeWithOptionalDistanceConstraint
-
- isSuppressZ() - Method in class CostOverlapWithinMidpointDistance
-
- isSuppressZ() - Method in class ImageMomentsBase
-
If true co-voariance is suprpessed in z-dimension
- isSuppressZ() - Method in class CenterOnMask
-
- isSuppressZ() - Method in class UniformRandom
-
- isSuppressZ() - Method in class SurfaceSizeMaskNonZero
-
- isSuppressZ() - Method in class EllipsoidBase
-
Iff true, surpresses covariance in the z-direction.
- isSuppressZCovariance() - Method in class FromObjects
-
- isSuppressZCovariance() - Method in class LinearLeastSquaresEllipsoidFitter
-
- isTemporary(int) - Method in class EncodedIntBuffer
-
- isTemporary(int) - Method in class EncodedVoxels
-
- isThreeChannels() - Method in class StackWriteAttributes
-
The number of channels is guaranteed to be 3 in the output.
- isThrowExceptionForInsufficientPoints() - Method in class CreateMarkFromPoints
-
- isThumbnailsEnabled() - Method in class FeatureCalculationContext
-
- isTime() - Method in class ExperimentIdentifierAuto
-
If true, the current time (HH.mm.ss) is included in the output.
- isTransposed() - Method in class CombineCSV
-
- isUnchanged(double, int) - Method in class UnchangedBase
-
Whether the current value is unchanged compared to the previous value.
- isUnchanged(double, int) - Method in class UnchangedScore
-
- isUnchanged(double, int) - Method in class UnchangedSize
-
- isUniformlySized() - Method in class StackNotUniformSized
-
Do all channels have identical dimensions?
- isUniformTyped() - Method in class StackNotUniformSized
-
Do all
Channel
s in the stack have identical voxel data-type?
- isUnsigned() - Method in class FloatVoxelType
-
- isUnsigned() - Method in class SignedVoxelType
-
- isUnsigned() - Method in class UnsignedVoxelType
-
- isUnsigned() - Method in class VoxelDataType
-
Whether the data-type is unsigned?
- isUnstarted() - Method in class JobStateMonitor
-
Is a job unstarted?
- isUnvisited(int) - Method in class EncodedIntBuffer
-
- isUnvisited(int) - Method in class EncodedVoxels
-
- isUseLastSeriesIndexOnly() - Method in class NamedChannels
-
- isUseLastSeriesIndexOnly() - Method in class Stacks
-
- isUseMax() - Method in class OverlapRatio
-
- isUseMax() - Method in class OverlapRatioMask
-
- isUseZ() - Method in class KernelApplicationParameters
-
Whether to additionally apply the kernel along the Z dimension, as well as X and Y?
- isUseZ() - Method in class KernelPointCursor
-
Whether to additionally apply the kernel along the Z dimension, as well as X and Y?
- isUseZ() - Method in class RemoveTouchingBorder
-
- isUseZ() - Method in class TraverseOuterContourOnImage
-
- isValidName(String, boolean) - Static method in class RGBChannelNames
-
Whether the channel-name is one of red, green, or blue, or alpha.
- isValidNameSet(Set<String>) - Static method in class RGBChannelNames
-
Do the channel-names correspond exactly to those expected either RGB or RGBA.
- isValidNameSet(Set<String>, boolean) - Static method in class RGBChannelNames
-
Do the channel-names correspond exactly to those expected for one of RGB or RGBA.
- isVaryColors() - Method in class SegmentInstanceWithModel
-
When true, the colors change for different objects in the image (using a default color set).
- isVaryImageLocation() - Method in class Montage
-
When true, the location of an image in the grid, as well as the number of images in each row
are both allowed to vary to fill space.
- isVaryImageSize() - Method in class Montage
-
When true, the images may vary in width/height in their respective rows to fill space, while
preserving the aspect-ratio of each image.
- isVaryNumberImagesPerRow() - Method in class Fill
-
When true the number of
Extent
s per row is allowed vary, to sensibly fill space.
- isVisuallyShortenDecimals() - Method in class ExportFeaturesStyle
-
When true, feature-values are shown as visually compressed as possible, including suppressing
decimal places.
- isVisuallyShortenDecimals() - Method in class FeatureExporterContext
-
When true double
values are printed to be as short as possible without losing
precision.
- isVoxelOn(Point3i) - Method in class Mask
-
Does a particular voxel have the on state?
- iterateEntries(CheckedBiConsumer<K, V, E>) - Method in class MapCreate
-
Iterate over each entry in the map, and apply an operation.
- IterateKernelHelper - Class in org.anchoranalysis.image.voxel.iterator.neighbor.kernel
-
- iterateMap(Map<K, V>, CheckedBiConsumer<K, V, E>) - Static method in class FunctionalIterate
-
Iterate through all entries in a
Map
.
- iterateOverSlices(Consumer<VoxelBuffer<T>>) - Method in interface SliceBufferIndex
-
Calls sliceConsumer
once for each slice with the respective buffer.
- iterateOverSlicesAndOffsets(ProcessVoxelBufferUnary<T>) - Method in interface SliceBufferIndex
-
Calls process
for each offset in each slice.
- iterateOverXY(OffsettedScalarTwoDimensionalConsumer<E>) - Method in class Extent
-
Calls processor once for each x and y-values in the range.
- iterateOverXY(PointTwoDimensionalConsumer) - Method in class Extent
-
Calls processor once for each x and y-values in the range.
- iterateOverXYOffset(CheckedIntConsumer<E>) - Method in class Extent
-
Calls processor once for each x and y-values but only passing an offset.
- iterateOverXYOffset(OffsettedPointTwoDimensionalConsumer) - Method in class Extent
-
Calls processor once for each x and y-values in the range.
- iterateOverXYWithShift(Point2i, PointTwoDimensionalConsumer) - Method in class Extent
-
Calls processor once for each x and y-values in the range, with a shift added.
- iterateOverYXOffset(OffsettedPointTwoDimensionalConsumer) - Method in class Extent
-
Calls processor once for each x and y-values in the range.
- iterateOverZ(CheckedIntConsumer<E>) - Method in class Extent
-
Calls processor once for each z-value in the range.
- iterateOverZUntil(IntPredicate) - Method in class Extent
-
Calls processor once for each z-value in the range unless indexPredicate
returns
false.
- iterateValues(Histogram.BinConsumer) - Method in class Histogram
-
Calls consumer
for every value, increasing from min to max.
- iterateValuesUntil(int, Histogram.BinConsumer) - Method in class Histogram
-
Calls consumer
for every value until a limit, increasing from min to limit
.
- IterateVoxelsAll - Class in org.anchoranalysis.image.voxel.iterator
-
Utilities for iterating over
all voxels in one or more
Voxels
.
- IterateVoxelsBoundingBox - Class in org.anchoranalysis.image.voxel.iterator
-
Utilities for iterating over the subset of image voxels within a bounding-box.
- IterateVoxelsEqualTo - Class in org.anchoranalysis.image.voxel.iterator
-
- IterateVoxelsIntersectingBounded - Class in org.anchoranalysis.image.voxel.iterator.intersecting
-
- IterateVoxelsMask - Class in org.anchoranalysis.image.core.mask
-
Utilities for iterating over the subset of voxels corresponding to an
on state in a
Mask
.
- IterateVoxelsNeighbors - Class in org.anchoranalysis.image.voxel.iterator.neighbor
-
Utilities for iterating over the neighboring voxels to a given point.
- IterateVoxelsObjectMask - Class in org.anchoranalysis.image.voxel.iterator
-
Utilities for iterating over the subset of voxels corresponding to an
on state in an
ObjectMask
.
- IterateVoxelsObjectMaskOptional - Class in org.anchoranalysis.image.voxel.iterator
-
Utilities for iterating over the subset of voxels corresponding to an
on state in an
optional
ObjectMask
.
- IterateVoxelsRemaining - Class in org.anchoranalysis.image.voxel.iterator
-
Utilities for iterating over
remaining voxels in one or more
VoxelBuffer
s.
- iterator() - Method in class SequenceInteger
-
An iterator for each element in the sequence.
- iterator() - Method in class DoubleList
-
- iterator() - Method in class DoubleSet
-
- iterator() - Method in class IntegerList
-
- iterator() - Method in class IntegerSet
-
- iterator() - Method in class StringList
-
- iterator() - Method in class StringSet
-
- iterator() - Method in class ColorList
-
- iterator() - Method in class NameValueMap
-
- iterator() - Method in class ConcurrentJobMonitor
-
- iterator() - Method in class FeatureList
-
- iterator() - Method in class CombinedName
-
- iterator() - Method in class SimpleName
-
- iterator() - Method in class FeatureNameList
-
- iterator() - Method in class ResultsVectorList
-
- iterator() - Method in class CacheTransferSourceCollection
-
- iterator() - Method in class SharedFeatures
-
- iterator() - Method in class NamedFeatureStore
-
- iterator() - Method in class StackArrangement
-
- iterator() - Method in class ObjectCollectionWithProperties
-
- iterator() - Method in class RGBStack
-
- iterator() - Method in class Stack
-
- iterator() - Method in class StackNotUniformSized
-
- iterator() - Method in class TimeSeries
-
- iterator() - Method in class ObjectCollection
-
- iterator() - Method in class InputsWithDirectory
-
Returns an iterator over the elements in this list in proper sequence.
- iterator() - Method in class EnergySavedInd
-
- iterator() - Method in class EnergySchemeSet
-
- iterator() - Method in class MemoList
-
- iterator() - Method in class UpdatableMarksList
-
- iterator() - Method in class ColoredMarks
-
- iterator() - Method in class MarkCollection
-
- iterator() - Method in class WeightedKernelList
-
- iterator() - Method in class ColoredOverlayCollection
-
- iterator() - Method in class OverlayCollection
-
- iterator() - Method in class ImageCounterList
-
- iterator() - Method in class LevelResultCollection
-
- iterator() - Method in class NamedChannels
-
- iterator() - Method in class ParsedFilePathBag
-
- iterator() - Method in class SortedSetChannel
-
- ObjectAggregationBase<T extends FeatureInputEnergy> - Class in org.anchoranalysis.plugin.image.feature.bean.shared.object
-
Calculates a feature for a set of objects using this stack as a energy-stack, and aggregates.
- ObjectAggregationBase() - Constructor for class ObjectAggregationBase
-
- ObjectAsMaskGenerator - Class in org.anchoranalysis.image.io.object.output.mask
-
Writes an object-mask as a mask (i.e.
- ObjectAsMaskGenerator() - Constructor for class ObjectAsMaskGenerator
-
Creates using a default image-resolution.
- ObjectAsMaskGenerator(Optional<Resolution>) - Constructor for class ObjectAsMaskGenerator
-
- ObjectAsPoints - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
-
- ObjectAsPoints() - Constructor for class ObjectAsPoints
-
- ObjectCollection - Class in org.anchoranalysis.image.voxel.object
-
- ObjectCollection(ArrayList<ObjectMask>) - Constructor for class ObjectCollection
-
Creates with the underlying list.
- ObjectCollection(Stream<ObjectMask>) - Constructor for class ObjectCollection
-
Creates with elements from a stream.
- ObjectCollectionFactory - Class in org.anchoranalysis.image.voxel.object
-
- ObjectCollectionProvider - Class in org.anchoranalysis.image.bean.provider
-
- ObjectCollectionProvider() - Constructor for class ObjectCollectionProvider
-
- ObjectCollectionProviderFilterBase - Class in org.anchoranalysis.plugin.image.bean.object.provider.filter
-
- ObjectCollectionProviderFilterBase() - Constructor for class ObjectCollectionProviderFilterBase
-
- ObjectCollectionProviderMorphological - Class in org.anchoranalysis.plugin.image.bean.object.provider.morphological
-
- ObjectCollectionProviderMorphological() - Constructor for class ObjectCollectionProviderMorphological
-
- ObjectCollectionProviderUnary - Class in org.anchoranalysis.image.bean.provider
-
- ObjectCollectionProviderUnary() - Constructor for class ObjectCollectionProviderUnary
-
- ObjectCollectionProviderWithFeature - Class in org.anchoranalysis.plugin.image.bean.object.provider.feature
-
- ObjectCollectionProviderWithFeature() - Constructor for class ObjectCollectionProviderWithFeature
-
- ObjectCollectionReader - Class in org.anchoranalysis.image.io.object.input
-
- ObjectCollectionWithProperties - Class in org.anchoranalysis.image.core.object.properties
-
- ObjectCollectionWithProperties(int) - Constructor for class ObjectCollectionWithProperties
-
Create with zero objects.
- ObjectCollectionWithProperties(ObjectMask) - Constructor for class ObjectCollectionWithProperties
-
Create with a single object.
- ObjectCollectionWithProperties(Stream<ObjectWithProperties>) - Constructor for class ObjectCollectionWithProperties
-
Create with a stream of objects with properties.
- ObjectCollectionWithProperties(ObjectCollection) - Constructor for class ObjectCollectionWithProperties
-
Create with a stream of objects, assign empty properties to each.
- ObjectCollectionWriter - Class in org.anchoranalysis.image.io.object.output.hdf5
-
- objectCopyTo(ObjectMask, Voxels<T>, BoundingBox) - Method in interface VoxelsExtracter
-
Copies an area corresponding to an object-mask to another
Voxels
.
- ObjectDrawAttributes - Class in org.anchoranalysis.overlay.writer
-
A means of extracting attributes associated with a particular object (e.g.
- ObjectDrawAttributes(ColorIndex) - Constructor for class ObjectDrawAttributes
-
Creates with a specific color-index and uses the iteration-index as both the ID and color-ID
- ObjectDrawAttributes(ColorIndex, IdentifierGetter<ObjectWithProperties>, IdentifierGetter<ObjectWithProperties>) - Constructor for class ObjectDrawAttributes
-
- ObjectFilter - Class in org.anchoranalysis.image.bean.object
-
Base class for filtering an
ObjectCollection
to remove objects according to a criteria.
- ObjectFilter() - Constructor for class ObjectFilter
-
- ObjectFilterCombine - Class in org.anchoranalysis.plugin.image.bean.object.filter.combine
-
A filter that combines other filters (in a list)
- ObjectFilterCombine() - Constructor for class ObjectFilterCombine
-
- ObjectFilterPredicate - Class in org.anchoranalysis.plugin.image.bean.object.filter
-
Uses a predicate to make a decision whether to keep objects or not.
- ObjectFilterPredicate() - Constructor for class ObjectFilterPredicate
-
- ObjectFilterRelation - Class in org.anchoranalysis.plugin.image.bean.object.filter
-
An independent object-filter that uses a relation in its predicate.
- ObjectFilterRelation() - Constructor for class ObjectFilterRelation
-
- objectFor(T) - Method in interface AccessObjectMask
-
An object-mask for a given element.
- objectFor(ObjectMask) - Method in class AccessObjectMaskSimple
-
- ObjectForReduction - Class in org.anchoranalysis.image.inference.bean.reduce
-
An object that can be reduced.
- ObjectForReduction(LabelledWithConfidence<ObjectMask>) - Constructor for class ObjectForReduction
-
Creates with a
ObjectMask
that is considered newly-added.
- ObjectForReduction(LabelledWithConfidence<ObjectMask>, int) - Constructor for class ObjectForReduction
-
- ObjectForReductionFactory - Class in org.anchoranalysis.image.inference.bean.reduce
-
- ObjectFromPointsFactory - Class in org.anchoranalysis.image.core.object
-
- ObjectInputStreamDeserializer<T> - Class in org.anchoranalysis.core.serialize
-
Deserializes using Java's Native serialization framework.
- ObjectInputStreamDeserializer() - Constructor for class ObjectInputStreamDeserializer
-
- ObjectIntersectionRemover - Class in org.anchoranalysis.plugin.image.object
-
- ObjectMask - Class in org.anchoranalysis.image.voxel.object
-
A localized-mask in an image, expressed as a
BoundingBox
, with a corresponding mask sized
to match the bounding-box.
- ObjectMask(Voxels<UnsignedByteBuffer>) - Constructor for class ObjectMask
-
Creates from a
Voxels
mask that is cornered at the origin.
- ObjectMask(BoundingBox) - Constructor for class ObjectMask
-
Creates as a bounding-box with all corresponding mask voxels set to off.
- ObjectMask(BoundedVoxels<UnsignedByteBuffer>) - Constructor for class ObjectMask
-
- ObjectMask(BinaryVoxels<UnsignedByteBuffer>) - Constructor for class ObjectMask
-
- ObjectMask(BoundingBox, Voxels<UnsignedByteBuffer>) - Constructor for class ObjectMask
-
- ObjectMask(BoundingBox, Voxels<UnsignedByteBuffer>, BinaryValuesInt) - Constructor for class ObjectMask
-
- ObjectMask(BoundingBox, BinaryVoxels<UnsignedByteBuffer>) - Constructor for class ObjectMask
-
Creates from a
BinaryVoxels
and a corresponding bounding-box.
- ObjectMask(BoundedVoxels<UnsignedByteBuffer>, BinaryValuesInt) - Constructor for class ObjectMask
-
- ObjectMask(BoundingBox, Voxels<UnsignedByteBuffer>, BinaryValuesByte) - Constructor for class ObjectMask
-
- ObjectMaskMerger - Class in org.anchoranalysis.image.core.merge
-
Merges one or more
ObjectMask
s into a single object.
- ObjectMaskStream - Class in org.anchoranalysis.image.voxel.object
-
A custom "stream" like class for various functional-programming operations on
ObjectCollection
- ObjectMaskStream(ObjectCollection) - Constructor for class ObjectMaskStream
-
- ObjectMatcher - Class in org.anchoranalysis.image.bean.object
-
Matches an object with other objects.
- ObjectMatcher() - Constructor for class ObjectMatcher
-
- ObjectOutputStreamGenerator<T extends Serializable> - Class in org.anchoranalysis.io.generator.serialized
-
- ObjectOutputStreamGenerator() - Constructor for class ObjectOutputStreamGenerator
-
- ObjectRadiusStandardDeviation - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shape
-
- ObjectRadiusStandardDeviation() - Constructor for class ObjectRadiusStandardDeviation
-
- objects() - Method in class ImageInitialization
-
- objects() - Method in class SegmentedObjectsAtScale
-
- objects() - Method in class MultiInput
-
- OBJECTS - Static variable in class OutputterDirectories
-
Where collections of objects are typically placed in a define-experiment output
- Objects - Class in org.anchoranalysis.plugin.annotation.bean.comparer
-
- Objects() - Constructor for class Objects
-
- objects(String) - Static method in class ReferenceFactory
-
- OBJECTS_ROOT_WITH_SEPERATORS - Static variable in class HDF5PathHelper
-
Hardcoded string that identifies in the HDF5 file for where the object-collection is stored.
- ObjectsAsGrayscaleGenerator - Class in org.anchoranalysis.image.io.object.output.grayscale
-
Base class for generators that accept a set of objects as input.
- ObjectsAsGrayscaleGenerator(Dimensions) - Constructor for class ObjectsAsGrayscaleGenerator
-
- ObjectsAsRGBGenerator - Class in org.anchoranalysis.image.io.object.output.rgb
-
- ObjectsAsRGBGenerator(DrawObject, ObjectDrawAttributes, Either<Dimensions, DisplayStack>) - Constructor for class ObjectsAsRGBGenerator
-
- ObjectsAsUniqueValueGenerator - Class in org.anchoranalysis.image.io.object.output.grayscale
-
Writes objects as an image with an incrementing unique integer id value for each object.
- ObjectsAsUniqueValueGenerator(Dimensions) - Constructor for class ObjectsAsUniqueValueGenerator
-
Create with a particular dimensions.
- ObjectScalingMethod - Interface in org.anchoranalysis.image.core.object.scale.method
-
A way to scale a group of
ObjectMask
s, scaling each object independently or collectively.
- ObjectScalingMethodFactory - Class in org.anchoranalysis.image.core.object.scale.method
-
- ObjectSerializerPeriodicReporter<T extends Serializable> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
-
- ObjectSerializerPeriodicReporter() - Constructor for class ObjectSerializerPeriodicReporter
-
- objectsForThumbnail(T) - Method in class CombineObjectsForFeatures
-
Selects objects from an input that will be used for thumbnail generation.
- objectsForThumbnail(FeatureInputSingleObject) - Method in class EachObjectIndependently
-
- objectsForThumbnail(FeatureInputPairObjects) - Method in class PairNeighbors
-
- ObjectsFromConnectedComponentsFactory - Class in org.anchoranalysis.image.voxel.binary.connected
-
Creates a
ObjectCollection
from the connected-components of a mask or binary-voxels.
- ObjectsFromConnectedComponentsFactory() - Constructor for class ObjectsFromConnectedComponentsFactory
-
Creates to use a small-neighborhood.
- ObjectsFromConnectedComponentsFactory(boolean) - Constructor for class ObjectsFromConnectedComponentsFactory
-
Creates to use a specified type of neighborhood.
- ObjectsFromConnectedComponentsFactory(int) - Constructor for class ObjectsFromConnectedComponentsFactory
-
Creates to use a minimum number of voxels for each connected component.
- ObjectsFromConnectedComponentsFactory(boolean, int) - Constructor for class ObjectsFromConnectedComponentsFactory
-
Creates to use a specified type of neighborhood, and minimum number of voxels.
- ObjectsMergedAsMaskGenerator - Class in org.anchoranalysis.image.io.object.output.grayscale
-
Writes objects merged together as a mask.
- ObjectsMergedAsMaskGenerator(Dimensions) - Constructor for class ObjectsMergedAsMaskGenerator
-
Create with particular size for the mask image.
- ObjectsToCompare - Class in org.anchoranalysis.plugin.annotation.comparison
-
- ObjectsToCompare(ObjectCollection, ObjectCollection) - Constructor for class ObjectsToCompare
-
- objectsToDraw(Dimensions) - Method in class ColoredBaseWithGenerator
-
The objects to draw (without any colors) on the background
- objectsToDraw(Dimensions) - Method in class ColoredObjects
-
- objectsToDraw(Dimensions) - Method in class ColoredMarks
-
- objectsWithProperties() - Method in class SegmentedObjectsAtScale
-
- ObjectVertex - Class in org.anchoranalysis.plugin.image.object.merge
-
A vertex in a merge graph representing an object (and and an associated payload)
- ObjectVertex(ObjectMask, double) - Constructor for class ObjectVertex
-
- ObjectVoxelIntersection - Class in org.anchoranalysis.annotation.io.assignment
-
Creates an assignment between intersecting voxels in two objects.
- ObjectVoxelIntersection(ObjectMask, ObjectMask) - Constructor for class ObjectVoxelIntersection
-
Determines a voxel-assignment between two objects.
- ObjectWithBoundingBoxGenerator - Class in org.anchoranalysis.image.io.object.output.mask
-
- ObjectWithBoundingBoxGenerator(Optional<Resolution>) - Constructor for class ObjectWithBoundingBoxGenerator
-
Create with a resolution, if it is known.
- objectWithColor(RGBColor) - Method in class RGBStack
-
- ObjectWithEllipse - Class in org.anchoranalysis.plugin.points.calculate.ellipse
-
- ObjectWithEllipse(ObjectMask, Ellipse) - Constructor for class ObjectWithEllipse
-
- ObjectWithMaximumFeature - Class in org.anchoranalysis.plugin.image.bean.object.provider.feature
-
Finds the object with the maximum feature-value from a collection.
- ObjectWithMaximumFeature() - Constructor for class ObjectWithMaximumFeature
-
- ObjectWithMaximumFeatureFromEachMatchedCollection - Class in org.anchoranalysis.plugin.image.bean.object.provider.feature
-
Finds the object with the maximum feature among a group of matches for each object.
- ObjectWithMaximumFeatureFromEachMatchedCollection() - Constructor for class ObjectWithMaximumFeatureFromEachMatchedCollection
-
- ObjectWithProperties - Class in org.anchoranalysis.image.core.object.properties
-
An
ObjectMask
with associated key-value properties.
- ObjectWithProperties(BoundingBox) - Constructor for class ObjectWithProperties
-
Creates as a bounding-box with all corresponding mask voxels set to off.
- ObjectWithProperties(ObjectMask) - Constructor for class ObjectWithProperties
-
Creates with an existing
ObjectMask
and empty properties.
- ObjectWithProperties(ObjectMask, Map<String, Object>) - Constructor for class ObjectWithProperties
-
- obtain(int, AggregateReceiver<T>, PeriodTriggerBank<T>) - Method in class AggregateTriggerBank
-
- obtain(int, PeriodReceiver<S>) - Method in class PeriodTriggerBank
-
- of(Stream<T>) - Static method in class FunctionalList
-
Creates a list from a stream.
- of(boolean) - Static method in class ObjectScalingMethodFactory
-
Determines which method to use, given circumstances.
- of(boolean, boolean) - Static method in enum OutsideKernelPolicy
-
Multiplexes between all three possible enums.
- of(boolean) - Static method in class NeighborhoodFactory
-
Gets an appropriate neighborhood
- of(ObjectMask...) - Static method in class ObjectCollectionFactory
-
Creates a new collection with elements from the parameter-list.
- of(ObjectCollection...) - Static method in class ObjectCollectionFactory
-
Creates a new collection with elements copied from existing collections.
- of(Optional<ObjectCollection>...) - Static method in class ObjectCollectionFactory
-
Creates a new collection with elements copied from existing collections, if they exist.
- of(Collection<ObjectMask>...) - Static method in class ObjectCollectionFactory
-
Creates a new collection with elements copied from existing collections.
- of(BinaryVoxels<UnsignedByteBuffer>...) - Static method in class ObjectCollectionFactory
-
Creates a new collection with elements from the parameter-list of
BinaryVoxels
converting the voxels in their entirety to an object-mask at the origin.
- of(CalculationPartResolver<FeatureInputSingleObject>, MorphologicalIterations, int, boolean) - Static method in class CalculateShellObjectMask
-
- of(CalculationPartResolver<FeatureInputSingleObject>, int, boolean) - Static method in class CalculateDilation
-
- of(CalculationPartResolver<FeatureInputSingleObject>, int, boolean) - Static method in class CalculateErosion
-
- of(FeatureCalculationInput<FeatureInputSingleObject>, boolean) - Static method in class CalculateEllipsoidLeastSquares
-
- offset(int, int) - Method in class Dimensions
-
Calculates a XY-offset of a point in a buffer whose dimensions are this extent.
- offset(Point3i) - Method in class Dimensions
-
Calculates a XYZ-offset of a point in a buffer whose dimensions are this extent.
- offset(int, int) - Method in class Extent
-
Calculates a XY-offset of a point in a buffer whose dimensions are this extent.
- offset(int, int, int) - Method in class Extent
-
Calculates a XYZ-offset of a point in a buffer whose dimensions are this extent.
- offset(ReadableTuple3i) - Method in class Extent
-
Calculates a XYZ-offset of a point in a buffer whose dimensions are this extent.
- offset(Point2i) - Method in class Extent
-
Calculates a XY-offset of a point in a buffer whose dimensions are this extent.
- offsetGlobal(int, int) - Method in class ObjectMask
-
Calculates an offset for locating a voxel inside the buffer, with global encoding of
coordinates.
- offsetRelative(int, int) - Method in class ObjectMask
-
Calculates an offset for locating a voxel inside the buffer, with local encoding of
coordinates.
- offsetSlice(Point3i) - Method in class Dimensions
-
Calculates a XY-offset of a point in a buffer whose dimensions are this extent.
- offsetSlice(ReadableTuple3i) - Method in class Extent
-
Calculates a XY-offset of a point in a buffer whose dimensions are this extent.
- OffsettedPointTwoDimensionalConsumer - Interface in org.anchoranalysis.spatial.point.consumer
-
- OffsettedScalarTwoDimensionalConsumer<E extends Exception> - Interface in org.anchoranalysis.spatial.point.consumer
-
- ofResolved(CalculationPartResolver<FeatureInputSingleObject>, int, boolean) - Static method in class CalculateErosion
-
- OMETiff - Class in org.anchoranalysis.io.bioformats.bean.writer
-
- OMETiff() - Constructor for class OMETiff
-
Default constructor.
- OMEXML - Class in org.anchoranalysis.io.bioformats.bean.writer
-
- OMEXML() - Constructor for class OMEXML
-
Default constructor.
- One - Class in org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels
-
Selects one specific channel from a set of stacks
- One() - Constructor for class One
-
- oneOnly(String, String, boolean, boolean) - Static method in class CheckMisconfigured
-
Checks that one of two properties is defined, but not both simultaneously.
- OneOrThreeChannelsWriter - Class in org.anchoranalysis.image.io.bean.stack.writer
-
A base-class for a
StackWriter
that writes an image that has either one or three
channels.
- OneOrThreeChannelsWriter() - Constructor for class OneOrThreeChannelsWriter
-
- OneStageGenerator<T> - Class in org.anchoranalysis.io.generator
-
- OneStageGenerator() - Constructor for class OneStageGenerator
-
- onInitialization(P) - Method in class InitializableBean
-
Called after initialization.
- onInitialization(NullInitialization) - Method in class NullParametersBean
-
- onInitialization() - Method in class NullParametersBean
-
As there's no parameters we expose a different method.
- onInitialization(DictionaryInitialization) - Method in class DictionaryProviderReference
-
- onInitialization(FeatureInitialization) - Method in class Feature
-
Called after initialization.
- onInitialization(FeatureRelatedInitialization) - Method in class ReferencingFeatureListProvider
-
- onInitialization(ImageInitialization) - Method in class BinarySegmentationReference
-
- onInitialization() - Method in class MarkWithIdentifierFactory
-
- onInitialization(ImageInitialization) - Method in class FromInput
-
- onInitialization(ImageInitialization) - Method in class FromChannel
-
- onInitialization(ImageInitialization) - Method in class Reference
-
- onInitialization(ImageInitialization) - Method in class FromStackChannel
-
- onInitialization(ImageInitialization) - Method in class ReferenceOrElse
-
- onInitialization(ImageInitialization) - Method in class FromInput
-
- onInitialization(FeatureRelatedInitialization) - Method in class PermuteFeature
-
- onInitialization(MarksInitialization) - Method in class FeatureValueCheckMark
-
- onInitialization(MarksInitialization) - Method in class MarkProposerReference
-
- onInitialization(MarksInitialization) - Method in class MarkMergeProposerReference
-
- onInitialization(MarksInitialization) - Method in class MarkSplitProposerReference
-
- onInitialization(MarksInitialization) - Method in class KernelMerge
-
- onInitialization(PointsInitialization) - Method in class Reference
-
- OnlyIf - Class in org.anchoranalysis.experiment.bean.log
-
Logs messages to a particular location ONLY if debug-mode is enabled.
- OnlyIf() - Constructor for class OnlyIf
-
- OnnxModel - Class in org.anchoranalysis.plugin.onnx.model
-
A model that can be used for inference using the
ONNX
Runtime's Java API.
- OnnxModel(OrtSession) - Constructor for class OnnxModel
-
- open(Logger) - Method in interface OpenedImageFile
-
Open the first series when we don't have a specific-type.
- open(int, Logger) - Method in interface OpenedImageFile
-
Open when we don't have a specific-type.
- open(Path) - Static method in class CSVReaderByLine
-
Opens a CSV file for reading.
- open(Path, String, boolean) - Static method in class CSVReaderByLine
-
Opens a CSV file for reading.
- open(Path, String, boolean, boolean) - Static method in class CSVReaderByLine
-
Opens a CSV file for reading.
- open(int, Logger) - Method in class OpenedMultiFile
-
- openChannelFromFilePath(Path) - Method in class TestLoaderImage
-
- openChannelFromTestPath(String) - Method in class TestLoaderImage
-
- openCheckType(int, VoxelDataType, Logger) - Method in interface OpenedImageFile
-
Opens a time-series, and checks that it is a particular type.
- OpenCV - Class in org.anchoranalysis.plugin.opencv.bean.interpolate
-
Interpolation using OpenCV for resizing an image.
- OpenCV() - Constructor for class OpenCV
-
- OpenCVModel - Class in org.anchoranalysis.plugin.opencv.segment
-
- OpenCVModel(Net) - Constructor for class OpenCVModel
-
- OpenCVReader - Class in org.anchoranalysis.plugin.opencv.bean.stack
-
Reads a stack from the file-system using OpenCV.
- OpenCVReader() - Constructor for class OpenCVReader
-
- OpenCVWriter - Class in org.anchoranalysis.plugin.opencv.bean.stack
-
Writes a stack to the file-system using OpenCV and a specified extension.
- OpenCVWriter() - Constructor for class OpenCVWriter
-
- OpenedCSVFile() - Constructor for class CSVReader.OpenedCSVFile
-
- OpenedImageFile - Interface in org.anchoranalysis.image.io.stack.input
-
An image file that has been opened for reading containing one or more series of image-
Stack
s.
- OpenedMultiFile - Class in org.anchoranalysis.plugin.io.multifile
-
A
OpenedImageFile
where the image is formed from more than one file on the file-system.
- OpenedMultiFile(StackReader, ParsedFilePathBag, ExecutionTimeRecorder) - Constructor for class OpenedMultiFile
-
- OpenedNamedChannels - Class in org.anchoranalysis.image.io.channel.map
-
- OpenedNamedChannels(OpenedImageFile, ChannelMap, int) - Constructor for class OpenedNamedChannels
-
- openFile(Path, StackReader, OperationContext) - Method in class FromStackReader
-
- openFile(Path, StackReader, OperationContext) - Method in class ImageMetadataReader
-
Opens a file containing one or more images but does not read an image.
- openFile(Path, ExecutionTimeRecorder) - Method in class StackReader
-
Opens a file containing one or more images.
- openFile(Path, CalculateOrientationChange, ExecutionTimeRecorder) - Method in class StackReaderOrientationCorrection
-
Opens a file containing one or more images but does not read an image.
- openFile(Path, ExecutionTimeRecorder) - Method in class BioformatsReader
-
- openFile(Path, CalculateOrientationChange, ExecutionTimeRecorder) - Method in class BioformatsReader
-
- openFile(Path, StackReader, OperationContext) - Method in class AlwaysReject
-
- openFile(Path, StackReader, OperationContext) - Method in class InferFromHeader
-
- openFile(Path, ExecutionTimeRecorder) - Method in class BranchExtension
-
- openFile(Path, ExecutionTimeRecorder) - Method in class FlattenAsChannel
-
- openFile(Path, ExecutionTimeRecorder) - Method in class ImposeResolution
-
- openFile(Path, ExecutionTimeRecorder) - Method in class MultiFileReader
-
- openFile(Path, ExecutionTimeRecorder) - Method in class ReadVoxelExtentXml
-
- openFile(Path, ExecutionTimeRecorder) - Method in class RejectIfConditionXYResolution
-
- openFile(Path, ExecutionTimeRecorder) - Method in class RotateImageToMatchEXIFOrientation
-
- openFile(Path, CalculateOrientationChange, ExecutionTimeRecorder) - Method in class RotateImageToMatchEXIFOrientation
-
- openFile(Path, ExecutionTimeRecorder) - Method in class OpenCVReader
-
- openLargestObjectFrom(String) - Method in class TestLoaderObjects
-
- openMask(StackReader, Path, BinaryValuesInt, OperationContext) - Static method in class MaskReader
-
Utility functions for opening a single-channeled stack as a
Mask
.
- openObjectsFromFilePath(Path) - Method in class TestLoaderImage
-
Opens an obj-mask-collection from a path to a file
- openObjectsFromTestPath(String) - Method in class TestLoaderImage
-
- openStackFromFilePath(Path) - Method in class TestLoaderImage
-
- openStackFromTestPath(String) - Method in class TestLoaderImage
-
- openXmlAbsoluteFilePath(String) - Static method in class TestLoader
-
Opens a XML document - with an absolute path on the filesystem.
- openXmlAbsoluteFilePath(Path) - Static method in class TestLoader
-
Opens a XML document - with an absolute path on the filesystem.
- openXmlFromTestPath(String) - Method in class TestLoader
-
Opens a XML document - with a path relative to the test root.
- OperationContext - Class in org.anchoranalysis.core.time
-
Context objects for general operations that allow for logging and recording execution time.
- OperationContext(Logger) - Constructor for class OperationContext
-
Creates with a
Logger
ignoring execution-times.
- OperationContext(ExecutionTimeRecorder, Logger) - Constructor for class OperationContext
-
- operationContext() - Method in interface InputOutputContext
-
- OperationFailedException - Exception in org.anchoranalysis.core.exception
-
Generic checked exception that can be thrown when a particular operation fails.
- OperationFailedException(String) - Constructor for exception OperationFailedException
-
Creates with only a message.
- OperationFailedException(Throwable) - Constructor for exception OperationFailedException
-
Creates with only a cause.
- OperationFailedException(String, Throwable) - Constructor for exception OperationFailedException
-
Creates with both a message and cause.
- OperationFailedRuntimeException - Exception in org.anchoranalysis.core.exception
-
Generic runtime exception that can be thrown when a particular operation fails.
- OperationFailedRuntimeException(String) - Constructor for exception OperationFailedRuntimeException
-
Creates with only a message.
- OperationFailedRuntimeException(Exception) - Constructor for exception OperationFailedRuntimeException
-
Creates with only a cause.
- OperationMap<T> - Class in org.anchoranalysis.mpp.io.input
-
Stores objects as operations
- OperationMap() - Constructor for class OperationMap
-
- OptimizationContext - Class in org.anchoranalysis.mpp.segment.optimization
-
- OptimizationContext(String, EnergySchemeWithSharedFeatures, DualStack, TriggerTerminationCondition, InputOutputContext, RandomNumberGenerator, MarkWithIdentifierFactory) - Constructor for class OptimizationContext
-
- OptimizationScheme<S,U,V> - Class in org.anchoranalysis.mpp.segment.bean.optimization
-
An optimization-scheme that uses kernels to make changes to state.
- OptimizationScheme() - Constructor for class OptimizationScheme
-
- OptimizationStep<S,T,V> - Class in org.anchoranalysis.mpp.segment.optimization.step
-
- OptimizationStep() - Constructor for class OptimizationStep
-
- OptimizationStepLogReporter - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
-
- OptimizationStepLogReporter() - Constructor for class OptimizationStepLogReporter
-
- OptimizationTerminatedEarlyException - Exception in org.anchoranalysis.mpp.segment.optimization
-
- OptimizationTerminatedEarlyException(String, Throwable) - Constructor for exception OptimizationTerminatedEarlyException
-
- OptionalBean - Annotation Type in org.anchoranalysis.bean.annotation
-
Indicates that a field of a class can be set to null (omitted), otherwise by default a bean must
always have a non-null value.
- OptionalComparator - Class in org.anchoranalysis.core.functional
-
- OptionalFactory - Class in org.anchoranalysis.core.functional
-
Utility functions to create
Optional
from flags.
- OptionalNameValue<V> - Class in org.anchoranalysis.io.generator.combined
-
A simple container expressing a value and an associationed optional name.
- OptionalNameValue(Optional<String>, V) - Constructor for class OptionalNameValue
-
- OptionalPointProposer - Interface in org.anchoranalysis.mpp.proposer
-
- OptionalProviderFactory - Class in org.anchoranalysis.bean
-
- OptionalUtilities - Class in org.anchoranalysis.core.functional
-
Additional utility functions for
Optional
and exceptions.
- or(StackWriteAttributes) - Method in class StackWriteAttributes
-
- Or - Class in org.anchoranalysis.plugin.image.bean.mask.provider.combine
-
Outputs the logical operation or voxelwise on both masks, modifying {mask} with the
result.
- Or() - Constructor for class Or
-
- Or - Class in org.anchoranalysis.plugin.image.bean.object.filter.combine
-
Applies multiples filter with logical OR i.e.
- Or() - Constructor for class Or
-
- OrderedFeatureList<T extends FeatureInput> - Interface in org.anchoranalysis.mpp.feature.addcriteria
-
- OrderedList - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
-
- OrderedList() - Constructor for class OrderedList
-
- orderedListOfFeatures() - Method in class AddCriteriaEnergyPair
-
- orderedListOfFeatures() - Method in class AddCriteriaNever
-
- orderedListOfFeatures() - Method in class AddCriteriaOr
-
- orderedListOfFeatures() - Method in class ArbitraryPointCommon
-
- orderedListOfFeatures() - Method in class BoundingBoxIntersection
-
- orderedListOfFeatures() - Method in interface OrderedFeatureList
-
- orderedListOfFeatures() - Method in class AddCriteriaFeatureRelationThreshold
-
- OrderedRadius - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.radii
-
- OrderedRadius() - Constructor for class OrderedRadius
-
- orElseGet(Optional<T>, CheckedSupplier<T, E>) - Static method in class OptionalUtilities
-
- orElseGetFlat(Optional<T>, CheckedSupplier<Optional<T>, E>...) - Static method in class OptionalUtilities
-
- orFlat(Iterable<Optional<T>>) - Static method in class OptionalUtilities
-
The first optional if it's present, or the second, or the third etc.
- orFlat(Stream<Optional<T>>) - Static method in class OptionalUtilities
-
The first optional if it's present, or the second, or the third etc.
- orFlat(Optional<T>...) - Static method in class OptionalUtilities
-
- orFlatSupplier(Iterable<CheckedSupplier<Optional<T>, E>>) - Static method in class OptionalUtilities
-
The first optional if it's present, or the second, or the third etc.
- orFlatSupplier(CheckedSupplier<Optional<T>, E>...) - Static method in class OptionalUtilities
-
- org.anchoranalysis.annotation - package org.anchoranalysis.annotation
-
Ground truth for an image in diverse forms.
- org.anchoranalysis.annotation.image - package org.anchoranalysis.annotation.image
-
Annotations that apply to an image as a whole.
- org.anchoranalysis.annotation.io - package org.anchoranalysis.annotation.io
-
Reading and writing annotations to the filesystem.
- org.anchoranalysis.annotation.io.assignment - package org.anchoranalysis.annotation.io.assignment
-
A pairing of objects from two collections (bipartite matching).
- org.anchoranalysis.annotation.io.assignment.generator - package org.anchoranalysis.annotation.io.assignment.generator
-
Generates output images to illustrate a
Assignment
between annotations.
- org.anchoranalysis.annotation.io.bean - package org.anchoranalysis.annotation.io.bean
-
Beans related to reading / writing / specifying annotations.
- org.anchoranalysis.annotation.io.bean.comparer - package org.anchoranalysis.annotation.io.bean.comparer
-
What to compare an annotation (ground truth) against?
- org.anchoranalysis.annotation.io.comparer - package org.anchoranalysis.annotation.io.comparer
-
Non-bean classes involving comparing results and annotations.
- org.anchoranalysis.annotation.io.image - package org.anchoranalysis.annotation.io.image
-
Reading and writing whole-image label annotations.
- org.anchoranalysis.annotation.io.image.findable - package org.anchoranalysis.annotation.io.image.findable
-
The outcome of searching for annotations or images on the file-system.
- org.anchoranalysis.annotation.io.mark - package org.anchoranalysis.annotation.io.mark
-
Reading and writing
Mark
-related annotations from/to the
file-system.
- org.anchoranalysis.annotation.mark - package org.anchoranalysis.annotation.mark
-
Annotations that use one or more marks to describe entities in an image.
- org.anchoranalysis.bean - package org.anchoranalysis.bean
-
- org.anchoranalysis.bean.annotation - package org.anchoranalysis.bean.annotation
-
- org.anchoranalysis.bean.define - package org.anchoranalysis.bean.define
-
- org.anchoranalysis.bean.define.adder - package org.anchoranalysis.bean.define.adder
-
- org.anchoranalysis.bean.exception - package org.anchoranalysis.bean.exception
-
Exceptions that can occur executing generic operations on
Anchor Beans.
- org.anchoranalysis.bean.initializable - package org.anchoranalysis.bean.initializable
-
Initializing beans with particular parameters, including recursively.
- org.anchoranalysis.bean.initializable.parameters - package org.anchoranalysis.bean.initializable.parameters
-
Some parameterization used when initializing beans.
- org.anchoranalysis.bean.initializable.property - package org.anchoranalysis.bean.initializable.property
-
Initializating a bean with parameters.
- org.anchoranalysis.bean.permute - package org.anchoranalysis.bean.permute
-
Applying permutations to a bean's fields.
- org.anchoranalysis.bean.permute.assign - package org.anchoranalysis.bean.permute.assign
-
Imposes a permutation value on one or more properties of a bean.
- org.anchoranalysis.bean.permute.property - package org.anchoranalysis.bean.permute.property
-
Applying permutations to the properties of a bean.
- org.anchoranalysis.bean.primitive - package org.anchoranalysis.bean.primitive
-
Beans that implement collections of primitive element types, as well as
String
.
- org.anchoranalysis.bean.shared - package org.anchoranalysis.bean.shared
-
Utility beans which have a generally broader use than a specific module.
- org.anchoranalysis.bean.shared.color - package org.anchoranalysis.bean.shared.color
-
Beans that specify colors.
- org.anchoranalysis.bean.shared.color.scheme - package org.anchoranalysis.bean.shared.color.scheme
-
Beans that create lists or indices of colors according to particular schemes.
- org.anchoranalysis.bean.shared.dictionary - package org.anchoranalysis.bean.shared.dictionary
-
Setting, referencing and initializing key-value parameters.
- org.anchoranalysis.bean.shared.path - package org.anchoranalysis.bean.shared.path
-
Defines a root path directory on the filesystem whre files are read / written.
- org.anchoranalysis.bean.shared.random - package org.anchoranalysis.bean.shared.random
-
Specifies a particular type of random-number generator.
- org.anchoranalysis.bean.shared.regex - package org.anchoranalysis.bean.shared.regex
-
Specifies regular-expressions.
- org.anchoranalysis.bean.shared.relation - package org.anchoranalysis.bean.shared.relation
-
Specifies a binary relation of some kind between scalars.
- org.anchoranalysis.bean.shared.relation.threshold - package org.anchoranalysis.bean.shared.relation.threshold
-
Specifies a unary relation to a threshold value.
- org.anchoranalysis.bean.xml - package org.anchoranalysis.bean.xml
-
Reading Beans from XML files.
- org.anchoranalysis.bean.xml.creator - package org.anchoranalysis.bean.xml.creator
-
Creates beans from XML.
- org.anchoranalysis.bean.xml.exception - package org.anchoranalysis.bean.xml.exception
-
Exceptions that can thrown when loading beans from XML.
- org.anchoranalysis.bean.xml.factory - package org.anchoranalysis.bean.xml.factory
-
Custom factories for loading beans in custom ways from XML.
- org.anchoranalysis.bean.xml.factory.primitive - package org.anchoranalysis.bean.xml.factory.primitive
-
Factories to create beans in org.anchoranalysis.bean.primitive
.
- org.anchoranalysis.core.cache - package org.anchoranalysis.core.cache
-
Caching (memozing) calls to a method so an operation does not need to be repeated.
- org.anchoranalysis.core.collection - package org.anchoranalysis.core.collection
-
Collection-related classes with general applicability that don't belong elsewhere.
- org.anchoranalysis.core.color - package org.anchoranalysis.core.color
-
Specifying particular colors and groups of colors.
- org.anchoranalysis.core.exception - package org.anchoranalysis.core.exception
-
Very general exceptions and base classes for exceptions with wide applicability.
- org.anchoranalysis.core.exception.combinable - package org.anchoranalysis.core.exception.combinable
-
Nested exceptions of similar type that can be combined together in a summary.
- org.anchoranalysis.core.exception.friendly - package org.anchoranalysis.core.exception.friendly
-
Particular types of exceptions that are guaranteed to have a text/form that gives user-friendly
error descriptions.
- org.anchoranalysis.core.format - package org.anchoranalysis.core.format
-
File formats and associated extensions.
- org.anchoranalysis.core.functional - package org.anchoranalysis.core.functional
-
Utilities and interfaces for applying functional-programming.
- org.anchoranalysis.core.functional.checked - package org.anchoranalysis.core.functional.checked
-
Versions of many functional-interfaces in java.util.function
that throw
checked-exceptions.
- org.anchoranalysis.core.functional.unchecked - package org.anchoranalysis.core.functional.unchecked
-
Adds additional functional-interfaces, that are unavailable in java.util.function
, and do
not throw checked exceptions.
- org.anchoranalysis.core.graph - package org.anchoranalysis.core.graph
-
Data-structures for directed and undirected graphs, with or without an edge payload.
- org.anchoranalysis.core.identifier.getter - package org.anchoranalysis.core.identifier.getter
-
Data structures for adding a unique name (a String or integer identifier) to other entities.
- org.anchoranalysis.core.identifier.name - package org.anchoranalysis.core.identifier.name
-
Data structures for name (String) and value associations.
- org.anchoranalysis.core.identifier.provider - package org.anchoranalysis.core.identifier.provider
-
A collection of named-elements, a
NamedProvider
and related operations.
- org.anchoranalysis.core.identifier.provider.store - package org.anchoranalysis.core.identifier.provider.store
-
Data structures like
NamedProvider
with
supporting for adding new elements.
- org.anchoranalysis.core.index - package org.anchoranalysis.core.index
-
Classes to support getting / setting / specifying unique-integers (indices) for elements.
- org.anchoranalysis.core.index.range - package org.anchoranalysis.core.index.range
-
A range of indices from minimum to maximum.
- org.anchoranalysis.core.log - package org.anchoranalysis.core.log
-
Interfaces to log messages, both information and error messages.
- org.anchoranalysis.core.log.error - package org.anchoranalysis.core.log.error
-
Mechanism for reporting errors (exceptions/throwables) to the user.
- org.anchoranalysis.core.random - package org.anchoranalysis.core.random
-
Generating random numbers.
- org.anchoranalysis.core.serialize - package org.anchoranalysis.core.serialize
-
Utilities for serializing and deserializing objects.
- org.anchoranalysis.core.system - package org.anchoranalysis.core.system
-
Utilities for interacting with the operating system or computer system generally
- org.anchoranalysis.core.system.path - package org.anchoranalysis.core.system.path
-
Utilities for converting/manipulating file-paths.
- org.anchoranalysis.core.time - package org.anchoranalysis.core.time
-
Recording the execution-time of operations for profiling.
- org.anchoranalysis.core.value - package org.anchoranalysis.core.value
-
Encapsulating values or sets of named-values.
- org.anchoranalysis.experiment - package org.anchoranalysis.experiment
-
Classes related to executing an experiment by calling jobs on inputs.
- org.anchoranalysis.experiment.arguments - package org.anchoranalysis.experiment.arguments
-
Arguments that can further specify an experiment in addition to its bean specification.
- org.anchoranalysis.experiment.bean - package org.anchoranalysis.experiment.bean
-
Beans related to executing an experiment by calling jobs on inputs.
- org.anchoranalysis.experiment.bean.identifier - package org.anchoranalysis.experiment.bean.identifier
-
Assigning unique names to experiments.
- org.anchoranalysis.experiment.bean.io - package org.anchoranalysis.experiment.bean.io
-
Generic experiments that handle input and output in structured ways.
- org.anchoranalysis.experiment.bean.log - package org.anchoranalysis.experiment.bean.log
-
Different approaches to where messages on the progress/status of an experiment are logged to.
- org.anchoranalysis.experiment.bean.processor - package org.anchoranalysis.experiment.bean.processor
-
How a task is executed on multiple inputs.
- org.anchoranalysis.experiment.bean.require - package org.anchoranalysis.experiment.bean.require
-
A test whether certain conditions on arguments to experiments are fulfilled.
- org.anchoranalysis.experiment.bean.task - package org.anchoranalysis.experiment.bean.task
-
Defines a
task,
which is a set of operations run on an input, that may or may not generate an output.
- org.anchoranalysis.experiment.io - package org.anchoranalysis.experiment.io
-
Interfaces for replacing attributes of an experiment: input, output, task etc.
- org.anchoranalysis.experiment.log - package org.anchoranalysis.experiment.log
-
Helpful classes for logging.
- org.anchoranalysis.experiment.task - package org.anchoranalysis.experiment.task
-
Non-bean classes related to a
Task
.
- org.anchoranalysis.experiment.task.processor - package org.anchoranalysis.experiment.task.processor
-
- org.anchoranalysis.experiment.time - package org.anchoranalysis.experiment.time
-
How long particular operations take to execute.
- org.anchoranalysis.feature.bean - package org.anchoranalysis.feature.bean
-
Beans pertaining to feature-calculation.
- org.anchoranalysis.feature.bean.list - package org.anchoranalysis.feature.bean.list
-
A feature-list (custom list type for features) and associated providers.
- org.anchoranalysis.feature.bean.operator - package org.anchoranalysis.feature.bean.operator
-
Features that are sufficiently generic to work on any input-type.
- org.anchoranalysis.feature.bean.provider - package org.anchoranalysis.feature.bean.provider
-
Provider of a single feature.
- org.anchoranalysis.feature.bean.results - package org.anchoranalysis.feature.bean.results
-
- org.anchoranalysis.feature.calculate - package org.anchoranalysis.feature.calculate
-
Sub-feature units of calculation that can be cached.
- org.anchoranalysis.feature.calculate.bound - package org.anchoranalysis.feature.calculate.bound
-
- org.anchoranalysis.feature.calculate.cache - package org.anchoranalysis.feature.calculate.cache
-
Classes to cache feature-results or parts of feature-results that occur repeatedly among features
or across calculations of the same feature.
- org.anchoranalysis.feature.calculate.cache.part - package org.anchoranalysis.feature.calculate.cache.part
-
Equivalent classes to org.anchoranalysis.feature.calculate.part
after having been
resolved against a cache.
- org.anchoranalysis.feature.calculate.part - package org.anchoranalysis.feature.calculate.part
-
A sub-part of the calculation of a feature, that can be cached, and reused by other features.
- org.anchoranalysis.feature.energy - package org.anchoranalysis.feature.energy
-
A particular stack used in feature-calculations called a
EnergyStack
together with related classes.
- org.anchoranalysis.feature.initialization - package org.anchoranalysis.feature.initialization
-
Initialization parameters used for beans in org.anchoranalysis.feature.bean
.
- org.anchoranalysis.feature.input - package org.anchoranalysis.feature.input
-
Base classes providing inputs to feature calculations.
- org.anchoranalysis.feature.io.csv - package org.anchoranalysis.feature.io.csv
-
Metadata for writing feature calculation-results in CSV format.
- org.anchoranalysis.feature.io.csv.metadata - package org.anchoranalysis.feature.io.csv.metadata
-
Writing the results of feature calculations to the file-system.
- org.anchoranalysis.feature.io.csv.results - package org.anchoranalysis.feature.io.csv.results
-
Writing the results from feature-calculation to a CSV file.
- org.anchoranalysis.feature.io.csv.table - package org.anchoranalysis.feature.io.csv.table
-
A
Generator
for writing a table of feature values as a
CSV.
- org.anchoranalysis.feature.io.name - package org.anchoranalysis.feature.io.name
-
Naming items in a weay that breaks down into multiple elements.
- org.anchoranalysis.feature.io.results - package org.anchoranalysis.feature.io.results
-
Writes feature-calculation results in different formats, also grouped results.
- org.anchoranalysis.feature.io.results.group - package org.anchoranalysis.feature.io.results.group
-
- org.anchoranalysis.feature.name - package org.anchoranalysis.feature.name
-
Data objects for the names of features.
- org.anchoranalysis.feature.results - package org.anchoranalysis.feature.results
-
Results from one or more feature calculations.
- org.anchoranalysis.feature.session - package org.anchoranalysis.feature.session
-
A defined context in which one or more features are provided inputs and produce results.
- org.anchoranalysis.feature.session.cache - package org.anchoranalysis.feature.session.cache
-
- org.anchoranalysis.feature.session.cache.finder - package org.anchoranalysis.feature.session.cache.finder
-
Strategies to determine which child-cache (among hierarchy) to employ for a particular feature
calculation.
- org.anchoranalysis.feature.session.calculator - package org.anchoranalysis.feature.session.calculator
-
Base classes for methods to calculate results from features.
- org.anchoranalysis.feature.session.replace - package org.anchoranalysis.feature.session.replace
-
Strategies on whether to reuse or invalidate a feature-input's cache.
- org.anchoranalysis.feature.shared - package org.anchoranalysis.feature.shared
-
Features shared for referencing among calculations.
- org.anchoranalysis.feature.store - package org.anchoranalysis.feature.store
-
- org.anchoranalysis.image.bean - package org.anchoranalysis.image.bean
-
Core (bean) classes for image processing.
- org.anchoranalysis.image.bean.channel - package org.anchoranalysis.image.bean.channel
-
Base classes for performing operations on
Channel
s.
- org.anchoranalysis.image.bean.displayer - package org.anchoranalysis.image.bean.displayer
-
- org.anchoranalysis.image.bean.interpolator - package org.anchoranalysis.image.bean.interpolator
-
Beans for specifying image interpolators.
- org.anchoranalysis.image.bean.nonbean - package org.anchoranalysis.image.bean.nonbean
-
Classes that are used elsewhere in this package but which aren't themselves AnchorBeans.
- org.anchoranalysis.image.bean.nonbean.init - package org.anchoranalysis.image.bean.nonbean.init
-
Classes that aren't AnchorBeans that pertain to the initialization of image-related beans.
- org.anchoranalysis.image.bean.nonbean.segment - package org.anchoranalysis.image.bean.nonbean.segment
-
Non-bean classes relating to image-segmentation.
- org.anchoranalysis.image.bean.nonbean.spatial.align - package org.anchoranalysis.image.bean.nonbean.spatial.align
-
Non-bean classes to help specify the position of one entity relative to the others.
- org.anchoranalysis.image.bean.nonbean.spatial.arrange - package org.anchoranalysis.image.bean.nonbean.spatial.arrange
-
Non-beans to specify how to form a single-image by spatially combining other images.
- org.anchoranalysis.image.bean.object - package org.anchoranalysis.image.bean.object
-
Beans pertaining to
ObjectMask
and their
collections.
- org.anchoranalysis.image.bean.provider - package org.anchoranalysis.image.bean.provider
-
Base classes for providers of different core data entities related to images.
- org.anchoranalysis.image.bean.provider.stack - package org.anchoranalysis.image.bean.provider.stack
-
- org.anchoranalysis.image.bean.segment - package org.anchoranalysis.image.bean.segment
-
Base classes to perform image segmentation, transforming an image into another meaningful entity
or entities.
- org.anchoranalysis.image.bean.segment.binary - package org.anchoranalysis.image.bean.segment.binary
-
Base classes to perform binary-segmentation.
- org.anchoranalysis.image.bean.segment.object - package org.anchoranalysis.image.bean.segment.object
-
Base classes to segment a channel into objects.
- org.anchoranalysis.image.bean.spatial - package org.anchoranalysis.image.bean.spatial
-
Beans to define entities or operate that consider Euclidian space.
- org.anchoranalysis.image.bean.spatial.arrange - package org.anchoranalysis.image.bean.spatial.arrange
-
Beans to specify how to form a single-image by spatially combining other images.
- org.anchoranalysis.image.bean.spatial.arrange.align - package org.anchoranalysis.image.bean.spatial.arrange.align
-
- org.anchoranalysis.image.bean.spatial.arrange.fill - package org.anchoranalysis.image.bean.spatial.arrange.fill
-
Montages images together to completely fill the available space, while preserving aspect ratio.
- org.anchoranalysis.image.bean.spatial.arrange.overlay - package org.anchoranalysis.image.bean.spatial.arrange.overlay
-
Combining other images through overlaying.
- org.anchoranalysis.image.bean.spatial.arrange.tile - package org.anchoranalysis.image.bean.spatial.arrange.tile
-
Combining other images through tiling.
- org.anchoranalysis.image.bean.spatial.direction - package org.anchoranalysis.image.bean.spatial.direction
-
Beans to specify a direction.
- org.anchoranalysis.image.bean.threshold - package org.anchoranalysis.image.bean.threshold
-
Base classes for thresholding and calculating levels for thresholding.
- org.anchoranalysis.image.bean.threshold.relation - package org.anchoranalysis.image.bean.threshold.relation
-
Reusable relations to a threshold.
- org.anchoranalysis.image.bean.unitvalue.distance - package org.anchoranalysis.image.bean.unitvalue.distance
-
Converting quantities of distance between units.
- org.anchoranalysis.image.bean.unitvalue.extent - package org.anchoranalysis.image.bean.unitvalue.extent
-
Converting quantities of extent (area or volume) between units.
- org.anchoranalysis.image.bean.unitvalue.extent.area - package org.anchoranalysis.image.bean.unitvalue.extent.area
-
Converting quantities of area between units.
- org.anchoranalysis.image.bean.unitvalue.extent.volume - package org.anchoranalysis.image.bean.unitvalue.extent.volume
-
Converting quantities of volume between units.
- org.anchoranalysis.image.core.bufferedimage - package org.anchoranalysis.image.core.bufferedimage
-
- org.anchoranalysis.image.core.channel - package org.anchoranalysis.image.core.channel
-
The
Channel
core data-class and related operations
and converters.
- org.anchoranalysis.image.core.channel.convert - package org.anchoranalysis.image.core.channel.convert
-
Converts a channel to other data-types.
- org.anchoranalysis.image.core.channel.convert.attached - package org.anchoranalysis.image.core.channel.convert.attached
-
Converts a channel to another data-type based upon another object to which it is attached.
- org.anchoranalysis.image.core.channel.convert.attached.channel - package org.anchoranalysis.image.core.channel.convert.attached.channel
-
Converts a channel to another data-type based upon a
Channel
to which it is
attached.
- org.anchoranalysis.image.core.channel.convert.attached.histogram - package org.anchoranalysis.image.core.channel.convert.attached.histogram
-
Converts a channel to another data-type based upon a
Histogram
to which it is
attached.
- org.anchoranalysis.image.core.channel.factory - package org.anchoranalysis.image.core.channel.factory
-
Factory classes for creating
Channel
for various
voxel data-types.
- org.anchoranalysis.image.core.contour - package org.anchoranalysis.image.core.contour
-
Finds outline voxels, the pixels on the contour/edge of the object.
- org.anchoranalysis.image.core.dimensions - package org.anchoranalysis.image.core.dimensions
-
Classes to describe the size of images or components of images both in voxels and physically.
- org.anchoranalysis.image.core.dimensions.size.suggestion - package org.anchoranalysis.image.core.dimensions.size.suggestion
-
Suggestions on a size for an image.
- org.anchoranalysis.image.core.mask - package org.anchoranalysis.image.core.mask
-
An image with only two permissible states.
- org.anchoranalysis.image.core.mask.combine - package org.anchoranalysis.image.core.mask.combine
-
Binary operations involving voxelwise combination of
Mask
.
- org.anchoranalysis.image.core.merge - package org.anchoranalysis.image.core.merge
-
Merges two or more entities.
- org.anchoranalysis.image.core.object - package org.anchoranalysis.image.core.object
-
The key data entity org.anchoranalysis.image.voxel.object
and related-classes and
operations.
- org.anchoranalysis.image.core.object.label - package org.anchoranalysis.image.core.object.label
-
Labelling elements (object-masks or similar) with unique successive integers in a channel.
- org.anchoranalysis.image.core.object.properties - package org.anchoranalysis.image.core.object.properties
-
- org.anchoranalysis.image.core.object.scale - package org.anchoranalysis.image.core.object.scale
-
Scaling object-collections, or lists of elements with object-representations.
- org.anchoranalysis.image.core.object.scale.method - package org.anchoranalysis.image.core.object.scale.method
-
Scaling elements with an associated
ObjectMask
either collectively or independently.
- org.anchoranalysis.image.core.points - package org.anchoranalysis.image.core.points
-
Operations that extract points from image data entities or vice versa.
- org.anchoranalysis.image.core.stack - package org.anchoranalysis.image.core.stack
-
Defines the key data object,
Stack
, and related
classes.
- org.anchoranalysis.image.core.stack.named - package org.anchoranalysis.image.core.stack.named
-
A collection of
Stack
s, each with a unique identifier
as a name.
- org.anchoranalysis.image.feature.bean - package org.anchoranalysis.image.feature.bean
-
Beans pertaining to feature definition and calculation.
- org.anchoranalysis.image.feature.bean.evaluator - package org.anchoranalysis.image.feature.bean.evaluator
-
Beans that define context (which feature, which energy-stack) for evaluating feature-inputs.
- org.anchoranalysis.image.feature.bean.histogram - package org.anchoranalysis.image.feature.bean.histogram
-
- org.anchoranalysis.image.feature.bean.object.collection - package org.anchoranalysis.image.feature.bean.object.collection
-
- org.anchoranalysis.image.feature.bean.object.pair - package org.anchoranalysis.image.feature.bean.object.pair
-
- org.anchoranalysis.image.feature.bean.object.single - package org.anchoranalysis.image.feature.bean.object.single
-
- org.anchoranalysis.image.feature.bean.physical - package org.anchoranalysis.image.feature.bean.physical
-
Features that convert to/from physical spatial units (e.g.
- org.anchoranalysis.image.feature.calculation - package org.anchoranalysis.image.feature.calculation
-
- org.anchoranalysis.image.feature.calculator - package org.anchoranalysis.image.feature.calculator
-
Implementations of
FeatureCalculatorMulti
related to images, especially to create tables of feature-calculations.
- org.anchoranalysis.image.feature.calculator.merged - package org.anchoranalysis.image.feature.calculator.merged
-
A particular implementation of
FeatureCalculatorMulti
for feature-calculations based
upon pairs of image-objects.
- org.anchoranalysis.image.feature.input - package org.anchoranalysis.image.feature.input
-
- org.anchoranalysis.image.inference - package org.anchoranalysis.image.inference
-
Inference of machine learning models on images.
- org.anchoranalysis.image.inference.bean.reduce - package org.anchoranalysis.image.inference.bean.reduce
-
Beans to reduce the number of results that are returned from inference, by removing overlaping
entities etc.
- org.anchoranalysis.image.inference.bean.segment.instance - package org.anchoranalysis.image.inference.bean.segment.instance
-
- org.anchoranalysis.image.inference.bean.segment.reduce - package org.anchoranalysis.image.inference.bean.segment.reduce
-
Non-bean classes to reduce the number of results that are returned from inference, by removing
overlapping entities etc.
- org.anchoranalysis.image.inference.segment - package org.anchoranalysis.image.inference.segment
-
Non-beans pertaining to segmentation of images via model inference.
- org.anchoranalysis.image.io - package org.anchoranalysis.image.io
-
Reading and writing of image-related data objects to and from the filesystem.
- org.anchoranalysis.image.io.bean.channel - package org.anchoranalysis.image.io.bean.channel
-
Beans pertaining to reading
Channel
s as input.
- org.anchoranalysis.image.io.bean.object.draw - package org.anchoranalysis.image.io.bean.object.draw
-
How to represent an object-mask in a raster that is being drawn.
- org.anchoranalysis.image.io.bean.object.feature - package org.anchoranalysis.image.io.bean.object.feature
-
- org.anchoranalysis.image.io.bean.stack.combine - package org.anchoranalysis.image.io.bean.stack.combine
-
Beans to combine multiple stacks into a single stack before outputting.
- org.anchoranalysis.image.io.bean.stack.metadata.reader - package org.anchoranalysis.image.io.bean.stack.metadata.reader
-
- org.anchoranalysis.image.io.bean.stack.reader - package org.anchoranalysis.image.io.bean.stack.reader
-
Bean classes for reading raster-files from the filesystem.
- org.anchoranalysis.image.io.bean.stack.writer - package org.anchoranalysis.image.io.bean.stack.writer
-
Bean classes for writing raster-files to the filesystem.
- org.anchoranalysis.image.io.channel.input - package org.anchoranalysis.image.io.channel.input
-
Non-bean classes for reading a
Channel
from the
filesystem.
- org.anchoranalysis.image.io.channel.map - package org.anchoranalysis.image.io.channel.map
-
Non-bean classes for a
mapping of names to Channel
s.
- org.anchoranalysis.image.io.channel.output - package org.anchoranalysis.image.io.channel.output
-
Non-bean classes for writing a
Channel
to the
filesystem.
- org.anchoranalysis.image.io.histogram.input - package org.anchoranalysis.image.io.histogram.input
-
Non-bean classes for reading a
Histogram
from the
filesystem.
- org.anchoranalysis.image.io.histogram.output - package org.anchoranalysis.image.io.histogram.output
-
Non-bean classes for writing a
Histogram
to the
filesystem.
- org.anchoranalysis.image.io.object - package org.anchoranalysis.image.io.object
-
Non-bean classes for reading / writing an
ObjectCollection
from and to the filesystem.
- org.anchoranalysis.image.io.object.input - package org.anchoranalysis.image.io.object.input
-
- org.anchoranalysis.image.io.object.output.grayscale - package org.anchoranalysis.image.io.object.output.grayscale
-
- org.anchoranalysis.image.io.object.output.hdf5 - package org.anchoranalysis.image.io.object.output.hdf5
-
- org.anchoranalysis.image.io.object.output.mask - package org.anchoranalysis.image.io.object.output.mask
-
Writing an
ObjectCollection
to the filesystem as
multiple binary singled-channeled images.
- org.anchoranalysis.image.io.object.output.rgb - package org.anchoranalysis.image.io.object.output.rgb
-
- org.anchoranalysis.image.io.stack - package org.anchoranalysis.image.io.stack
-
Non-bean classes for reading / writing a
Stack
from
and to the filesystem.
- org.anchoranalysis.image.io.stack.input - package org.anchoranalysis.image.io.stack.input
-
Non-bean classes for reading a
Stack
from the
filesystem.
- org.anchoranalysis.image.io.stack.output - package org.anchoranalysis.image.io.stack.output
-
Non-bean classes for writing a
Stack
to the
filesystem.
- org.anchoranalysis.image.io.stack.output.box - package org.anchoranalysis.image.io.stack.output.box
-
Base classes for generators that ultimately write
only a bounding-box portion of a
Stack
to the filesystem.
- org.anchoranalysis.image.io.stack.output.generator - package org.anchoranalysis.image.io.stack.output.generator
-
Base classes for generators that ultimately write a
Stack
to the filesystem.
- org.anchoranalysis.image.io.stack.time - package org.anchoranalysis.image.io.stack.time
-
A time-sequence of
Stack
s.
- org.anchoranalysis.image.voxel - package org.anchoranalysis.image.voxel
-
Data-structures to store and manipulate image raster-data or voxels.
- org.anchoranalysis.image.voxel.arithmetic - package org.anchoranalysis.image.voxel.arithmetic
-
Arithmetic operations for
Voxels
.
- org.anchoranalysis.image.voxel.assigner - package org.anchoranalysis.image.voxel.assigner
-
Assigns values to some or all voxels.
- org.anchoranalysis.image.voxel.binary - package org.anchoranalysis.image.voxel.binary
-
- org.anchoranalysis.image.voxel.binary.connected - package org.anchoranalysis.image.voxel.binary.connected
-
- org.anchoranalysis.image.voxel.binary.values - package org.anchoranalysis.image.voxel.binary.values
-
Defining on and off intensity-values to interpret an image in a binary way.
- org.anchoranalysis.image.voxel.buffer - package org.anchoranalysis.image.voxel.buffer
-
A buffer of voxel-values, usually corresponding to a single z-slice in
Voxels
.
- org.anchoranalysis.image.voxel.buffer.primitive - package org.anchoranalysis.image.voxel.buffer.primitive
-
Conversion of both primitive data types and image structures between Anchor's data-structures and
other representations.
- org.anchoranalysis.image.voxel.buffer.slice - package org.anchoranalysis.image.voxel.buffer.slice
-
A container with voxel-buffers for each z-slice.
- org.anchoranalysis.image.voxel.convert - package org.anchoranalysis.image.voxel.convert
-
Converting
Voxels
to different data-types.
- org.anchoranalysis.image.voxel.convert.bufferedimage - package org.anchoranalysis.image.voxel.convert.bufferedimage
-
- org.anchoranalysis.image.voxel.convert.imglib2 - package org.anchoranalysis.image.voxel.convert.imglib2
-
Converts anchor data-structures to those used by
ImgLib2.
- org.anchoranalysis.image.voxel.datatype - package org.anchoranalysis.image.voxel.datatype
-
The different data-types that can be used to represent voxels.
- org.anchoranalysis.image.voxel.extracter - package org.anchoranalysis.image.voxel.extracter
-
Methods to read/copy/duplicate portions of voxels.
- org.anchoranalysis.image.voxel.extracter.predicate - package org.anchoranalysis.image.voxel.extracter.predicate
-
Methods to find or count voxels that satisfy a predicate.
- org.anchoranalysis.image.voxel.factory - package org.anchoranalysis.image.voxel.factory
-
- org.anchoranalysis.image.voxel.iterator - package org.anchoranalysis.image.voxel.iterator
-
Utilities to iterate over voxel-locations in images and sub-regions of images.
- org.anchoranalysis.image.voxel.iterator.intersecting - package org.anchoranalysis.image.voxel.iterator.intersecting
-
Like org.anchoranalysis.image.voxel.iterator
but refers to iterators that operation over
the intersecting regions of two entities.
- org.anchoranalysis.image.voxel.iterator.neighbor - package org.anchoranalysis.image.voxel.iterator.neighbor
-
Iterating over a point's neighboring voxels.
- org.anchoranalysis.image.voxel.iterator.neighbor.kernel - package org.anchoranalysis.image.voxel.iterator.neighbor.kernel
-
- org.anchoranalysis.image.voxel.iterator.predicate - package org.anchoranalysis.image.voxel.iterator.predicate
-
Functional-interfaces for processing different combinations of points and buffers that return a
boolean.
- org.anchoranalysis.image.voxel.iterator.process - package org.anchoranalysis.image.voxel.iterator.process
-
Functional-interfaces for processing different combinations of points and buffers that do not
return a value.
- org.anchoranalysis.image.voxel.iterator.process.buffer - package org.anchoranalysis.image.voxel.iterator.process.buffer
-
Functional-interfaces for processing different combinations of points and raw buffers, but not
VoxelBuffer
.
- org.anchoranalysis.image.voxel.iterator.process.voxelbuffer - package org.anchoranalysis.image.voxel.iterator.process.voxelbuffer
-
Functional-interfaces for processing different combinations of points and
VoxelBuffer
but not raw buffers.
- org.anchoranalysis.image.voxel.kernel - package org.anchoranalysis.image.voxel.kernel
-
Applying a
kernel via
convolution to voxels.
- org.anchoranalysis.image.voxel.kernel.count - package org.anchoranalysis.image.voxel.kernel.count
-
Kernels to count the number of voxels that are equal to a particular value.
- org.anchoranalysis.image.voxel.kernel.morphological - package org.anchoranalysis.image.voxel.kernel.morphological
-
Kernels that apply morphological operations.
- org.anchoranalysis.image.voxel.kernel.outline - package org.anchoranalysis.image.voxel.kernel.outline
-
Kernel to find outline voxels on an object.
- org.anchoranalysis.image.voxel.neighborhood - package org.anchoranalysis.image.voxel.neighborhood
-
A region in proximity to a voxel, encompassing this voxel as well as others.
- org.anchoranalysis.image.voxel.object - package org.anchoranalysis.image.voxel.object
-
The fundamental data class that is an
ObjectMask
and related structures.
- org.anchoranalysis.image.voxel.object.morphological - package org.anchoranalysis.image.voxel.object.morphological
-
- org.anchoranalysis.image.voxel.object.morphological.predicate - package org.anchoranalysis.image.voxel.object.morphological.predicate
-
Predicates to match certain voxels as used in org.anchoranalysis.image.voxel.object.morphological
.
- org.anchoranalysis.image.voxel.projection - package org.anchoranalysis.image.voxel.projection
-
Classes for calculating differnet kind of projections of voxel values across multiple buffers.
- org.anchoranalysis.image.voxel.projection.extrema - package org.anchoranalysis.image.voxel.projection.extrema
-
- org.anchoranalysis.image.voxel.resizer - package org.anchoranalysis.image.voxel.resizer
-
Different interpolator methods to use when scaling voxels.
- org.anchoranalysis.image.voxel.statistics - package org.anchoranalysis.image.voxel.statistics
-
Statistics about aggregated voxel intensities.
- org.anchoranalysis.image.voxel.thresholder - package org.anchoranalysis.image.voxel.thresholder
-
Thresholding operations on voxels.
- org.anchoranalysis.inference - package org.anchoranalysis.inference
-
High-level classes for performing machine learning model inference.
- org.anchoranalysis.inference.concurrency - package org.anchoranalysis.inference.concurrency
-
Specifying how many CPUs and GPUs can be allocated for some purpose.
- org.anchoranalysis.io.bioformats - package org.anchoranalysis.io.bioformats
-
Non-bean classes for filesystem I/O using
Bioformats.
- org.anchoranalysis.io.bioformats.bean - package org.anchoranalysis.io.bioformats.bean
-
- org.anchoranalysis.io.bioformats.bean.options - package org.anchoranalysis.io.bioformats.bean.options
-
User-specified options that can modify metadata or other attributes of a loaded Bioformats image.
- org.anchoranalysis.io.bioformats.bean.writer - package org.anchoranalysis.io.bioformats.bean.writer
-
Writing stacks to the file system using the Bioformats library.
- org.anchoranalysis.io.bioformats.copyconvert - package org.anchoranalysis.io.bioformats.copyconvert
-
Converts the byte stream opened by Bioformats into channels of particular data-type.
- org.anchoranalysis.io.bioformats.copyconvert.tobyte - package org.anchoranalysis.io.bioformats.copyconvert.tobyte
-
Converts the byte stream opened by Bioformats into channels of
ByteBuffer
.
- org.anchoranalysis.io.bioformats.copyconvert.tofloat - package org.anchoranalysis.io.bioformats.copyconvert.tofloat
-
Converts the byte stream opened by Bioformats into channels of
FloatBuffer
.
- org.anchoranalysis.io.bioformats.copyconvert.toint - package org.anchoranalysis.io.bioformats.copyconvert.toint
-
Converts the byte stream opened by Bioformats into channels of
IntBuffer
.
- org.anchoranalysis.io.bioformats.copyconvert.toshort - package org.anchoranalysis.io.bioformats.copyconvert.toshort
-
Converts the byte stream opened by Bioformats into channels of
ShortBuffer
.
- org.anchoranalysis.io.bioformats.metadata - package org.anchoranalysis.io.bioformats.metadata
-
Reading metadata information from files using EXIF and/or other metadata headers.
- org.anchoranalysis.io.generator - package org.anchoranalysis.io.generator
-
Base-classes and utilities for generators, which write different types of objects to the file
system.
- org.anchoranalysis.io.generator.collection - package org.anchoranalysis.io.generator.collection
-
Outputting more than one element collectively using a generator.
- org.anchoranalysis.io.generator.combined - package org.anchoranalysis.io.generator.combined
-
Combining multiple generators into one.
- org.anchoranalysis.io.generator.sequence - package org.anchoranalysis.io.generator.sequence
-
Writing a sequence of elements using a generator.
- org.anchoranalysis.io.generator.sequence.pattern - package org.anchoranalysis.io.generator.sequence.pattern
-
A particular naming pattern files follow when outputted.
- org.anchoranalysis.io.generator.serialized - package org.anchoranalysis.io.generator.serialized
-
Generators for writing serialized objects.
- org.anchoranalysis.io.generator.tabular - package org.anchoranalysis.io.generator.tabular
-
Generators for writing tabular data, including CSV.
- org.anchoranalysis.io.generator.text - package org.anchoranalysis.io.generator.text
-
Generators for writing textual data, including strings.
- org.anchoranalysis.io.generator.xml - package org.anchoranalysis.io.generator.xml
-
Generators for writing XML data.
- org.anchoranalysis.io.imagej.bean.interpolator - package org.anchoranalysis.io.imagej.bean.interpolator
-
Performing interpolation with ImageJ.
- org.anchoranalysis.io.imagej.bean.stack.writer - package org.anchoranalysis.io.imagej.bean.stack.writer
-
Raster-writers that use ImageJ to write images to the filesystem.
- org.anchoranalysis.io.imagej.convert - package org.anchoranalysis.io.imagej.convert
-
Converts to and from ImageJ data-structures for images.
- org.anchoranalysis.io.imagej.resizer - package org.anchoranalysis.io.imagej.resizer
-
Image interpolation when scaling using ImageJ.
- org.anchoranalysis.io.input - package org.anchoranalysis.io.input
-
Classes relating to creating inputs for an experiment / task.
- org.anchoranalysis.io.input.bean - package org.anchoranalysis.io.input.bean
-
Beans related to collecting inputs from the file-system for an experiment.
- org.anchoranalysis.io.input.bean.dictionary - package org.anchoranalysis.io.input.bean.dictionary
-
- org.anchoranalysis.io.input.bean.files - package org.anchoranalysis.io.input.bean.files
-
Methods to provide a collection of
File
s.
- org.anchoranalysis.io.input.bean.grouper - package org.anchoranalysis.io.input.bean.grouper
-
Determines how inputs are aggregated into groups, if at all.
- org.anchoranalysis.io.input.bean.namer - package org.anchoranalysis.io.input.bean.namer
-
Beans to derive names (compact unique identifiers) from files.
- org.anchoranalysis.io.input.bean.path - package org.anchoranalysis.io.input.bean.path
-
Beans pertaining to manipulating and matching against file-paths.
- org.anchoranalysis.io.input.bean.path.matcher - package org.anchoranalysis.io.input.bean.path.matcher
-
Beans to find a subset of files that match a particular conditions on their paths.
- org.anchoranalysis.io.input.bean.path.provider - package org.anchoranalysis.io.input.bean.path.provider
-
Methods to provide a single file-path.
- org.anchoranalysis.io.input.csv - package org.anchoranalysis.io.input.csv
-
Classes for reading comma-separated-values (CSV) files.
- org.anchoranalysis.io.input.file - package org.anchoranalysis.io.input.file
-
Non-bean classes that relate to using files during inputting.
- org.anchoranalysis.io.input.grouper - package org.anchoranalysis.io.input.grouper
-
Non-bean classes pertaining grouping inputs.
- org.anchoranalysis.io.input.path - package org.anchoranalysis.io.input.path
-
Non-bean classes pertaining to getting/extracting/manipulating paths as used in inputting.
- org.anchoranalysis.io.input.path.matcher - package org.anchoranalysis.io.input.path.matcher
-
Non-bean classes to help with org.anchoranalysis.io.input.bean.path.matcher
.
- org.anchoranalysis.io.output.bean - package org.anchoranalysis.io.output.bean
-
Beans for the framework around writing files to the file-system.
- org.anchoranalysis.io.output.bean.enabled - package org.anchoranalysis.io.output.bean.enabled
-
Beans indicating whether a particular output is enabled or not.
- org.anchoranalysis.io.output.bean.path.prefixer - package org.anchoranalysis.io.output.bean.path.prefixer
-
Beans for generating paths for outputting files by adding a prefix, suffix etc.
- org.anchoranalysis.io.output.bean.rules - package org.anchoranalysis.io.output.bean.rules
-
Rules for determining if a particular output is enabled or not in a context of a hierarchy.
- org.anchoranalysis.io.output.enabled - package org.anchoranalysis.io.output.enabled
-
Non-beans pertaining to whether a particular output is enabled or not.
- org.anchoranalysis.io.output.enabled.multi - package org.anchoranalysis.io.output.enabled.multi
-
Non-beans that pertain to whether multiple-levels have outputs that are enabled or not.
- org.anchoranalysis.io.output.enabled.single - package org.anchoranalysis.io.output.enabled.single
-
Non-beans that pertain to whether a single level has outputs that are enabled or not.
- org.anchoranalysis.io.output.error - package org.anchoranalysis.io.output.error
-
Exceptions that may be thrown when writing files to the file-system.
- org.anchoranalysis.io.output.namestyle - package org.anchoranalysis.io.output.namestyle
-
Methods of naming a file with an index in the file-name.
- org.anchoranalysis.io.output.outputter - package org.anchoranalysis.io.output.outputter
-
Classes for outputting to particular directories.
- org.anchoranalysis.io.output.outputter.directory - package org.anchoranalysis.io.output.outputter.directory
-
BoundDirectory
and related classes.
- org.anchoranalysis.io.output.path.prefixer - package org.anchoranalysis.io.output.path.prefixer
-
Non-beans for generating paths for outputting files by adding a prefix, suffix etc.
- org.anchoranalysis.io.output.recorded - package org.anchoranalysis.io.output.recorded
-
Classes for recording the output-names used as they are written / queried.
- org.anchoranalysis.io.output.writer - package org.anchoranalysis.io.output.writer
-
Allows a generators to write element(s) to the filesystem.
- org.anchoranalysis.io.output.xml - package org.anchoranalysis.io.output.xml
-
Outputting XML to the file-system.
- org.anchoranalysis.launcher - package org.anchoranalysis.launcher
-
Parent package and entry-point classes for the Anchor command-line launcher application.
- org.anchoranalysis.launcher.config - package org.anchoranalysis.launcher.config
-
Specifies a configuration of the launcher for a particular application.
- org.anchoranalysis.launcher.executor - package org.anchoranalysis.launcher.executor
-
Runs a particular experiment after identifying necessary paths and input files.
- org.anchoranalysis.launcher.executor.selectparam - package org.anchoranalysis.launcher.executor.selectparam
-
Different methods of selecting a object T
that is used as a parameter for an experiment.
- org.anchoranalysis.launcher.executor.selectparam.experiment - package org.anchoranalysis.launcher.executor.selectparam.experiment
-
- org.anchoranalysis.launcher.executor.selectparam.path - package org.anchoranalysis.launcher.executor.selectparam.path
-
SelectParam
s for loading a
Optional<Path>
for inputs, outputs or tasks.
- org.anchoranalysis.launcher.executor.selectparam.path.convert - package org.anchoranalysis.launcher.executor.selectparam.path.convert
-
Converting paths to/from different formats as needed by org.anchoranalysis.launcher.executor.selectparam.path
.
- org.anchoranalysis.launcher.options - package org.anchoranalysis.launcher.options
-
A centralized location for all command-line options used by the launcher.
- org.anchoranalysis.launcher.options.process - package org.anchoranalysis.launcher.options.process
-
Adding/removing/changing the arguments (input and output) from the experiment via
command-line-options.
- org.anchoranalysis.launcher.resources - package org.anchoranalysis.launcher.resources
-
Reading and integrating resources for the launcher.
- org.anchoranalysis.launcher.run - package org.anchoranalysis.launcher.run
-
Parses command-line arguments and runs an experiment.
- org.anchoranalysis.launcher.run.tasks - package org.anchoranalysis.launcher.run.tasks
-
Loading and displaying pre-defined tasks.
- org.anchoranalysis.math.arithmetic - package org.anchoranalysis.math.arithmetic
-
Performing primitive type conversion, counting and summing.
- org.anchoranalysis.math.equation - package org.anchoranalysis.math.equation
-
Solving or manipulating equations.
- org.anchoranalysis.math.histogram - package org.anchoranalysis.math.histogram
-
The
Histogram
data class and related operations.
- org.anchoranalysis.math.optimization - package org.anchoranalysis.math.optimization
-
- org.anchoranalysis.math.relation - package org.anchoranalysis.math.relation
-
Different kinds of binary-relations.
- org.anchoranalysis.math.statistics - package org.anchoranalysis.math.statistics
-
Data structures and algorithms to calculate statistics.
- org.anchoranalysis.math.statistics.moment - package org.anchoranalysis.math.statistics.moment
-
Calculates first and second
image
moments from a covariance matrix of points.
- org.anchoranalysis.mpp.bean - package org.anchoranalysis.mpp.bean
-
- org.anchoranalysis.mpp.bean.bound - package org.anchoranalysis.mpp.bean.bound
-
Lower and upper limits set around variables.
- org.anchoranalysis.mpp.bean.bound.rotation - package org.anchoranalysis.mpp.bean.bound.rotation
-
Bounds on how to rotate an entity in Euclidean space.
- org.anchoranalysis.mpp.bean.mark - package org.anchoranalysis.mpp.bean.mark
-
Beans generally related to
Mark
s.
- org.anchoranalysis.mpp.bean.mark.factory - package org.anchoranalysis.mpp.bean.mark.factory
-
Beans related to creating
Mark
s.
- org.anchoranalysis.mpp.bean.points - package org.anchoranalysis.mpp.bean.points
-
Operations based on sets of points.
- org.anchoranalysis.mpp.bean.points.fitter - package org.anchoranalysis.mpp.bean.points.fitter
-
Fitting structures to sets of points.
- org.anchoranalysis.mpp.bean.proposer - package org.anchoranalysis.mpp.bean.proposer
-
Proposing
Mark
s or other data-structures with particular
attributes.
- org.anchoranalysis.mpp.bean.provider - package org.anchoranalysis.mpp.bean.provider
-
- org.anchoranalysis.mpp.bean.regionmap - package org.anchoranalysis.mpp.bean.regionmap
-
Voxel subregions of
Mark
s.
- org.anchoranalysis.mpp.feature.addcriteria - package org.anchoranalysis.mpp.feature.addcriteria
-
Criteria for adding edges during optimization of marked-point-processes.
- org.anchoranalysis.mpp.feature.bean.energy.element - package org.anchoranalysis.mpp.feature.bean.energy.element
-
Implementations and helper classes for calculating energy during an energy-minimization
optimization scheme.
- org.anchoranalysis.mpp.feature.bean.energy.scheme - package org.anchoranalysis.mpp.feature.bean.energy.scheme
-
- org.anchoranalysis.mpp.feature.bean.mark - package org.anchoranalysis.mpp.feature.bean.mark
-
Features calculated on a
Mark
.
- org.anchoranalysis.mpp.feature.bean.mark.collection - package org.anchoranalysis.mpp.feature.bean.mark.collection
-
Features calculated on a org.anchoranalysis.mpp.feature.bean.mark.collection
.
- org.anchoranalysis.mpp.feature.energy - package org.anchoranalysis.mpp.feature.energy
-
Non-bean classes pertaining to calculating energy during an energy-minimization optimization
scheme.
- org.anchoranalysis.mpp.feature.energy.marks - package org.anchoranalysis.mpp.feature.energy.marks
-
Non-bean classes pertaining to calculating energy of {org.anchoranalysis.mpp.mark.Mark}s.
- org.anchoranalysis.mpp.feature.energy.saved - package org.anchoranalysis.mpp.feature.energy.saved
-
Saved snapshots of energy-calculations.
- org.anchoranalysis.mpp.feature.energy.scheme - package org.anchoranalysis.mpp.feature.energy.scheme
-
Factorized form of storing the energy during an energy-minimization optimization scheme.
- org.anchoranalysis.mpp.feature.error - package org.anchoranalysis.mpp.feature.error
-
Exceptions relating to
Feature
s involving classes from
anchor-mpp
.
- org.anchoranalysis.mpp.feature.input - package org.anchoranalysis.mpp.feature.input
-
Inputs to mark-point-processes related
Feature
s.
- org.anchoranalysis.mpp.feature.mark - package org.anchoranalysis.mpp.feature.mark
-
Non-bean classes for calculating feature-values related to
Mark
s.
- org.anchoranalysis.mpp.index - package org.anchoranalysis.mpp.index
-
Indexing voxel-values in different ways.
- org.anchoranalysis.mpp.index.factory - package org.anchoranalysis.mpp.index.factory
-
Factories for classes in org.anchoranalysis.mpp.index
.
- org.anchoranalysis.mpp.init - package org.anchoranalysis.mpp.init
-
Parameters used to initialize certain types of beans.
- org.anchoranalysis.mpp.io.bean.input - package org.anchoranalysis.mpp.io.bean.input
-
Beans for reading data structures related to marked point processes from the file system.
- org.anchoranalysis.mpp.io.bean.report.feature - package org.anchoranalysis.mpp.io.bean.report.feature
-
Beans for communicating feature-values from data-structures in human-readable manner.
- org.anchoranalysis.mpp.io.input - package org.anchoranalysis.mpp.io.input
-
Non-beans for reading data structures related to marked point processes from the file system.
- org.anchoranalysis.mpp.io.marks - package org.anchoranalysis.mpp.io.marks
-
Non-beans to help write visualization of
Mark
s to the
filesystem.
- org.anchoranalysis.mpp.io.marks.generator - package org.anchoranalysis.mpp.io.marks.generator
-
Generator
base classes to help write visualization of
Mark
s to the filesystem.
- org.anchoranalysis.mpp.io.output - package org.anchoranalysis.mpp.io.output
-
Non-beans for writing data structures related to marked point processes from the file system.
- org.anchoranalysis.mpp.mark - package org.anchoranalysis.mpp.mark
-
Non-bean classes related to
Mark
s.
- org.anchoranalysis.mpp.mark.conic - package org.anchoranalysis.mpp.mark.conic
-
- org.anchoranalysis.mpp.mark.points - package org.anchoranalysis.mpp.mark.points
-
Mark
s implementing structures based on points.
- org.anchoranalysis.mpp.mark.voxelized - package org.anchoranalysis.mpp.mark.voxelized
-
A mark after a voxel-representation has been inferred.
- org.anchoranalysis.mpp.mark.voxelized.memo - package org.anchoranalysis.mpp.mark.voxelized.memo
-
- org.anchoranalysis.mpp.overlap - package org.anchoranalysis.mpp.overlap
-
Calculating overlaps between two
Mark
s.
- org.anchoranalysis.mpp.overlay - package org.anchoranalysis.mpp.overlay
-
- org.anchoranalysis.mpp.pair - package org.anchoranalysis.mpp.pair
-
- org.anchoranalysis.mpp.proposer - package org.anchoranalysis.mpp.proposer
-
Non-bean classes for proposing
Mark
s or other data-structures
with particular attributes.
- org.anchoranalysis.mpp.proposer.error - package org.anchoranalysis.mpp.proposer.error
-
Recording errors related to proposing
Mark
s or other
data-structures with particular attributes.
- org.anchoranalysis.mpp.segment.bean - package org.anchoranalysis.mpp.segment.bean
-
Beans for segmentation algorithms related to marked-point-processes.
- org.anchoranalysis.mpp.segment.bean.define - package org.anchoranalysis.mpp.segment.bean.define
-
- org.anchoranalysis.mpp.segment.bean.optimization - package org.anchoranalysis.mpp.segment.bean.optimization
-
Schemes for finding optima (minima or maxima) via optimization.
- org.anchoranalysis.mpp.segment.bean.optimization.feedback - package org.anchoranalysis.mpp.segment.bean.optimization.feedback
-
- org.anchoranalysis.mpp.segment.bean.optimization.kernel - package org.anchoranalysis.mpp.segment.bean.optimization.kernel
-
Base classes for kernels that transition a configuration of marks (a
MarkCollection
) into an altered version.
- org.anchoranalysis.mpp.segment.bean.optimization.termination - package org.anchoranalysis.mpp.segment.bean.optimization.termination
-
- org.anchoranalysis.mpp.segment.define - package org.anchoranalysis.mpp.segment.define
-
Non-bean classes used in org.anchoranalysis.mpp.segment.bean.define
- org.anchoranalysis.mpp.segment.optimization - package org.anchoranalysis.mpp.segment.optimization
-
Non-bean classes used in org.anchoranalysis.mpp.segment.bean.optimization
- org.anchoranalysis.mpp.segment.optimization.feedback - package org.anchoranalysis.mpp.segment.optimization.feedback
-
Non-bean classes used in org.anchoranalysis.mpp.segment.bean.optimization.feedback
- org.anchoranalysis.mpp.segment.optimization.feedback.aggregate - package org.anchoranalysis.mpp.segment.optimization.feedback.aggregate
-
Aggregating optimization feedback over time.
- org.anchoranalysis.mpp.segment.optimization.feedback.period - package org.anchoranalysis.mpp.segment.optimization.feedback.period
-
Collecting optimization feedback periodically.
- org.anchoranalysis.mpp.segment.optimization.kernel - package org.anchoranalysis.mpp.segment.optimization.kernel
-
Non-bean classes used in org.anchoranalysis.mpp.segment.bean.optimization.kernel
- org.anchoranalysis.mpp.segment.optimization.step - package org.anchoranalysis.mpp.segment.optimization.step
-
Describes an individual step in the optimization.
- org.anchoranalysis.mpp.segment.transformer - package org.anchoranalysis.mpp.segment.transformer
-
Mapping one type of optimization state to another.
- org.anchoranalysis.overlay - package org.anchoranalysis.overlay
-
Overlay
s and related classes involving drawing entities on top
of an image.
- org.anchoranalysis.overlay.bean - package org.anchoranalysis.overlay.bean
-
Beans relating to drawing an
Overlay
on an image.
- org.anchoranalysis.overlay.collection - package org.anchoranalysis.overlay.collection
-
- org.anchoranalysis.overlay.object - package org.anchoranalysis.overlay.object
-
- org.anchoranalysis.overlay.writer - package org.anchoranalysis.overlay.writer
-
Drawing an overlay on an image.
- org.anchoranalysis.plugin.annotation.bean.aggregate - package org.anchoranalysis.plugin.annotation.bean.aggregate
-
Beans to combine two or more annotations.
- org.anchoranalysis.plugin.annotation.bean.comparer - package org.anchoranalysis.plugin.annotation.bean.comparer
-
Comparing the similarity of annotations from two images to each other.
- org.anchoranalysis.plugin.annotation.bean.comparison - package org.anchoranalysis.plugin.annotation.bean.comparison
-
Task to compare a set of annotations to a segmentation or another set of annotations.
- org.anchoranalysis.plugin.annotation.bean.comparison.assigner - package org.anchoranalysis.plugin.annotation.bean.comparison.assigner
-
Pairs annotations from two different sets, creating an assignment of some type.
- org.anchoranalysis.plugin.annotation.bean.file - package org.anchoranalysis.plugin.annotation.bean.file
-
- org.anchoranalysis.plugin.annotation.bean.label - package org.anchoranalysis.plugin.annotation.bean.label
-
A label as used for annotating.
- org.anchoranalysis.plugin.annotation.bean.strategy - package org.anchoranalysis.plugin.annotation.bean.strategy
-
Strategies for how to annotate an image, such label per image etc.
- org.anchoranalysis.plugin.annotation.comparison - package org.anchoranalysis.plugin.annotation.comparison
-
Non-bean classes for comparing two sets of annotations.
- org.anchoranalysis.plugin.annotation.counter - package org.anchoranalysis.plugin.annotation.counter
-
Utility classes for counting images incrementally.
- org.anchoranalysis.plugin.fiji.bean.channel.grayscalereconstruction - package org.anchoranalysis.plugin.fiji.bean.channel.grayscalereconstruction
-
Morphological grayscale-reconstruction algorithm.
- org.anchoranalysis.plugin.fiji.bean.channel.provider - package org.anchoranalysis.plugin.fiji.bean.channel.provider
-
- org.anchoranalysis.plugin.fiji.bean.channel.provider.distance - package org.anchoranalysis.plugin.fiji.bean.channel.provider.distance
-
- org.anchoranalysis.plugin.fiji.bean.define - package org.anchoranalysis.plugin.fiji.bean.define
-
- org.anchoranalysis.plugin.fiji.bean.mask.provider - package org.anchoranalysis.plugin.fiji.bean.mask.provider
-
- org.anchoranalysis.plugin.fiji.bean.threshold - package org.anchoranalysis.plugin.fiji.bean.threshold
-
- org.anchoranalysis.plugin.image.bean.blur - package org.anchoranalysis.plugin.image.bean.blur
-
Filters that perform blurring.
- org.anchoranalysis.plugin.image.bean.channel.aggregator - package org.anchoranalysis.plugin.image.bean.channel.aggregator
-
- org.anchoranalysis.plugin.image.bean.channel.convert - package org.anchoranalysis.plugin.image.bean.channel.convert
-
- org.anchoranalysis.plugin.image.bean.channel.provider - package org.anchoranalysis.plugin.image.bean.channel.provider
-
Implementations of
ChannelProvider
that are
generic base-classes or otherwise abstract or general.
- org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic - package org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
-
- org.anchoranalysis.plugin.image.bean.channel.provider.assign - package org.anchoranalysis.plugin.image.bean.channel.provider.assign
-
- org.anchoranalysis.plugin.image.bean.channel.provider.convert - package org.anchoranalysis.plugin.image.bean.channel.provider.convert
-
- org.anchoranalysis.plugin.image.bean.channel.provider.gradient - package org.anchoranalysis.plugin.image.bean.channel.provider.gradient
-
Implementations of
ChannelProvider
that calculate
the gradient of a
Channel
's voxels in one or more
dimensions.
- org.anchoranalysis.plugin.image.bean.channel.provider.intensity - package org.anchoranalysis.plugin.image.bean.channel.provider.intensity
-
- org.anchoranalysis.plugin.image.bean.channel.provider.mask - package org.anchoranalysis.plugin.image.bean.channel.provider.mask
-
- org.anchoranalysis.plugin.image.bean.channel.provider.object - package org.anchoranalysis.plugin.image.bean.channel.provider.object
-
- org.anchoranalysis.plugin.image.bean.channel.provider.score - package org.anchoranalysis.plugin.image.bean.channel.provider.score
-
Implementations of
ChannelProvider
that assign a
score to particular subregions of a channel.
- org.anchoranalysis.plugin.image.bean.channel.provider.slice - package org.anchoranalysis.plugin.image.bean.channel.provider.slice
-
Implementations of
ChannelProvider
that process 3D
channels slice-by-slice.
- org.anchoranalysis.plugin.image.bean.color.provider - package org.anchoranalysis.plugin.image.bean.color.provider
-
- org.anchoranalysis.plugin.image.bean.dictionary - package org.anchoranalysis.plugin.image.bean.dictionary
-
- org.anchoranalysis.plugin.image.bean.dimensions.provider - package org.anchoranalysis.plugin.image.bean.dimensions.provider
-
- org.anchoranalysis.plugin.image.bean.histogram.provider - package org.anchoranalysis.plugin.image.bean.histogram.provider
-
- org.anchoranalysis.plugin.image.bean.histogram.threshold - package org.anchoranalysis.plugin.image.bean.histogram.threshold
-
Thresholding of intensity values represented in at
Histogram
.
- org.anchoranalysis.plugin.image.bean.mask.provider - package org.anchoranalysis.plugin.image.bean.mask.provider
-
- org.anchoranalysis.plugin.image.bean.mask.provider.combine - package org.anchoranalysis.plugin.image.bean.mask.provider.combine
-
Implementations of
MaskProvider
that combine
existing providers.
- org.anchoranalysis.plugin.image.bean.mask.provider.convert - package org.anchoranalysis.plugin.image.bean.mask.provider.convert
-
- org.anchoranalysis.plugin.image.bean.mask.provider.morphological - package org.anchoranalysis.plugin.image.bean.mask.provider.morphological
-
Implementations of
MaskProvider
that implement
morphological operations.
- org.anchoranalysis.plugin.image.bean.mask.provider.predicate - package org.anchoranalysis.plugin.image.bean.mask.provider.predicate
-
- org.anchoranalysis.plugin.image.bean.mask.provider.segment - package org.anchoranalysis.plugin.image.bean.mask.provider.segment
-
- org.anchoranalysis.plugin.image.bean.mask.provider.slice - package org.anchoranalysis.plugin.image.bean.mask.provider.slice
-
Implementations of
MaskProvider
that process 3D
masks slice-by-slice.
- org.anchoranalysis.plugin.image.bean.object.filter - package org.anchoranalysis.plugin.image.bean.object.filter
-
- org.anchoranalysis.plugin.image.bean.object.filter.collective - package org.anchoranalysis.plugin.image.bean.object.filter.collective
-
Implementations of
ObjectFilter
that assess each
element in a collection
collectively.
- org.anchoranalysis.plugin.image.bean.object.filter.combine - package org.anchoranalysis.plugin.image.bean.object.filter.combine
-
- org.anchoranalysis.plugin.image.bean.object.filter.independent - package org.anchoranalysis.plugin.image.bean.object.filter.independent
-
Implementations of
ObjectFilter
that
independently assess each element in a collection.
- org.anchoranalysis.plugin.image.bean.object.match - package org.anchoranalysis.plugin.image.bean.object.match
-
- org.anchoranalysis.plugin.image.bean.object.provider - package org.anchoranalysis.plugin.image.bean.object.provider
-
- org.anchoranalysis.plugin.image.bean.object.provider.connected - package org.anchoranalysis.plugin.image.bean.object.provider.connected
-
- org.anchoranalysis.plugin.image.bean.object.provider.feature - package org.anchoranalysis.plugin.image.bean.object.provider.feature
-
- org.anchoranalysis.plugin.image.bean.object.provider.filter - package org.anchoranalysis.plugin.image.bean.object.provider.filter
-
- org.anchoranalysis.plugin.image.bean.object.provider.mask - package org.anchoranalysis.plugin.image.bean.object.provider.mask
-
- org.anchoranalysis.plugin.image.bean.object.provider.merge - package org.anchoranalysis.plugin.image.bean.object.provider.merge
-
- org.anchoranalysis.plugin.image.bean.object.provider.morphological - package org.anchoranalysis.plugin.image.bean.object.provider.morphological
-
- org.anchoranalysis.plugin.image.bean.object.provider.segment - package org.anchoranalysis.plugin.image.bean.object.provider.segment
-
- org.anchoranalysis.plugin.image.bean.object.provider.slice - package org.anchoranalysis.plugin.image.bean.object.provider.slice
-
- org.anchoranalysis.plugin.image.bean.object.provider.split - package org.anchoranalysis.plugin.image.bean.object.provider.split
-
- org.anchoranalysis.plugin.image.bean.object.segment.channel - package org.anchoranalysis.plugin.image.bean.object.segment.channel
-
- org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima - package org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima
-
- org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction - package org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction
-
- org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong - package org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong
-
- org.anchoranalysis.plugin.image.bean.object.segment.reduce - package org.anchoranalysis.plugin.image.bean.object.segment.reduce
-
Strategies for reducing the number of elements with a list by merging/removing lower-confidence
elements that overlap.
- org.anchoranalysis.plugin.image.bean.scale - package org.anchoranalysis.plugin.image.bean.scale
-
Implementations of
ScaleCalculator
for calculating
a scaling-factor from dimensions.
- org.anchoranalysis.plugin.image.bean.segment.binary - package org.anchoranalysis.plugin.image.bean.segment.binary
-
- org.anchoranalysis.plugin.image.bean.stack.provider - package org.anchoranalysis.plugin.image.bean.stack.provider
-
- org.anchoranalysis.plugin.image.bean.stack.provider.color - package org.anchoranalysis.plugin.image.bean.stack.provider.color
-
Implementations of
StackProvider
that color
portions of an image.
- org.anchoranalysis.plugin.image.bean.thumbnail.object - package org.anchoranalysis.plugin.image.bean.thumbnail.object
-
- org.anchoranalysis.plugin.image.bean.thumbnail.stack - package org.anchoranalysis.plugin.image.bean.thumbnail.stack
-
- org.anchoranalysis.plugin.image.channel - package org.anchoranalysis.plugin.image.channel
-
Non-beans for operations or calculations relating to
Channel
s.
- org.anchoranalysis.plugin.image.feature.bean.dimensions - package org.anchoranalysis.plugin.image.feature.bean.dimensions
-
- org.anchoranalysis.plugin.image.feature.bean.histogram.statistic - package org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
-
- org.anchoranalysis.plugin.image.feature.bean.histogram.threshold - package org.anchoranalysis.plugin.image.feature.bean.histogram.threshold
-
- org.anchoranalysis.plugin.image.feature.bean.list - package org.anchoranalysis.plugin.image.feature.bean.list
-
- org.anchoranalysis.plugin.image.feature.bean.list.pair - package org.anchoranalysis.plugin.image.feature.bean.list.pair
-
- org.anchoranalysis.plugin.image.feature.bean.list.permute - package org.anchoranalysis.plugin.image.feature.bean.list.permute
-
- org.anchoranalysis.plugin.image.feature.bean.metadata - package org.anchoranalysis.plugin.image.feature.bean.metadata
-
- org.anchoranalysis.plugin.image.feature.bean.morphological - package org.anchoranalysis.plugin.image.feature.bean.morphological
-
- org.anchoranalysis.plugin.image.feature.bean.object.collection - package org.anchoranalysis.plugin.image.feature.bean.object.collection
-
- org.anchoranalysis.plugin.image.feature.bean.object.combine - package org.anchoranalysis.plugin.image.feature.bean.object.combine
-
- org.anchoranalysis.plugin.image.feature.bean.object.pair - package org.anchoranalysis.plugin.image.feature.bean.object.pair
-
- org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap - package org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap
-
Features that calculate the degree of overlap between two
ObjectMask
s.
- org.anchoranalysis.plugin.image.feature.bean.object.pair.touching - package org.anchoranalysis.plugin.image.feature.bean.object.pair.touching
-
Features that calculate how many other objects an
ObjectMask
directly neighbors.
- org.anchoranalysis.plugin.image.feature.bean.object.single - package org.anchoranalysis.plugin.image.feature.bean.object.single
-
- org.anchoranalysis.plugin.image.feature.bean.object.single.border - package org.anchoranalysis.plugin.image.feature.bean.object.single.border
-
Implementations of
FeatureSingleObject
that determine if an
object lies at the border of an image.
- org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox - package org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox
-
- org.anchoranalysis.plugin.image.feature.bean.object.single.energy - package org.anchoranalysis.plugin.image.feature.bean.object.single.energy
-
- org.anchoranalysis.plugin.image.feature.bean.object.single.intensity - package org.anchoranalysis.plugin.image.feature.bean.object.single.intensity
-
- org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient - package org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient
-
- org.anchoranalysis.plugin.image.feature.bean.object.single.moments - package org.anchoranalysis.plugin.image.feature.bean.object.single.moments
-
- org.anchoranalysis.plugin.image.feature.bean.object.single.morphological - package org.anchoranalysis.plugin.image.feature.bean.object.single.morphological
-
- org.anchoranalysis.plugin.image.feature.bean.object.single.shape - package org.anchoranalysis.plugin.image.feature.bean.object.single.shape
-
- org.anchoranalysis.plugin.image.feature.bean.object.single.shared - package org.anchoranalysis.plugin.image.feature.bean.object.single.shared
-
- org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting - package org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting
-
- org.anchoranalysis.plugin.image.feature.bean.object.single.slice - package org.anchoranalysis.plugin.image.feature.bean.object.single.slice
-
Implementations of
FeatureSingleObject
that processes an object
slice-by-slice in the z-dimension.
- org.anchoranalysis.plugin.image.feature.bean.object.single.surface - package org.anchoranalysis.plugin.image.feature.bean.object.single.surface
-
- org.anchoranalysis.plugin.image.feature.bean.physical - package org.anchoranalysis.plugin.image.feature.bean.physical
-
Beans involving physical units for measurement.
- org.anchoranalysis.plugin.image.feature.bean.score - package org.anchoranalysis.plugin.image.feature.bean.score
-
- org.anchoranalysis.plugin.image.feature.bean.shared - package org.anchoranalysis.plugin.image.feature.bean.shared
-
- org.anchoranalysis.plugin.image.feature.bean.shared.object - package org.anchoranalysis.plugin.image.feature.bean.shared.object
-
- org.anchoranalysis.plugin.image.feature.bean.stack.intensity - package org.anchoranalysis.plugin.image.feature.bean.stack.intensity
-
- org.anchoranalysis.plugin.image.feature.bean.stack.object - package org.anchoranalysis.plugin.image.feature.bean.stack.object
-
- org.anchoranalysis.plugin.image.feature.object - package org.anchoranalysis.plugin.image.feature.object
-
Non-bean classes that help calculate features from
ObjectMask
s.
- org.anchoranalysis.plugin.image.feature.object.calculation.delegate - package org.anchoranalysis.plugin.image.feature.object.calculation.delegate
-
Implementations of
CalculationPart
as used by
features elsewhere in this package.
- org.anchoranalysis.plugin.image.feature.object.calculation.single - package org.anchoranalysis.plugin.image.feature.object.calculation.single
-
- org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological - package org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological
-
- org.anchoranalysis.plugin.image.feature.stack.calculation - package org.anchoranalysis.plugin.image.feature.stack.calculation
-
Implementations of
CalculationPart
that process
Stack
s as used by features elsewhere in this package.
- org.anchoranalysis.plugin.image.intensity - package org.anchoranalysis.plugin.image.intensity
-
Non-bean for operations or calculations relating to intensity.
- org.anchoranalysis.plugin.image.intensity.level - package org.anchoranalysis.plugin.image.intensity.level
-
Non-beans for calculating a thresholding level from itensity values.
- org.anchoranalysis.plugin.image.object - package org.anchoranalysis.plugin.image.object
-
- org.anchoranalysis.plugin.image.object.merge - package org.anchoranalysis.plugin.image.object.merge
-
- org.anchoranalysis.plugin.image.object.merge.condition - package org.anchoranalysis.plugin.image.object.merge.condition
-
- org.anchoranalysis.plugin.image.object.merge.priority - package org.anchoranalysis.plugin.image.object.merge.priority
-
- org.anchoranalysis.plugin.image.provider - package org.anchoranalysis.plugin.image.provider
-
Non-bean classes pertaining to
Provider
s.
- org.anchoranalysis.plugin.image.segment.thresholder.slice - package org.anchoranalysis.plugin.image.segment.thresholder.slice
-
Non-beans pertaining to segmenting a z-stack slice-by-slice.
- org.anchoranalysis.plugin.image.segment.watershed.encoding - package org.anchoranalysis.plugin.image.segment.watershed.encoding
-
Encoding voxels in a watershed-transformation implementation.
- org.anchoranalysis.plugin.image.task.bean - package org.anchoranalysis.plugin.image.task.bean
-
A parent package for many different kinds of tasks.
- org.anchoranalysis.plugin.image.task.bean.combine - package org.anchoranalysis.plugin.image.task.bean.combine
-
Combining multiple images together into a single image.
- org.anchoranalysis.plugin.image.task.bean.feature - package org.anchoranalysis.plugin.image.task.bean.feature
-
- org.anchoranalysis.plugin.image.task.bean.feature.source - package org.anchoranalysis.plugin.image.task.bean.feature.source
-
Source of rows in feature-tables with
FeatureSource
and derived classes.
- org.anchoranalysis.plugin.image.task.bean.format - package org.anchoranalysis.plugin.image.task.bean.format
-
Tasks for converting image-formats.
- org.anchoranalysis.plugin.image.task.bean.format.convertstyle - package org.anchoranalysis.plugin.image.task.bean.format.convertstyle
-
Different approaches for converting sets of channels (RGB, independently etc.) to another image
format.
- org.anchoranalysis.plugin.image.task.bean.grouped - package org.anchoranalysis.plugin.image.task.bean.grouped
-
Tasks that involved stacks (usually each channel from an image) that are somehow
grouped-together.
- org.anchoranalysis.plugin.image.task.bean.grouped.histogram - package org.anchoranalysis.plugin.image.task.bean.grouped.histogram
-
Task(s) to export histograms of intensity values.
- org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels - package org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels
-
Selecting a subset of a set of channels.
- org.anchoranalysis.plugin.image.task.bean.labeller - package org.anchoranalysis.plugin.image.task.bean.labeller
-
Associating labels with images.
- org.anchoranalysis.plugin.image.task.bean.scale - package org.anchoranalysis.plugin.image.task.bean.scale
-
Tasks to scale an image.
- org.anchoranalysis.plugin.image.task.bean.segment - package org.anchoranalysis.plugin.image.task.bean.segment
-
Tasks to segment an image.
- org.anchoranalysis.plugin.image.task.bean.slice - package org.anchoranalysis.plugin.image.task.bean.slice
-
Tasks that process on one or more slices from a z-stack.
- org.anchoranalysis.plugin.image.task.channel.aggregator - package org.anchoranalysis.plugin.image.task.channel.aggregator
-
Combines multiple
Channel
s voxel-wise to form a
single aggregated
Channel
.
- org.anchoranalysis.plugin.image.task.feature - package org.anchoranalysis.plugin.image.task.feature
-
Non-bean classes pertaining to
Feature
s as used in tasks.
- org.anchoranalysis.plugin.image.task.feature.calculator - package org.anchoranalysis.plugin.image.task.feature.calculator
-
Non-beans for calculating
Feature
s.
- org.anchoranalysis.plugin.image.task.grouped - package org.anchoranalysis.plugin.image.task.grouped
-
Non-bean classes about grouping channels or other inputs.
- org.anchoranalysis.plugin.image.task.labeller - package org.anchoranalysis.plugin.image.task.labeller
-
Non-bean classes about labelling images.
- org.anchoranalysis.plugin.image.task.segment - package org.anchoranalysis.plugin.image.task.segment
-
Non-bean classes for image-segmentation.
- org.anchoranalysis.plugin.image.task.size - package org.anchoranalysis.plugin.image.task.size
-
Non-bean classes pertaining to determining the size of an image.
- org.anchoranalysis.plugin.image.task.slice - package org.anchoranalysis.plugin.image.task.slice
-
Non-bean classes pertaining to combining stacks into a single stack.
- org.anchoranalysis.plugin.image.task.stack - package org.anchoranalysis.plugin.image.task.stack
-
Non-bean classes pertaining to stacks and channels as used in tasks.
- org.anchoranalysis.plugin.image.thumbnail - package org.anchoranalysis.plugin.image.thumbnail
-
Non-bean classes for thumbnail creation.
- org.anchoranalysis.plugin.imagej.bean.channel.provider - package org.anchoranalysis.plugin.imagej.bean.channel.provider
-
- org.anchoranalysis.plugin.imagej.bean.channel.provider.filter - package org.anchoranalysis.plugin.imagej.bean.channel.provider.filter
-
- org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.moments - package org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.moments
-
- org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank - package org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank
-
- org.anchoranalysis.plugin.imagej.bean.define - package org.anchoranalysis.plugin.imagej.bean.define
-
- org.anchoranalysis.plugin.imagej.bean.mask.provider - package org.anchoranalysis.plugin.imagej.bean.mask.provider
-
- org.anchoranalysis.plugin.imagej.bean.object.provider - package org.anchoranalysis.plugin.imagej.bean.object.provider
-
- org.anchoranalysis.plugin.imagej.bean.object.segment - package org.anchoranalysis.plugin.imagej.bean.object.segment
-
- org.anchoranalysis.plugin.imagej.bean.stack.provider - package org.anchoranalysis.plugin.imagej.bean.stack.provider
-
- org.anchoranalysis.plugin.imagej.bean.threshold - package org.anchoranalysis.plugin.imagej.bean.threshold
-
- org.anchoranalysis.plugin.imagej.channel.provider - package org.anchoranalysis.plugin.imagej.channel.provider
-
- org.anchoranalysis.plugin.imagej.mask - package org.anchoranalysis.plugin.imagej.mask
-
- org.anchoranalysis.plugin.io.bean.channel.map - package org.anchoranalysis.plugin.io.bean.channel.map
-
- org.anchoranalysis.plugin.io.bean.file.copy.method - package org.anchoranalysis.plugin.io.bean.file.copy.method
-
Methods for copying files on the file-system.
- org.anchoranalysis.plugin.io.bean.file.copy.naming - package org.anchoranalysis.plugin.io.bean.file.copy.naming
-
Rules for preserving or changing the naming of files when copying on the file-system.
- org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster - package org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster
-
- org.anchoranalysis.plugin.io.bean.file.group - package org.anchoranalysis.plugin.io.bean.file.group
-
Grouping files together so that they collectively represent a single entity.
- org.anchoranalysis.plugin.io.bean.file.group.check - package org.anchoranalysis.plugin.io.bean.file.group.check
-
Tests that are applied when grouping files in org.anchoranalysis.plugin.io.bean.file.group
- org.anchoranalysis.plugin.io.bean.file.group.parser - package org.anchoranalysis.plugin.io.bean.file.group.parser
-
Parsing file-paths to determine file-grouping in org.anchoranalysis.plugin.io.bean.file.group
- org.anchoranalysis.plugin.io.bean.file.namer - package org.anchoranalysis.plugin.io.bean.file.namer
-
- org.anchoranalysis.plugin.io.bean.file.namer.patternspan - package org.anchoranalysis.plugin.io.bean.file.namer.patternspan
-
Implementations of
FileNamer
that look for a
pattern across many files.
- org.anchoranalysis.plugin.io.bean.file.path - package org.anchoranalysis.plugin.io.bean.file.path
-
Beans to specify a file-path.
- org.anchoranalysis.plugin.io.bean.file.path.prefixer - package org.anchoranalysis.plugin.io.bean.file.path.prefixer
-
- org.anchoranalysis.plugin.io.bean.file.pattern - package org.anchoranalysis.plugin.io.bean.file.pattern
-
Extracting a pattern from a file-path.
- org.anchoranalysis.plugin.io.bean.file.provider - package org.anchoranalysis.plugin.io.bean.file.provider
-
- org.anchoranalysis.plugin.io.bean.grouper - package org.anchoranalysis.plugin.io.bean.grouper
-
- org.anchoranalysis.plugin.io.bean.input - package org.anchoranalysis.plugin.io.bean.input
-
- org.anchoranalysis.plugin.io.bean.input.channel - package org.anchoranalysis.plugin.io.bean.input.channel
-
- org.anchoranalysis.plugin.io.bean.input.files - package org.anchoranalysis.plugin.io.bean.input.files
-
- org.anchoranalysis.plugin.io.bean.input.files.provider - package org.anchoranalysis.plugin.io.bean.input.files.provider
-
- org.anchoranalysis.plugin.io.bean.input.filter - package org.anchoranalysis.plugin.io.bean.input.filter
-
- org.anchoranalysis.plugin.io.bean.input.stack - package org.anchoranalysis.plugin.io.bean.input.stack
-
- org.anchoranalysis.plugin.io.bean.metadata.header - package org.anchoranalysis.plugin.io.bean.metadata.header
-
Different types of image-file-formats whose headers can provide
ImageMetadata
.
- org.anchoranalysis.plugin.io.bean.metadata.reader - package org.anchoranalysis.plugin.io.bean.metadata.reader
-
- org.anchoranalysis.plugin.io.bean.path.derive - package org.anchoranalysis.plugin.io.bean.path.derive
-
- org.anchoranalysis.plugin.io.bean.stack.reader - package org.anchoranalysis.plugin.io.bean.stack.reader
-
- org.anchoranalysis.plugin.io.bean.stack.writer - package org.anchoranalysis.plugin.io.bean.stack.writer
-
- org.anchoranalysis.plugin.io.bean.summarizer - package org.anchoranalysis.plugin.io.bean.summarizer
-
Summarizing a set of elements into a descriptive-string.
- org.anchoranalysis.plugin.io.bean.summarizer.image - package org.anchoranalysis.plugin.io.bean.summarizer.image
-
Implementations of
Summarizer
that summarize
images.
- org.anchoranalysis.plugin.io.bean.summarizer.input - package org.anchoranalysis.plugin.io.bean.summarizer.input
-
- org.anchoranalysis.plugin.io.bean.summarizer.path - package org.anchoranalysis.plugin.io.bean.summarizer.path
-
- org.anchoranalysis.plugin.io.bean.task - package org.anchoranalysis.plugin.io.bean.task
-
Implementations of
Task
related to file-system
I/O.
- org.anchoranalysis.plugin.io.file.copy - package org.anchoranalysis.plugin.io.file.copy
-
Non-bean classes to help tasks in org.anchoranalysis.plugin.io.bean.file.copy
.
- org.anchoranalysis.plugin.io.input.filter - package org.anchoranalysis.plugin.io.input.filter
-
Non-bean classes to help tasks in org.anchoranalysis.plugin.io.bean.input.filter
.
- org.anchoranalysis.plugin.io.input.path - package org.anchoranalysis.plugin.io.input.path
-
Non-bean classes to help in processing paths.
- org.anchoranalysis.plugin.io.multifile - package org.anchoranalysis.plugin.io.multifile
-
Non-bean classes to help use multiple files to represent a single
Stack
.
- org.anchoranalysis.plugin.io.multifile.buffer - package org.anchoranalysis.plugin.io.multifile.buffer
-
Buffers used in org.anchoranalysis.plugin.io.multifile
.
- org.anchoranalysis.plugin.io.naming.interval - package org.anchoranalysis.plugin.io.naming.interval
-
How to write parts of a time-interval in a file-name.
- org.anchoranalysis.plugin.io.shared - package org.anchoranalysis.plugin.io.shared
-
Objects used in shared-state in
Task
s in this
plugin.
- org.anchoranalysis.plugin.io.xml - package org.anchoranalysis.plugin.io.xml
-
Reading and writing metadata XML.
- org.anchoranalysis.plugin.ml.bean.classifier - package org.anchoranalysis.plugin.ml.bean.classifier
-
Beans that perform classification in some way.
- org.anchoranalysis.plugin.ml.bean.cluster - package org.anchoranalysis.plugin.ml.bean.cluster
-
Beans that perform clustering in some way.
- org.anchoranalysis.plugin.mpp.bean.addcriteria - package org.anchoranalysis.plugin.mpp.bean.addcriteria
-
- org.anchoranalysis.plugin.mpp.bean.bound - package org.anchoranalysis.plugin.mpp.bean.bound
-
- org.anchoranalysis.plugin.mpp.bean.check - package org.anchoranalysis.plugin.mpp.bean.check
-
- org.anchoranalysis.plugin.mpp.bean.contour - package org.anchoranalysis.plugin.mpp.bean.contour
-
Retrieving the contour
outline pixels along the exterior
outer contour of an
ObjectMask
.
- org.anchoranalysis.plugin.mpp.bean.contour.visitscheduler - package org.anchoranalysis.plugin.mpp.bean.contour.visitscheduler
-
- org.anchoranalysis.plugin.mpp.bean.define - package org.anchoranalysis.plugin.mpp.bean.define
-
Beans related to
Define
involving
Mark
or related classes.
- org.anchoranalysis.plugin.mpp.bean.object.provider - package org.anchoranalysis.plugin.mpp.bean.object.provider
-
- org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection - package org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection
-
- org.anchoranalysis.plugin.mpp.bean.proposer.mark.single - package org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
-
- org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection - package org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection
-
- org.anchoranalysis.plugin.mpp.bean.proposer.merge - package org.anchoranalysis.plugin.mpp.bean.proposer.merge
-
- org.anchoranalysis.plugin.mpp.bean.proposer.orientation - package org.anchoranalysis.plugin.mpp.bean.proposer.orientation
-
- org.anchoranalysis.plugin.mpp.bean.proposer.points - package org.anchoranalysis.plugin.mpp.bean.proposer.points
-
- org.anchoranalysis.plugin.mpp.bean.proposer.points.contour - package org.anchoranalysis.plugin.mpp.bean.proposer.points.contour
-
Finding a point on the external
outer contour of an
ObjectMask
.
- org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation - package org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation
-
- org.anchoranalysis.plugin.mpp.bean.proposer.position - package org.anchoranalysis.plugin.mpp.bean.proposer.position
-
- org.anchoranalysis.plugin.mpp.bean.proposer.radii - package org.anchoranalysis.plugin.mpp.bean.proposer.radii
-
- org.anchoranalysis.plugin.mpp.bean.proposer.scalar - package org.anchoranalysis.plugin.mpp.bean.proposer.scalar
-
- org.anchoranalysis.plugin.mpp.bean.proposer.split - package org.anchoranalysis.plugin.mpp.bean.proposer.split
-
- org.anchoranalysis.plugin.mpp.bean.provider.collection - package org.anchoranalysis.plugin.mpp.bean.provider.collection
-
- org.anchoranalysis.plugin.mpp.bean.provider.single - package org.anchoranalysis.plugin.mpp.bean.provider.single
-
- org.anchoranalysis.plugin.mpp.bean.region - package org.anchoranalysis.plugin.mpp.bean.region
-
- org.anchoranalysis.plugin.mpp.bean.segment.binary - package org.anchoranalysis.plugin.mpp.bean.segment.binary
-
- org.anchoranalysis.plugin.mpp.bean.stack.provider - package org.anchoranalysis.plugin.mpp.bean.stack.provider
-
- org.anchoranalysis.plugin.mpp.contour - package org.anchoranalysis.plugin.mpp.contour
-
Performs a walk on every voxel on the contour of an object-mask.
- org.anchoranalysis.plugin.mpp.contour.distance - package org.anchoranalysis.plugin.mpp.contour.distance
-
A list of visited pixels which forms one contiguous path where each voxel neighbors each other.
- org.anchoranalysis.plugin.mpp.contour.path - package org.anchoranalysis.plugin.mpp.contour.path
-
A set of contiguously neighboring points along the outline of an object.
- org.anchoranalysis.plugin.mpp.contour.path.merge - package org.anchoranalysis.plugin.mpp.contour.path.merge
-
- org.anchoranalysis.plugin.mpp.contour.path.merge.strategy - package org.anchoranalysis.plugin.mpp.contour.path.merge.strategy
-
- org.anchoranalysis.plugin.mpp.experiment.bean.convert - package org.anchoranalysis.plugin.mpp.experiment.bean.convert
-
- org.anchoranalysis.plugin.mpp.experiment.bean.define - package org.anchoranalysis.plugin.mpp.experiment.bean.define
-
- org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task - package org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task
-
- org.anchoranalysis.plugin.mpp.experiment.bean.feature.source - package org.anchoranalysis.plugin.mpp.experiment.bean.feature.source
-
- org.anchoranalysis.plugin.mpp.experiment.bean.objects - package org.anchoranalysis.plugin.mpp.experiment.bean.objects
-
- org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition - package org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition
-
- org.anchoranalysis.plugin.mpp.experiment.bean.segment - package org.anchoranalysis.plugin.mpp.experiment.bean.segment
-
- org.anchoranalysis.plugin.mpp.experiment.objects - package org.anchoranalysis.plugin.mpp.experiment.objects
-
Non-bean classes used in org.anchoranalysis.plugin.mpp.experiment.bean.objects
.
- org.anchoranalysis.plugin.mpp.experiment.objects.csv - package org.anchoranalysis.plugin.mpp.experiment.objects.csv
-
Reading rows from a CSV file.
- org.anchoranalysis.plugin.mpp.experiment.shared - package org.anchoranalysis.plugin.mpp.experiment.shared
-
Shared-state use across tasks in this JAR.
- org.anchoranalysis.plugin.mpp.feature.bean.mark.collection - package org.anchoranalysis.plugin.mpp.feature.bean.mark.collection
-
- org.anchoranalysis.plugin.mpp.feature.bean.mark.direction - package org.anchoranalysis.plugin.mpp.feature.bean.mark.direction
-
- org.anchoranalysis.plugin.mpp.feature.bean.mark.radii - package org.anchoranalysis.plugin.mpp.feature.bean.mark.radii
-
Implementations of
FeatureMark
to measure or
calculate radii.
- org.anchoranalysis.plugin.mpp.feature.bean.mark.region - package org.anchoranalysis.plugin.mpp.feature.bean.mark.region
-
- org.anchoranalysis.plugin.mpp.feature.bean.memo.all - package org.anchoranalysis.plugin.mpp.feature.bean.memo.all
-
- org.anchoranalysis.plugin.mpp.feature.bean.memo.ind - package org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
-
- org.anchoranalysis.plugin.mpp.feature.bean.memo.pair - package org.anchoranalysis.plugin.mpp.feature.bean.memo.pair
-
- org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.distance - package org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.distance
-
- org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap - package org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap
-
- org.anchoranalysis.plugin.mpp.feature.bean.unit - package org.anchoranalysis.plugin.mpp.feature.bean.unit
-
Beans to convert between units.
- org.anchoranalysis.plugin.mpp.feature.overlap - package org.anchoranalysis.plugin.mpp.feature.overlap
-
Implementations of
CalculationPart
to calculate
overlap between two entities.
- org.anchoranalysis.plugin.mpp.segment.bean.annealing - package org.anchoranalysis.plugin.mpp.segment.bean.annealing
-
- org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark - package org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark
-
- org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent - package org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent
-
- org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.voxelized - package org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.voxelized
-
Implementations of
KernelBirth
that are
independent but use the voxelized state of a
Mark
.
- org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer - package org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer
-
- org.anchoranalysis.plugin.mpp.segment.bean.marks - package org.anchoranalysis.plugin.mpp.segment.bean.marks
-
Beans to perform segmentation involving
Mark
s and related
classes.
- org.anchoranalysis.plugin.mpp.segment.bean.marks.dual - package org.anchoranalysis.plugin.mpp.segment.bean.marks.dual
-
- org.anchoranalysis.plugin.mpp.segment.bean.marks.partition - package org.anchoranalysis.plugin.mpp.segment.bean.marks.partition
-
- org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized - package org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized
-
- org.anchoranalysis.plugin.mpp.segment.bean.marks.weight - package org.anchoranalysis.plugin.mpp.segment.bean.marks.weight
-
Deriving a weight for a
Mark
.
- org.anchoranalysis.plugin.mpp.segment.bean.optimization - package org.anchoranalysis.plugin.mpp.segment.bean.optimization
-
Beans related to performing optimization with marked-point-processes.
- org.anchoranalysis.plugin.mpp.segment.bean.optimization.extract - package org.anchoranalysis.plugin.mpp.segment.bean.optimization.extract
-
- org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge - package org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge
-
- org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode - package org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode
-
- org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter - package org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
-
- org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme - package org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme
-
- org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter - package org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter
-
- org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination - package org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination
-
- org.anchoranalysis.plugin.mpp.segment.kernel.assigner - package org.anchoranalysis.plugin.mpp.segment.kernel.assigner
-
- org.anchoranalysis.plugin.mpp.segment.kernel.updater - package org.anchoranalysis.plugin.mpp.segment.kernel.updater
-
- org.anchoranalysis.plugin.mpp.segment.optimization - package org.anchoranalysis.plugin.mpp.segment.optimization
-
Non-bean classes to help with optimization in org.anchoranalysis.plugin.mpp.segment.bean.optimization
and sub-packages.
- org.anchoranalysis.plugin.mpp.segment.shared - package org.anchoranalysis.plugin.mpp.segment.shared
-
Stared-state for segmentation tasks involving mark-point-processes.
- org.anchoranalysis.plugin.onnx.bean.object.segment.decode.instance.maskrcnn - package org.anchoranalysis.plugin.onnx.bean.object.segment.decode.instance.maskrcnn
-
Decodes the outputted tensors from a
Mask
R-CNN implementation.
- org.anchoranalysis.plugin.onnx.bean.object.segment.decode.instance.text - package org.anchoranalysis.plugin.onnx.bean.object.segment.decode.instance.text
-
Decodes the outputted tensors from text-segmentation models.
- org.anchoranalysis.plugin.onnx.bean.object.segment.stack - package org.anchoranalysis.plugin.onnx.bean.object.segment.stack
-
- org.anchoranalysis.plugin.onnx.model - package org.anchoranalysis.plugin.onnx.model
-
Non-bean classes for running an inference model with the
ONNX
Runtime.
- org.anchoranalysis.plugin.opencv - package org.anchoranalysis.plugin.opencv
-
- org.anchoranalysis.plugin.opencv.bean.color - package org.anchoranalysis.plugin.opencv.bean.color
-
Operations involving color-spaces and
OpenCV.
- org.anchoranalysis.plugin.opencv.bean.feature - package org.anchoranalysis.plugin.opencv.bean.feature
-
Extracting features using
OpenCV.
- org.anchoranalysis.plugin.opencv.bean.interpolate - package org.anchoranalysis.plugin.opencv.bean.interpolate
-
Interpolation beans that use OpenCV.
- org.anchoranalysis.plugin.opencv.bean.object.segment.stack - package org.anchoranalysis.plugin.opencv.bean.object.segment.stack
-
Segmentation of a
Stack
using OpenCV.
- org.anchoranalysis.plugin.opencv.bean.stack - package org.anchoranalysis.plugin.opencv.bean.stack
-
- org.anchoranalysis.plugin.opencv.convert - package org.anchoranalysis.plugin.opencv.convert
-
Conversion to/from
OpenCV data-structures.
- org.anchoranalysis.plugin.opencv.resizer - package org.anchoranalysis.plugin.opencv.resizer
-
Interpolation non-beans that use OpenCV.
- org.anchoranalysis.plugin.opencv.segment - package org.anchoranalysis.plugin.opencv.segment
-
Non-bean classes pertaining to segmentation.
- org.anchoranalysis.plugin.operator.feature.bean - package org.anchoranalysis.plugin.operator.feature.bean
-
Features that combine or convert other features in a generic way.
- org.anchoranalysis.plugin.operator.feature.bean.arithmetic - package org.anchoranalysis.plugin.operator.feature.bean.arithmetic
-
Arithmetic involving features.
- org.anchoranalysis.plugin.operator.feature.bean.conditional - package org.anchoranalysis.plugin.operator.feature.bean.conditional
-
Conditional operations involving features.
- org.anchoranalysis.plugin.operator.feature.bean.list - package org.anchoranalysis.plugin.operator.feature.bean.list
-
Operations that extract a single value from a list of features.
- org.anchoranalysis.plugin.operator.feature.bean.range - package org.anchoranalysis.plugin.operator.feature.bean.range
-
Features that compare against a range of values.
- org.anchoranalysis.plugin.operator.feature.bean.replace - package org.anchoranalysis.plugin.operator.feature.bean.replace
-
Replaces particular values if they are returned from a feature.
- org.anchoranalysis.plugin.operator.feature.bean.statistics - package org.anchoranalysis.plugin.operator.feature.bean.statistics
-
Converts feature values based upon a statistical measure of distribution.
- org.anchoranalysis.plugin.operator.feature.physical - package org.anchoranalysis.plugin.operator.feature.physical
-
Converting to/from physical units.
- org.anchoranalysis.plugin.operator.feature.statistics - package org.anchoranalysis.plugin.operator.feature.statistics
-
Non-bean statistical operations.
- org.anchoranalysis.plugin.points.bean - package org.anchoranalysis.plugin.points.bean
-
Beans that fit or otherwise manipulate sets of points.
- org.anchoranalysis.plugin.points.bean.convexhull - package org.anchoranalysis.plugin.points.bean.convexhull
-
Convex hull operations.
- org.anchoranalysis.plugin.points.bean.feature - package org.anchoranalysis.plugin.points.bean.feature
-
Features related to points and fitting points to conics.
- org.anchoranalysis.plugin.points.bean.fitter - package org.anchoranalysis.plugin.points.bean.fitter
-
Fitting geometric structures to points.
- org.anchoranalysis.plugin.points.calculate.ellipse - package org.anchoranalysis.plugin.points.calculate.ellipse
-
- org.anchoranalysis.plugin.points.calculate.ellipsoid - package org.anchoranalysis.plugin.points.calculate.ellipsoid
-
- org.anchoranalysis.plugin.points.convexhull - package org.anchoranalysis.plugin.points.convexhull
-
Non-bean convex hull operations.
- org.anchoranalysis.plugin.quick.bean.experiment - package org.anchoranalysis.plugin.quick.bean.experiment
-
Quickly defining experiments via several assumptions, including particular file-paths.
- org.anchoranalysis.plugin.quick.bean.input - package org.anchoranalysis.plugin.quick.bean.input
-
Specifying inputs when quickly defining an experiment.
- org.anchoranalysis.plugin.quick.bean.input.filepathappend - package org.anchoranalysis.plugin.quick.bean.input.filepathappend
-
Appending other entities to inputs when quickly defining experiments.
- org.anchoranalysis.plugin.quick.bean.structure - package org.anchoranalysis.plugin.quick.bean.structure
-
Specifying a structure of subdirectories and filenames when quickly defining an experiment.
- org.anchoranalysis.spatial.axis - package org.anchoranalysis.spatial.axis
-
Identifying the three standard axes in 3D cartesian coordinates.
- org.anchoranalysis.spatial.box - package org.anchoranalysis.spatial.box
-
Axis-aligned bounding-boxes and related operations.
- org.anchoranalysis.spatial.orientation - package org.anchoranalysis.spatial.orientation
-
Various methods to specify the orientation (general direction) of an entity.
- org.anchoranalysis.spatial.point - package org.anchoranalysis.spatial.point
-
A cartesian-coordinate, across varying primitive types, in 2D and 3D space.
- org.anchoranalysis.spatial.point.consumer - package org.anchoranalysis.spatial.point.consumer
-
Functional interfaces that accept cartesian coordinate points specified in different ways.
- org.anchoranalysis.spatial.rtree - package org.anchoranalysis.spatial.rtree
-
R-Tree data structure and related operations.
- org.anchoranalysis.spatial.scale - package org.anchoranalysis.spatial.scale
-
How to much to scale an entity in Cartesian space by.
- org.anchoranalysis.test - package org.anchoranalysis.test
-
Testing utilities and fixtures with no greater downstream dependency than anchor-core.
- org.anchoranalysis.test.experiment - package org.anchoranalysis.test.experiment
-
Testing utilities and fixtures with no greater downstream dependency than
anchor-experiment or anchor-mpp or anchor-mpp-io.
- org.anchoranalysis.test.experiment.launcher - package org.anchoranalysis.test.experiment.launcher
-
Launches an anchor binary from a shell and runs an experiment.
- org.anchoranalysis.test.experiment.task - package org.anchoranalysis.test.experiment.task
-
Helper classes to execute
Task
s in tests.
- org.anchoranalysis.test.feature - package org.anchoranalysis.test.feature
-
Testing utilities and fixtures with no greater downstream dependency than anchor-feature.
- org.anchoranalysis.test.feature.plugins - package org.anchoranalysis.test.feature.plugins
-
Testing utilities and fixtures with no greater downstream dependency than
anchor-image-feature or anchor-mpp.
- org.anchoranalysis.test.feature.plugins.mockfeature - package org.anchoranalysis.test.feature.plugins.mockfeature
-
A mocked feature internally using a feature-calculation.
- org.anchoranalysis.test.feature.plugins.objects - package org.anchoranalysis.test.feature.plugins.objects
-
Fixtures for creating object-masks and related feature-inputs.
- org.anchoranalysis.test.image - package org.anchoranalysis.test.image
-
Testing utilities and fixtures with no greater downstream dependency than anchor-image-io
or anchor-io-bioformats or anchor-imagej.
- org.anchoranalysis.test.image.csv - package org.anchoranalysis.test.image.csv
-
Comparing two CSV files for equality (by a certain definition).
- org.anchoranalysis.test.image.io - package org.anchoranalysis.test.image.io
-
Utilities for testing-related reading and writing to the filesystem.
- org.anchoranalysis.test.image.load - package org.anchoranalysis.test.image.load
-
Load test image data.
- org.anchoranalysis.test.image.object - package org.anchoranalysis.test.image.object
-
Fixtures for creating object-masks.
- org.anchoranalysis.test.image.rasterwriter.comparison - package org.anchoranalysis.test.image.rasterwriter.comparison
-
Different ways for comparing images.
- org.anchoranalysis.test.image.segment - package org.anchoranalysis.test.image.segment
-
Fixtures or other helper classes for testing image segmentation algorithms.
- org.anchoranalysis.test.image.stackwriter - package org.anchoranalysis.test.image.stackwriter
-
- org.anchoranalysis.test.io.output - package org.anchoranalysis.test.io.output
-
- Orientation - Class in org.anchoranalysis.spatial.orientation
-
The
orientation (direction) in
2D or 3D Euclidean space.
- Orientation() - Constructor for class Orientation
-
- Orientation2D - Class in org.anchoranalysis.spatial.orientation
-
A simple angular orientation the 2D plane, relative to the x-axis.
- Orientation2D(double) - Constructor for class Orientation2D
-
- Orientation2D() - Constructor for class Orientation2D
-
- Orientation3DEulerAngles - Class in org.anchoranalysis.spatial.orientation
-
An orientation using three angle parameters for the rotation.
- Orientation3DEulerAngles(double, double, double) - Constructor for class Orientation3DEulerAngles
-
- OrientationAndRadiiProposer - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
-
Proposes both an orientation and radii for a
ConicBase
- OrientationAndRadiiProposer(RadiiProposer, OrientationProposer) - Constructor for class OrientationAndRadiiProposer
-
- OrientationAxisAngle - Class in org.anchoranalysis.spatial.orientation
-
An orientation in axis-angle representation.
- OrientationAxisAngle(Vector3d, double) - Constructor for class OrientationAxisAngle
-
- OrientationChange - Enum in org.anchoranalysis.image.core.dimensions
-
Changes orientation of an image in the XY plane.
- OrientationProposer - Class in org.anchoranalysis.mpp.bean.proposer
-
- OrientationProposer() - Constructor for class OrientationProposer
-
- OrientationReader - Class in org.anchoranalysis.io.bioformats.metadata
-
Reads the image-orientation from EXIF metadata, if specified in an image-file.
- OrientationRotationMatrix - Class in org.anchoranalysis.spatial.orientation
-
Orients an object by rotating anti-clockwise with an explicit
RotationMatrix
.
- OrientationRotationMatrix() - Constructor for class OrientationRotationMatrix
-
- OrientationRotationMatrix(RotationMatrix) - Constructor for class OrientationRotationMatrix
-
- ORIGIN - Static variable in class Point3i
-
A constant
Point3i
where all dimensions are zero.
- otherVertex(V) - Method in class TypedEdge
-
The other vertex on the edge
- Otsu - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold
-
Performs auto-thresholding using Otsu's method.
- Otsu() - Constructor for class Otsu
-
- OtsuWeighted - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold
-
Similar to Otsu, but weighs the variances differently of background and foreground.
- OtsuWeighted() - Constructor for class OtsuWeighted
-
- OtsuWeighted(double, double) - Constructor for class OtsuWeighted
-
- outFilePrefix(NamedPath, Optional<String>, PathPrefixerContext) - Method in class PathPrefixer
-
Provides a prefix which can be prepended to all output files.
- outFilePrefix(NamedPath, Optional<String>, PathPrefixerContext) - Method in class PathPrefixerAvoidResolve
-
- outFilePrefix(NamedPath, Optional<String>, PathPrefixerContext) - Method in class HomeSubdirectory
-
- outFilePrefix(NamedPath, Optional<String>, PathPrefixerContext) - Method in class Rooted
-
- outFilePrefix(NamedPath, Optional<String>, PathPrefixerContext) - Method in class ExperimentStructure
-
- outFilePrefixAvoidResolve(NamedPath, Optional<String>, PathPrefixerContext) - Method in class PathPrefixerAvoidResolve
-
Provides a prefix which can be prepended to all output files.
- outFilePrefixFromPath(NamedPath, Path, PathPrefixerContext) - Method in class IncrementingNumber
-
- outFilePrefixFromPath(NamedPath, Path, PathPrefixerContext) - Method in class PathPrefixerAvoidResolve
-
Determines the out-file prefix from a path
- outFilePrefixFromPath(NamedPath, Path, PathPrefixerContext) - Method in class DirectoryStructure
-
- outFilePrefixFromPath(NamedPath, Path, PathPrefixerContext) - Method in class FromDescriptiveName
-
- outFilePrefixFromPath(NamedPath, Path, PathPrefixerContext) - Method in class IfIncrementingNumberRequested
-
- outFilePrefixFromPath(NamedPath, Path, PathPrefixerContext) - Method in class LastDirectoryAsPrefix
-
- outFilePrefixFromPath(NamedPath, Path, PathPrefixerContext) - Method in class PathRegEx
-
- outgoingEdgesFor(V) - Method in class GraphWithPayload
-
All outgoing edges for a given vertex.
- Outline - Class in org.anchoranalysis.image.io.bean.object.draw
-
Draws the outline of each object-mask.
- Outline() - Constructor for class Outline
-
Creates with an outline-width of 1 voxel.
- Outline(int) - Constructor for class Outline
-
Create with a particular outline-width.
- Outline(int, boolean) - Constructor for class Outline
-
- OutlineKernel - Class in org.anchoranalysis.image.voxel.kernel.outline
-
Sets voxels on the outline of an object to be on and otherwise off.
- OutlineKernel() - Constructor for class OutlineKernel
-
- OutlineKernelBase - Class in org.anchoranalysis.image.voxel.kernel.outline
-
A base class for kernels that find the outline of an
ObjectMask
.
- OutlineKernelBase() - Constructor for class OutlineKernelBase
-
Default constructor.
- OutlineKernelBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single
-
- OutlineKernelBase() - Constructor for class OutlineKernelBase
-
- OutlineKernelNeighborMatchValue - Class in org.anchoranalysis.image.voxel.kernel.outline
-
Outputs the outline of an object-mask, but only for voxels on the exterior which neighbor a
binary-mask.
- OutlineKernelNeighborMatchValue(BinaryVoxels<UnsignedByteBuffer>) - Constructor for class OutlineKernelNeighborMatchValue
-
Creates for an object.
- OutlinePreserveRelativeSize - Class in org.anchoranalysis.plugin.image.bean.thumbnail.object
-
Create a thumbnail by drawing an outline of an object at a particular-scale, and placing it
centered in a window of a certain size.
- OutlinePreserveRelativeSize() - Constructor for class OutlinePreserveRelativeSize
-
- outlineSingleColor(int, DisplayStack, RGBColor) - Static method in class DrawObjectsGenerator
-
Creates a generator that draws an outline around objects on a background using a single color
for all objects.
- outlineVariedColors(int, int, DisplayStack) - Static method in class DrawObjectsGenerator
-
Creates a generator that draws an outline around objects on a background using varied colors
for the objects.
- outlineVariedColors(int, int, Either<Dimensions, DisplayStack>) - Static method in class DrawObjectsGenerator
-
Creates a generator that draws an outline around objects on a background using varied colors
for the objects.
- outlineWithColorIndex(int, ColorIndex) - Static method in class DrawObjectsGenerator
-
Creates a generator that draws an outline around objects using a particular
ColorIndex
.
- output() - Method in class ExecutionArguments
-
Arguments to help specify the outputs from the experiment.
- output(InputOutputContext) - Method in class OutputFeatureTable
-
Outputs the feature-table.
- output(NamedProvider<Stack>, String, boolean, OutputterChecked) - Static method in class NamedStacksOutputter
-
Writes all or a subset from a set of named-stacks to a directory as a raster.
- output(String, boolean) - Method in class NamedProviderOutputter
-
Outputs the entities using a particular output-name.
- OUTPUT_BY_GROUP - Static variable in class CompareAnnotations
-
- OUTPUT_DEFAULT_NON_AGGREGATED - Static variable in class FeatureOutputNames
-
If not otherwise specified, the output name for a non-aggregated CSV of the results.
- OUTPUT_ENERGY_STACK_DIRECTORY - Static variable in class EnergyStackWriter
-
- OUTPUT_EXECUTION_TIME - Static variable in class OutputExperiment
-
The name for the output that records the total execution-time of the experiment.
- OUTPUT_FEATURE_TABLE - Static variable in class OutputFeatureTable
-
The output-name for a CSV table of feature-values.
- OUTPUT_RESULTS - Static variable in class ExportFeatures
-
- OUTPUT_SUFFIX_AGGREGATED - Static variable in class FeatureOutputNames
-
- OUTPUT_SUFFIX_AGGREGATED_GROUP - Static variable in class FeatureOutputNames
-
- OUTPUT_SUFFIX_GROUP - Static variable in class FeatureOutputNames
-
- OUTPUT_THUMBNAILS - Static variable in class FeatureExporter
-
The output-name for writing thumbnails.
- outputAfterAllTasksAreExecuted(Outputter) - Method in interface ExperimentState
-
- outputAfterAllTasksAreExecuted(Outputter) - Method in class SegmentMarksState
-
- outputAnyRemainingGroups() - Method in class GroupMapByName
-
Outputs any groups that have not already been outputted.
- OutputArguments - Class in org.anchoranalysis.experiment.arguments
-
Arguments that can further specify an experiment's output in addition to its bean
specification.
- OutputArguments() - Constructor for class OutputArguments
-
- outputBeforeAnyTasksAreExecuted(Outputter) - Method in interface ExperimentState
-
- outputBeforeAnyTasksAreExecuted(Outputter) - Method in class SegmentMarksState
-
- OutputDirectoryAlreadyExistsException - Exception in org.anchoranalysis.io.output.error
-
When an output-directory already exists.
- OutputDirectoryAlreadyExistsException(String) - Constructor for exception OutputDirectoryAlreadyExistsException
-
- OutputEnabled - Class in org.anchoranalysis.io.output.bean.enabled
-
Whether a particular output, identified by a textual name, is enabled or not.
- OutputEnabled() - Constructor for class OutputEnabled
-
- OutputEnabledDelta - Class in org.anchoranalysis.io.output.recorded
-
Additional output-names to enable or disable from an existing set of output-enabled rules.
- OutputEnabledDelta() - Constructor for class OutputEnabledDelta
-
- OutputEnabledMutable - Class in org.anchoranalysis.io.output.enabled
-
A specific set of first-level outputs are enabled, to which more can be added.
- OutputEnabledMutable(String...) - Constructor for class OutputEnabledMutable
-
Creates with one or more enabled outputs.
- OutputEnabledMutable(SingleLevelOutputEnabled, String...) - Constructor for class OutputEnabledMutable
-
Creates with one or more enabled outputs.
- OutputEnabledRules - Class in org.anchoranalysis.io.output.bean.rules
-
- OutputEnabledRules() - Constructor for class OutputEnabledRules
-
- OutputEnableRulesSpecify - Class in org.anchoranalysis.io.output.bean.rules
-
Base class for an
OutputEnabledRules
that specifies particular output-names for first and
second levels.
- OutputEnableRulesSpecify(StringSet) - Constructor for class OutputEnableRulesSpecify
-
Create with a specific set of first-level output names.
- OutputEnableRulesSpecify() - Constructor for class OutputEnableRulesSpecify
-
- OutputExperiment - Class in org.anchoranalysis.experiment.bean.io
-
- OutputExperiment() - Constructor for class OutputExperiment
-
- OutputFactory - Class in org.anchoranalysis.launcher.executor.selectparam.path
-
SelectParam<Path>
factory for outputs.
- OutputFeatureTable - Class in org.anchoranalysis.image.io.bean.object.feature
-
Specifies a table of feature-calculations on objects.
- OutputFeatureTable() - Constructor for class OutputFeatureTable
-
- outputFormatString() - Method in class IndexableOutputNameStyle
-
- outputFormatString() - Method in class IntegerSuffixOutputNameStyle
-
- outputFormatString() - Method in class StringSuffixOutputNameStyle
-
- outputGroupIntoSubdirectory(Collection<Map.Entry<String, T>>, Function<Boolean, InputOutputContext>, Optional<String>) - Method in class GroupMapByName
-
Output a particular group into a subdirectory.
- outputHeaderToWriter(PrintWriter, String) - Method in class AggIDCounter
-
- outputHeaderToWriter(PrintWriter) - Method in class Aggregator
-
- OutputManager - Class in org.anchoranalysis.io.output.bean
-
Responsible for making decisions on where output goes and what form it takes.
- OutputManager() - Constructor for class OutputManager
-
- OutputManagerFixture - Class in org.anchoranalysis.test.io.output
-
- outputMetadata - Variable in class LabelledResultsCSVWriter
-
Metadata defining which CSV file to write to, and which headers.
- outputName() - Method in class FeatureCSVMetadataForOutput
-
Names for the produced output.
- outputNameForGroups() - Method in class AggregateChannelTask
-
- outputNameForGroups() - Method in class GroupedStackBase
-
The first-level output-name used for determining if groups are written.
- outputNameForGroups() - Method in class ExportImageHistograms
-
- outputNames() - Method in class FeatureOutputMetadata
-
- OutputNameStyle - Class in org.anchoranalysis.io.output.namestyle
-
- OutputNameStyle(String) - Constructor for class OutputNameStyle
-
- OutputNameStyle() - Constructor for class OutputNameStyle
-
- OutputPattern - Class in org.anchoranalysis.io.generator.sequence.pattern
-
A particular naming pattern files follow when outputted.
- OutputPattern(Optional<String>, IndexableOutputNameStyle, boolean) - Constructor for class OutputPattern
-
- OutputPatternIntegerSuffix - Class in org.anchoranalysis.io.generator.sequence.pattern
-
A
OutputPattern
that outputs a file-name with a trailing integer index.
- OutputPatternIntegerSuffix(String, boolean) - Constructor for class OutputPatternIntegerSuffix
-
Creates in a subdirectory, using the outputName as both the subdirectory name and the prefix.
- OutputPatternIntegerSuffix(String, String) - Constructor for class OutputPatternIntegerSuffix
-
Creates in a subdirectory, using the output-name as the subdirectory name, and a specific
prefix.
- OutputPatternIntegerSuffix(String, int, boolean) - Constructor for class OutputPatternIntegerSuffix
-
- OutputPatternIntegerSuffix(String, String, int, boolean) - Constructor for class OutputPatternIntegerSuffix
-
- OutputPatternIntegerSuffix(String, boolean, String, int, boolean) - Constructor for class OutputPatternIntegerSuffix
-
Creates with a full set of flexibility about how the filename appears and whether a
subdirectory is used.
- OutputPatternStringSuffix - Class in org.anchoranalysis.io.generator.sequence.pattern
-
A
OutputPattern
that outputs a file-name with a trailing string index.
- OutputPatternStringSuffix(String, boolean) - Constructor for class OutputPatternStringSuffix
-
Creates without a prefix.
- OutputPatternStringSuffix(String, boolean, String) - Constructor for class OutputPatternStringSuffix
-
Creates with a prefix.
- OutputPrefixerSettings - Class in org.anchoranalysis.io.output.path.prefixer
-
Arguments influencing into which directory outputs are written, and how identifiers are
expressed.
- OutputPrefixerSettings() - Constructor for class OutputPrefixerSettings
-
- OutputPrefixWithExtension - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming
-
Copies files using whatever prefix is assigned to an input by the
OutputManager
as the
file-name, adding the same extension as the source file.
- OutputPrefixWithExtension() - Constructor for class OutputPrefixWithExtension
-
- outputSelectParam(CommandLine) - Static method in class SelectParamFactory
-
Can point to either:
a path ending in .xml, assumed to BeanXML for an output manager
a directory, set as the outputDirectory in the input-context
- outputsEnabled() - Method in class Outputter
-
- OutputSequence - Interface in org.anchoranalysis.io.generator.sequence
-
A sequence of elements that are written to the same directory.
- OutputSequenceFactory<T> - Class in org.anchoranalysis.io.generator.sequence
-
Creates and starts a
OutputSequence
with a particular generator and context.
- OutputSequenceFactory(Generator<T>, OutputterChecked) - Constructor for class OutputSequenceFactory
-
- OutputSequenceIncrementing<T> - Class in org.anchoranalysis.io.generator.sequence
-
A sequence of outputs that use the same generator, where each output increments an index by one
in the filename.
- OutputSequenceIncrementing(BoundOutputter<T>) - Constructor for class OutputSequenceIncrementing
-
- OutputSequenceIndexed<T,S> - Class in org.anchoranalysis.io.generator.sequence
-
A sequence of outputs that use the same generator with non-incrementing indexes for each output.
- OutputSequenceStackFactory - Class in org.anchoranalysis.image.io.stack.output
-
Creates
OutputSequence
of different kinds for writing stacks to a directory.
- outputSharedObjects(SharedObjects, Optional<EnergyStack>, Outputter) - Method in class DefineOutputter
-
- Outputter - Class in org.anchoranalysis.io.output.outputter
-
- Outputter(OutputterChecked, ErrorReporter) - Constructor for class Outputter
-
- outputter(Optional<Path>) - Static method in class OutputterFixture
-
- outputter(OutputManager, OutputEnabledRules) - Static method in class OutputterFixture
-
- OutputterChecked - Class in org.anchoranalysis.io.output.outputter
-
A particular directory on the filesystem in which outputting can occur.
- outputterChecked(Optional<Path>) - Static method in class OutputterFixture
-
- OutputterCheckedFixture - Class in org.anchoranalysis.test.io.output
-
- OutputterDirectories - Class in org.anchoranalysis.mpp.segment.define
-
Directories into which collections of different types of objects are written to in a
define experiment
- OutputterFixture - Class in org.anchoranalysis.test.image.io
-
- OutputterTarget - Class in org.anchoranalysis.io.output.outputter.directory
-
The directory and prefix an outputter writes to.
- OutputterTarget(DirectoryWithPrefix, DirectoryCreationParameters) - Constructor for class OutputterTarget
-
Creates for a particular directory, with optionally an associated prefix.
- outputToWriter(PrintWriter) - Method in class AggIDCounter
-
- outputToWriter(PrintWriter) - Method in class Aggregator
-
- OutputWriteContext - Class in org.anchoranalysis.io.output.outputter
-
Settings and user-arguments for writing files.
- OutputWriteContext() - Constructor for class OutputWriteContext
-
Create with default state, including no default beans assigned.
- OutputWriteContext(OutputWriteSettings) - Constructor for class OutputWriteContext
-
- OutputWriteContext(OutputWriteSettings, Optional<ImageFileFormat>, ExecutionTimeRecorder) - Constructor for class OutputWriteContext
-
- OutputWriteFailedException - Exception in org.anchoranalysis.io.output.error
-
- OutputWriteFailedException(String) - Constructor for exception OutputWriteFailedException
-
- OutputWriteFailedException(String, HasFriendlyErrorMessage) - Constructor for exception OutputWriteFailedException
-
- OutputWriteFailedException(String, AnchorCombinableException) - Constructor for exception OutputWriteFailedException
-
- OutputWriteFailedException(Throwable) - Constructor for exception OutputWriteFailedException
-
- OutputWriteSettings - Class in org.anchoranalysis.io.output.bean
-
Settings for how to write output, including default writers.
- OutputWriteSettings() - Constructor for class OutputWriteSettings
-
- OutsideKernelPolicy - Enum in org.anchoranalysis.image.voxel.kernel
-
How to handle voxels whose neighbors are outside the scene.
- OutsideRange - Class in org.anchoranalysis.plugin.image.feature.bean.score
-
- OutsideRange() - Constructor for class OutsideRange
-
- overAll(Kernel, BinaryVoxels<UnsignedByteBuffer>, KernelApplicationParameters, ProcessKernelPointCursor) - Static method in class IterateKernelHelper
-
Iterates over all voxels.
- overBox(Kernel, BinaryVoxels<UnsignedByteBuffer>, BoundingBox, KernelApplicationParameters, ProcessKernelPointCursor) - Static method in class IterateKernelHelper
-
Iterates over only voxels contained within a bounding-box.
- overBoxUntil(Kernel, BinaryVoxels<UnsignedByteBuffer>, BoundingBox, KernelApplicationParameters, PredicateKernelPointCursor) - Static method in class IterateKernelHelper
-
Iterates over only voxels contained within a bounding-box until a predicate is matched
on a voxel.
- OverlapMaskBase - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap
-
- OverlapMaskBase() - Constructor for class OverlapMaskBase
-
- OverlapMIPBase - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap
-
- OverlapMIPBase() - Constructor for class OverlapMIPBase
-
- OverlapNumberVoxelsMask - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap
-
- OverlapNumberVoxelsMask() - Constructor for class OverlapNumberVoxelsMask
-
- OverlapNumVoxels - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap
-
- OverlapNumVoxels() - Constructor for class OverlapNumVoxels
-
- overlappingNumVoxels(FeatureCalculationInput<FeatureInputPairMemo>) - Method in class FeaturePairMemoSingleRegion
-
- overlappingNumVoxels(FeatureCalculationInput<FeatureInputPairMemo>) - Method in class OverlapMaskBase
-
- overlappingNumVoxels(FeatureCalculationInput<FeatureInputPairMemo>) - Method in class OverlapMIPBase
-
- OverlappingObject<T> - Class in org.anchoranalysis.image.core.object.label
-
An object-mask that is founded to overlap with another during labelling.
- OverlappingObject(T, ObjectMask) - Constructor for class OverlappingObject
-
- OverlappingObjects - Class in org.anchoranalysis.annotation.io.assignment
-
- OverlappingObjects() - Constructor for class OverlappingObjects
-
- OverlapRatio - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap
-
- OverlapRatio() - Constructor for class OverlapRatio
-
- OverlapRatioMask - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap
-
- OverlapRatioMask() - Constructor for class OverlapRatioMask
-
- OverlapRelative - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap
-
Expresses the number of intersecting pixels between two objects as a ratio to something else
(denominator)
- OverlapRelative() - Constructor for class OverlapRelative
-
- OverlapRelativeToFirst - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap
-
- OverlapRelativeToFirst() - Constructor for class OverlapRelativeToFirst
-
- OverlapRelativeToMaxVolume - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap
-
Overlap ratio to the maximum number of pixels
- OverlapRelativeToMaxVolume() - Constructor for class OverlapRelativeToMaxVolume
-
- OverlapRelativeToMerged - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap
-
- OverlapRelativeToMerged() - Constructor for class OverlapRelativeToMerged
-
- OverlapRelativeToSecond - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap
-
- OverlapRelativeToSecond() - Constructor for class OverlapRelativeToSecond
-
- OverlapUtilities - Class in org.anchoranalysis.mpp.overlap
-
- overlapWith(VoxelizedMarkMemo, VoxelizedMarkMemo, int) - Static method in class OverlapUtilities
-
- overlapWithGlobalMask(FeatureCalculationInput<FeatureInputPairMemo>) - Method in class OverlapMaskBase
-
- overlapWithMaskGlobal(VoxelizedMarkMemo, VoxelizedMarkMemo, int, Voxels<UnsignedByteBuffer>, byte) - Static method in class OverlapUtilities
-
- Overlay - Class in org.anchoranalysis.image.bean.spatial.arrange.overlay
-
Overlays one image on the other.
- Overlay(String, String, String) - Constructor for class Overlay
-
Creates with alignment text for each axis.
- Overlay() - Constructor for class Overlay
-
- Overlay(Align) - Constructor for class Overlay
-
- Overlay - Class in org.anchoranalysis.overlay
-
An entity that will eventually be drawn on top of an image.
- Overlay() - Constructor for class Overlay
-
- OverlayCollection - Class in org.anchoranalysis.overlay.collection
-
- OverlayCollection() - Constructor for class OverlayCollection
-
Creates an empty collection.
- OverlayCollection(Stream<Overlay>) - Constructor for class OverlayCollection
-
Creates the collection from a stream of
Overlay
s.
- OverlayCollectionMarkFactory - Class in org.anchoranalysis.mpp.overlay
-
Two-way factory.
- OverlayMark - Class in org.anchoranalysis.mpp.overlay
-
An implementation of
Overlay
that draws an
Mark
on an image.
- OverlayMark(Mark, RegionMembershipWithFlags) - Constructor for class OverlayMark
-
- OverlayObjectMask - Class in org.anchoranalysis.overlay.object
-
- OverlayObjectMask(ObjectMask, int) - Constructor for class OverlayObjectMask
-
Creates with a particular
ObjectMask
and identifier.
- RadiiMinRatio - Class in org.anchoranalysis.plugin.mpp.bean.check
-
- RadiiMinRatio() - Constructor for class RadiiMinRatio
-
- radiiOrdered() - Method in class ConicBase
-
- radiiOrderedResolved(Optional<Resolution>) - Method in class ConicBase
-
- RadiiProposer - Class in org.anchoranalysis.mpp.bean.proposer
-
- RadiiProposer() - Constructor for class RadiiProposer
-
- RadiiProposerRepeat - Class in org.anchoranalysis.plugin.mpp.bean.proposer.radii
-
- RadiiProposerRepeat() - Constructor for class RadiiProposerRepeat
-
- RadiiRandomizer - Class in org.anchoranalysis.mpp.mark.conic
-
Utility functions for generating random radii for
ConicBase
- RadiiRatio - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.radii
-
- RadiiRatio() - Constructor for class RadiiRatio
-
- radiusForRegion(int) - Method in class MarkWithPositionAndSingleRadius
-
- radiusForRegionSquared(int) - Method in class MarkWithPositionAndSingleRadius
-
- RandomCollection<T> - Class in org.anchoranalysis.mpp.pair
-
A collection of items from which one can randomly sample
- RandomCollection() - Constructor for class RandomCollection
-
- RandomCollectionWithAddCriteria<T> - Class in org.anchoranalysis.mpp.feature.addcriteria
-
- RandomCollectionWithAddCriteria(Class<?>) - Constructor for class RandomCollectionWithAddCriteria
-
- randomIndex(RandomNumberGenerator) - Method in class MarkCollection
-
- randomizeRadii(Bound, RandomNumberGenerator, Optional<Resolution>, boolean) - Static method in class RadiiRandomizer
-
- randomMark(RandomNumberGenerator) - Method in class MarkCollection
-
- RandomNumberGenerator - Interface in org.anchoranalysis.core.random
-
Generates random numbers from various distributions.
- RandomNumberGeneratorBean - Class in org.anchoranalysis.bean.shared.random
-
- RandomNumberGeneratorBean() - Constructor for class RandomNumberGeneratorBean
-
- RandomNumberGeneratorMersenne - Class in org.anchoranalysis.core.random
-
Implements a random-number generator using the MersenneTwister
algorithm.
- RandomNumberGeneratorMersenne(boolean) - Constructor for class RandomNumberGeneratorMersenne
-
Creates indicating whether to use a fixed-seed or not.
- RandomOrder - Class in org.anchoranalysis.plugin.io.bean.file.provider
-
- RandomOrder() - Constructor for class RandomOrder
-
- randomOrientation(RandomNumberGenerator, Optional<Resolution>) - Method in class BoundRotation
-
- randomOrientation(RandomNumberGenerator, Optional<Resolution>) - Method in class BoundRotation2D
-
- randomOrientation(RandomNumberGenerator, Optional<Resolution>) - Method in class BoundRotation3D
-
- RandomOrientation - Class in org.anchoranalysis.plugin.mpp.bean.proposer.orientation
-
- RandomOrientation() - Constructor for class RandomOrientation
-
- RandomOrientation(BoundRotation) - Constructor for class RandomOrientation
-
- RandomXY - Class in org.anchoranalysis.plugin.mpp.bean.proposer.orientation
-
- RandomXY() - Constructor for class RandomXY
-
- randOpen(RandomNumberGenerator) - Method in class ResolvedBound
-
A random value between the bounds (open interval)
- Range - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
-
The range (difference in values) between two quantiles
- Range() - Constructor for class Range
-
- Range<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.range
-
The statistical range between two values i.e.
- Range() - Constructor for class Range
-
- rangeChannelNum() - Method in class ParsedFilePathBag
-
- RangeCompareBase<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.range
-
- RangeCompareBase() - Constructor for class RangeCompareBase
-
- RangeCompareFromScalars<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.range
-
A base-class for setting the boundaries of the range using constant scalars
- RangeCompareFromScalars() - Constructor for class RangeCompareFromScalars
-
- rangeCPresent() - Method in class SizeExtents
-
- rangeSliceNum() - Method in class ParsedFilePathBag
-
- rangeTimeIndex() - Method in class ParsedFilePathBag
-
- rangeTPresent() - Method in class SizeExtents
-
- RasterDirectoryObjectsGenerator - Class in org.anchoranalysis.image.io.object.output.mask
-
Writes each object as a binary
Mask
in a directory.
- RasterGenerator<T> - Class in org.anchoranalysis.image.io.stack.output.generator
-
Transforms an entity to a
Stack
and writes it to the file-system.
- RasterGenerator() - Constructor for class RasterGenerator
-
- RasterGeneratorBridge<T,V> - Class in org.anchoranalysis.image.io.stack.output.generator
-
Allows us to call an RasterGenerator<S>
as if it was an RasterGenerator<T>
using
an function to connect the two.
- RasterGeneratorBridge(RasterGenerator<V>, CheckedFunction<T, V, ? extends Throwable>) - Constructor for class RasterGeneratorBridge
-
Creates with a delegate and a function to bridge the exposed element-type to the delegate
element-type.
- RasterGeneratorDelegateToDisplayStack<T> - Class in org.anchoranalysis.image.io.stack.output.generator
-
- RasterGeneratorDelegateToDisplayStack(SingleFileTypeGenerator<T, DisplayStack>, boolean) - Constructor for class RasterGeneratorDelegateToDisplayStack
-
- RasterGeneratorDelegateToRaster<S,T> - Class in org.anchoranalysis.image.io.stack.output.generator
-
- RasterGeneratorDelegateToRaster(RasterGenerator<S>) - Constructor for class RasterGeneratorDelegateToRaster
-
- RasterGeneratorSelectFormat<T> - Class in org.anchoranalysis.image.io.stack.output.generator
-
A
RasterGenerator
that selects an appropriate output-format based upon each generated
image.
- RasterGeneratorSelectFormat() - Constructor for class RasterGeneratorSelectFormat
-
- RasterTask<S,U> - Class in org.anchoranalysis.plugin.image.task.bean
-
An experiment that takes (primarily) a series of raster images as an input.
- RasterTask() - Constructor for class RasterTask
-
- RatioFirstToSecond - Class in org.anchoranalysis.image.feature.bean.object.pair
-
Ratio of first-object to second-object in a pair.
- RatioFirstToSecond() - Constructor for class RatioFirstToSecond
-
- RatioNonMode - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
-
- RatioNonMode() - Constructor for class RatioNonMode
-
- RatioPrincipalAxisLength - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.moments
-
Calculates the ratio of prinicpal-axis length using Image Moments.
- RatioPrincipalAxisLength() - Constructor for class RatioPrincipalAxisLength
-
- RatioThreshold - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.threshold
-
- RatioThreshold() - Constructor for class RatioThreshold
-
- read(Path, OperationContext) - Method in interface AnnotationReader
-
Reads an annotation, if possible, from the file-system.
- read(Path, OperationContext) - Method in class ImageLabelAnnotationReader
-
- read(Path, OperationContext) - Method in class DualMarksAnnotationReader
-
- read(Path) - Method in class CSVReader
-
Opens a CSV for reading.
- read(ProcessCSVLine) - Method in class ReadByLine
-
Reads a CSV-file iterating through each row and passing it to lineProcessor
- ReadableTuple3i - Interface in org.anchoranalysis.spatial.point
-
A tuple with three-values, respectively for the X, Y and Z dimensions.
- readAcquisitionDate(Path) - Static method in class AcquisitionDateReader
-
Reads an image acquisition-date from a file identified by path, based on the present of EXIF
data.
- readAcquisitionDate(Metadata) - Static method in class AcquisitionDateReader
-
Reads an image acquisition-date from metadata, based on the present of EXIF data.
- ReadAnnotationFromFile - Class in org.anchoranalysis.plugin.annotation.bean.strategy
-
- readAssumeExists(Path, OperationContext) - Static method in class ReadAnnotationFromFile
-
- ReadByLine - Class in org.anchoranalysis.io.input.csv
-
An opened-CSV file that is read line-by-line and processed.
- ReadByLine(Path, CSVReader) - Constructor for class ReadByLine
-
- readCheckExists(Path, OperationContext) - Static method in class ReadAnnotationFromFile
-
- readDate(Metadata, Class<T>, int[], int[]) - Static method in class ReadMetadataUtilities
-
Reads a metadata entry of type Date
from the first directory of type directoryType
.
- readDate(Directory, int) - Static method in class ReadMetadataUtilities
-
Reads a metadata entry of type Date
from a Directory
.
- readDefaultMarks(Path, OperationContext) - Method in class DualMarksAnnotationReader
-
- readFromCSV(Path, boolean) - Static method in class FileLabelMap
-
- readFromFile(Path) - Static method in class Dictionary
-
- ReadFromFile - Class in org.anchoranalysis.io.input.bean.dictionary
-
- ReadFromFile() - Constructor for class ReadFromFile
-
- readFromWidthHeightTags(Metadata, Class<T>, int, int) - Static method in class ReadMetadataUtilities
-
Reads two metadata entries, representing width and height, and use them to form a
Extent
.
- readFromWidthHeightTags(Directory, int, int) - Static method in class ReadMetadataUtilities
-
Reads two metadata entries, representing width and height, and use them to form a
Extent
.
- readHistogramFromFile(Path) - Static method in class HistogramCSVReader
-
Reads a CSV file from the file-system that describes a histogram of voxel values.
- readInt(Metadata, Class<T>, int) - Static method in class ReadMetadataUtilities
-
Reads a metadata entry of type int
from the first directory of type directoryType
.
- readInt(Directory, int) - Static method in class ReadMetadataUtilities
-
Reads a metadata entry of type int
from a Directory
.
- readLine() - Method in class CSVReader.OpenedCSVFile
-
Reads the next-line from the open CSV file.
- readMetadata(Path) - Static method in class ReadMetadataUtilities
-
Reads metadata, if it exists, from an image.
- readMetadata(Path, boolean) - Static method in class ReadVoxelExtentXml
-
Looks for a metadata file describing the resolution
- ReadMetadataUtilities - Class in org.anchoranalysis.io.bioformats.metadata
-
Reads various image properties from tags in Metadata
.
- ReadOptions - Class in org.anchoranalysis.io.bioformats.bean.options
-
- ReadOptions() - Constructor for class ReadOptions
-
- ReadOptionsDelegate - Class in org.anchoranalysis.io.bioformats.bean.options
-
Forces a particular settings, but otherwise uses settings from a delegate
- ReadOptionsDelegate() - Constructor for class ReadOptionsDelegate
-
- readResolutionXml(File) - Static method in class ResolutionAsXml
-
- readStack(Path, OperationContext) - Method in class StackReader
-
Opens a file at path
that should contain only a single-stack.
- ReadVoxelExtentXml - Class in org.anchoranalysis.plugin.io.bean.stack.reader
-
Reads
Resolution
from an XML file associated an image.
- ReadVoxelExtentXml() - Constructor for class ReadVoxelExtentXml
-
- reconstruction(VoxelsUntyped, VoxelsUntyped, Optional<ObjectMask>) - Method in class GrayscaleReconstruction2DIJ
-
- reconstruction(VoxelsUntyped, VoxelsUntyped, Optional<ObjectMask>) - Method in class GrayscaleReconstructionByErosion
-
- reconstruction(VoxelsUntyped, VoxelsUntyped, Optional<ObjectMask>) - Method in class GrayscaleReconstructionRobinson
-
- recordCopiedOutput(Path, Optional<Path>, int) - Method in class RecordingCounter
-
Records an copy operation in the log / CSV path mapping.
- RecordedExecutionTimes - Class in org.anchoranalysis.core.time
-
Recorded execution-times for operations.
- RecordedExecutionTimes(Stream<RecordedExecutionTimes.RecordedOperation>) - Constructor for class RecordedExecutionTimes
-
Create with the running-times.
- RecordedExecutionTimes.RecordedOperation - Class in org.anchoranalysis.core.time
-
A particular type of operation that has been recorded (en aggregate).
- RecordedOperation(String, int, double, double, int) - Constructor for class RecordedExecutionTimes.RecordedOperation
-
- RecordedOutputs - Class in org.anchoranalysis.io.output.recorded
-
Outputs recorded from RecordOutputNamesForWriter
.
- RecordedOutputs() - Constructor for class RecordedOutputs
-
- recordedOutputs() - Method in class RecordingWriters
-
If defined, all output-names that are passed as arguments to both writers are recorded here.
- RecordedOutputsWithRules - Class in org.anchoranalysis.io.output.recorded
-
Rules to determine what outputting occurs, together with maybe an entity that records the
output-names that are used when writing / querying.
- RecordedOutputsWithRules() - Constructor for class RecordedOutputsWithRules
-
Creates with no rules or outputs defined.
- RecordedOutputsWithRules(MultiLevelRecordedOutputs, MultiLevelOutputEnabled, OutputEnabledDelta) - Constructor for class RecordedOutputsWithRules
-
Creates with all elements defined.
- recordedTimes() - Method in class ExecutionTimeRecorder
-
The execution-times that have been recorded.
- recordedTimes() - Method in class ExecutionTimeRecorderIgnore
-
- recordError(Class<?>, String, Throwable) - Method in interface ErrorReporter
-
Reports an error that occurred as an exception, with a message first introducing it.
- recordError(Class<?>, Throwable) - Method in interface ErrorReporter
-
Reports an error that occurred as an exception
- recordError(Class<?>, String) - Method in interface ErrorReporter
-
Reports an error with a constant string error message.
- recordError(Class<?>, Throwable) - Method in class ErrorReporterBase
-
- recordError(Class<?>, String) - Method in class ErrorReporterBase
-
- recordError(Class<?>, String, Throwable) - Method in class ErrorReporterBase
-
- recordError(Class<?>, Throwable) - Method in class ErrorReporterForTask
-
- recordError(Class<?>, String) - Method in class ErrorReporterForTask
-
- recordError(Class<?>, String, Throwable) - Method in class ErrorReporterForTask
-
- recordErrorFormatted(Class<?>, String, Object...) - Method in interface ErrorReporter
-
Reports an error with a string derived from a format-string.
- recordExecutionTime(String, long) - Method in class ExecutionTimeRecorder
-
Records the execution-time of a particular operation.
- recordExecutionTime(String, CheckedRunnable<E>) - Method in class ExecutionTimeRecorder
-
Executes an operation
while recording the execution-time - without a return
type.
- recordExecutionTime(String, CheckedSupplier<T, E>) - Method in class ExecutionTimeRecorder
-
Executes an operation
while recording the execution-time - with a return type.
- recordExecutionTime(String, long) - Method in class ExecutionTimeRecorderIgnore
-
- recordExecutionTimeUnchecked(String, Runnable) - Method in class ExecutionTimeRecorder
-
Executes an operation
while recording the execution-time - without a return type,
and without throwing an exception..
- RecordingCounter<T> - Class in org.anchoranalysis.plugin.io.shared
-
A counter that also records outputs in a message-log and CSV file.
- RecordingCounter(Counter, Outputter, T) - Constructor for class RecordingCounter
-
- RecordingWriters - Class in org.anchoranalysis.io.output.recorded
-
Two writers that record any output-names that are passed as arguments.
- RecordingWriters(ElementOutputter, Optional<WriterExecuteBeforeEveryOperation>, Optional<MultiLevelRecordedOutputs>) - Constructor for class RecordingWriters
-
Creates the two writers.
- recordTimeDifferenceBetween(String, long, long) - Method in class ExecutionTimeRecorder
-
Records the execution-time of a particular operation by subtracting the start-time from the
end time.
- recordWarning(String) - Method in interface ErrorReporter
-
Reports an warning with a constant string error message.
- recordWarning(String) - Method in class ErrorReporterBase
-
- recordWarning(String) - Method in class ErrorReporterForTask
-
- recordWarningFormatted(String, Object...) - Method in interface ErrorReporter
-
Reports an warning with a string derived from a format-string.
- RecursivelyDescribeExceptionStack - Class in org.anchoranalysis.core.exception.friendly
-
Generates a nice string representation of an Exception and its causes according to certain rules.
- RED - Static variable in class RGBChannelNames
-
Name for the red channel.
- red() - Method in class RGBStack
-
The red channel.
- reduce(List<LabelledWithConfidence<ObjectMask>>, Extent, ExecutionTimeRecorder) - Method in class ReduceElementsGreedy
-
- reduce(List<LabelledWithConfidence<T>>, Extent, ExecutionTimeRecorder) - Method in class ReduceElements
-
Reduce a list of elements (each with a confidence score and a label) to a
smaller-list.
- reduce(ReduceElements<ObjectMask>, boolean, ExecutionTimeRecorder) - Method in class SegmentedObjects
-
Reduces the segmented-objects, applying a reduction algorithm separately to each
object-class.
- reduce() - Method in class HungarianAlgorithm
-
Reduce the cost matrix by subtracting the smallest element of each row from all elements of
the row as well as the smallest element of each column from all elements of the column.
- reduce(List<LabelledWithConfidence<ObjectMask>>, Extent, ExecutionTimeRecorder) - Method in class ThresholdConfidence
-
- ReduceElements<T> - Class in org.anchoranalysis.image.inference.bean.segment.reduce
-
Reduces the number or spatial-extent of elements by favoring higher-confidence elements over
lower-confidence elements.
- ReduceElements() - Constructor for class ReduceElements
-
- ReduceElementsGreedy - Class in org.anchoranalysis.image.inference.bean.reduce
-
Reduces the number or spatial-extent of elements by favouring higher-confidence elements over
lower-confidence elements.
- ReduceElementsGreedy() - Constructor for class ReduceElementsGreedy
-
- ReduceFirstAndSecond - Class in org.anchoranalysis.plugin.image.feature.bean.list.pair
-
- ReduceFirstAndSecond() - Constructor for class ReduceFirstAndSecond
-
- ReduceObjectsGraph - Class in org.anchoranalysis.image.inference.bean.reduce
-
Combines a
PriorityQueue
(ordering by highest confidence) and a graph-structure
indicating which objects overlap with each other.
- ReduceObjectsGraph(List<LabelledWithConfidence<ObjectMask>>) - Constructor for class ReduceObjectsGraph
-
Create with a list of elements.
- ReduceRatioFirstAndSecond - Class in org.anchoranalysis.plugin.image.feature.bean.list.pair
-
- ReduceRatioFirstAndSecond() - Constructor for class ReduceRatioFirstAndSecond
-
- ReductionOutcome<T> - Class in org.anchoranalysis.image.inference.segment
-
The result of a reduction operation.
- ReductionOutcome() - Constructor for class ReductionOutcome
-
Create with an empty list of retained-indices.
- ReductionOutcome(List<Integer>) - Constructor for class ReductionOutcome
-
- ReductionOutcome(List<Integer>, List<T>) - Constructor for class ReductionOutcome
-
- Reference<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.operator
-
Uses another feature to calculate the value.
- Reference(String) - Constructor for class Reference
-
Create with a specific identifier.
- Reference() - Constructor for class Reference
-
- Reference - Class in org.anchoranalysis.plugin.image.bean.channel.provider
-
- Reference(String) - Constructor for class Reference
-
- Reference() - Constructor for class Reference
-
- Reference - Class in org.anchoranalysis.plugin.image.bean.histogram.provider
-
- Reference(String) - Constructor for class Reference
-
- Reference() - Constructor for class Reference
-
- Reference - Class in org.anchoranalysis.plugin.image.bean.mask.provider
-
- Reference(String) - Constructor for class Reference
-
- Reference() - Constructor for class Reference
-
- Reference - Class in org.anchoranalysis.plugin.image.bean.object.provider
-
- Reference(String) - Constructor for class Reference
-
- Reference() - Constructor for class Reference
-
- Reference - Class in org.anchoranalysis.plugin.image.bean.stack.provider
-
Retrieves an existing stack.
- Reference(String) - Constructor for class Reference
-
- Reference() - Constructor for class Reference
-
- Reference - Class in org.anchoranalysis.plugin.mpp.bean.provider.collection
-
- Reference() - Constructor for class Reference
-
- Reference(String) - Constructor for class Reference
-
- Reference - Class in org.anchoranalysis.plugin.points.bean.fitter
-
- Reference() - Constructor for class Reference
-
- ReferenceFactory - Class in org.anchoranalysis.plugin.image.provider
-
Creates reference (i.e.
- ReferenceOrElse - Class in org.anchoranalysis.plugin.image.bean.object.provider
-
Returns a object-collection by name if it exists, or else calls objectsElse
if it doesn't
exist.
- ReferenceOrElse() - Constructor for class ReferenceOrElse
-
- ReferenceOrEmpty - Class in org.anchoranalysis.plugin.mpp.bean.provider.collection
-
Returns an existing marks-collection or an empty set if it doesn't exist
- ReferenceOrEmpty() - Constructor for class ReferenceOrEmpty
-
- ReferencingFeatureListProvider<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.list
-
A base class for implementations of
FeatureListProvider
that may reference features
created elsewhere.
- ReferencingFeatureListProvider() - Constructor for class ReferencingFeatureListProvider
-
- ReflectInAxesWithinDistance - Class in org.anchoranalysis.plugin.points.bean.fitter
-
Reflects points in each axes if all points are within a certain distance from it
- ReflectInAxesWithinDistance() - Constructor for class ReflectInAxesWithinDistance
-
- reflectThroughOrigin() - Method in class BoundingBox
-
Reflects the bounding box through the origin.
- RegEx - Class in org.anchoranalysis.bean.shared.regex
-
The regular-expression to use for matching groups.
- RegEx() - Constructor for class RegEx
-
- RegExList - Class in org.anchoranalysis.bean.shared.regex
-
Combines one or more
RegEx
together, by successively trying to match each
RegEx
until success.
- RegExList() - Constructor for class RegExList
-
- RegExMatcher - Class in org.anchoranalysis.plugin.io.bean.file.namer
-
- RegExMatcher() - Constructor for class RegExMatcher
-
- RegExSimple - Class in org.anchoranalysis.bean.shared.regex
-
Matches a Java-style regular expression against the string.
- RegExSimple(String) - Constructor for class RegExSimple
-
Creates with an expression that should match one or more groups.
- RegExSimple() - Constructor for class RegExSimple
-
- RegExSimple(String, Pattern) - Constructor for class RegExSimple
-
- region() - Method in interface AnnotationWithMarks
-
The region(s) of the marks that specifies the annotation.
- region() - Method in class DualMarksAnnotation
-
- region(BoundingBox, boolean) - Method in class Mask
-
Creates an
ObjectMask
corresponding to the on/off state in a bounding-box.
- region(BoundingBox, boolean) - Method in class BoundedVoxels
-
A (sub-)region of the voxels.
- region(BoundingBox, boolean) - Method in interface VoxelsExtracter
-
A (sub-)region of the voxels.
- region(BoundingBox, boolean) - Method in class ObjectMask
-
A (sub-)region of the object-mask.
- regionIntersecting(BoundingBox, int) - Method in class BoundedVoxels
-
- regionIntersecting(BoundingBox) - Method in class ObjectMask
-
Creates an object-mask covering the a bounding-box (that is required to intersect at least
partially)
- RegionMap - Class in org.anchoranalysis.mpp.bean.regionmap
-
Maps integer IDs to sub-regions in the map
- RegionMap(int) - Constructor for class RegionMap
-
- RegionMap() - Constructor for class RegionMap
-
- RegionMapSingleton - Class in org.anchoranalysis.mpp.bean.regionmap
-
- RegionMembership - Class in org.anchoranalysis.mpp.bean.regionmap
-
- RegionMembership(int) - Constructor for class RegionMembership
-
- RegionMembership() - Constructor for class RegionMembership
-
- RegionMembershipAnd - Class in org.anchoranalysis.mpp.bean.regionmap
-
- RegionMembershipAnd() - Constructor for class RegionMembershipAnd
-
- RegionMembershipAnd(int) - Constructor for class RegionMembershipAnd
-
- RegionMembershipOr - Class in org.anchoranalysis.mpp.bean.regionmap
-
- RegionMembershipOr() - Constructor for class RegionMembershipOr
-
- RegionMembershipUtilities - Class in org.anchoranalysis.mpp.bean.regionmap
-
- RegionMembershipWithFlags - Class in org.anchoranalysis.mpp.bean.regionmap
-
- RegionMembershipWithFlags(RegionMembership, int) - Constructor for class RegionMembershipWithFlags
-
- regionZ(int, int, VoxelsFactoryTypeBound<T>) - Method in class BoundedVoxels
-
Creates an box with a subrange of the slices.
- regionZ(int, int) - Method in class ObjectMask
-
Creates an object-mask with a subrange of the slices.
- register(String, AnchorBeanFactory) - Static method in class RegisterBeanFactories
-
Registers a specific factory.
- register(String, Function<List<T>, Object>) - Static method in class RegisterBeanFactories
-
Registers a bean that creates a {link java.util.List}.
- registerAllPackageBeanFactories() - Static method in class RegisterBeanFactories
-
Registers the factories for the beans that exist in this package
- RegisterBeanFactories - Class in org.anchoranalysis.bean.xml
-
Utility class for registering the Bean-factories that are found in anchor-bean (or any other).
- registerBeanFactories() - Static method in class RegisterFeatureBeanFactories
-
Registers all custom feature-related beans.
- RegisterFeatureBeanFactories - Class in org.anchoranalysis.feature.bean
-
- RegularExpression - Class in org.anchoranalysis.plugin.io.bean.file.group.parser
-
- RegularExpression() - Constructor for class RegularExpression
-
- RegularExpressionBase - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming
-
- RegularExpressionBase() - Constructor for class RegularExpressionBase
-
- rejected() - Method in interface DualMarks
-
The rejected marks.
- RejectIfConditionXYResolution - Class in org.anchoranalysis.plugin.io.bean.stack.reader
-
If the XY resolution of an opened-image meets a certain condition then the resolution is scaled
by a factor.
- RejectIfConditionXYResolution() - Constructor for class RejectIfConditionXYResolution
-
- RejectIfIntensityLessThan - Class in org.anchoranalysis.plugin.image.feature.bean.score
-
- RejectIfIntensityLessThan() - Constructor for class RejectIfIntensityLessThan
-
- RejectIfNotConnected - Class in org.anchoranalysis.plugin.image.bean.object.provider.connected
-
Rejects a set of objects, if any object is not fully connected (pixels form two or more separate
connected components)
- RejectIfNotConnected() - Constructor for class RejectIfNotConnected
-
- rejectProposal() - Method in class OptimizationStep
-
- relation() - Method in class RelationToConstant
-
- relation() - Method in class RelationToThreshold
-
The relation to the threshold.
- relation() - Method in class BinaryNotOffVoxels
-
- relation() - Method in class BinaryNotOnVoxels
-
- relation() - Method in class BinaryOffVoxels
-
- relation() - Method in class BinaryOnVoxels
-
- RelationBean - Class in org.anchoranalysis.bean.shared.relation
-
Base class that specifies a
relation between two
double
s.
- RelationBean() - Constructor for class RelationBean
-
- RelationToConstant - Class in org.anchoranalysis.bean.shared.relation.threshold
-
Defines a constant threshold, and a relation to it.
- RelationToConstant() - Constructor for class RelationToConstant
-
- RelationToConstant(RelationBean, double) - Constructor for class RelationToConstant
-
- RelationToThreshold - Class in org.anchoranalysis.bean.shared.relation.threshold
-
A base class specifying a threshold and a relation to it.
- RelationToThreshold() - Constructor for class RelationToThreshold
-
- RelationWithMatches - Class in org.anchoranalysis.plugin.image.bean.object.filter.collective
-
Matches each object with others, and keeps only those where a relation holds true for all matches
(in terms of features)
- RelationWithMatches() - Constructor for class RelationWithMatches
-
- relativeMaskTo(BoundingBox) - Method in class ObjectMask
-
Creates a new object-mask with coordinates changed to be relative to another box.
- relativePositionTo(BoundingBox) - Method in class BoundingBox
-
The relative position of the corner to another bounding box.
- relativePositionToBox(BoundingBox) - Method in class BoundingBox
-
A new bounding-box using relative position coordinates to another box.
- relativeScale(Extent, Extent, boolean) - Static method in class RelativeScaleCalculator
-
- relativeScale(Extent, Extent) - Static method in class RelativeScaleCalculator
-
Calculates a scaling factor so as to scale source
to target
.
- RelativeScaleCalculator - Class in org.anchoranalysis.spatial.scale
-
Determine the scaling-factor needed to scale an
Extent
to become equal in size to another
Extent
.
- relativeScalePreserveAspectRatio(Extent, Extent) - Static method in class RelativeScaleCalculator
-
Calculates a scaling factor so as to maximally scale source
to target
-
while preserving the aspect ratio.
- RelativeToDirectory - Class in org.anchoranalysis.plugin.io.bean.file.namer
-
Constructs a name by finding the relative-path between the file and the input-directory.
- RelativeToDirectory() - Constructor for class RelativeToDirectory
-
- releaseKeepBest() - Method in class DualState
-
- releaseKeepBest() - Method in class OptimizationStep
-
- rememberConverted(NamedChannelsInput, U, StringBuilder) - Method in class SharedStateRememberConverted
-
Remembers a converted input.
- remove(K, V) - Method in class MapCreate
-
Removes the entry for the specified key only if it is currently mapped to the specified
value.
- remove(int) - Method in class ColorList
-
Remove an element at a particular index.
- remove(T) - Method in class IntersectingObjects
-
Removes an object-mask, so that it is no longer considered in queries.
- remove(MemoForIndex, VoxelizedMarkMemo) - Method in class RandomCollectionWithAddCriteria
-
- remove(EnergyMemoList, VoxelizedMarkMemo, EnergyStackWithoutParameters) - Method in class MarksWithEnergyBreakdown
-
- remove(EnergyMemoList, int, VoxelizedMarkMemo, EnergyStackWithoutParameters) - Method in class MarksWithEnergyBreakdown
-
- remove(int) - Method in class MarksWithEnergyBreakdown
-
- remove(int) - Method in class MarksWithTotalEnergy
-
- remove(int, EnergyStackWithoutParameters) - Method in class VoxelizedMarksWithEnergy
-
- remove(VoxelizedMarkMemo, EnergyStackWithoutParameters) - Method in class VoxelizedMarksWithEnergy
-
- remove(MemoForIndex, VoxelizedMarkMemo) - Method in class EnergySavedPairs
-
- remove(EnergySavedInd, int) - Method in class EnergyMemoList
-
- remove(int) - Method in class MemoList
-
- remove(VoxelizedMarkMemo) - Method in class MemoList
-
- remove(MemoForIndex, VoxelizedMarkMemo) - Method in class UpdatableMarksList
-
- remove(Object) - Method in class UpdatableMarksList
-
- remove(int) - Method in class UpdatableMarksList
-
- remove(int) - Method in class ColoredMarks
-
- remove(int) - Method in class MarkCollection
-
- remove(MemoForIndex, VoxelizedMarkMemo) - Method in interface UpdatableMarks
-
- remove(BoundingBox, T) - Method in class BoundingBoxRTree
-
Removes a particular item from the r-tree, identified by its bounding-box and payload.
- remove(double, double, T) - Method in class IntervalRTree
-
Removes a particular item from the r-tree, identified by its interval and payload.
- remove(Rectangle, T) - Method in class RTree
-
Removes a particular item from the r-tree, identified by its Rectangle
and payload.
- removeAll(Collection<?>) - Method in class UpdatableMarksList
-
- removeAndUpdateEnergy(MarksFromPartition, ProposerContext) - Method in class KernelDeathPartition
-
- removeAndUpdateEnergy(T, ProposerContext) - Method in class KernelDeath
-
- removeAndUpdateEnergy(VoxelizedMarksWithEnergy, ProposerContext) - Method in class KernelDeathVoxelized
-
- removeAnyLeadingPeriod(String) - Static method in class FormatExtensions
-
Removes a single leading period from a string, if one exists.
- removeBelowThreshold(int) - Method in class Histogram
-
All values less than threshold
are removed.
- removeClosestToUnitZ() - Method in class ImageMoments
-
Removes the entry that is closest to having an eigenVector in direction (0,0,1).
- removeEdge(V, V) - Method in class GraphWithoutPayload
-
Remove an edge between two vertices.
- removeEdge(V, V) - Method in class GraphWithPayload
-
Remove an edge between two vertices.
- removeEdge(ObjectForReduction, ObjectForReduction) - Method in class ReduceObjectsGraph
-
Remove an edge between two vertices.
- removeExtension(String) - Static method in class ExtensionUtilities
-
Removes an extension from a filename or path.
- removeExtension(Path) - Static method in class ExtensionUtilities
-
- RemoveExtension - Class in org.anchoranalysis.plugin.io.bean.file.namer
-
Removes extensions from the identifier (but not from the file) and only if the extension
hasn't already been removed upstream.
- RemoveExtension(FileNamer) - Constructor for class RemoveExtension
-
- RemoveExtension() - Constructor for class RemoveExtension
-
- removeIfExists(T) - Method in class NameValueMap
-
Removes an element from the set, if it exists.
- removeIfExists(FeatureList<FeatureInput>) - Method in class SharedFeatures
-
Remove all features, if they currently exist, from features
.
- removeInstanceFor(Class<? extends T>) - Method in class BeanInstanceMap
-
Removes any instance in the map of a particular family-type.
- RemoveIntersectingVoxels - Class in org.anchoranalysis.plugin.image.bean.object.provider.split
-
Considers all possible pairs of objects in a provider, and removes any intersecting pixels
- RemoveIntersectingVoxels() - Constructor for class RemoveIntersectingVoxels
-
- removeIntersectingVoxels(ObjectCollection, Dimensions, boolean) - Static method in class ObjectIntersectionRemover
-
- RemoveLastElement - Class in org.anchoranalysis.plugin.io.bean.grouper
-
Splits an identifier into elements by the directory separator, and removes the final element.
- RemoveLastElement() - Constructor for class RemoveLastElement
-
- removeLeft(int) - Method in class ContiguousVoxelPath
-
Removes the first numToRemove pixels from the left
- RemoveMatching - Class in org.anchoranalysis.plugin.io.bean.file.provider
-
- RemoveMatching() - Constructor for class RemoveMatching
-
- removeNonMatching(List<T>) - Method in class FilterDescriptiveNameEqualsContains
-
- removeOrReplace(boolean, boolean, boolean) - Method in class MergeCandidate
-
Chops of one-side of keep, and one-side of merge
- RemoveOverlappingObjects - Class in org.anchoranalysis.image.inference.bean.reduce
-
Intersecting objects are removed if they have sufficient overlap.
- RemoveOverlappingObjects() - Constructor for class RemoveOverlappingObjects
-
- RemovePartition - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.partition
-
- RemovePartition() - Constructor for class RemovePartition
-
- RemovePartitionAndThen<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.partition
-
- RemovePartitionAndThen() - Constructor for class RemovePartitionAndThen
-
- removeRight(int) - Method in class ContiguousVoxelPath
-
Removes the last numToRemove pixels from the right
- removeStackWriter() - Static method in class BeanInstanceMapFixture
-
- RemoveTouchingBorder - Class in org.anchoranalysis.plugin.image.bean.object.provider.filter
-
Considers all possible pairs of objects in a provider, and removes those that touch the border.
- RemoveTouchingBorder() - Constructor for class RemoveTouchingBorder
-
- removeTouchingBorderXY(Extent) - Method in class OverlappingObjects
-
Removes any objects from the assignment if they touch the X or Y scene border.
- RemoveTrailingDirectory - Class in org.anchoranalysis.plugin.io.bean.path.derive
-
- RemoveTrailingDirectory() - Constructor for class RemoveTrailingDirectory
-
- removeTwo(EnergyMemoList, int, int, EnergyStackWithoutParameters) - Method in class MarksWithEnergyBreakdown
-
- removeTwo(int, int, EnergyStackWithoutParameters) - Method in class VoxelizedMarksWithEnergy
-
- removeTwo(EnergySavedInd, int, int) - Method in class EnergyMemoList
-
- removeTwo(int, int) - Method in class MarkCollection
-
- removeVertex(V) - Method in class GraphWithoutPayload
-
Removes a vertex and any edges connected to it.
- removeVertex(V) - Method in class GraphWithPayload
-
Removes a vertex and any edges connected to it.
- removeVertex(ObjectForReduction) - Method in class ReduceObjectsGraph
-
Removes a vertex and any edges connected to it.
- RemoveWhitespace - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming
-
Removes any whitespace characters from the path
- RemoveWhitespace() - Constructor for class RemoveWhitespace
-
- Repeat - Class in org.anchoranalysis.bean.shared.color.scheme
-
- Repeat() - Constructor for class Repeat
-
- repeat(int, CheckedRunnable<E>) - Static method in class FunctionalIterate
-
Repeats an operation a number of times.
- repeat(int, Supplier<T>) - Static method in class FunctionalList
-
Creates a list of elements, by repeatedly calling the same operation.
- REPEAT - Static variable in class PositionChoicesConstants
-
The choice which will cause a single-slice in the z-dimension to be duplicated across the
z-dimension to match the z-size onto which it is projected.
- Repeat - Class in org.anchoranalysis.plugin.image.bean.segment.binary
-
- Repeat() - Constructor for class Repeat
-
- Repeat - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection
-
- Repeat() - Constructor for class Repeat
-
- Repeat - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
-
- Repeat() - Constructor for class Repeat
-
- Repeat - Class in org.anchoranalysis.plugin.mpp.bean.proposer.position
-
- Repeat() - Constructor for class Repeat
-
- repeatAsStream(int, Class<? extends E>, CheckedSupplier<T, E>) - Static method in class FunctionalIterate
-
Repeats an operation a number of times, to form a
Stream
.
- repeatCountSuccessful(int, CheckedBooleanSupplier<E>) - Static method in class FunctionalIterate
-
Repeats an operation a number of times, counting the number of times the operation returns
true.
- RepeatSlice - Class in org.anchoranalysis.plugin.image.bean.channel.provider.slice
-
Creates a new channel with specific dimensions that repeatedly duplicates a slice from an
existing channel
- RepeatSlice() - Constructor for class RepeatSlice
-
- RepeatSlice - Class in org.anchoranalysis.plugin.image.bean.mask.provider.slice
-
Creates a new mask with specific dimensions that repeatedly duplicates a slice from an existing
mask
- RepeatSlice() - Constructor for class RepeatSlice
-
- repeatUntil(int, CheckedBooleanSupplier<E>) - Static method in class FunctionalIterate
-
Repeats an operation until a true value is returned.
- repeatWithIndex(int, CheckedIntConsumer<E>) - Static method in class FunctionalIterate
-
Repeats an operation a number of times, passing an increment index to operation
each
time.
- Replace - Class in org.anchoranalysis.plugin.io.bean.path.derive
-
Generates a file-path by replacing all occurrences of a string-pattern with another
- Replace() - Constructor for class Replace
-
- replaceBy(BinaryVoxels<UnsignedByteBuffer>) - Method in class Mask
-
Replaces the underlying voxels in the mask with new voxels.
- replaceError(ErrorNode) - Method in class ProposerContext
-
- replaceError(ErrorNode) - Method in class KernelCalculationContext
-
- replaceError(ErrorNode) - Method in class TransformationContext
-
- ReplaceInfinity<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.replace
-
- ReplaceInfinity() - Constructor for class ReplaceInfinity
-
- replaceInput(T) - Method in class SessionInputSequential
-
Replaces existing input with new input
- replaceInputManager(InputManager<T>) - Method in class InputOutputExperiment
-
- ReplaceInputManager<T extends InputFromManager> - Interface in org.anchoranalysis.experiment.io
-
Indicates and provides a mechanism that the
InputManager
can be replaced.
- replaceInputManager(InputManager<T>) - Method in interface ReplaceInputManager
-
Replace the existing @{link InputManager} associated with this class.
- replaceInputManager(InputManager<T>) - Method in class QuickMultiDatasetExperiment
-
- replaceInputManager(InputManager<T>) - Method in class QuickMultiDatasetStructuredExperiment
-
- ReplaceNaN<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.replace
-
- ReplaceNaN() - Constructor for class ReplaceNaN
-
- replaceOutputManager(OutputManager) - Method in class InputOutputExperiment
-
- ReplaceOutputManager - Interface in org.anchoranalysis.experiment.io
-
Indicates and provides a mechanism that the
OutputManager
can be replaced.
- replaceOutputManager(OutputManager) - Method in interface ReplaceOutputManager
-
- replaceOutputManager(OutputManager) - Method in class QuickMultiDatasetExperiment
-
- replaceOutputManager(OutputManager) - Method in class QuickMultiDatasetStructuredExperiment
-
- ReplacePropertyBeanFactory<T extends AnchorBean<T>> - Class in org.anchoranalysis.bean.xml.factory
-
Replaces a property (an XML element of attribute) on a bean before loading it.
- ReplacePropertyBeanFactory(BeanInstanceMap) - Constructor for class ReplacePropertyBeanFactory
-
- replaceSlice(int, VoxelBuffer<T>) - Method in class BoundedVoxels
-
Assigns a new buffer for a slice.
- replaceSlice(int, VoxelBuffer<UnsignedByteBuffer>) - Method in class FromByte
-
- replaceSlice(int, VoxelBuffer<FloatBuffer>) - Method in class FromFloat
-
- replaceSlice(int, VoxelBuffer<UnsignedIntBuffer>) - Method in class FromInt
-
- replaceSlice(int, VoxelBuffer<UnsignedShortBuffer>) - Method in class FromShort
-
- replaceSlice(int, VoxelBuffer<T>) - Method in interface SliceBufferIndex
-
Replaces the voxels for a particular z-slice.
- replaceSlice(int, VoxelBuffer<T>) - Method in class Voxels
-
Assigns a new buffer for a particular slice.
- replaceSlice(int, VoxelsUntyped, int, boolean) - Method in class VoxelsUntyped
-
Copies one particular z-slice of voxels from a source into the current voxels.
- ReplaceStrategy<T extends FeatureInput> - Interface in org.anchoranalysis.feature.session.replace
-
- replaceTask(Task<T, S>) - Method in class InputOutputExperiment
-
- replaceTask(Task<T, S>) - Method in class JobProcessor
-
- ReplaceTask<T extends InputFromManager,S> - Interface in org.anchoranalysis.experiment.io
-
Indicates and provides a mechanism that the
Task
can be replaced.
- replaceTask(Task<T, S>) - Method in interface ReplaceTask
-
Replace the currently-assigned
Task
with another.
- replaceTask(Task<U, S>) - Method in class ConvertNamedChannels
-
- ReplaceUnusualValue<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.replace
-
Calculates the underlying feature, but replaces the result with a constant if it happens to be an
"unusual" value
- ReplaceUnusualValue() - Constructor for class ReplaceUnusualValue
-
- replaceVoxels(Voxels<?>) - Method in class Channel
-
Assigns new voxels to replace the existing voxels.
- replaceVoxels(Voxels<T>) - Method in class BoundedVoxels
-
Replaces the voxels in the box.
- replaceVoxels(Voxels<UnsignedByteBuffer>) - Method in class ObjectMask
-
Replaces the voxels in the object-mask.
- reportBegin(FeedbackBeginParameters<T>) - Method in class FeedbackReceiverList
-
- reportBegin(FeedbackBeginParameters<T>) - Method in class FeedbackReceiverRequireArguments
-
- reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class PeriodicSubdirectoryReporter
-
- reportBegin(FeedbackBeginParameters<T>) - Method in class ReporterAggregate
-
- reportBegin(FeedbackBeginParameters<T>) - Method in interface FeedbackReceiver
-
- reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class ConsoleAccepted
-
- reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class ConsoleAggregatedReporter
-
- reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class CSVReporterAggregated
-
- reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class CSVReporterBest
-
- reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class MinimalExecutionTimeStatsReporter
-
- reportBegin(FeedbackBeginParameters<T>) - Method in class NullReporter
-
- reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class ObjectSerializerPeriodicReporter
-
- reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class OptimizationStepLogReporter
-
- reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class TextFile
-
- reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class TextFileMarksReporter
-
- reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class VoxelizedMarksChangeReporter
-
- reportEnd(FeedbackEndParameters<T>) - Method in class FeedbackReceiverList
-
- reportEnd(FeedbackEndParameters<T>) - Method in class FeedbackReceiverRequireArguments
-
- reportEnd(FeedbackEndParameters<VoxelizedMarksWithEnergy>) - Method in class PeriodicSubdirectoryReporter
-
- reportEnd(FeedbackEndParameters<T>) - Method in class ReporterAggregate
-
- reportEnd(FeedbackEndParameters<T>) - Method in interface FeedbackReceiver
-
- reportEnd(FeedbackEndParameters<VoxelizedMarksWithEnergy>) - Method in class ConsoleAccepted
-
- reportEnd(FeedbackEndParameters<VoxelizedMarksWithEnergy>) - Method in class ConsoleAggregatedReporter
-
- reportEnd(FeedbackEndParameters<VoxelizedMarksWithEnergy>) - Method in class CSVReporterAggregated
-
- reportEnd(FeedbackEndParameters<VoxelizedMarksWithEnergy>) - Method in class CSVReporterBest
-
- reportEnd(FeedbackEndParameters<VoxelizedMarksWithEnergy>) - Method in class MinimalExecutionTimeStatsReporter
-
- reportEnd(FeedbackEndParameters<T>) - Method in class NullReporter
-
- reportEnd(FeedbackEndParameters<VoxelizedMarksWithEnergy>) - Method in class OptimizationStepLogReporter
-
- reportEnd(FeedbackEndParameters<VoxelizedMarksWithEnergy>) - Method in class TextFile
-
- reportEnd(FeedbackEndParameters<VoxelizedMarksWithEnergy>) - Method in class VoxelizedMarksChangeReporter
-
- ReporterAggregate<T> - Class in org.anchoranalysis.mpp.segment.bean.optimization.feedback
-
- ReporterAggregate(double) - Constructor for class ReporterAggregate
-
- ReporterAggregate() - Constructor for class ReporterAggregate
-
- ReporterException - Exception in org.anchoranalysis.mpp.segment.optimization.feedback
-
- ReporterException(String) - Constructor for exception ReporterException
-
- ReporterException(Throwable) - Constructor for exception ReporterException
-
- ReporterInterval<T> - Class in org.anchoranalysis.mpp.segment.bean.optimization.feedback
-
- ReporterInterval() - Constructor for class ReporterInterval
-
- ReporterInterval(double) - Constructor for class ReporterInterval
-
- ReportFeature<T> - Class in org.anchoranalysis.io.output.bean
-
- ReportFeature() - Constructor for class ReportFeature
-
- ReportFeatureEvaluator<T extends FeatureInput> - Class in org.anchoranalysis.mpp.io.bean.report.feature
-
- ReportFeatureEvaluator() - Constructor for class ReportFeatureEvaluator
-
- ReportFeatureForMarks<T extends FeatureInput> - Class in org.anchoranalysis.mpp.io.bean.report.feature
-
- ReportFeatureForMarks() - Constructor for class ReportFeatureForMarks
-
- ReportFeatureForSharedObjects - Class in org.anchoranalysis.mpp.io.bean.report.feature
-
- ReportFeatureForSharedObjects() - Constructor for class ReportFeatureForSharedObjects
-
- ReportFeatureOnMark - Class in org.anchoranalysis.mpp.io.bean.report.feature
-
- ReportFeatureOnMark() - Constructor for class ReportFeatureOnMark
-
- ReportFeatureOnMarks - Class in org.anchoranalysis.mpp.io.bean.report.feature
-
- ReportFeatureOnMarks() - Constructor for class ReportFeatureOnMarks
-
- ReportFeatureOnObject - Class in org.anchoranalysis.mpp.io.bean.report.feature
-
- ReportFeatureOnObject() - Constructor for class ReportFeatureOnObject
-
- ReportFeatureOnObjectCollection - Class in org.anchoranalysis.mpp.io.bean.report.feature
-
- ReportFeatureOnObjectCollection() - Constructor for class ReportFeatureOnObjectCollection
-
- ReportFeatureOnObjectsBase<T extends FeatureInput> - Class in org.anchoranalysis.mpp.io.bean.report.feature
-
- ReportFeatureOnObjectsBase() - Constructor for class ReportFeatureOnObjectsBase
-
- ReportFeatureWrapError - Class in org.anchoranalysis.mpp.io.bean.report.feature
-
- ReportFeatureWrapError() - Constructor for class ReportFeatureWrapError
-
- reporting(int, StateReporter<T, U>, TransformationContext) - Method in class OptimizationStep
-
- Reporting<S> - Class in org.anchoranalysis.mpp.segment.optimization.step
-
Exposes data which is only needed by reporting tools
- reportIteration(Reporting<T>) - Method in class FeedbackReceiverList
-
- reportIteration(Reporting<T>) - Method in class FeedbackReceiverRequireArguments
-
- reportIteration(Reporting<T>) - Method in class ReporterInterval
-
- reportIteration(Reporting<T>) - Method in interface FeedbackReceiver
-
- reportIteration(Reporting<VoxelizedMarksWithEnergy>) - Method in class ConsoleAccepted
-
- reportIteration(Reporting<VoxelizedMarksWithEnergy>) - Method in class CSVReporterBest
-
- reportIteration(Reporting<VoxelizedMarksWithEnergy>) - Method in class MinimalExecutionTimeStatsReporter
-
- reportIteration(Reporting<T>) - Method in class NullReporter
-
- reportIteration(Reporting<VoxelizedMarksWithEnergy>) - Method in class VoxelizedMarksChangeReporter
-
- reportNewBest(Reporting<T>) - Method in class FeedbackReceiverList
-
- reportNewBest(Reporting<T>) - Method in class FeedbackReceiverRequireArguments
-
- reportNewBest(Reporting<T>) - Method in interface FeedbackReceiver
-
- reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class ConsoleAccepted
-
- reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class ConsoleAggregatedReporter
-
- reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class CSVReporterAggregated
-
- reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class CSVReporterBest
-
- reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class KernelIterDescriptionSerializerPeriodicReporter
-
- reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class Log4JReporter
-
- reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class MemoryUsageReporter
-
- reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class MinimalExecutionTimeStatsReporter
-
- reportNewBest(Reporting<T>) - Method in class NullReporter
-
- reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class OptimizationStepLogReporter
-
- reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class TextFile
-
- reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class TextFileMarksReporter
-
- reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class VoxelizedMarksChangeReporter
-
- reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class VoxelizedMarksPeriodicReporter
-
- requestOmitExperimentIdentifier(String) - Method in class OutputArguments
-
Requests that the experiment-identifier (name and index) is not included in the
output-directory path.
- requestOmitExperimentIdentifier() - Method in class OutputPrefixerSettings
-
Requests that the experiment-identifier (name and index) is not included in the
output-directory path.
- requestOutputIncrementingNumberSequence() - Method in class OutputArguments
-
Requests outputting with an incrementing number sequence, rather than the usual outputter
(normally based upon input filenames).
- requestOutputIncrementingNumberSequence() - Method in class OutputPrefixerSettings
-
Requests outputting with an incrementing number sequence, rather than the usual outputter
(normally based upon input filenames).
- requestOutputSuppressDirectories() - Method in class OutputArguments
-
Requests suppressing directories (replacing subdirectory separators with an underscore) in
the identifiers that are outputted.
- requestOutputSuppressDirectories() - Method in class OutputPrefixerSettings
-
Requests suppressing directories (replacing subdirectory separators with an underscore) in
the identifiers that are outputted.
- RequireArguments - Class in org.anchoranalysis.experiment.bean.require
-
A predicate on whether all necessary arguments exist for some purpose.
- RequireArguments() - Constructor for class RequireArguments
-
- RequireDebugMode - Class in org.anchoranalysis.experiment.bean.require
-
Require that debug-mode has been enabled.
- RequireDebugMode() - Constructor for class RequireDebugMode
-
- RequireFeatureRelationThreshold - Class in org.anchoranalysis.plugin.mpp.bean.provider.single
-
- RequireFeatureRelationThreshold() - Constructor for class RequireFeatureRelationThreshold
-
- requiresImageMetadata() - Method in class SummarizerImageMetadata
-
- requiresImageMetadata() - Method in class ExtractIdentifier
-
- requiresImageMetadata() - Method in class ExtractIdentifierAndPath
-
- requiresImageMetadata() - Method in class ExtractPath
-
- requiresImageMetadata() - Method in class SummarizerPath
-
- requiresImageMetadata() - Method in class Summarizer
-
- requiresImageMetadata() - Method in class SummarizerAggregate
-
- requiresImageMetadata() - Method in class SummarizerCount
-
- requiresImageMetadata() - Method in class SummarizerListMultiline
-
- requiresImageMetadata() - Method in class SummarizerSplitMoreThan
-
- reset() - Method in class CachedSupplierBase
-
Ensures the object is unevaluated, deleting any cached result if it exists.
- reset() - Method in class RunningSum
-
Reset the sum and count to zero.
- reset() - Method in class RunningSumCollection
-
Resets all items to zero.
- reset() - Method in class Histogram
-
Sets the count for all values to 0.
- reset() - Method in class VoxelizedMarkMemo
-
- reset() - Method in class AggIDCounter
-
- reset() - Method in class Aggregator
-
- reset() - Method in class PeriodTriggerBank
-
- resetInd() - Method in class EnergySavedInd
-
- ResettableCalculation - Interface in org.anchoranalysis.feature.calculate.cache
-
A calculation that be invalidated (resetted), removing any existing cached value.
- resize(VoxelsUntyped, VoxelsUntyped) - Method in class VoxelsResizer
-
Copies voxels slice-by-slice from source
to destination
performing necessary
interpolation.
- resizeByte(VoxelBuffer<UnsignedByteBuffer>, VoxelBuffer<UnsignedByteBuffer>, Extent, Extent) - Method in class VoxelsResizer
-
Interpolates from voxelsSource
to voxelsDestination
for unsigned 8-bit
buffers.
- resizeByte(VoxelBuffer<UnsignedByteBuffer>, VoxelBuffer<UnsignedByteBuffer>, Extent, Extent) - Method in class VoxelsResizerExecutionTime
-
- resizeByte(VoxelBuffer<UnsignedByteBuffer>, VoxelBuffer<UnsignedByteBuffer>, Extent, Extent) - Method in class VoxelsResizerImgLib2
-
- resizeByte(VoxelBuffer<UnsignedByteBuffer>, VoxelBuffer<UnsignedByteBuffer>, Extent, Extent) - Method in class VoxelsResizerNone
-
- resizeByte(VoxelBuffer<UnsignedByteBuffer>, VoxelBuffer<UnsignedByteBuffer>, Extent, Extent) - Method in class VoxelsResizerImageJ
-
- resizeByte(VoxelBuffer<UnsignedByteBuffer>, VoxelBuffer<UnsignedByteBuffer>, Extent, Extent) - Method in class VoxelsResizerOpenCV
-
- resizedXY(int, int, VoxelsResizer) - Method in interface VoxelsExtracter
-
Creates a new voxels that are a resized version of the current voxels (only in X and Y
dimensions), interpolating as needed.
- resizeFloat(VoxelBuffer<FloatBuffer>, VoxelBuffer<FloatBuffer>, Extent, Extent) - Method in class VoxelsResizer
-
Interpolates from voxelsSource
to voxelsDestination
for float buffers.
- resizeFloat(VoxelBuffer<FloatBuffer>, VoxelBuffer<FloatBuffer>, Extent, Extent) - Method in class VoxelsResizerExecutionTime
-
- resizeFloat(VoxelBuffer<FloatBuffer>, VoxelBuffer<FloatBuffer>, Extent, Extent) - Method in class VoxelsResizerImgLib2
-
- resizeFloat(VoxelBuffer<FloatBuffer>, VoxelBuffer<FloatBuffer>, Extent, Extent) - Method in class VoxelsResizerNone
-
- resizeFloat(VoxelBuffer<FloatBuffer>, VoxelBuffer<FloatBuffer>, Extent, Extent) - Method in class VoxelsResizerImageJ
-
- resizeFloat(VoxelBuffer<FloatBuffer>, VoxelBuffer<FloatBuffer>, Extent, Extent) - Method in class VoxelsResizerOpenCV
-
- resizeShort(VoxelBuffer<UnsignedShortBuffer>, VoxelBuffer<UnsignedShortBuffer>, Extent, Extent) - Method in class VoxelsResizer
-
Interpolates from voxelsSource
to voxelsDestination
for unsigned 16-bit
buffers.
- resizeShort(VoxelBuffer<UnsignedShortBuffer>, VoxelBuffer<UnsignedShortBuffer>, Extent, Extent) - Method in class VoxelsResizerExecutionTime
-
- resizeShort(VoxelBuffer<UnsignedShortBuffer>, VoxelBuffer<UnsignedShortBuffer>, Extent, Extent) - Method in class VoxelsResizerImgLib2
-
- resizeShort(VoxelBuffer<UnsignedShortBuffer>, VoxelBuffer<UnsignedShortBuffer>, Extent, Extent) - Method in class VoxelsResizerNone
-
- resizeShort(VoxelBuffer<UnsignedShortBuffer>, VoxelBuffer<UnsignedShortBuffer>, Extent, Extent) - Method in class VoxelsResizerImageJ
-
- resizeShort(VoxelBuffer<UnsignedShortBuffer>, VoxelBuffer<UnsignedShortBuffer>, Extent, Extent) - Method in class VoxelsResizerOpenCV
-
- resizeXY(Extent, VoxelsResizer) - Method in class Channel
-
Resizes the dimensions of the channel, interpolating the existing voxel values to match.
- resizeXY(int, int, VoxelsResizer) - Method in class Channel
-
- resizeXY(int, int) - Method in class Dimensions
-
Resizes the dimensions to have new sizes in the X and Y dimension.
- resolution() - Method in class EnergyStack
-
The image-resolution associated with the energy-stack.
- resolution() - Method in class Channel
-
The resolution of the voxel that describes a physical size for each voxel.
- resolution() - Method in class Dimensions
-
Resolution of voxels to physical measurements.
- resolution(Resolution) - Method in enum OrientationChange
-
A
Resolution
that describes
resolution
after the orientation change.
- Resolution - Class in org.anchoranalysis.image.core.dimensions
-
The resolution of an image.
- Resolution() - Constructor for class Resolution
-
Creates with a default resolution with value 1.0 in each dimension.
- Resolution(double, double, double) - Constructor for class Resolution
-
Creates with a resolution from three double values for each dimension.
- Resolution(Tuple3d) - Constructor for class Resolution
-
Constructs a resolution from a tuple.
- resolution() - Method in class Mask
-
Resolution of voxels to physical measurements.
- resolution() - Method in class DisplayStack
-
Resolution of voxels to physical measurements.
- resolution() - Method in class Stack
-
Resolution of voxels to physical measurements.
- ResolutionAsXml - Class in org.anchoranalysis.plugin.io.xml
-
Reads and writes a metadata XML file specifying the image-resolution.
- ResolutionFixture - Class in org.anchoranalysis.test.image
-
- resolutionRequired() - Method in class MergeBase
-
- resolve(Path, Path) - Static method in class ResolvePathAbsolute
-
- resolve(Optional<UnitConverter>, DirectionVector) - Method in class DistancePhysical
-
- resolve(Optional<UnitConverter>, DirectionVector) - Method in class DistanceVoxels
-
- resolve(Optional<UnitConverter>, Point3d, Point3d) - Method in class UnitValueDistance
-
Resolves the distance using the direction between two points of type
Point3d
.
- resolve(Optional<UnitConverter>, Point3i, Point3i) - Method in class UnitValueDistance
-
Resolves the distance using the direction between two points of type
Point3i
.
- resolve(Optional<UnitConverter>, DirectionVector) - Method in class UnitValueDistance
-
- resolve(String) - Method in class SegmentStackIntoObjectsPooled
-
Resolves a relative filename for a model into a path, relative to the model directory.
- resolve(Optional<Resolution>, boolean) - Method in class Bound
-
- resolveArea(double, Optional<Resolution>) - Method in class FeatureSingleMemoRegion
-
- resolveArea(double, Optional<Resolution>) - Method in class UnitConverter
-
Convert area into another unit representation
- ResolvedBound - Class in org.anchoranalysis.mpp.bean.bound
-
A bound resolved into pixel units
- ResolvedBound(ResolvedBound) - Constructor for class ResolvedBound
-
- ResolvedBound() - Constructor for class ResolvedBound
-
- ResolvedBound(double, double) - Constructor for class ResolvedBound
-
- resolveDistance(double, Optional<Resolution>, DirectionVector) - Method in class UnitConverter
-
Convert distance into another unit representation
- ResolvedPart<S,T extends FeatureInput> - Class in org.anchoranalysis.feature.calculate.cache.part
-
Like a
CalculationPart
but has been resolved against a cache to reuse any existing
identical instance.
- ResolvedPart(CalculationPart<S, T>) - Constructor for class ResolvedPart
-
- ResolvedPartMap<S,T extends FeatureInput,U> - Class in org.anchoranalysis.feature.calculate.cache.part
-
- ResolvedPartMap(CalculationPartMap<S, T, U, FeatureCalculationException>) - Constructor for class ResolvedPartMap
-
Creates with a map.
- resolveFeatureIdentifier(String) - Method in interface FeatureSymbolCalculator
-
- resolveForAxis(Optional<UnitConverter>, Axis) - Method in class UnitValueDistance
-
Resolves the distance in a direction aligned to a particular axis.
- resolveName(String) - Method in class DefineAdderWithPrefixBean
-
Prepends a prefix before the name.
- resolvePath(Path) - Method in class PathPrefixer
-
Converts a relative-path to an absolute-path (relative to the file-path associated with this
current bean)
- resolvePath(String) - Method in class PathPrefixer
-
An absolute path to the prefix
- ResolvePathAbsolute - Class in org.anchoranalysis.core.system.path
-
- resolver() - Method in interface FeatureCalculationInput
-
A resolver for calculations.
- resolver() - Method in class SessionInputSequential
-
- resolveTestPath(String) - Method in class TestLoaderImage
-
- resolveTestPath(String) - Method in class TestLoader
-
Resolves a path to test-data (relative path to the test-data root) to an absolute path on the
file system.
- resolveToVoxels(Optional<UnitConverter>) - Method in class AreaPhysical
-
- resolveToVoxels(Optional<UnitConverter>) - Method in class AreaPixels
-
- resolveToVoxels(Optional<UnitConverter>) - Method in class UnitValueExtent
-
Resolves a measurement of area/volume (in whatever units) to units corresponding to the image
pixels/voxels.
- resolveToVoxels(Optional<UnitConverter>) - Method in class VolumePhysical
-
- resolveToVoxels(Optional<UnitConverter>) - Method in class VolumeVoxels
-
- resolveVolume(double, Optional<Resolution>) - Method in class FeatureSingleMemoRegion
-
- resolveVolume(double, Optional<Resolution>) - Method in class UnitConverter
-
Convert volume into another unit representation
- resources() - Method in class LauncherConfig
-
Config for resources sued by the launcher
- Resources - Class in org.anchoranalysis.launcher.resources
-
Accesses resource-files associated with this application.
- Resources(ClassLoader, String, String, String, String, Optional<String>) - Constructor for class Resources
-
- ResultsVector - Class in org.anchoranalysis.feature.results
-
A vector of results of applying a feature-calculations to many entities.
- ResultsVector(int) - Constructor for class ResultsVector
-
Creates with a particular size.
- ResultsVectorList - Class in org.anchoranalysis.feature.results
-
- ResultsVectorList(ResultsVector) - Constructor for class ResultsVectorList
-
Creates with the list containing a single item.
- ResultsVectorList() - Constructor for class ResultsVectorList
-
- ResultsVectorTestUtilities - Class in org.anchoranalysis.test.feature.plugins
-
- ResultsVectorWithThumbnail - Class in org.anchoranalysis.plugin.image.task.feature
-
A results-vector with an optional thumbnails associated with it.
- ResultsVectorWithThumbnail(CheckedSupplier<ResultsVector, OperationFailedException>) - Constructor for class ResultsVectorWithThumbnail
-
- ResultsVectorWithThumbnail(CheckedSupplier<ResultsVector, OperationFailedException>, CheckedSupplier<Optional<DisplayStack>, OperationFailedException>) - Constructor for class ResultsVectorWithThumbnail
-
- retainAll(Collection<?>) - Method in class UpdatableMarksList
-
- retrieveCreateAggregatedChannel() - Method in class ChannelAggregator
-
Retrieve or create an aggregated-channel of type outputType
.
- retrieveCreateAggregatedChannel() - Method in class ProjectableBufferAggregator
-
- RetrieveDestinationFromDual - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.dual
-
- RetrieveDestinationFromDual() - Constructor for class RetrieveDestinationFromDual
-
- RetrieveDestinationFromVoxelized<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized
-
- RetrieveDestinationFromVoxelized() - Constructor for class RetrieveDestinationFromVoxelized
-
- RetrieveSingleMarkOnly - Class in org.anchoranalysis.plugin.mpp.bean.provider.single
-
Retrieves a mark from a marks, assuming there is only one mark in a marks, otherwise throwing an
exception
- RetrieveSingleMarkOnly() - Constructor for class RetrieveSingleMarkOnly
-
- RetrieveSourceFromDual - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.dual
-
- RetrieveSourceFromDual() - Constructor for class RetrieveSourceFromDual
-
- RetrieveSourceFromVoxelized<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized
-
- RetrieveSourceFromVoxelized() - Constructor for class RetrieveSourceFromVoxelized
-
- reuseByte(Voxels<UnsignedByteBuffer>) - Static method in class BinaryVoxelsFactory
-
- reuseByte(Voxels<UnsignedByteBuffer>, BinaryValuesInt) - Static method in class BinaryVoxelsFactory
-
Reuses an existing voxel-buffer (of type unsigned byte) as a binary-version which should have
only two intensity-values representing off and on.
- reuseInt(Voxels<UnsignedIntBuffer>, BinaryValuesInt) - Static method in class BinaryVoxelsFactory
-
Reuses an existing voxel-buffer (of type unsigned int) as a binary-version which should have
only two intensity-values representing off and on.
- ReuseSingletonStrategy<T extends FeatureInput> - Class in org.anchoranalysis.feature.session.replace
-
- ReuseSingletonStrategy(CacheCreator) - Constructor for class ReuseSingletonStrategy
-
- ReuseSingletonStrategy(CacheCreator, ChildCacheFinder) - Constructor for class ReuseSingletonStrategy
-
- reverse() - Method in class MergeCandidate
-
- reverseIterateArray(T[], CheckedConsumer<T, E>) - Static method in class FunctionalIterate
-
Iterates through every element in an array in reverse order
- rewind() - Method in class UnsignedByteBuffer
-
- rgb(boolean) - Method in class StackWriteAttributes
-
- rgb(boolean, boolean) - Static method in class StackWriteAttributesFactory
-
- RGBChannelNames - Class in org.anchoranalysis.image.core.stack
-
Constants for referring to the channels in a RGB-stack or RGBA-stack.
- RGBColor - Class in org.anchoranalysis.core.color
-
- RGBColor() - Constructor for class RGBColor
-
Create with black color.
- RGBColor(Color) - Constructor for class RGBColor
-
- RGBColor(int) - Constructor for class RGBColor
-
Creates with an RGB value encoded as an int, as in the constructor for
Color
.
- RGBColor(int, int, int) - Constructor for class RGBColor
-
Creates with specific values for the red, green and blue components.
- RGBColorBean - Class in org.anchoranalysis.bean.shared.color
-
- RGBColorBean() - Constructor for class RGBColorBean
-
Creates with a completely black color.
- RGBColorBean(RGBColor) - Constructor for class RGBColorBean
-
- RGBColorBean(Color) - Constructor for class RGBColorBean
-
- RGBColorBean(int, int, int) - Constructor for class RGBColorBean
-
Create from values for red, green and blue.
- RGBIfNamesMatch - Class in org.anchoranalysis.plugin.image.task.bean.format.convertstyle
-
Converts a set of channels to a single RGB-stack if the channel-names match, otherwise uses
fallback
.
- RGBIfNamesMatch() - Constructor for class RGBIfNamesMatch
-
- rgbMaybe3D(boolean) - Static method in class StackWriteAttributesFactory
-
- RGBStack - Class in org.anchoranalysis.image.core.stack
-
A stack with exactly three channels, respectively for red, green and blue
colors.
- RGBStack(Extent) - Constructor for class RGBStack
-
Creates a particularly-sized stack with unsigned byte voxel data type, with all voxels
initialized to 0.
- RGBStack(Extent, Color) - Constructor for class RGBStack
-
Creates a particularly-sized stack with
unsigned byte voxel data type, with all voxels
initialized to a specific
Color
.
- RGBStack(Extent, RGBColor) - Constructor for class RGBStack
-
Creates a particularly-sized stack with
unsigned byte voxel data type, with all voxels
initialized to a specific
RGBColor
.
- RGBStack(Extent, ChannelFactorySingleType) - Constructor for class RGBStack
-
Creates a particularly-sized stack with all channels initialized to 0.
- RGBStack(Dimensions, ChannelFactorySingleType) - Constructor for class RGBStack
-
Creates a particularly-sized stack with all channels initialized to 0.
- RGBStack(Stack) - Constructor for class RGBStack
-
Creates from an existing stack (which must have 1 or 3 channels).
- RGBStack(Channel, Channel, Channel) - Constructor for class RGBStack
-
Create with
Channel
s for each color.
- RIGHT - Static variable in class PositionChoicesConstants
-
Align to the right in the X-dimension/
- rightPad(String, int) - Static method in class StringUtilities
-
Right-pad a string with whitespace, so it reaches a fixed length.
- rightSize() - Method in class OverlappingObjects
-
The total number of objects in the right set.
- rmv(int) - Method in class EnergySavedInd
-
- rmvFromUpdatablePairList(UpdatableMarksList, Mark) - Method in class VoxelizedMarksWithEnergy
-
- rootDirectory(InputContextParameters) - Method in class FilesProvider
-
A root directory for these files, if it exists.
- rootDirectory(InputContextParameters) - Method in class FilesProviderUnary
-
- rootDirectory(InputContextParameters) - Method in class FilesProviderWithDirectory
-
- rootDirectory(InputContextParameters) - Method in class FilesProviderWithoutDirectory
-
- rootDirectory(InputContextParameters) - Method in class SpecificPathList
-
- rootDirectoryPrefix(Optional<String>, PathPrefixerContext) - Method in class PathPrefixer
-
Provides a prefix that becomes the root-folder.
- rootDirectoryPrefix(Optional<String>, PathPrefixerContext) - Method in class PathPrefixerAvoidResolve
-
- rootDirectoryPrefix(Optional<String>, PathPrefixerContext) - Method in class HomeSubdirectory
-
- rootDirectoryPrefix(Optional<String>, PathPrefixerContext) - Method in class Rooted
-
- rootDirectoryPrefix(Optional<String>, PathPrefixerContext) - Method in class ExperimentStructure
-
- rootDirectoryPrefixAvoidResolve(Optional<String>) - Method in class PathPrefixerAvoidResolve
-
Provides a prefix that becomes the root-folder.
- Rooted - Class in org.anchoranalysis.plugin.io.bean.file.path.prefixer
-
Prepend a 'root' before the file-path-prefix obtained from a delegate
- Rooted() - Constructor for class Rooted
-
- Rooted(PathPrefixerAvoidResolve, String) - Constructor for class Rooted
-
- Rooted - Class in org.anchoranalysis.plugin.io.bean.file.provider
-
Represents a set of files, with a different path-root depending on context.
- Rooted() - Constructor for class Rooted
-
- Rooted - Class in org.anchoranalysis.plugin.io.bean.path.derive
-
- Rooted() - Constructor for class Rooted
-
- RootedExperiment - Class in org.anchoranalysis.plugin.quick.bean.structure
-
- RootedExperiment() - Constructor for class RootedExperiment
-
- RootedFilePath - Class in org.anchoranalysis.plugin.io.bean.file.path
-
- RootedFilePath() - Constructor for class RootedFilePath
-
- RootedFilePathUtilities - Class in org.anchoranalysis.plugin.io.input.path
-
- RootPath - Class in org.anchoranalysis.bean.shared.path
-
Defines a root path.
- RootPath() - Constructor for class RootPath
-
- RootPathMap - Class in org.anchoranalysis.plugin.io.input.path
-
A collection of root-paths indexed by their name.
- RotatableBoundingBox - Class in org.anchoranalysis.mpp.mark.points
-
A two-dimensional bounding-box rotated at arbitrary angle in XY plane around a point.
- RotatableBoundingBox() - Constructor for class RotatableBoundingBox
-
- RotatableBoundingBoxFactory - Class in org.anchoranalysis.mpp.mark.points
-
- RotateImageToMatchEXIFOrientation - Class in org.anchoranalysis.plugin.io.bean.stack.reader
-
Rotates an image to match any EXIF orientation information, if it exists.
- RotateImageToMatchEXIFOrientation() - Constructor for class RotateImageToMatchEXIFOrientation
-
- RotateImageToMatchEXIFOrientation(StackReaderOrientationCorrection) - Constructor for class RotateImageToMatchEXIFOrientation
-
- rotatePoint(Tuple3d) - Method in class RotationMatrix
-
Performs a rotation on a single point, encoded as a
Point3d
.
- rotatePointInplace(Point3d) - Method in class RotationMatrix
-
Performs a rotation on a single point, replacing the existing value of the point.
- RotationMatrix - Class in org.anchoranalysis.spatial.orientation
-
A
matrix that performs a rotation in
Euclidean space.
- RotationMatrix(int) - Constructor for class RotationMatrix
-
Creates a rotation-matrix populated only with zeros.
- RotationMatrix(DoubleMatrix2D) - Constructor for class RotationMatrix
-
Creates a rotation-matrix from an existing DoubleMatrix2D
.
- RowLabels - Class in org.anchoranalysis.feature.io.csv.metadata
-
Labels for each row of feature-results in the outputted CSV row.
- RowLabels(String) - Constructor for class RowLabels
-
Creates with a single string as an identifier.
- RowLabels(Optional<String[]>, Optional<MultiName>) - Constructor for class RowLabels
-
- RTree<T> - Class in org.anchoranalysis.spatial.rtree
-
Bases class for implementations of R-Trees that store objects with associated geometry.
- RTree(int) - Constructor for class RTree
-
Creates an empty R-Tree.
- RTree(int, int) - Constructor for class RTree
-
Creates an empty R-Tree with a specified number of children.
- run() - Method in interface CheckedRunnable
-
- runCommandLineApplication(String[], LauncherConfig, Logger) - Static method in class Launch
-
Runs a command-line application, by parsing arguments, and then executing an experiment.
- runExperiment(String) - Method in class ExperimentLauncherFromShell
-
Runs an experiment identified by an XML found in the resources
- runExperiment(String, Optional<String>, Optional<String>) - Method in class ExperimentLauncherFromShell
-
Runs an experiment identified by an XML found in the resources
- runExperimentInTemporaryDirectory(String, Path) - Method in class ExperimentLauncherFromShell
-
Creates a temporary-folder, copies data all data from the associated test-loader, and runs an
experiment
- runExperimentInTemporaryDirectory(String, Optional<String>, Optional<String>, Path, String[]) - Method in class ExperimentLauncherFromShell
-
Creates a temporary-folder, copies data all data from the associated test-loader, and runs an
experiment
- RunningSum - Class in org.anchoranalysis.math.arithmetic
-
Mutable class that allows for incrementing jointly sum and count variables, so as to eventually
calculate the mean.
- RunningSum() - Constructor for class RunningSum
-
- RunningSum(double, long) - Constructor for class RunningSum
-
- RunningSumCollection - Class in org.anchoranalysis.math.arithmetic
-
A collection of
RunningSum
where an operation is executed on all objects in the
collection.
- RunningSumCollection(int) - Constructor for class RunningSumCollection
-
Constructor.
- RunningSumExtrema - Class in org.anchoranalysis.math.arithmetic
-
Like a
RunningSum
but also remembers the
mean and
max across all the added
values.
- RunningSumExtrema() - Constructor for class RunningSumExtrema
-
- RunningSumParented - Class in org.anchoranalysis.experiment.time
-
Wraps a
RunningSum
with an additional variable, indicating the total number of parent
operations.
- RunningSumParented(int) - Constructor for class RunningSumParented
-
- RunningSumPoint - Class in org.anchoranalysis.spatial.point
-
A running sum for tracking points separately in each dimension.
- RunningSumPoint() - Constructor for class RunningSumPoint
-
- sampleDoubleFromRange(double) - Method in interface RandomNumberGenerator
-
Generates a uniformly random floating-point number within a range from 0
(exclusive) to endExclusive
.
- sampleDoubleFromRange(double, double) - Method in interface RandomNumberGenerator
-
Generates a uniformly random floating-point number within a range.
- sampleDoubleFromZeroCenteredRange(double) - Method in interface RandomNumberGenerator
-
Generates a uniformly random floating-point number centered around 0
ranging from
[-halfWidth,+halfWidth]
(both exclusive).
- sampleDoubleZeroAndOne() - Method in interface RandomNumberGenerator
-
Samples from a uniformly-distributed range between 0.0 (exclusive) and 1.0
(exclusive).
- sampleDoubleZeroAndOne() - Method in class RandomNumberGeneratorMersenne
-
- sampleFromAvailable(int) - Method in class PartitionedMarks
-
Samples from the available marks
- sampleFromList(List<T>) - Method in interface RandomNumberGenerator
-
Samples uniformly an element from a list.
- sampleInteger(int) - Method in class ProposerContext
-
Samples an integer uniformally between [0..maxVal)
- sampleIntFromRange(int) - Method in interface RandomNumberGenerator
-
Generates a uniformly random discrete number within a range from 0 (inclusive) to
endExclusive
.
- sampleIntFromRange(int, int) - Method in interface RandomNumberGenerator
-
Samples from a uniformly random discrete number within a range.
- sampleLongFromRange(long) - Method in interface RandomNumberGenerator
-
Generates a uniformly random discrete number within a range from 0 (inclusive) to
endExclusive
.
- sampleRandomPairNonUniform(RandomNumberGenerator) - Method in class RandomCollectionWithAddCriteria
-
- sampleRandomPairNonUniform(RandomNumberGenerator) - Method in class RandomCollection
-
- SampleWithDirectory - Class in org.anchoranalysis.plugin.io.bean.file.provider
-
- SampleWithDirectory() - Constructor for class SampleWithDirectory
-
- SavedFiles - Class in org.anchoranalysis.test.image.stackwriter
-
Access previously saved-files in resources.
- ScalarProposer - Class in org.anchoranalysis.mpp.bean.proposer
-
- ScalarProposer() - Constructor for class ScalarProposer
-
- ScalarThreeDimensionalConsumer - Interface in org.anchoranalysis.spatial.point.consumer
-
Like a
IntConsumer
but accepts three coordinates of a point as scalar arguments.
- ScalarTwoDimensionalConsumer - Interface in org.anchoranalysis.spatial.point.consumer
-
Like a
IntConsumer
but accepts two coordinates of a point as scalar arguments.
- scale(ScaleFactor, VoxelsResizer, Optional<Extent>) - Method in class BoundedVoxels
-
Creates a scaled-version (in XY dimensions only) of the current bounding-box.
- scale(ScaleFactor) - Method in class ObjectMask
-
Produces a scaled-version of an object-mask.
- scale(ScaleFactor, Optional<Extent>) - Method in class ObjectMask
-
Produces a scaled-version of an object-mask.
- scale(double) - Method in class Bound
-
- scale(double) - Method in class BoundMinMax
-
- scale(double) - Method in class ResolvedBound
-
- scale(ScaleFactor) - Method in class Ellipse
-
- scale(ScaleFactor) - Method in class Ellipsoid
-
- scale(ScaleFactor) - Method in class MarkWithPositionAndSingleRadius
-
Objects are scaled in pre-rotated position.
- scale(ScaleFactor) - Method in class Mark
-
Scales the mark in X and Y dimensions.
- scale(ScaleFactor) - Method in class MarkWithPosition
-
- scale(ScaleFactor) - Method in class LineSegment
-
- scale(ScaleFactor) - Method in class PointList
-
- scale(ScaleFactor) - Method in class Polygon
-
- scale(ScaleFactor) - Method in class PolygonCurve
-
- scale(ScaleFactor) - Method in class RotatableBoundingBox
-
- Scale - Class in org.anchoranalysis.plugin.image.bean.object.provider
-
Scales all the objects in the collection by a particular scale-factor.
- Scale() - Constructor for class Scale
-
- Scale - Class in org.anchoranalysis.plugin.mpp.bean.proposer.scalar
-
- Scale() - Constructor for class Scale
-
- scale(ScaleFactor) - Method in class BoundingBox
-
Scales the bounding-box, both the corner-point and the extent.
- scale(ScaleFactor, Extent) - Method in class BoundingBox
-
Scales the bounding-box corner-point, and assigns a new extent.
- scale(double) - Method in class Point2d
-
Arithmetically multiplies each dimension's value by a factor.
- scale(double) - Method in class Point2f
-
Multiplies each dimension's component by a factor.
- scale(double) - Method in class Tuple3d
-
Arithmetically multiply values across each dimension.
- scale(int) - Method in class Tuple3i
-
Arithmetically multiplies by a value across each dimension.
- scale(double) - Method in class Tuple3i
-
Arithmetically multiplies by a value across each dimension.
- scale(Point3d) - Method in class ScaleFactor
-
Multiplies a
Point3d
by the respective scaling-factor in each X and Y dimensions.
- scale(int, int) - Method in class ScaleFactorInt
-
Multiplies a point by the respective scaling-factor in each dimension.
- scale(Point2i) - Method in class ScaleFactorInt
-
Multiplies a
Point2i
by the respective scaling-factor in each dimension.
- scale(Extent) - Method in class ScaleFactorInt
-
Multiplies an
Extent
by the respective scaling-factor in each dimension.
- scale(ScaleFactor, Point3i) - Static method in class Scaler
-
Scales a point in XY by multiplying each dimension by its corresponding scaling-factor.
- ScaleableBackground - Class in org.anchoranalysis.image.io.stack.output.box
-
A stack that can be used as a background (and maybe scaled).
- scaleAndThreshold(Voxels<FloatBuffer>, Extent, VoxelsResizer, float) - Static method in class ScaleAndThresholdVoxels
-
Scales voxels representing a mask to a target size, and then thresholds.
- ScaleAndThresholdVoxels - Class in org.anchoranalysis.image.inference.segment
-
Scales the size of a Voxels<FloatBuffer>
and then thresholds it.
- scaleBy(DisplayStack, ScaleFactor, VoxelsResizer) - Static method in class ScaleableBackground
-
Creates a background from a stack with scaling.
- ScaleByDictionary - Class in org.anchoranalysis.plugin.image.bean.channel.convert
-
Scales by compressing a certain range of values into the 8-bit signal.
- ScaleByDictionary() - Constructor for class ScaleByDictionary
-
- ScaleByMinMaxValue - Class in org.anchoranalysis.plugin.image.bean.channel.convert
-
Scales by compressing a certain range of values into the 8-bit signal
- ScaleByMinMaxValue() - Constructor for class ScaleByMinMaxValue
-
- ScaleByTypeToByte - Class in org.anchoranalysis.plugin.image.bean.channel.convert
-
- ScaleByTypeToByte() - Constructor for class ScaleByTypeToByte
-
- ScaleCalculator - Class in org.anchoranalysis.image.bean.spatial
-
Calculating a scaling-factor from dimensions.
- ScaleCalculator() - Constructor for class ScaleCalculator
-
- scaleCalculator - Variable in class ScaleImage
-
Calculates what scale-factor to apply on the image.
- scaleCeil(ScaleFactor, Point3i) - Static method in class Scaler
-
Scales a point in XY by multiplying each dimension by its corresponding scaling-factor.
- scaleCeil(double, int) - Static method in class Scaler
-
Multiplies a quantity (integer) by a scaling-factor, returning it as an integer via
ceil.
- scaleClampTo(ScaleFactor, Extent) - Method in class BoundingBox
-
Scales the bounding-box, both the corner-point and the extent - ensuring it remains inside a
containing-extent.
- ScaledElements<T> - Class in org.anchoranalysis.image.core.object.scale
-
A list of elements, with an
ObjectMask
representation, that have been scaled.
- ScaledElements(List<T>, ScaleFactor, ObjectScalingMethod, Optional<UnaryOperator<T>>, Optional<UnaryOperator<T>>, AccessObjectMask<T>) - Constructor for class ScaledElements
-
Creates elements to be scaled.
- scaledObjectFor(T) - Method in class ScaledElements
-
Gets the scaled version of an element given the unscaled element.
- scaleElements(List<T>, ScaleFactor, AccessObjectMask<T>) - Method in interface ObjectScalingMethod
-
Applies a scaling factor to elements, where each element is associated with a unique
ObjectMask
.
- scaleElements(List<T>, ScaleFactor, Optional<UnaryOperator<T>>, Optional<UnaryOperator<T>>, AccessObjectMask<T>) - Method in interface ObjectScalingMethod
-
Applies a scaling factor to elements, where each element is associated with a unique
ObjectMask
.
- scaleElements(List<T>, ScaleFactor, boolean, Extent, AccessObjectMask<T>) - Static method in class Scaler
-
Scales every element in a list collectively, ensuring the results remain inside a particular
region.
- ScaleFactor - Class in org.anchoranalysis.spatial.scale
-
What to scale X and Y dimensions by.
- ScaleFactor(double) - Constructor for class ScaleFactor
-
Create with an identical scaling-factor for all dimensions.
- ScaleFactor(double, double) - Constructor for class ScaleFactor
-
Create with specific scaling-factors for each dimension.
- ScaleFactorInt - Class in org.anchoranalysis.spatial.scale
-
Like
ScaleFactor
but only allows integer scaling-factors in each dimension.
- ScaleFactorInt(int, int) - Constructor for class ScaleFactorInt
-
- scaleFactorUpscale() - Method in class ImageInferenceContext
-
The scaling-factors needed to upscale the model output to match the desired scale.
- scaleFloor(double, int) - Static method in class Scaler
-
Multiplies a quantity (integer) by a scaling-factor, returning it as an integer via
floor.
- ScaleImage<S> - Class in org.anchoranalysis.plugin.image.task.bean.scale
-
Base class for tasks whose primary aim is to scale (resize) an image.
- ScaleImage() - Constructor for class ScaleImage
-
- ScaleImageCommonSize - Class in org.anchoranalysis.plugin.image.task.bean.scale
-
Creates a scaled copy of images, ensuring all images have identical output size.
- ScaleImageCommonSize() - Constructor for class ScaleImageCommonSize
-
- ScaleImageIndependently - Class in org.anchoranalysis.plugin.image.task.bean.scale
-
Creates a scaled copy of images, treating each image independently, and without any padding or
alignment.
- ScaleImageIndependently() - Constructor for class ScaleImageIndependently
-
- scaleMultiplex(double, int, boolean) - Static method in class Scaler
-
- scaleObjects(ObjectCollection, ScaleFactor) - Static method in class Scaler
-
Scales every object-mask in a collection collectively.
- scaleObjects(ObjectCollection, ScaleFactor, boolean, Extent) - Static method in class Scaler
-
Scales every object-mask in a collection collectively, ensuring the results remain
inside a particular region.
- scaleObjects(ObjectCollection, ScaleFactor, boolean, Optional<UnaryOperator<ObjectMask>>, Optional<UnaryOperator<ObjectMask>>) - Static method in class Scaler
-
Scales every object-mask in a collection collectively (if not overlappjng), allowing
for additional manipulation before and after scaling.
- Scaler - Class in org.anchoranalysis.image.core.object.scale
-
Scales object-masks (or other more generic elements) collectively to avoid undesired overlap.
- Scaler - Class in org.anchoranalysis.spatial.scale
-
- scaleRadii(double) - Method in class Ellipse
-
- scaleRound(double, int) - Static method in class Scaler
-
Multiplies a quantity (integer) by a scaling-factor, returning it as an integer via
rounding.
- scaleStack(Stack, Optional<ImageSizeSuggestion>, VoxelsResizer, S) - Method in class ScaleImage
-
Produce a scaled version of a
Stack
, mapping each channel to a scaled version of
itself.
- scaleStack(Stack, Optional<ImageSizeSuggestion>, VoxelsResizer, CommonSize) - Method in class ScaleImageCommonSize
-
- scaleStack(Stack, Optional<ImageSizeSuggestion>, VoxelsResizer, NoSharedState) - Method in class ScaleImageIndependently
-
- scaleToMatchRow(double, int) - Method in class ExtentToArrange
-
Changes the size of the image to match a row that has a total width of rowWidth
,
preserving aspect-ratio.
- ScaleToSize - Class in org.anchoranalysis.plugin.image.bean.thumbnail.stack
-
Create a thumbnail by scales an image to a particular size.
- ScaleToSize() - Constructor for class ScaleToSize
-
- scaleToWidth(List<List<ExtentToArrange>>, boolean, int) - Static method in class FitCombinedScaler
-
Calculates the size of the combined image to use for the montage, and scales the associated
Extent
each to match.
- scaleX(double) - Method in class Tuple3i
-
Arithmetically multiplies the X-axis component by a value.
- scaleXY(ScaleFactor) - Method in class DualMarksAnnotation
-
Scales the marks in the annotation in X and Y dimensions.
- scaleXY(ScaleFactor, VoxelsResizer) - Method in class Channel
-
Resizes the dimensions of the channel, by scaling the existing size by a factor.
- scaleXY(ScaleFactor) - Method in class Resolution
-
Multiplies the X and Y components of the resolution by a factor.
- scaleXY(ScaleFactor) - Method in class Mask
-
Creates a new
Mask
whose X- and Y- dimensions are scaled by
scaleFactor
.
- scaleXY(ScaleFactor) - Method in class MarkCollection
-
Scales the mark in X and Y dimensions.
- ScaleXY - Class in org.anchoranalysis.plugin.image.bean.channel.provider.intensity
-
Scales the channel in the X and Y dimensions.
- ScaleXY() - Constructor for class ScaleXY
-
- ScaleXY - Class in org.anchoranalysis.plugin.image.bean.mask.provider
-
Scales the mask in XY dimensions, but not in Z dimension.
- ScaleXY() - Constructor for class ScaleXY
-
- ScaleXY - Class in org.anchoranalysis.plugin.mpp.bean.provider.collection
-
- ScaleXY() - Constructor for class ScaleXY
-
- scaleXY(double) - Method in class Tuple3d
-
Arithmetically multiply values by a factor only in X and Y dimensions.
- scaleXY(double) - Method in class Tuple3i
-
Arithmetically multiplies the X- and Y-axis components by a value.
- scaleXYBy(ScaleFactor) - Method in class Dimensions
-
Scales the X- and Y- dimensions by a scaling-factor.
- scaleXYBy(ScaleFactor) - Method in class SizeMapping
-
Scales the XY dimensions the factor.
- scaleXYBy(ScaleFactor, boolean) - Method in class Extent
-
Scales the X- and Y- dimensions by a scaling-factor.
- scaleXYBy(double, boolean) - Method in class Extent
-
Scales all dimensions by a scaling-factor.
- scaleY(double) - Method in class Tuple3i
-
Arithmetically multiplies the Y-axis component by a value.
- scaling - Variable in class ToUnsignedByteWithScaling
-
- sceneContains(Point2i) - Static method in class CircleObjectFixture
-
- ScoreObjects - Class in org.anchoranalysis.plugin.image.bean.channel.provider.score
-
- ScoreObjects() - Constructor for class ScoreObjects
-
- ScoreVoxels - Class in org.anchoranalysis.plugin.image.bean.channel.provider.score
-
Assigns a score (a value indicating how probable something is) to each voxel
- ScoreVoxels() - Constructor for class ScoreVoxels
-
- search(CalculationPart<S, T>) - Method in interface CalculationPartResolver
-
Searches for an equivalent calculation to calculation
.
- search(CalculationPartMap<S, T, U, FeatureCalculationException>) - Method in interface CalculationPartResolver
-
Searches for an equivalent calculation to calculation
.
- SearchClosestValueMonoticallyIncreasing - Class in org.anchoranalysis.math.optimization
-
Given a
monotonically
increasing function of an integer, determine the input value that provides an output value as
close to
target
as possible.
- SearchClosestValueMonoticallyIncreasing(double, SearchClosestValueMonoticallyIncreasing.ValueFunction) - Constructor for class SearchClosestValueMonoticallyIncreasing
-
Create without an upper bound.
- SearchClosestValueMonoticallyIncreasing(double, SearchClosestValueMonoticallyIncreasing.ValueFunction, IntPredicate) - Constructor for class SearchClosestValueMonoticallyIncreasing
-
- SearchClosestValueMonoticallyIncreasing.ValueFunction - Interface in org.anchoranalysis.math.optimization
-
The function that calculates the output value for a particular input int
.
- SearchDirectory - Class in org.anchoranalysis.io.input.bean.files
-
Searches a directory for files whose paths match a particular predicate.
- SearchDirectory(String) - Constructor for class SearchDirectory
-
Create for a specific directory.
- SearchDirectory() - Constructor for class SearchDirectory
-
- Second - Class in org.anchoranalysis.image.feature.bean.object.pair
-
Evaluates the first-object in a pair only
- Second(Feature<FeatureInputSingleObject>) - Constructor for class Second
-
- Second() - Constructor for class Second
-
- second(String) - Method in class MultiLevelBinary
-
- second(String) - Method in class MultiLevelNot
-
- second(String) - Method in interface MultiLevelOutputEnabled
-
A second-level of
OutputEnabled
for a particular
outputName
as used in
first-level.
- second(String) - Method in class OutputEnabledMutable
-
- second(String) - Method in class MultiLevelRecordedOutputs
-
A
RecordedOutputs
for recording second-level outputs for a given
outputName
from the first-level.
- secondaryReport() - Method in class StateReporter
-
- secondaryReport() - Method in class StateReporterIdentity
-
- secondaryReport() - Method in class StateReporterToPixelized
-
- secondaryReport() - Method in class StateReporterTransformer
-
- secondEntries() - Method in class MultiLevelRecordedOutputs
-
All second-level recorded output entries.
- secondLevel(String) - Method in class RecordingWriters
-
A writer that performs a second-level check on which outputs occur, but writes to the
top-level directory.
- secondLevelOutputs(String, OutputEnabled) - Method in class OutputEnableRulesSpecify
-
- secondPart() - Method in class CombinedName
-
- secondPart() - Method in interface MultiName
-
The second part of the name.
- secondPart() - Method in class SimpleName
-
- seek(int) - Method in class SlidingBuffer
-
Moves buffer to a particular z-slice.
- segment(VoxelsUntyped, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class BinarySegmentation
-
Performs a segmentation on voxels so that each voxel has an on or off state
after the operation.
- segment(VoxelsUntyped, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class BinarySegmentationReference
-
- segment(VoxelsUntyped, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class BinarySegmentationThreshold
-
- segment(VoxelsUntyped, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class BinarySegmentationUnary
-
- segment(Channel, Optional<ObjectMask>, Optional<ObjectCollection>) - Method in class SegmentChannelIntoObjects
-
Segments a channel to produce an object-collection.
- segment(Channel, Optional<ObjectMask>, Optional<ObjectCollection>) - Method in class SegmentChannelIntoObjectsUnary
-
- segment(Channel, Optional<ObjectMask>, Optional<ObjectCollection>, SegmentChannelIntoObjects) - Method in class SegmentChannelIntoObjectsUnary
-
Creates an
ObjectCollection
given the segmentation-results provided by the delegate.
- segment(Stack, ExecutionTimeRecorder) - Method in class SegmentStackIntoObjectsPooled
-
Segments individually using a pool of size 1 just for one stack.
- segment(Stack, ConcurrentModelPool<T>, ExecutionTimeRecorder) - Method in class SegmentStackIntoObjectsPooled
-
Segments a stack to produce an object-collection.
- segment(Stack, ConcurrentModelPool<S>, ExecutionTimeRecorder) - Method in class SegmentStackIntoObjectsScaleDecode
-
- segment(Stack, ConcurrentModelPool<T>, ExecutionTimeRecorder) - Method in class SuppressNonMaximum
-
- segment(SharedObjects, Optional<Dictionary>, InputOutputContext) - Method in class SegmentIntoMarks
-
- segment(Channel, Optional<ObjectMask>, Optional<ObjectCollection>, SegmentChannelIntoObjects) - Method in class AtScale
-
- segment(Channel, Optional<ObjectMask>, Optional<ObjectCollection>) - Method in class ConnectedComponentsFromBinarySegmentation
-
- segment(Channel, Optional<ObjectMask>, Optional<ObjectCollection>, SegmentChannelIntoObjects) - Method in class Filter
-
- segment(Channel, Optional<ObjectMask>, Optional<ObjectCollection>, SegmentChannelIntoObjects) - Method in class ImposeMinima
-
- segment(Channel, Optional<ObjectMask>, Optional<ObjectCollection>) - Method in class Mser
-
- segment(Channel, Optional<ObjectMask>, Optional<ObjectCollection>, SegmentChannelIntoObjects) - Method in class SegmentOnMaximumIntensityAndExpandInZ
-
- segment(Channel, Optional<ObjectMask>, Optional<ObjectCollection>) - Method in class WatershedYeong
-
- segment(VoxelsUntyped, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class Sequence
-
- segment(VoxelsUntyped, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class ThresholdAgainstChannel
-
- segment(Channel, Optional<ObjectMask>, Optional<ObjectCollection>) - Method in class FloodFillEachIntensityLevel
-
- segment(VoxelsUntyped, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class SegmentThresholdAboveMinBound
-
- segment(SharedObjects, Optional<Dictionary>, InputOutputContext) - Method in class SegmentWithMarkedPointProcess
-
- segmentAll(Voxels<?>, Voxels<?>, Voxels<UnsignedByteBuffer>) - Method in class SliceThresholder
-
- segmentAll(Voxels<?>, Voxels<?>, Voxels<UnsignedByteBuffer>) - Method in class SliceThresholderMask
-
- segmentAll(Voxels<?>, Voxels<?>, Voxels<UnsignedByteBuffer>) - Method in class SliceThresholderWithoutMask
-
- SegmentationBean<T> - Class in org.anchoranalysis.image.bean.segment
-
Performs some kind of segmentation on an image.
- SegmentationBean() - Constructor for class SegmentationBean
-
- SegmentationFailedException - Exception in org.anchoranalysis.image.bean.nonbean.segment
-
When a segmentation cannot successfully complete.
- SegmentationFailedException(String) - Constructor for exception SegmentationFailedException
-
Create with a message only.
- SegmentationFailedException(Throwable) - Constructor for exception SegmentationFailedException
-
Create with a cause only.
- SegmentationFailedException(String, Throwable) - Constructor for exception SegmentationFailedException
-
Create with a message and a cause.
- SegmentChannel - Class in org.anchoranalysis.plugin.image.bean.mask.provider.segment
-
- SegmentChannel() - Constructor for class SegmentChannel
-
- SegmentChannel - Class in org.anchoranalysis.plugin.image.bean.object.provider.segment
-
- SegmentChannel() - Constructor for class SegmentChannel
-
- SegmentChannelByObject - Class in org.anchoranalysis.plugin.image.bean.object.provider.segment
-
Performs segmentation of a channel using each object in the upstream collection as a mask.
- SegmentChannelByObject() - Constructor for class SegmentChannelByObject
-
- SegmentChannelIntoObjects - Class in org.anchoranalysis.image.bean.segment.object
-
A base class for algorithms to segment a channel into one or more objects.
- SegmentChannelIntoObjects() - Constructor for class SegmentChannelIntoObjects
-
- SegmentChannelIntoObjectsUnary - Class in org.anchoranalysis.image.bean.segment.object
-
- SegmentChannelIntoObjectsUnary() - Constructor for class SegmentChannelIntoObjectsUnary
-
- SegmentedBackground - Class in org.anchoranalysis.image.inference.segment
-
The background to a segmentation.
- SegmentedBackground(DualScale<Stack>, StackDisplayer) - Constructor for class SegmentedBackground
-
- SegmentedObjects - Class in org.anchoranalysis.image.inference.segment
-
Objects that are a result of an instance-segmentation.
- SegmentedObjects(String, Collection<WithConfidence<MultiScaleObject>>, SegmentedBackground, ExecutionTimeRecorder) - Constructor for class SegmentedObjects
-
Create for a collection of objects with an identical label.
- SegmentedObjects(List<LabelledWithConfidence<MultiScaleObject>>, SegmentedBackground, ExecutionTimeRecorder) - Constructor for class SegmentedObjects
-
Create for a collection of objects with potentially differing labels.
- SegmentedObjectsAtScale - Class in org.anchoranalysis.image.inference.segment
-
Exposes a particular set of segmented-objects at a particular scale.
- SegmentedObjectsAtScale(List<LabelledWithConfidence<MultiScaleObject>>, Function<MultiScaleObject, ObjectMask>, Stack, StackDisplayer, ExecutionTimeRecorder, String) - Constructor for class SegmentedObjectsAtScale
-
- segmentFromExistingSegmentation(VoxelsUntyped, BinarySegmentationParameters, Optional<ObjectMask>, BinarySegmentation) - Method in class BinarySegmentationUnary
-
- segmentFromExistingSegmentation(VoxelsUntyped, BinarySegmentationParameters, Optional<ObjectMask>, BinarySegmentation) - Method in class Invert
-
- segmentFromExistingSegmentation(VoxelsUntyped, BinarySegmentationParameters, Optional<ObjectMask>, BinarySegmentation) - Method in class Repeat
-
- SegmentInstanceWithModel<T extends InferenceModel> - Class in org.anchoranalysis.plugin.image.task.bean.segment
-
Using a model-pool, performs instance segmentation on an image producing zero, one or more
objects per image.
- SegmentInstanceWithModel() - Constructor for class SegmentInstanceWithModel
-
- SegmentIntoMarks - Class in org.anchoranalysis.mpp.segment.bean
-
- SegmentIntoMarks() - Constructor for class SegmentIntoMarks
-
- SegmentMarksFromImage - Class in org.anchoranalysis.plugin.mpp.experiment.bean.segment
-
Segments an image into a collection of
Mark
s.
- SegmentMarksFromImage() - Constructor for class SegmentMarksFromImage
-
- SegmentMarksState - Class in org.anchoranalysis.plugin.mpp.segment.shared
-
State that only needs to be initialized once can be shared across many calls to the algorithm.
- SegmentMarksState(KernelProposer<VoxelizedMarksWithEnergy, UpdatableMarksList>, Define) - Constructor for class SegmentMarksState
-
- SegmentObjectsFromONNXModel - Class in org.anchoranalysis.plugin.onnx.bean.object.segment.stack
-
Performs instance-segmentation using the ONNX Runtime and an .onnx
model file.
- SegmentObjectsFromONNXModel() - Constructor for class SegmentObjectsFromONNXModel
-
- SegmentObjectsFromTensorFlowModel - Class in org.anchoranalysis.plugin.opencv.bean.object.segment.stack
-
Performs instance-segmentation using OpenCV's DNN module and a TensorFlow
.pb
SavedModel file.
- SegmentObjectsFromTensorFlowModel() - Constructor for class SegmentObjectsFromTensorFlowModel
-
- SegmentOnMaximumIntensityAndExpandInZ - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel
-
Perform a segmentation in a MIP instead of z-stacks, and fits the result back into a 3D
segmentation.
- SegmentOnMaximumIntensityAndExpandInZ() - Constructor for class SegmentOnMaximumIntensityAndExpandInZ
-
- SegmentStack<T extends InferenceModel> - Class in org.anchoranalysis.plugin.image.bean.object.provider.segment
-
Segments a stack into objects.
- SegmentStack() - Constructor for class SegmentStack
-
- SegmentStackIntoObjectsPooled<T extends InferenceModel> - Class in org.anchoranalysis.image.inference.bean.segment.instance
-
A base class for algorithms to segment a stack into one or more objects - using a pool of models
- SegmentStackIntoObjectsPooled() - Constructor for class SegmentStackIntoObjectsPooled
-
- SegmentStackIntoObjectsScaleDecode<T,S extends ImageInferenceModel<T>> - Class in org.anchoranalysis.image.inference.bean.segment.instance
-
- SegmentStackIntoObjectsScaleDecode() - Constructor for class SegmentStackIntoObjectsScaleDecode
-
- SegmentThresholdAboveMinBound - Class in org.anchoranalysis.plugin.mpp.bean.segment.binary
-
- SegmentThresholdAboveMinBound() - Constructor for class SegmentThresholdAboveMinBound
-
- SegmentWithMarkedPointProcess - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks
-
- SegmentWithMarkedPointProcess() - Constructor for class SegmentWithMarkedPointProcess
-
- SegmentWithSeeds - Class in org.anchoranalysis.plugin.image.bean.object.provider.segment
-
Takes each object one-by-one from objectsSource
, and finds matching seeds from objectsSeeds
- SegmentWithSeeds() - Constructor for class SegmentWithSeeds
-
- select(ExecutionArguments) - Method in interface SelectParam
-
Retrieves the parameter.
- select(ExecutionArguments) - Method in class UseDefaultManager
-
- selectChannels(ChannelSource, boolean) - Method in class All
-
- selectChannels(ChannelSource, boolean) - Method in class FromStacks
-
Takes a stack-collection and extracts a set of references to particular channels (each with a
name)
- selectChannels(ChannelSource, boolean) - Method in class One
-
- selectChannels(ChannelSource, boolean) - Method in class SpecificAndRename
-
- selectDelegate(StackWriteOptions) - Method in class BranchChannels
-
- selectDelegate(StackWriteOptions) - Method in class BranchStack
-
- selectDelegate(StackWriteOptions) - Method in class BranchSuggestedFormat
-
- selectDelegate(StackWriteOptions) - Method in class StackWriterDelegateBase
-
- selectDerivePath() - Method in class FromDerivePath
-
- selectDerivePath() - Method in class RemoveLastElement
-
- selectFileExtension(OutputWriteSettings, Optional<Logger>) - Method in class HDF5ObjectsGenerator
-
- selectFileExtension(Stack, StackWriteOptions, OutputWriteSettings, Optional<Logger>) - Method in class RasterGenerator
-
Selects the file-extension to use for a particular stack.
- selectFileExtension(Stack, StackWriteOptions, OutputWriteSettings, Optional<Logger>) - Method in class RasterGeneratorSelectFormat
-
Combines stack-write-options derived for a particular stack with the general write-options
associated with the
RasterGenerator
.
- selectFileExtension(OutputWriteSettings, Optional<Logger>) - Method in class DictionaryGenerator
-
- selectFileExtension(OutputWriteSettings, Optional<Logger>) - Method in class SerializedGenerator
-
- selectFileExtension(OutputWriteSettings, Optional<Logger>) - Method in class SingleFileTypeGenerator
-
Selects the file/extension to be used for outputting the file.
- selectFileExtension(OutputWriteSettings, Optional<Logger>) - Method in class SingleFileTypeGeneratorBridge
-
- selectFileExtension(OutputWriteSettings, Optional<Logger>) - Method in class CSVGenerator
-
- selectFileExtension(OutputWriteSettings, Optional<Logger>) - Method in class StringGenerator
-
- selectFileExtension(OutputWriteSettings, Optional<Logger>) - Method in class XMLGenerator
-
- selectIndexToRmv(MarkCollection, ProposerContext) - Static method in class KernelDeath
-
- selective() - Method in class RecordingWriters
-
A writer that allows only certain selected output-names, and records the written output-names
- selectMarkFrom(MarkCollection, ProposerContext) - Method in class MarkFromCollectionProposer
-
- selectMarkFrom(MarkCollection, MarkFromCollectionProposer, ProposerContext) - Method in class Check
-
- selectMarkFrom(MarkCollection, ProposerContext) - Method in class MarkFromCollectionProposerUnary
-
- selectMarkFrom(MarkCollection, MarkFromCollectionProposer, ProposerContext) - Method in class MarkFromCollectionProposerUnary
-
- selectMarkFrom(MarkCollection, MarkFromCollectionProposer, ProposerContext) - Method in class Repeat
-
- selectMarkFrom(MarkCollection, MarkFromCollectionProposer, ProposerContext) - Method in class UniformRandom
-
- selectOutputEnabled(Optional<OutputEnabledRules>) - Method in class RecordedOutputsWithRules
-
- SelectParam<T> - Interface in org.anchoranalysis.launcher.executor.selectparam
-
Different methods of selecting a object T
that is used as a parameter for an experiment.
- SelectParamFactory - Class in org.anchoranalysis.launcher.executor.selectparam
-
Creates an appropriate
SelectParam
based upon the options passed to the command-line.
- SelectSlicesBase - Class in org.anchoranalysis.plugin.mpp.bean.region
-
- SelectSlicesBase() - Constructor for class SelectSlicesBase
-
- SelectSlicesWithIndexBase - Class in org.anchoranalysis.plugin.mpp.bean.region
-
- SelectSlicesWithIndexBase() - Constructor for class SelectSlicesWithIndexBase
-
- separate(Collection<T>) - Method in class SpatiallySeparate
-
Splits a collection of elements into spatially separate clusters, without consuming
all elements in elements
.
- Sequence - Class in org.anchoranalysis.plugin.image.bean.segment.binary
-
Performs a sequence of succesive segmentations
- Sequence() - Constructor for class Sequence
-
- SequenceInteger - Class in org.anchoranalysis.bean.permute.property
-
A sequence of integers.
- SequenceInteger() - Constructor for class SequenceInteger
-
- sequenceIterator() - Method in class PermutePropertySequence
-
Iterates each element in sequence
.
- SequenceMemory - Class in org.anchoranalysis.io.generator.sequence
-
- SequenceMemory() - Constructor for class SequenceMemory
-
- SequentialProcessor<T extends InputFromManager,S> - Class in org.anchoranalysis.experiment.bean.processor
-
Executes jobs sequentially, without any parallelism.
- SequentialProcessor() - Constructor for class SequentialProcessor
-
- SequentialSession<T extends FeatureInput> - Class in org.anchoranalysis.feature.session
-
Calculates features with successively different inputs, without caching any results from one
input to the next.
- SerializedGenerator<T> - Class in org.anchoranalysis.io.generator.serialized
-
- SerializedGenerator() - Constructor for class SerializedGenerator
-
- serializeObjectToFile(T, Path) - Static method in class XStreamSerializer
-
Writes a file with a serialized representation of an object.
- SessionInputSequential<T extends FeatureInput> - Class in org.anchoranalysis.feature.session
-
- SessionInputSequential(T, CacheCreator) - Constructor for class SessionInputSequential
-
Creates for a particular input and
CacheCreator
, otherwise using defaults.
- SessionInputSequential(T, CacheCreator, ChildCacheFinder) - Constructor for class SessionInputSequential
-
- set() - Method in class DoubleSet
-
The underlying set of values.
- set() - Method in class IntegerSet
-
The underlying set of values.
- set() - Method in class StringSet
-
The underlying set of values.
- set(int, double) - Method in class ResultsVector
-
Assigns a result at a particular position.
- set(int, ResultsVector) - Method in class ResultsVector
-
Assigns many results, starting at a particular position, and incrementing thereafter.
- set(int, VoxelizedMarkMemo) - Method in class MemoList
-
- set(int, UpdatableMarks) - Method in class UpdatableMarksList
-
- set(int, Mark) - Method in class MarkCollection
-
- setAboveMaxValue(double) - Method in class RangeCompareBase
-
Constant to return if outside the range (above the maximum allowed)
- setAcceptDirectoryErrors(boolean) - Method in class SearchDirectory
-
If true, continues when a directory-access-error occurs (logging it), otherwise throws an
exception.
- setAcceptMissingResolution(boolean) - Method in class WithResolutionBase
-
Whether to throw an exception (if true) if image-resolution is missing, or return Double.Nan
(if false).
- setAcceptMissingResolution(boolean) - Method in class VoxelPhysicalSize
-
Whether to throw an exception (if true) if image-resolution is missing, or return Double.Nan
(if false).
- setAcceptNoResolution(boolean) - Method in class ReadVoxelExtentXml
-
If false, an exception is thrown if the resolution file is missing for a particular image.
- setAcceptOutsideScene(boolean) - Method in class CheckMarkWithMask
-
- setAdd(DefineAdderBean) - Method in class VisualizeOnBackground
-
- setAddCriteria(AddCriteria<T>) - Method in class RandomCollectionWithAddCriteria
-
- setAdditionalBackgrounds(List<DerivePath>) - Method in class MarkProposerStrategy
-
Additional background-stacks that are possible to use while annotating.
- setAdditionalChannels(List<IndexedChannel>) - Method in class MultiInputManagerQuick
-
Additional channels other than the main one, which are located in the main raster file
- setAdditionalChannels(List<IndexedChannel>) - Method in class NamedChannelsQuick
-
Additional channels other than the main one, which are located in the main raster file
- setAdditionalPropertyPaths(StringSet) - Method in class PermuteProperty
-
Additional property paths that are also changed, together with propertyPath
.
- setAddName(boolean) - Method in class CombineCSV
-
- setAddOne(boolean) - Method in class Quantile
-
- setAddSum(int) - Method in class GradientBaseAddSum
-
Added to all gradients (so we can store negative gradients)
- setAdjacentChannels(List<AdjacentFile>) - Method in class NamedChannelsQuick
-
Channels that are located in a separate raster file adjacent to the main raster file
- setAggIntervalLog10(double) - Method in class ReporterInterval
-
How many iterations before printing a new report? Encoded in log10.
- setAggregateTriggerBank(AggregateTriggerBank<T>) - Method in class FeedbackBeginParameters
-
- setAggregator(ChannelAggregator) - Method in class AggregateChannelTask
-
- setAlign(Align) - Method in class Grow
-
How to align the box after it is grown, as much as possible.
- setAlign(Align) - Method in class Overlay
-
Indicates how to align the image across the three axes.
- setAlign(Align) - Method in class ScaleImageCommonSize
-
How a smaller image (after scaling) is aligned to the larger image (with the common size).
- setAligner(BoxAligner) - Method in class Tile
-
How to align a smaller image inside a larger cell.
- setAligner(BoxAligner) - Method in class Montage
-
When varyImageSize==false
and varyImageLocation==false
, how to align a
smaller image inside a larger cell.
- setAlignerLabel(BoxAligner) - Method in class Montage
-
When label==false
and varyImageLocation==false
, how to align the label with
its associated image.
- setAlignX(String) - Method in class Align
-
Indicates how to align the image across the X-axis (i.e.
- setAlignY(String) - Method in class Align
-
Indicates how to align the image across the Y-axis (i.e.
- setAlignZ(String) - Method in class Align
-
Indicates how to align the image across the Z-axis: one of top, bottom, center,
repeat
.
- setAll(EnergySavedAll) - Method in class MarksWithEnergyBreakdown
-
Certain features are stored for every object, so that we can reference them in our
calculations for the 'all' component
- setAnnealScheme(AnnealScheme) - Method in class SimulatedAnnealing
-
- setAnnotations(AnnotationInputManager<NamedChannelsInputPart, T>) - Method in class FromAnnotations
-
- setAnnotatorStrategy(S) - Method in class AnnotationInputManager
-
The strategy to be used for annotating.
- setAppendChannels(List<AppendStack>) - Method in class NamedChannelsQuick
-
Channels that are located in a separate raster file somewhere else in the project's structure
- setAppendCSV(DerivePath) - Method in class FromCSVInputManager
-
- setAppendCsv(AppendCsv) - Method in class MatchedAppendCsv
-
- setAppendDictionary(List<NamedBean<DerivePath>>) - Method in class MultiInputManager
-
- setAppendFilePath(List<NamedBean<DerivePath>>) - Method in class MultiInputManager
-
- setAppendHistogram(List<NamedBean<DerivePath>>) - Method in class MultiInputManager
-
- setAppendMarks(List<NamedBean<DerivePath>>) - Method in class MultiInputManager
-
- setAppendMarksFromAnnotation(List<NamedBean<DerivePath>>) - Method in class MultiInputManager
-
- setAppendMarksFromAnnotationAcceptedOnly(List<NamedBean<DerivePath>>) - Method in class MultiInputManager
-
- setAppendMarksFromAnnotationRejectedOnly(List<NamedBean<DerivePath>>) - Method in class MultiInputManager
-
- setAppendObjects(List<NamedBean<DerivePath>>) - Method in class MultiInputManager
-
- setAppendStack(List<NamedBean<DerivePath>>) - Method in class MultiInputManager
-
- setApplyResolution(boolean) - Method in class DistanceTransform3D
-
Multiples the values by the x-resolution, if it exists.
- setApplyToPath(boolean) - Method in class MatchRegularExpression
-
If true, the filter is applied to the path, not just the filename (using forward slashes as
directory separators)
- setArrange(StackArranger) - Method in class Arrange
-
Determines how the stacks in list
are arranged.
- setArrange(StackArranger) - Method in class Cell
-
How to arrange any
RGBStack
s in this particular cell.
- setAsMemberFlag(byte, byte) - Static method in class RegionMembershipUtilities
-
- setAsPercentage(boolean) - Method in class Quantile
-
If true, the quantile is interpreted as a percentage rather than a decimal.
- setAssigner(AnnotationComparisonAssigner<T>) - Method in class CompareAnnotations
-
- setAssignMode(AssignMode<S, T, U>) - Method in class SimulatedAnnealing
-
- setAvoidBulletOnFirst(boolean) - Method in class SummarizerAggregate
-
Iff true no bullet is added for the very first-item in the list
- setAvoidDivideByZero(boolean) - Method in class Divide
-
- setAvoidOverlappingObjects(boolean) - Method in class PairNeighbors
-
If true, no overlapping objects are treated as pairs
- setAxis(String) - Method in class AxisAlignedUnitVector
-
Which axis the unit-vector will align with.
- setAxis(String) - Method in class CenterOfGravity
-
- setAxis(String) - Method in class GradientForAxis
-
Which axis? X=0, Y=1, Z=2
- setAxis(String) - Method in class ForSpecificAxis
-
- setAxis(String) - Method in class ArbitraryInsidePoint
-
- setAxis(String) - Method in class BoundingBoxAlongAxisBase
-
- setAxis(String) - Method in class GradientMeanForAxis
-
- setAxis(String) - Method in class PrincipalAxisOrientation
-
Which axis to read from (x,y,z)
- setAxis(String) - Method in class BoundingBoxExtent
-
- setBackground(AnnotationBackground) - Method in class AnnotatorStrategy
-
The visual background to use while annotating.
- setBackground(Either<Dimensions, DisplayStack>) - Method in class ObjectsAsRGBGenerator
-
A background image or dimensions to define an empty background.
- setBackground(String) - Method in class CompareAnnotations
-
The name of the stack to use as background to the annotations.
- setBackground(ProviderAsStack) - Method in class ColoredBase
-
The background.
- setBackgroundChannelIndex(int) - Method in class OutlinePreserveRelativeSize
-
Uses only this channel (identified by an index in the stack) as the background, -1 disables.
- setBackgroundChannelProvider(ChannelProvider) - Method in class MorphologicalOperatorBase
-
- setBackgroundID(String) - Method in class VisualizeOnBackground
-
- setBackgroundIntensity(int) - Method in class ScaleImageCommonSize
-
The background intensity to use in each channel when the scaled image does not cover the
entire canvas.
- setBackgroundStackMap(StringMap) - Method in class AnnotationBackground
-
If non-null, maps underlying stack-name to a background.
- setBackgroundStackName(String) - Method in class SegmentIntoMarks
-
- setBeanExtension(String) - Method in class QuickMultiDatasetExperiment
-
- setBeanExtension(String) - Method in class QuickMultiDatasetStructuredExperiment
-
- setBelowMinValue(double) - Method in class RangeCompareBase
-
Constant to return if outside the range (below the minimum allowed)
- setBest(boolean) - Method in class VoxelizedMarksChangeReporter
-
- setBigNeighborhood(boolean) - Method in class Dilate
-
- setBigNeighborhood(boolean) - Method in class ConnectedComponentsFromMask
-
If true uses 8 neighborhood rather than 4 neighborhood etc.
- setBigNeighborhood(boolean) - Method in class DecomposeIntoConnectedComponents
-
if true, uses 8 neighborhood instead of 4, and similarly in 3d
- setBigNeighborhood(boolean) - Method in class Dilate
-
- setBigNeighborhood(boolean) - Method in class TraverseOuterContourOnImage
-
- setBinary(boolean) - Method in class ScaleImage
-
Iff true the image to be scaled is treated as a binary-mask, and interpolation during scaling
ensures only two binary-values are outputted.
- setBinaryInputChannelID(String) - Method in class AddDistanceTransform
-
The ID of the binary input mask that determines the region of the Watershed.
- setBinarySgmn(BinarySegmentation) - Method in class BinarySegmentByObject
-
- setBirthRepeats(int) - Method in class KernelReplace
-
- setBit0(boolean) - Method in class RegionMembership
-
- setBit1(boolean) - Method in class RegionMembership
-
- setBit2(boolean) - Method in class RegionMembership
-
- setBit3(boolean) - Method in class RegionMembership
-
- setBit4(boolean) - Method in class RegionMembership
-
- setBit5(boolean) - Method in class RegionMembership
-
- setBit6(boolean) - Method in class RegionMembership
-
- setBit7(boolean) - Method in class RegionMembership
-
- setBitsPerPixel(int) - Method in class ForceBitsPerPixel
-
- setBlockSize(SizeXY) - Method in class HOGParameters
-
The block-size as per OpenCV implementation (identical default-size).
- setBlockStride(SizeXY) - Method in class HOGParameters
-
The block-stride as per OpenCV implementation (identical default-size).
- setBlue(int) - Method in class RGBColorBean
-
Sets the blue component value.
- setBlue(int) - Method in class RGBColor
-
Sets the blue component value.
- setBlue(ChannelProvider) - Method in class ThreeChannels
-
- setBold(boolean) - Method in class TextStyle
-
Whether to bold the drawn text
- setBorderWidth(int) - Method in class MontageSlices
-
Adds a border around each part of the montage
- setBounds(BoundRotation) - Method in class RandomOrientation
-
- setBridgeMatcher(ObjectMatcher) - Method in class Bridge
-
Used to match each input-object to an intermediary-object
- setBundleSize(int) - Method in class ObjectSerializerPeriodicReporter
-
- setBundleSize(int) - Method in class VoxelizedMarksChangeReporter
-
- setBySlices(boolean) - Method in class ConnectedComponentsFromMask
-
- setCacheSize(int) - Method in class RelationWithMatches
-
Size of feature evaluation cache for featureEvaluatorMatch
- setCalculateLevel(CalculateLevel) - Method in class CalculateLevelUnary
-
- setCalculateLevel(CalculateLevel) - Method in class ThresholderGlobal
-
- setCalculateLevel(CalculateLevel) - Method in class LevelPerObjectBase
-
Method to calculate the level for a particular object.
- setCalculateLevel(CalculateLevel) - Method in class GreaterThanThreshold
-
Calculates the level for the threshold
- setCalculateLevel(CalculateLevel) - Method in class LevelFromHistogram
-
- setCalculateLevel(CalculateLevel) - Method in class ThresholdHistogram
-
- setCalculateLevel(CalculateLevel) - Method in class CalculateLevelBase
-
- setCalculateLevelElse(CalculateLevel) - Method in class CalculateLevelRelativeToThreshold
-
- setCaseSensitive(boolean) - Method in class PatternSpan
-
Iff true, a case sensitive search is used to match patterns.
- setCellDefault(StackArranger) - Method in class Tile
-
Used to define an individual cell, when no specific entry is found in cells
for a
particular cell.
- setCells(List<Cell>) - Method in class Tile
-
Defines the corresponding
StackArranger
for an individual cell in table.
- setCellSize(SizeXY) - Method in class HOGParameters
-
The cell-size as per OpenCV implementation (identical default-size).
- setCenterPoint(Point3d) - Method in class FitResult
-
- setChangeExisting(boolean) - Method in class ConvertBase
-
If true, the existing channel can be changed.
- setChannel(ChannelProvider) - Method in class ChannelProviderUnary
-
- setChannel(ChannelProvider) - Method in class FromChannel
-
- setChannel(ChannelProvider) - Method in class FromChannel
-
- setChannel(ChannelProvider) - Method in class FromChannelBase
-
- setChannel(ChannelProvider) - Method in class IntensityGreaterEqualThan
-
- setChannel(ChannelProvider) - Method in class UnaryWithChannelBase
-
- setChannel(ChannelProvider) - Method in class WithChannelBase
-
- setChannel(ChannelProvider) - Method in class FromChannelOrMask
-
A channel that is provided to the stack.
- setChannel1(ChannelProvider) - Method in class ChannelProviderBinary
-
- setChannel1(ChannelProvider) - Method in class ChannelProviderTernary
-
- setChannel2(ChannelProvider) - Method in class ChannelProviderBinary
-
- setChannel2(ChannelProvider) - Method in class ChannelProviderTernary
-
- setChannel3(ChannelProvider) - Method in class ChannelProviderTernary
-
- setChannelAssignFrom(ChannelProvider) - Method in class AssignFromChannel
-
- setChannelConversionStyle(ChannelConvertStyle) - Method in class ConvertImageFormat
-
To convert as RGB or independently or in another way.
- setChannelConverter(ConvertChannelTo<T>) - Method in class Convert
-
- setChannelConverter(ConvertChannelTo<?>) - Method in class ConvertImageFormat
-
Optionally, how to convert from one bit-depth to another (scaling, clamping etc.)
- setChannelElse(ChannelProvider) - Method in class IfParamEquals
-
- setChannelFirst(int) - Method in class Difference
-
Index of first channel
- setChannelGroupID(int) - Method in class RegularExpression
-
- setChannelID(String) - Method in class AddEdgeFilters
-
The ID of the channel that provides the input to the filter.
- setChannelIfVoxelZero(ChannelProvider) - Method in class IfVoxelZero
-
If a pixel is zero in the input-channel, the output is formed from the corresponding pixel in
this channel instead
- setChannelIndex(int) - Method in class FromStack
-
- setChannelIndex(int) - Method in class FromStackChannel
-
- setChannelIndex(int) - Method in class One
-
The index of the channel to retrieve from stackName
.
- setChannelIndex(int) - Method in class MultiInputManagerQuick
-
If either stackAsChannel==true or we have specified additionalChannels this indicated which
channel to use from the stack
- setChannelLookup(ChannelProvider) - Method in class NormalizeDifferenceToMedian
-
- setChannelMap(ChannelMapCreator) - Method in class NamedChannels
-
- setChannelMask(String) - Method in class ExportImageHistograms
-
If defined, this is the name of channel used as a mask over the values which are fed into the
histogram
- setChannelName(String) - Method in class SingleChannel
-
- setChannelName(String) - Method in class ConvertNamedChannelsToStack
-
By default all channels are converted into a stack.
- setChannelSecond(int) - Method in class Difference
-
Index of second channel
- setChannelsExtra(List<ChannelProvider>) - Method in class ScoreVoxels
-
- setChannelsPerByteArray(int) - Method in class ForceChannelsPerByteArray
-
- setChannelThreshold(ChannelProvider) - Method in class ThresholdAgainstChannel
-
- setCheck(CheckMark) - Method in class Not
-
- setCheckMark(CheckMark) - Method in class FromObjects
-
- setCheckMark(CheckMark) - Method in class Check
-
- setCheckMark(CheckMark) - Method in class Check
-
- setCheckParsedFilePathBag(CheckParsedFilePathBag) - Method in class GroupFiles
-
Imposes a condition on each parsed-file-path-bag which must be-fulfilled if a file is to be
included.
- setClassifierProvider(FeatureListProvider<FeatureInputStack>) - Method in class BinaryClassifierImageLabeller
-
- setClassLabelsPath(String) - Method in class SegmentStackIntoObjectsScaleDecode
-
Relative-path to the class-labels file, a text file where each line specifies a class label
in order, relative to the models/ directory in the Anchor distribution.
- setClearOutsideMask(boolean) - Method in class ThresholdAgainstChannel
-
- setCollapseFilename(boolean) - Method in class FilePathAppendBase
-
- setColor(RGBColorBean) - Method in class FromSingle
-
The single color to repeat.
- setColor(RGBColorBean) - Method in class AnnotationLabel
-
An optional color associated with the label when displayed via GUI
- setColor(RGBColorBean) - Method in class ColoredMask
-
- setColors(ColorScheme) - Method in class ColorSchemeUnary
-
The delegate that creates the color-list before subsequent processing.
- setColors(List<RGBColorBean>) - Method in class FromList
-
The list of colors to specify.
- setColors(ColorScheme) - Method in class ColoredBaseWithGenerator
-
Colors to use for drawing objects
- setColorScheme(ColorScheme) - Method in class GenerateToMatchObjects
-
- setColorsUnpaired(ColorScheme) - Method in class CompareAnnotations
-
- setColorUnselectedObjects(RGBColorBean) - Method in class OutlinePreserveRelativeSize
-
Optionally outline the other (unselected for the thumbnail) objects in this particular color.
- setColumn(int) - Method in class Cell
-
The column in the table that the cell refers to (zero-indexed).
- setColumnDefinition(ColumnDefinition) - Method in class ExportObjectsFromCSV
-
Column definition for the CSV files
- setColumnGroup(String) - Method in class ColumnDefinition
-
Name of CSV column used to group results (the same values, are outputted together)
- setColumnID(String) - Method in class ColumnDefinition
-
Name of CSV column with the file identifier
- setColumns(int) - Method in class MontageSlices
-
How many columns to use in the montage, or 0 to guess an approximately square output
- setColumnUniquePixel(String) - Method in class ColumnDefinition
-
Name of CSV column with X coordinate of point for the first Object
- setCombine(CombineObjectsForFeatures<T>) - Method in class FromObjects
-
- setCommand(String) - Method in class MorphologicalOperation
-
One of: open, close, fill, erode, dilate, skel, outline
- setComparerLeft(ComparableSource) - Method in class AnnotationComparisonInputManager
-
- setComparerRight(ComparableSource) - Method in class AnnotationComparisonInputManager
-
- setCondition(DictionaryCondition) - Method in class IfParamEquals
-
- setCondition(DictionaryCondition) - Method in class IfKeyValueCondition
-
- setConstant(double) - Method in class MaxWithConstant
-
- setContains(String) - Method in class DescriptiveNameContainsImageLabeller
-
- setContains(String) - Method in class FilterDescriptiveName
-
A descriptive-name must contain (case-sensitive) this string.
- setConvert(ConvertChannelToWithHistogram<T>) - Method in class ConvertWithHistogram
-
- setConvexHull(boolean) - Method in class FitPointsFromObjects
-
If true, Reduces the set of points by applying a convex-hull operation
- setCopyFilesNaming(CopyFilesNaming<NoSharedState>) - Method in class CopyFilesNamingOne
-
- setCountThreshold(int) - Method in class SummarizerSplitMoreThan
-
If there are more than countThreshold
elements, use summarizerGreaterThan
,
else summarizerElse
.
- setCov(boolean) - Method in class ObjectRadiusStandardDeviation
-
- setCreateMark(CreateMarkFromPoints) - Method in class PointsFitter
-
- setCreateShort(boolean) - Method in class Arrange
-
If true, the created raster has unsigned short voxel data type.
- setCreateShort(boolean) - Method in class TileWithLabels
-
When true, the voxel-data-type of the created image is unsigned short, otherwise
unsigned byte.
- setCreateShort(boolean) - Method in class WriteText
-
When true, text
is drawn across all z-slices in the stack.
- setCreateShort(boolean) - Method in class DistanceTransform3D
-
- setCreateShort(boolean) - Method in class DistanceTransformForEachObject3D
-
- setCreateShort(boolean) - Method in class CreateNew
-
If True creates an unsigned short-image
- setCsvFilePath(DerivePath) - Method in class FilterCSVColumn
-
- setCsvIgnoreZeros(boolean) - Method in class ExportImageHistograms
-
Iff true, bins with zero-counts are not written as a row in the CSV file.
- setCurrentTemp(double) - Method in class Geometry
-
- setCustomName(String) - Method in class Feature
-
An optional additional name that be associated with the feature (defaults to an empty
string).
- setDatasetName(String) - Method in class ExperimentResultsExperimentStructure
-
The name of the experiment including version suffix
- setDatasetNameSubdirectory(boolean) - Method in class ExperimentResultsExperimentStructure
-
If true the datasetName is appended as a subdirectory e.g.
- setDatasets(StringSet) - Method in class QuickMultiDatasetExperiment
-
- setDatasets(StringSet) - Method in class QuickMultiDatasetStructuredExperiment
-
- setDatasetSpecific(String) - Method in class QuickMultiDatasetExperiment
-
- setDatasetSpecific(String) - Method in class QuickMultiDatasetStructuredExperiment
-
- setDatasetSuffix(String) - Method in class FilePathAppendBase
-
A suffix appended to the dataset name extracted from the reg exp
- setDatasetVersion(String) - Method in class ExperimentResultsExperimentStructure
-
A version-suffix appended to the dataset name extracted from the reg exp
- setDay(boolean) - Method in class ExperimentIdentifierAuto
-
If true, the current day (yyyy.MM.dd) is included in the output.
- setDebug(boolean) - Method in class RootPath
-
If true this root is preferred, when executing a job in debugging mode.
- setDebug(boolean) - Method in class ThresholdedFeature
-
- setDebugModeParameters(Optional<DebugModeParameters>) - Method in class InputContextParameters
-
Parameters for debug-mode (only defined if we are in debug mode).
- setDecode(DecodeInstanceSegmentation<T>) - Method in class SegmentStackIntoObjectsScaleDecode
-
Decodes inference output into segmented objects.
- setDefaultBehaviourString(Optional<String>) - Method in class ExperimentExecutor
-
If present, a string is printed in the description if the default-experiment is used,
otherwise ignored.
- setDefaultColors(ColorScheme) - Method in class OutputWriteSettings
-
The default color-scheme used for outputs, if no other scheme is specified.
- setDefaultStackReaderForMetadata(StackReader) - Method in class ConvertNamedChannels
-
Supplies to the imageMetadataReader
to use, if no other reader is specified.
- setDefine(Define) - Method in class MarkEvaluator
-
- setDefine(Define) - Method in class DefineOutputter
-
- setDefine(DefineOutputter) - Method in class Develop
-
Defines entities (chanels, stacks etc.) that are derived from inputs and other entities.
- setDefine(DefineOutputter) - Method in class ExportReportFeatures
-
- setDefine(DefineOutputterWithEnergy) - Method in class FromObjects
-
- setDefine(DefineOutputter) - Method in class ExportObjectsAsCroppedImages
-
- setDefine(DefineOutputterWithEnergy) - Method in class SegmentWithMarkedPointProcess
-
Adds definitions of stacks/objects etc.
- setDelegate(ResolvedBound) - Method in class BoundMinMax
-
- setDelimiter(String) - Method in class DirectoryWithPrefix
-
Added between prefix
and the filename, if the filename is defined.
- setDelimiter(String) - Method in class SubsetRangeIfRequested
-
Character used to split the name into groups.
- setDelimiter(String) - Method in class LastDirectoryAsPrefix
-
- setDelta(double) - Method in class Mser
-
- setDeltat(double) - Method in class AnisotropicDiffusion
-
the integration constant for the numerical integration scheme.
- setDepth(double) - Method in class ImposeResolution
-
Physical pixel size of a voxel in z-dimension.
- setDerivePath(DerivePath) - Method in class DualMarksAnnotationAsObjects
-
- setDerivePath(DerivePath) - Method in class MarksAsObjects
-
- setDerivePath(DerivePath) - Method in class MaskAsObject
-
Where to find the
Mask
to compare, as a function of the source file-path.
- setDerivePath(DerivePath) - Method in class Objects
-
Where to find the objects to compare, as a function of the source file-path.
- setDerivePath(DerivePath) - Method in class CollapseFileName
-
Called as a delegate to provide a
source
Path
.
- setDerivePath(DerivePath) - Method in class RemoveTrailingDirectory
-
- setDictionary(DictionaryProvider) - Method in class FeatureEvaluator
-
Parameters to optionally associated with stackEnergy
, and meaningless if stackEnergy
is not specified.
- setDictionary(DictionaryProvider) - Method in class EnergySchemeCreatorByElement
-
- setDictionary(DictionaryProvider) - Method in class ScaleByDictionary
-
- setDictionary(DictionaryProvider) - Method in class AssignFromDictionary
-
The dictionary from which an assignment will occur.
- setDictionary(DictionaryProvider) - Method in class ScoreVoxels
-
- setDictionary(DictionaryProvider) - Method in class DictionaryCondition
-
The dictionary to provide a value to check.
- setDictionary(DictionaryProvider) - Method in class IfParamEqual
-
- setDictionary(String) - Method in class ParamFromCollection
-
- setDictionary(DictionaryProvider) - Method in class FeatureListProviderLDAClassifier
-
- setDictionary(DictionaryProvider) - Method in class FeatureValueCheckMark
-
- setDictionary(DictionaryProvider) - Method in class DefineOutputterWithEnergy
-
- setDictionary(DictionaryProvider) - Method in class GaussianSampler
-
The dictionary that parameterizes the Gaussian-distribution that is sampled from.
- setDictionary(String) - Method in class Develop
-
If non-empty, the identifier for a dictionary that is treated as part of the energy-stack.
- setDictionary(DictionaryProvider) - Method in class SegmentMarksFromImage
-
If non-empty, a dictionary that is passed to the segmentation procedure.
- setDimensions(DimensionsProvider) - Method in class ReportFeatureForMarks
-
- setDimensions(DimensionsProvider) - Method in class FromDimensionsBase
-
- setDimensions(DimensionsProvider) - Method in class FromDimensionsBase
-
- setDimensions(DimensionsProvider) - Method in class RepeatSlice
-
Dimensions to create new mask
- setDimensions(DimensionsProvider) - Method in class MergeBase
-
- setDimensions(DimensionsProvider) - Method in class WithDimensionsBase
-
- setDimensions(DimensionsProvider) - Method in class WithOptionalDimensionsBase
-
- setDimensions(DimensionsProvider) - Method in class ToDimensions
-
The dimensions the source image/entity is desired to be scaled to.
- setDimensions(DimensionsProvider) - Method in class FromMarks
-
- setDimensions(DimensionsProvider) - Method in class RequireFeatureRelationThreshold
-
- setDimensions(DimensionsProvider) - Method in class PointsFitterToMark
-
- setDimensionsSourceFallback(DimensionsProvider) - Method in class ToDimensions
-
- setDirection(DirectionVectorBean) - Method in class ConvertToPhysicalDistance
-
Direction of the distance being converted, defaults to a unit vector along the X-axis
- setDirection(SpecifyVector) - Method in class FeatureMarkDirection
-
- setDirectionVector(SpecifyVector) - Method in class FromUnitValueDistance
-
- setDirectory(String) - Method in class FilesProviderWithDirectoryString
-
A directory in which to look for files.
- setDirectory(Path) - Method in class DirectoryWithPrefix
-
- setDirectory(String) - Method in class HomeSubdirectory
-
A relative-path (to the user home directory) which is used as an output directory
- setDirectoryDataset(String) - Method in class QuickMultiDatasetExperiment
-
- setDirectoryDistance(int) - Method in class QuickMultiDatasetStructuredExperiment
-
How many directories to recurse back from the current file to the Experiments/ directory
- setDirectoryOutput(String) - Method in class QuickExperiment
-
- setDisableDebugMode(boolean) - Method in class RootedFilePath
-
- setDisableDebugMode(boolean) - Method in class Rooted
-
- setDisplayer(StackDisplayer) - Method in class SegmentStackIntoObjectsScaleDecode
-
How to convert an image to be displayed to the user.
- setDisplayer(StackDisplayer) - Method in class CompareAnnotations
-
How to convert an image to be displayed to the user.
- setDisplayer(StackDisplayer) - Method in class ColoredBase
-
How to convert an image to be displayed to the user.
- setDisplayer(StackDisplayer) - Method in class OutlinePreserveRelativeSize
-
How to convert an image so that it can be displayed.
- setDisplayer(StackDisplayer) - Method in class ScaleToSize
-
How to convert an image to be displayed to the user.
- setDisplayer(StackDisplayer) - Method in class Montage
-
How to convert an image to be displayed to the user.
- setDisplayer(StackDisplayer) - Method in class ExportObjectsAsCroppedImages
-
How to convert an image to be displayed to the user.
- setDisplayer(StackDisplayer) - Method in class ExportObjectsFromCSV
-
How to convert an image to be displayed to the user.
- setDisplayer(StackDisplayer) - Method in class SegmentMarksFromImage
-
How to convert an image to be displayed to the user.
- setDisplayer(StackDisplayer) - Method in class SegmentWithMarkedPointProcess
-
How to convert an image to be displayed to the user.
- setDistance(int) - Method in class LevelPerObjectNeighbors
-
How many neighbors to include by distance (distance==1 implies all directly touching
neighbors, distance==2 implies those touching the directly touching etc.)
- setDistanceMapProvider(ChannelProvider) - Method in class MergeSpatialClusters
-
A distance map which can also be used for making decisions on merging
- setDistanceMax(double) - Method in class CalculateLevel
-
- setDistanceTransformMultiplyBy(float) - Method in class AddDistanceTransform
-
Multiplies the distance transform by this factor to make it more meaningful in a short.
- setDistanceTransformSmoothSigmaMeters(double) - Method in class AddDistanceTransform
-
If non-zero, a Gaussian blur is applied to the distance transform using the sigma in meters
below.
- setDistanceX(double) - Method in class ReflectInAxesWithinDistance
-
- setDistanceY(double) - Method in class ReflectInAxesWithinDistance
-
- setDistanceZ(double) - Method in class ReflectInAxesWithinDistance
-
- setDistanceZEndIfEmpty(UnitValueDistance) - Method in class XYOrientationExtendToZ
-
- setDivideByZeroValue(double) - Method in class Divide
-
- setDivisor(double) - Method in class PermutePropertySequenceDouble
-
What to divide the integer-sequence by.
- setDo3D(boolean) - Method in class AnisotropicDiffusion
-
Whether to perform the diffusion in 3D direction, or rather only in the 2D plane.
- setDo3D(boolean) - Method in class ObjectCollectionProviderMorphological
-
- setDo3D(boolean) - Method in class MorphologicalIterations
-
Whether to perform the morphological dimensions in 3D or 2D
- setDo3D(boolean) - Method in class PairNeighbors
-
- setDo3D(boolean) - Method in class TouchingVoxels
-
- setDo3D(boolean) - Method in class Erode
-
- setDo3D(boolean) - Method in class NumberRemovedVoxelsAfterClosing
-
- setDo3D(boolean) - Method in class OutlineKernelBase
-
- setDo3D(boolean) - Method in class UniformRandomRadiiProposer
-
- setDuplicate(boolean) - Method in class Reference
-
If true the channel is duplicated after it is retrieved, to prevent overwriting existing data
This is a shortcut to avoid embedding beans in a ChannelProviderDuplicate
- setDuplicate(boolean) - Method in class Reference
-
If true the channel is duplicated after it is retrieved, to prevent overwriting exisiting
data This is a shortcut to avoid embedding beans in a ChannelProviderDuplicate
- setElemAllCreator(FeatureListProvider<FeatureInputAllMemo>) - Method in class EnergySchemeCreatorByElement
-
- setElemIndCreator(FeatureListProvider<FeatureInputSingleMemo>) - Method in class EnergySchemeCreatorByElement
-
- setElemPairCreator(FeatureListProvider<FeatureInputPairMemo>) - Method in class EnergySchemeCreatorByElement
-
- setEmptyValue(double) - Method in class CenterOfGravity
-
- setEmptyValue(double) - Method in class Intersection
-
- setEmptyValue(double) - Method in class ArbitraryInsidePoint
-
- setEmptyValue(int) - Method in class IntensityMeanMaxSlice
-
- setEmptyValue(double) - Method in class IntensityMeanShellBase
-
- setEmptyValue(double) - Method in class DerivedObject
-
- setEnd(int) - Method in class SequenceInteger
-
An index beyond which we cannot iterate (inclusive).
- setEnergyChannelIndex(int) - Method in class Identity
-
- setEnergyChannelIndex(int) - Method in class RejectIfIntensityLessThan
-
- setEnergyChannelIndex(int) - Method in class SingleChannel
-
- setEnergyChannelIndex(int) - Method in class QuantileAcrossConnectedComponents
-
- setEnergyChannelIndexCheck(int) - Method in class IdentityImposeValueRelationToHistogram
-
- setEnergyChannelIndexFail(int) - Method in class IdentityImposeValueRelationToHistogram
-
- setEnergyIndex(int) - Method in class NumberNeighboringVoxels
-
Index of which channel in the energy-stack to select
- setEnergyIndex(int) - Method in class SpecificEnergyChannelBase
-
Index of which channel in the energy-stack to select
- setEnergyIndex(int) - Method in class FeatureEnergyChannel
-
Index of channel to use in the energy-stack (0 is the first channel, 1 is second etc.)
- setEnergyIndex(int) - Method in class OutsideRange
-
- setEnergyIndex(int) - Method in class Intensity
-
The channel that that forms the histogram.
- setEnergyIndex(int) - Method in class AsObjectMask
-
The channel that that forms an object-mask with the bounding-box set to entire channel's
dimensions
- setEnergyIndex(int) - Method in class OverlapMaskBase
-
- setEnergyIndexGradient(int) - Method in class TextureScore
-
- setEnergyIndexMask(int) - Method in class IntensityMeanShellBase
-
A channel of the energyStack that is used as an additional mask using default byte values for
on and off.
- setEnergyIndexMask(int) - Method in class Intensity
-
Optionally, index of another channel that masks the histogram.
- setEnergyIndexX(int) - Method in class IntensityGradientBase
-
- setEnergyIndexY(int) - Method in class IntensityGradientBase
-
- setEnergyIndexZ(int) - Method in class IntensityGradientBase
-
- setEnergySchemeCreator(EnergySchemeCreator) - Method in class MarkEvaluator
-
- setEnergySchemeCreator(EnergySchemeCreator) - Method in class SegmentWithMarkedPointProcess
-
Creates an energy scheme that assigns an energy score to each collection of marks.
- setEnergyStack(EnergyStack) - Method in class FeatureInputEnergy
-
Assigns an
EnergyStack
to be associated with the input.
- setEnergyStack(Optional<EnergyStack>) - Method in class FeatureInputEnergy
-
Assigns an optional
EnergyStack
to be associated with the input.
- setEnergyTotal(double) - Method in class MarksWithTotalEnergy
-
The pre-annealed total energy
- setEnergyTotal(double) - Method in class EnergySavedInd
-
- setEquals(String) - Method in class FilterDescriptiveName
-
A descriptive-name must be exactly equal to (case-sensitive) this string.
- setErodeAtBoundary(boolean) - Method in class ConvexHullBase
-
- setError(int, Exception) - Method in class ResultsVector
-
Set an error state at a particular position.
- setErrorAll(Exception) - Method in class ResultsVector
-
Set an error state at all positions.
- setErrorDisconnectedObjects(boolean) - Method in class RemoveIntersectingVoxels
-
If true, throws an error if there is a disconnected object after the erosion
- setErrorTree(DefaultTreeModel) - Method in class ProposerFailureDescription
-
- setExactDepth(int) - Method in class DirectoryDepth
-
- setExceptionIfEmpty(boolean) - Method in class FeatureHistogramStatistic
-
- setExcludeZero(boolean) - Method in class Intensity
-
Iff true, zero-valued voxels are excluded from the histogram
- setExcludeZero(boolean) - Method in class IntensityMeanMaxSlice
-
- setExcludeZero(boolean) - Method in class Intensity
-
If true, zeros are excluded from considering in the histogram
- setExecutionTime(long) - Method in class OptimizationStep
-
- setExitBeforeOptimization(boolean) - Method in class SegmentWithMarkedPointProcess
-
Iff true the algorithm exits before optimization begins (useful for debugging).
- setExitWithMinima(boolean) - Method in class WatershedYeong
-
If true, exits early and just returns the minima, without any further segmentation
- setExpandLabelZ(boolean) - Method in class TileWithLabels
-
When true, the label is repeated across all z-slices in the stack.
- setExperiment(RootedExperiment) - Method in class ExperimentResultsExperimentStructure
-
- setExperiment(RootedExperiment) - Method in class ExperimentStructure
-
- setExperimentIdentifier(ExperimentIdentifier) - Method in class OutputExperiment
-
A name for the experiment.
- setExperimentType(String) - Method in class FilePathAppendBase
-
A folder identifying the type of experiment (where the outputs are all put in the same
directory
- setExperimentType(String) - Method in class QuickMultiDatasetStructuredExperiment
-
The value of $1 (see comment above) in naming-structure.
- setExperimentType(String) - Method in class RootedExperiment
-
A directory identifying the type of experiment.
- setExpression(String) - Method in class RegExSimple
-
A Java-style regular expression containing groups.
- setExpression(String) - Method in class MatchRegularExpression
-
The regular-expression, Java-style as described in
Pattern
.
- setExpression(String) - Method in class RegularExpression
-
- setExtendInZ(boolean) - Method in class ExportObjectsAsCroppedImages
-
Extends the objects in z-dimension (uses maximum intensity for the segmentation, but in all
slices)
- setExtension(String) - Method in class OneOrThreeChannelsWriter
-
Which extension to use to write the image (without any leading period).
- setExtension(String) - Method in class AppendStack
-
- setExtension(String) - Method in class AppendStackDirect
-
- setExtensions(StringSet) - Method in class MatchExtensions
-
A set of file-extensions (without the period), one of which must match the end of a path.
- setExtensions(StringSet) - Method in class BranchExtension
-
Any extensions to match (case insensitive) excluding any leading period.
- setExtractScoreSize(ExtractScoreSize<S>) - Method in class DirectAssignMode
-
- setExtractScoreSize(ExtractScoreSize<S>) - Method in class UniformProposal
-
- setExtractScoreSizeReport(ExtractScoreSize<S>) - Method in class TransformationAssignMode
-
- setExtractScoreSizeState(ExtractScoreSize<T>) - Method in class TransformationAssignMode
-
- setExtractWeight(ExtractWeightFromMark) - Method in class KernelInitialMarksFromPartition
-
- setFactor(double) - Method in class ScoreObjects
-
- setFactor(double) - Method in class Scale
-
- setFactorHigh(double) - Method in class Identity
-
- setFactorLow(double) - Method in class Identity
-
- setFactorStandardDeviation(double) - Method in class GaussianSampler
-
Multiples the standard deviation of the distribution found in keyStandardDeviation
.
- setFallback(FilesProvider) - Method in class SpecificPathList
-
If no paths can be found either from listPaths or the input-context, then the fallback is
called if exists, otherwise an error is thrown
- setFallback(ScaleCalculator) - Method in class ToSuggested
-
- setFallback(ChannelConvertStyle) - Method in class ExtractToRGB
-
If a channel doesn't match an RGB pattern, this conversion-style can be used instead.
- setFallback(ChannelConvertStyle) - Method in class RGBIfNamesMatch
-
If a channel doesn't match an RGB pattern, this conversion-style can be used instead.
- setFallback(ImageMetadataReader) - Method in class InferFromHeader
-
Fallback to use if EXIF information is non-existing or absent.
- setFallbackName(String) - Method in class ExperimentIdentifierAuto
-
If there's no task-name, then this constant is used as a fallback name.
- setFeature(Feature<T>) - Method in class FeatureProviderDefine
-
The feature to provide.
- setFeature(Feature<T>) - Method in class FeatureEvaluator
-
The single feature that will be calculated (possibly repeatedly) in the session.
- setFeature(FeatureListEvaluator<FeatureInputSingleObject>) - Method in class OutputFeatureTable
-
A list of features to calculate in an evaluation context.
- setFeature(Feature<FeatureInputSingleObject>) - Method in class ScoreObjects
-
Feature that calculates the score for an object.
- setFeature(Feature<T>) - Method in class PermuteFeatureBase
-
- setFeature(Feature<FeatureInputPairMemo>) - Method in class AddCriteriaFeatureRelationThreshold
-
- setFeature(FeatureProvider<T>) - Method in class FeatureValueCheckMark
-
- setFeature(FeatureProvider<FeatureInputMark>) - Method in class RequireFeatureRelationThreshold
-
- setFeatureCondition(Feature<T>) - Method in class IfCondition
-
- setFeatureCondition(Feature<T>) - Method in class IfConditionWithinRange
-
Calculates value for the condition - which is checked if it lies within a certain range
- setFeatureElse(Feature<T>) - Method in class IfCondition
-
- setFeatureEvaluator(FeatureEvaluator<FeatureInputPairObjects>) - Method in class MultipleComparer
-
Calculates the cost used when making assignments.
- setFeatureEvaluator(FeatureEvaluator<T>) - Method in class ReportFeatureEvaluator
-
- setFeatureEvaluator(FeatureEvaluator<FeatureInputPairObjects>) - Method in class FeatureCostAssigner
-
- setFeatureEvaluator(FeatureEvaluator<FeatureInputSingleObject>) - Method in class DiscardOutliers
-
- setFeatureEvaluator(FeatureEvaluator<FeatureInputSingleObject>) - Method in class RelationWithMatches
-
- setFeatureEvaluator(FeatureEvaluator<FeatureInputSingleObject>) - Method in class ThresholdedFeature
-
- setFeatureEvaluator(FeatureEvaluator<FeatureInputSingleObject>) - Method in class ObjectCollectionProviderWithFeature
-
- setFeatureEvaluator(FeatureEvaluator<FeatureInputSingleObject>) - Method in class MergeGreedyToIncreaseObjectFeature
-
- setFeatureEvaluator(FeatureEvaluator<FeatureInputSingleObject>) - Method in class MergeToIncreaseObjectFeature
-
- setFeatureEvaluatorMatch(FeatureEvaluator<FeatureInputSingleObject>) - Method in class RelationWithMatches
-
- setFeatureEvaluatorMerge(FeatureEvaluator<FeatureInputPairObjects>) - Method in class MergePairs
-
- setFeatureEvaluatorThreshold(FeatureEvaluator<FeatureInputNull>) - Method in class MergePairs
-
Allows merge only if the feature-value satisfies a relation to this threshold
- setFeatureProvider(FeatureProvider<T>) - Method in class FeatureEvaluator
-
The single feature that will be calculated (possibly repeatedly) in the session
- setFeatures(List<FeatureProvider<T>>) - Method in class FeatureListEvaluator
-
A list of providers, combined together to form a list of features, to be calculated in a
session
- setFeatures(List<NamedBean<FeatureListProvider<U>>>) - Method in class ExportFeatures
-
The features to be exported (after possibly some manipulation or augmentation).
- setFeatures(List<NamedBean<FeatureListProvider<FeatureInputSingleObject>>>) - Method in class SegmentInstanceWithModel
-
Features to calculate for objects in the features output.
- setFeaturesAggregate(List<NamedBean<FeatureListProvider<FeatureInputResults>>>) - Method in class ExportFeatures
-
- setFeaturesImage(List<NamedBean<FeatureListProvider<FeatureInputStack>>>) - Method in class PairNeighbors
-
Additional features that only depend on the image, so do not need to be replicated for every
object.
- setFeaturesPair(List<NamedBean<FeatureListProvider<FeatureInputPairObjects>>>) - Method in class PairNeighbors
-
Additional features that are processed on the pair of images (i.e.
- setFeatureTables(List<OutputFeatureTable>) - Method in class Develop
-
Specifies a feature-table that can also be outputted.
- setFeedbackReceiver(FeedbackReceiverBean<T>) - Method in class FeedbackReceiverRequireArguments
-
- setFeedbackReceiver(FeedbackReceiverBean<VoxelizedMarksWithEnergy>) - Method in class SegmentWithMarkedPointProcess
-
Processes feedback from the segmentation algorithm for outputting / debugging.
- setFileFilter(String) - Method in class ExperimentResultsExperimentStructure
-
Files to search for
- setFileFilterAndDirectory(Path) - Method in class SearchDirectory
-
Sets both the directory and the glob from a string containing both.
- setFileId(String) - Method in class AppendCsv
-
Unique identifier for the stack, object-mask-collection etc.
- setFileId(String) - Method in class FilePathBaseAppendToManagerWithFileID
-
Unique identifier for the stack, object-mask-collection etc.
- setFileInput(NamedFiles) - Method in class GroupFiles
-
- setFileInput(InputManager<FileInput>) - Method in class NamedChannels
-
- setFileInput(InputManager<FileInput>) - Method in class Stacks
-
- setFileInput(String) - Method in class QuickExperiment
-
A string indicating the input file(s)
- setFilePath(String) - Method in class SortedSetSlice
-
- setFilePath(String) - Method in class FromSerializedMarks
-
- setFilePath(String) - Method in class FromSerializedObject
-
- setFilePathParser(FilePathParser) - Method in class MultiFileReader
-
- setFilePathProviderSVM(FilePathProvider) - Method in class FeatureListProviderSVMClassifier
-
- setFiles(FilesProvider) - Method in class ReadFromFile
-
Provides a single file containing a dictionary.
- setFiles(FilesProvider) - Method in class FilesProviderUnary
-
- setFiles(FilesProviderWithDirectory) - Method in class FilesProviderWithDirectoryUnary
-
- setFiles(FilesProvider) - Method in class FromFiles
-
A provider that should return exactly one
File
whose path is employed.
- setFiles(FilesProviderWithDirectory) - Method in class Rooted
-
- setFiles(FilesProvider) - Method in class NamedFiles
-
The files to use as inputs.
- setFiles(FilesProviderWithDirectory) - Method in class NamedFilesWithDirectory
-
The files to use as inputs.
- setFiles(FilesProviderWithDirectory) - Method in class QuickBase
-
A path to the main channel of each file
- setFilter(ObjectFilter) - Method in class IfObjectFilter
-
- setFilter(ObjectFilter) - Method in class ObjectCollectionProviderFilterBase
-
- setFilter(ObjectFilter) - Method in class Filter
-
- setFilter(ImageLabeller<T>) - Method in class ImageLabellerStringMap
-
- setFilterFilesCsv(MatchedAppendCsv) - Method in class QuickBase
-
If set, a CSV is read with two columns: the names of images and a
- setFindMaxima(boolean) - Method in class ExtractSlice
-
If true, the maxima of the score is searched for.
- setFindOutlinePixelAngle(FindPointOnContour) - Method in class TraversePointsOnContour
-
- setFirst(StringSet) - Method in class OutputEnableRulesSpecify
-
Output-names in the first-level.
- setFirst(boolean) - Method in class AsSingle
-
Iff true, first object is used, otherwise the second
- setFirst(StateTransformerBean<S, U>) - Method in class Compose
-
First transformation from S
to U
- setFirstLineHeaders(boolean) - Method in class CombineCSV
-
- setFixedSizeScaler(ScaleCalculator) - Method in class Montage
-
How to calculate the size of each image, when varyImageSize==false
.
- setFixRandomSeed(boolean) - Method in class SegmentWithMarkedPointProcess
-
Iff true uses a constant seed for the random-number-generator (useful for debugging).
- setFlatten(boolean) - Method in class MultipleComparer
-
If true, a maximum-intensity-projection is first applied to any 3D objects into a 2D plane,
before comparison.
- setFlatten(boolean) - Method in class CompareAnnotations
-
If true, a maximum-intensity-projection is first applied to any 3D objects into a 2D plane,
before comparison.
- setFlatten(boolean) - Method in class ExteriorContour
-
If true, any 3D mask is flattened in the z-dimension (maximum intensity projection) to make
it 2D
- setFlatten(boolean) - Method in class ColoredBase
-
If true, objects and the background are flattened in the z dimension (via maximum intensity
projection), so that a 2D image is produced.
- setFontColor(RGBColorBean) - Method in class TextStyle
-
Font-color of drawn text
- setFontName(String) - Method in class TextStyle
-
Font-name of drawn text
- setFontSize(int) - Method in class TextStyle
-
Font-size of drawn text
- setForceChangeBytes(boolean) - Method in class Invert
-
If true, rather than modifying the binary-values (an index) bytes are modified in the buffer
to reflect the existing binary-values.
- setForceDetailedLogging(boolean) - Method in class OutputExperiment
-
Whether more detailed log-messages around each experiment occur.
- setForceEagerEvaluation(boolean) - Method in class NamedChannelsAppend
-
- setForceRGB(boolean) - Method in class Arrange
-
Iff true, ensures every stack is converted into 3 channels.
- setFormats(List<HeaderFormat>) - Method in class InferFromHeader
-
The formats whose headers will be searched, to find sufficient metadata to populate
ImageMetadata
.
- setForwardDirectionOnly(boolean) - Method in class XYOrientationExtendToZ
-
- setFrom3i(ObjectMask) - Static method in class PointsFromObject
-
A sorted-set of three-dimensional integer points from the entire object-mask
- setFromContour(ObjectMask) - Static method in class PointsFromObject
-
A set of points from the contour of object
in three dimensions.
- setGaussian(boolean) - Method in class AddEdgeFilters
-
If true, the Gaussian filter is included.
- setGaussianSigmaMeters(double) - Method in class AddEdgeFilters
-
- setGlob(String) - Method in class MatchGlob
-
The string describing a glob e.g.
- setGradient(ChannelProvider) - Method in class ScoreVoxels
-
- setGrayscaleReconstruction(GrayscaleReconstructionByErosion) - Method in class MinimaImpositionGrayscaleReconstruction
-
- setGreen(int) - Method in class RGBColorBean
-
Sets the green component value.
- setGreen(int) - Method in class RGBColor
-
Sets the green component value.
- setGreen(ChannelProvider) - Method in class ThreeChannels
-
- setGroup(String) - Method in class AnnotationLabel
-
Specifies a group for the label (similar labels that are displayed together)
- setGroup(Grouper) - Method in class ExportFeatures
-
Includes an additional group column in CSVs, and creates group-specific feature files.
- setGroup(Grouper) - Method in class GroupedStackBase
-
How to partition the inputs into groups.
- setGroup(Grouper) - Method in class IfGroupIndexRange
-
Fallback to use when no group-index-range is specified.
- setGroup(String) - Method in class CSVRow
-
- setGroup(String) - Method in class AppendHistogram
-
- setHeight(int) - Method in class SizeXY
-
Size in Y dimension.
- setHeight(double) - Method in class ImposeResolution
-
Physical pixel size of a voxel in y-dimension.
- setHighestTwoRadiiOnly(boolean) - Method in class RadiiRatio
-
- setHistogram(HistogramProvider) - Method in class HistogramProviderUnary
-
- setHistogram(HistogramProvider) - Method in class ConvertWithHistogram
-
If set, a histogram used in conversion to describe input intensities (across perhaps multiple
images).
- setHistogram(HistogramProvider) - Method in class SegmentChannel
-
An optional histogram of voxel intensity values which can be used by segment
- setHistogram(HistogramProvider) - Method in class FromHistogram
-
If non-null, a histogram is extracted from this provider rather than the histogram from the
inputted CSV.
- setHistogramChannelIndex(int) - Method in class CalculateLevelBase
-
- setHistogramIndex(int) - Method in class IdentityImposeValueRelationToHistogram
-
- setHistogramsExtra(List<HistogramProvider>) - Method in class ScoreVoxels
-
- setId(String) - Method in class DictionaryProviderReference
-
- setId(String) - Method in class Reference
-
The identifier that uniquely determines the other feature to reference.
- setId(String) - Method in class FeatureProviderReference
-
The name of the feature to reference.
- setId(String) - Method in class FeatureResultsStatistic
-
The name of the feature, whose results will provide the statistic.
- setId(String) - Method in class BinarySegmentationReference
-
- setId(String) - Method in class FilePathProviderReference
-
- setId(int) - Method in class Mark
-
- setId(String) - Method in class Reference
-
- setId(String) - Method in class FromChannel
-
- setId(String) - Method in class Reference
-
- setId(String) - Method in class Reference
-
- setId(String) - Method in class Reference
-
- setId(String) - Method in class ReferenceOrElse
-
- setId(String) - Method in class Reference
-
- setId(String) - Method in class FeatureIntersectingObjects
-
ID for the particular object-collection
- setId(DerivePath) - Method in class ExportFeatures
-
Translates an input file name to a unique ID.
- setId(String) - Method in class MarkBoundsReference
-
- setId(String) - Method in class MarkProposerReference
-
- setId(String) - Method in class MarkMergeProposerReference
-
- setId(String) - Method in class MarkSplitProposerReference
-
- setId(String) - Method in class Reference
-
- setId(String) - Method in class ReferenceOrEmpty
-
- setId(int) - Method in class CreateEllipse
-
- setId(String) - Method in class CSVRow
-
- setId(String) - Method in class Reference
-
- setIdentifierSubrange(Optional<IndexRangeNegative>) - Method in class InputContextParameters
-
If defined, this indicates and specifies only a subset of the naming-elements to use.
- setIdentifierSuffix(String) - Method in class QuickMultiDatasetExperiment
-
- setIdentifierSuffix(String) - Method in class QuickMultiDatasetStructuredExperiment
-
- setIdGenerator(DerivePath) - Method in class ExportObjectsFromCSV
-
- setIgnoreAtThreshold(boolean) - Method in class OutlineKernelBase
-
- setIgnoreCase(boolean) - Method in class FilePathPattern
-
if true, case is ignored in the pattern matching.
- setIgnoreContains(String) - Method in class AnnotationBackground
-
If non-empty, to not display any stacks in backgroundStackMap
whose name contains
this string.
- setIgnoreFileNotFoundAppend(boolean) - Method in class NamedChannelsAppend
-
- setIgnoreFittingFailure(boolean) - Method in class FitPointsFromObjects
-
If true, if too few points exist to make a mark, or otherwise a fitting errors, it is simply
not included (with only a log error) If false, an exception is thrown
- setIgnoreHidden(boolean) - Method in class SearchDirectory
-
If true, case is ignored in the pattern matching.
- setIgnoreHidden(boolean) - Method in class FilePathPattern
-
Iff true, any hidden-path is not considered, and simply ignored
- setIgnoreHigherSide(boolean) - Method in class GaussianCumulative
-
- setIgnoreLowerSide(boolean) - Method in class GaussianCumulative
-
- setIgnoreMissingChannel(boolean) - Method in class IndependentChannels
-
Iff true and we cannot find a channel in the file, we ignore it and carry on
- setIgnoreNaN(boolean) - Method in class Sum
-
If true, we ignore any NaN values.
- setIgnoreNoObjects(boolean) - Method in class SegmentInstanceWithModel
-
When true, then the outputs (outline, mask, image etc.) are not written for images that
produce no objects.
- setIgnoreZero(boolean) - Method in class RatioNonMode
-
- setIgnoreZeros(boolean) - Method in class HistogramCSVGenerator
-
Iff true bins in the histogram with a zero count are not written
- setIgnoreZIfNaN(boolean) - Method in class DistanceTransform3D
-
If the z-resolution is undefined, the z dimenion is ignored.
- setImageLabeller(ImageLabeller<T>) - Method in class ImageAssignLabel
-
Maps a label to an image
- setImageMetadataReader(ImageMetadataReader) - Method in class Montage
-
- setImageMetadataReader(ImageMetadataReader) - Method in class ScaleImageCommonSize
-
- setImageMetadataReader(ImageMetadataReader) - Method in class ConvertNamedChannels
-
- setImgChannelMapCreator(ChannelMapCreator) - Method in class GroupFiles
-
- setIncludeBatchDimension(boolean) - Method in class SegmentObjectsFromONNXModel
-
If true, a 4-dimensional tensor is created (with the first dimension describing a batch-size
of 1), instead of the usual 3-dimensional tensor describing channel, height, width.
- setIncludeDirectories(boolean) - Method in class DirectoryStructure
-
If false, the folders are ignored, and only the file-name is used in the output
- setIncludeFeatureNames(boolean) - Method in class EnergySchemeCreatorByElement
-
If true, the names of the imageFeatures are taken as a combination of the namedItem and the
actual features
- setIncludeFileName(boolean) - Method in class AppendDictionary
-
- setIncludeFirst(boolean) - Method in class PairNeighbors
-
Include features for the First-object of the pair
- setIncludeMerged(boolean) - Method in class PairNeighbors
-
Include features for the Merged-object of the pair
- setIncludeSecond(boolean) - Method in class PairNeighbors
-
Include features for the Second-object of the pair
- setIncludeShell(boolean) - Method in class MaxOverlapRatio
-
- setIncludeZ(boolean) - Method in class Outline
-
If true the outline is also applied in the z-dimension, otherwise this is ignored as possible
boundary
- setIncludeZ(boolean) - Method in class NotTouchingSceneBorder
-
- setIncrement(int) - Method in class SequenceInteger
-
Size of step to use when incrementing.
- setIndex(int) - Method in class IndexedChannel
-
The index (starting at zero) of this
Channel
relative to others.
- setIndex(int) - Method in class KernelPointCursor
-
The index in the buffer that the kernel currently is focussed on.
- setIndex(int) - Method in class AtIndex
-
- setIndex(int) - Method in class SliceAt
-
Index in z-dimension of slice to extract
- setIndex(int) - Method in class SpecificAxisBase
-
Specifies which principal-axis to use for calculations (0=largest eigenvalue,
1=second-largest eigenvalue etc.)
- setIndex(int) - Method in class IndexedRegionBase
-
- setIndex(int) - Method in class OrderedRadius
-
- setIndex(int) - Method in class AsObject
-
- setIndex(int) - Method in class HOGFeature
-
Which index to return from the HOG descriptor.
- setIndex(int, double) - Method in class DirectionVector
-
Sets an element of the vector by the index of its position.
- setIndexDay(int) - Method in class TimestampPattern
-
The index of the group in regularExpression
that encodes the day, starting
from 0 for the first group.
- setIndexEnd(int) - Method in class NameElementRange
-
The index of the last element (inclusive) for the range.
- setIndexEnd(int) - Method in class ExtractSliceRange
-
Slice index to end extracting from (inclusive).
- setIndexHours(int) - Method in class TimestampPattern
-
The index of the group in regularExpression
that encodes the hours, starting
from 0 for the first group.
- setIndexMinutes(int) - Method in class TimestampPattern
-
The index of the group in regularExpression
that encodes the minutes, starting
from 0 for the first group.
- setIndexMonth(int) - Method in class TimestampPattern
-
The index of the group in regularExpression
that encodes the month, starting
from 0 for the first group.
- setIndexNonZero(int) - Method in class SelectSlicesWithIndexBase
-
- setIndexSeconds(int) - Method in class TimestampPattern
-
The index of the group in regularExpression
that encodes the seconds, starting
from 0 for the first group.
- setIndexStart(int) - Method in class NameElementRange
-
The index of the first element (inclusive) for the range.
- setIndexStart(int) - Method in class ExtractSliceRange
-
Slice index to start extracting from (inclusive).
- setIndexYear(int) - Method in class TimestampPattern
-
The index of the group in regularExpression
that encodes the year, starting
from 0 for the first group.
- setInitContext(OptimizationContext) - Method in class FeedbackBeginParameters
-
- setInitialKernel(Kernel<T, S>) - Method in class KernelProposer
-
- setInnerCoreDistance(double) - Method in class Ellipsoid
-
- setInput(InputManager<T>) - Method in class AnnotationInputManager
-
The inputs to be annotated.
- setInput(InputManager<T>) - Method in class InputOutputExperiment
-
The input-manager to specify where/which/how necessary inputs for the experiment occur.
- setInput(InputManager<T>) - Method in class InputManagerUnary
-
The delegate input-manager which will be circumstantially called by the current
input-manager.
- setInput(SelectParam<Optional<Path>>) - Method in class ExperimentExecutor
-
- setInput(InputManager<? extends ProvidesStackInput>) - Method in class MultiInputManager
-
- setInput(InputManager<T>) - Method in class AnnotationComparisonInputManager
-
- setInput(InputManager<NamedChannelsInputPart>) - Method in class NamedChannelsAppend
-
- setInput(InputManager<NamedChannelsInput>) - Method in class ConvertNamedChannelsToStack
-
- setInput(MultiInputManager) - Method in class FromCSVInputManager
-
- setInputDebug(InputManager<T>) - Method in class BranchIfDebug
-
If defined, this provides an input to the manager when in debug-mode, rather than than
otherwise inputs
.
- setInputDirectory(Optional<Path>) - Method in class InputContextParameters
-
If defined, a directory which can be used by beans to find input.
- setInputFilterExtensions(Optional<StringSetTrie>) - Method in class InputContextParameters
-
A trie of extensions that can be used filter inputs.
- setInputFilterGlob(Optional<String>) - Method in class InputContextParameters
-
A glob that can be used by beans to filter input.
- setInputName(String) - Method in class MultiInputManager
-
- setInputName(String) - Method in class SegmentObjectsFromONNXModel
-
The name of the input in the ONNX model.
- setInputName(String) - Method in class QuickExperiment
-
- setInputName(String) - Method in class MultiInputManagerQuick
-
- setInputPaths(Optional<List<Path>>) - Method in class InputContextParameters
-
A list of paths referring to specific inputs.
- setInputPointShift(float) - Method in class ConicFitterBase
-
- setIntensity(ChannelProvider) - Method in class ScoreVoxels
-
- setInterleaveChannels(boolean) - Method in class SegmentObjectsFromONNXModel
-
If true, the channels are placed as the final position of the tensor (**after** width/height)
instead of **before** width/height.
- setInterpolator(Interpolator) - Method in class Arrange
-
The interpolator to use for scaling images, if needed.
- setInterpolator(Interpolator) - Method in class SegmentStackIntoObjectsScaleDecode
-
The interpolator to use for scaling images.
- setInterpolator(Interpolator) - Method in class ScaleXY
-
The interpolator to use for scaling images.
- setInterpolator(Interpolator) - Method in class AtScale
-
The interpolator to use.
- setInterpolator(Interpolator) - Method in class OutlinePreserveRelativeSize
-
Interpolator used when scaling the background
- setInterpolator(Interpolator) - Method in class ScaleToSize
-
- setInterpolator(Interpolator) - Method in class CombineObjectsForFeatures
-
Interpolator used to resize images in thumbnail generation.
- setInterpolator(Interpolator) - Method in class Montage
-
How to resize images.
- setInterpolator(Interpolator) - Method in class GroupedStackBase
-
The interpolator to use for scaling images.
- setInterpolator(Interpolator) - Method in class ScaleImage
-
The interpolator to use for scaling images.
- setInterpolator(Interpolator) - Method in class SegmentInstanceWithModel
-
The interpolator to use for scaling images.
- setInterpolator(Interpolator) - Method in class DecodeMaskRCNN
-
The interpolator to use for scaling images.
- setInterpolator(Interpolator) - Method in class HOGParameters
-
The interpolator to use for scaling images.
- setInverse(boolean) - Method in class IntersectsWithContainer
-
- setInverse(boolean) - Method in class IntensityMeanShellBase
-
Iff true, calculates instead on the inverse of the object-mask (what's left when the shell is
removed).
- setInverseMask(boolean) - Method in class IntensityMeanShellBase
-
If true, uses the inverse of the passed mask.
- setInvert(boolean) - Method in class MaskAsObject
-
- setInvert(boolean) - Method in class FromObjects
-
- setInvert(boolean) - Method in class FilterWithRegularExpression
-
Iff true, then a file is rejected if the regular-expression matches and vice-versa.
- setInvertDecisionValue(boolean) - Method in class FeatureListProviderSVMClassifier
-
- setItem(T) - Method in class NamedBean
-
The item that is to be named, the underlying bean.
- setItem(Feature<T>) - Method in class DefineSingle
-
The sole feature that forms the list.
- setItem(FeatureListProvider<FeatureInput>) - Method in class PrependName
-
Provides the features and names before any prepending.
- setItem(Feature<S>) - Method in class FeatureUnary
-
- setItem(Feature<FeatureInputSingleObject>) - Method in class FeatureDeriveFromPair
-
- setItem(ReportFeature<MarksInitialization>) - Method in class ReportFeatureWrapError
-
- setItem(Feature<FeatureInputHistogram>) - Method in class ThresholdHistogram
-
- setItem(FeatureListProvider<FeatureInputSingleObject>) - Method in class DeriveFromPair
-
- setItem(FeatureListProvider<FeatureInputSingleObject>) - Method in class FeatureListProviderAggregatePair
-
For each feature in the list, a corresponding aggregate feature is created in the
output list.
- setItem(Feature<FeatureInputHistogram>) - Method in class Intensity
-
Feature to apply to the histogram
- setItem(Feature<FeatureInputSingleObject>) - Method in class DerivedObject
-
- setItem(Feature<FeatureInputPairObjects>) - Method in class FeatureIntersectingObjectsSingleElement
-
- setItem(FeaturePairObjects) - Method in class PairedWithMask
-
- setItem(VoxelScore) - Method in class RejectIfIntensityLessThan
-
- setItem(Feature<FeatureInputSingleObject>) - Method in class FeatureSingleObjectFromShared
-
- setItem(Feature<FeatureInputHistogram>) - Method in class Intensity
-
Feature to apply to the histogram.
- setItem(Feature<FeatureInputSingleObject>) - Method in class AsObjectMask
-
- setItem(Feature<FeatureInputSingleObject>) - Method in class QuantileAcrossConnectedComponents
-
- setItem(DerivePath) - Method in class Rooted
-
- setItem(Feature<FeatureInputSingleMemo>) - Method in class CoefficientOfVarianceFromAll
-
- setItem(Feature<FeatureInputSingleMemo>) - Method in class MeanFromAll
-
- setItem(Feature<FeatureInputHistogram>) - Method in class Intensity
-
Feature to apply to the histogram
- setItem(Feature<FeatureInputSingleMemo>) - Method in class FeaturePairMemoOne
-
- setItem1(Feature<T>) - Method in class FeatureBinary
-
Provides the first value for the binary-function.
- setItem2(Feature<T>) - Method in class FeatureBinary
-
Provides the second value for the binary-function.
- setItemMean(Feature<T>) - Method in class StatisticalBase
-
- setItemProportionate(Feature<FeatureInputSingleMemo>) - Method in class FeatureAsIndividualProportionate
-
- setItemStdDev(Feature<T>) - Method in class StatisticalBase
-
- setIterations(int) - Method in class AnisotropicDiffusion
-
How many iterations to perform diffusion.
- setIterations(int) - Method in class MorphologicalOperatorBase
-
- setIterations(int) - Method in class ObjectCollectionProviderMorphological
-
- setIterations(int) - Method in class Repeat
-
The maximum number of iterations.
- setIterations(MorphologicalIterations) - Method in class Intersection
-
The number of dilations and erosions to apply to determine if two objects intersect
- setIterations(MorphologicalIterations) - Method in class IntensityMeanShellBase
-
The number of dilations and erosions to apply and whether to do in the Z dimension.
- setIterations(int) - Method in class Erode
-
- setIterations(int) - Method in class NumberRemovedVoxelsAfterClosing
-
- setIterations(MorphologicalIterations) - Method in class Shell
-
The number of dilations and erosions to apply and whether to do in the Z dimension
- setIterations(int) - Method in class MorphologicalOperation
-
iterations for erode, dilate, open, close
- setIterations(int) - Method in class UniformProposal
-
- setIterations(int) - Method in class NumberIterationsBase
-
The number of iterations for which the number-of-marks must remain constant.
- setIterationsDilation(int) - Method in class MorphologicalIterations
-
Number of times to perform morphological dilation
- setIterationsErosion(int) - Method in class MorphologicalIterations
-
Number of times to perform morphological erosion
- setKappa(double) - Method in class AnisotropicDiffusion
-
A parameter kappa associated with the diffusion functions.
- setKeepEntireImage(boolean) - Method in class ExportObjectsAsCroppedImages
-
If true, rather than writing out a bounding-box around the object-mask, the entire image is
written
- setKeepExtension(boolean) - Method in class CollapseFileName
-
When true, the extension is appended to the directory.
- setKeepExtremes(boolean) - Method in class Identity
-
- setKeepProcessorsFree(int) - Method in class DebugDependentProcessor
-
How many processors to avoid using for the tasks.
- setKeepProcessorsFree(int) - Method in class ParallelProcessor
-
How many processors to avoid using for the tasks.
- setKeepZ(boolean) - Method in class ImposeResolution
-
Keep the z-resolution if it is already defined
- setKernel(Kernel<T, S>) - Method in class WeightedKernel
-
- setKernel(Kernel<T, S>) - Method in class KernelProposerOptionSingle
-
- setKernelFactoryList(WeightedKernelList<?, ?>) - Method in class FeedbackBeginParameters
-
- setKernelHalfWidth(int) - Method in class Median
-
Kernel will be a square kernel of size (2*kernelHalfWidth+1)x(2*kernelHalfWidth+1)
- setKernelNegative(KernelPosNeg<T, S>) - Method in class KernelProposerOptionDual
-
- setKernelPositive(KernelPosNeg<T, S>) - Method in class KernelProposerOptionDual
-
- setKernelProposer(KernelProposer<VoxelizedMarksWithEnergy, UpdatableMarksList>) - Method in class SegmentWithMarkedPointProcess
-
Proposes kernel-changes during iterations of hte marked-point-processes.
- setKernelStateBridge(KernelStateBridge<U, T>) - Method in class TransformationAssignMode
-
- setKey(String) - Method in class AssignFromDictionary
-
The key of the value in the dictionary that will be assigned.
- setKey(String) - Method in class DictionaryCondition
-
The key in the dictionary whose value is checked.
- setKey(String) - Method in class IfParamEqual
-
- setKey(String) - Method in class ParamFromCollection
-
The name of the key in the dictionary, whose corresponding value will be returned.
- setKey(String) - Method in class FromDictionary
-
- setKeyGroupID(int) - Method in class RegularExpression
-
- setKeyLower(String) - Method in class ScaleByDictionary
-
- setKeyMean(String) - Method in class GaussianSampler
-
The name of the key in the dictionary with the mean of the distribution.
- setKeyPrefix(String) - Method in class FromDictionary
-
Prefix prepended to key
- setKeyRequired(boolean) - Method in class RegularExpression
-
- setKeyStandardDeviation(String) - Method in class GaussianSampler
-
The name of the key in the dictionary with the standard-deviation.
- setKeySuffix(String) - Method in class FromDictionary
-
- setKeyUpper(String) - Method in class ScaleByDictionary
-
- setLabel(String) - Method in class StackProviderWithLabel
-
The label associated with stack
.
- setLabel(boolean) - Method in class MontageSlices
-
If true a label is added beside every image showing the slice index
- setLabels(List<AnnotationLabel>) - Method in class ImageLabelStrategy
-
- setLevel(int) - Method in class Constant
-
- setLimitUpper(Optional<Either<Integer, Double>>) - Method in class InputContextParameters
-
If defined, an upper limit that is imposed on the number of inputs.
- setLine(String[]) - Method in class CSVRow
-
- setList(List<DefineAdderBean>) - Method in class Concatenate
-
- setList(List<RegEx>) - Method in class RegExList
-
The list of
RegEx
es that are successively tried to be matched.
- setList(List<StringMapItem>) - Method in class StringMap
-
A list of mappings between a single-items in the respective sets.
- setList(List<LoggingDestination>) - Method in class ToMultiple
-
The list of loggers to log to
- setList(List<Feature<T>>) - Method in class Define
-
The list that specifies features.
- setList(List<NamedBean<FeatureListProvider<T>>>) - Method in class DefinedNamed
-
- setList(List<Feature<T>>) - Method in class FeatureList
-
The list of features.
- setList(List<Feature<T>>) - Method in class FeatureFromList
-
Assigns the list of features to use.
- setList(FeatureList<T>) - Method in class FeatureFromList
-
Assigns the list of features to use.
- setList(List<Provider<Stack>>) - Method in class Arrange
-
The stacks that are passed in respect order into arrange
.
- setList(List<StackProviderWithLabel>) - Method in class TileWithLabels
-
- setList(List<RegionMembership>) - Method in class RegionMap
-
- setList(List<AddCriteriaPair>) - Method in class AddCriteriaOr
-
- setList(List<FeedbackReceiver<T>>) - Method in class FeedbackReceiverList
-
- setList(List<TerminationCondition>) - Method in class TerminationConditionListOr
-
- setList(List<ColorProvider>) - Method in class Concatenate
-
- setList(List<CalculateLevel>) - Method in class CalculateLevelListBase
-
- setList(List<ObjectFilter>) - Method in class ObjectFilterCombine
-
A list of other filters from which the sub-classes implement filtering behaviour.
- setList(List<ObjectCollectionProvider>) - Method in class Concatenate
-
- setList(List<BinarySegmentation>) - Method in class Sequence
-
A list of binary-segmentations that are applied successively (the output of the predecessor
becomes the input of the sucecssor)
- setList(List<ProviderAsStack>) - Method in class Concatenate
-
- setList(List<NamedBean<FromStack>>) - Method in class SpecificAndRename
-
- setList(List<IndexedChannel>) - Method in class FromEntries
-
- setList(List<FilesProvider>) - Method in class Combine
-
- setList(List<InputManager<T>>) - Method in class Concatenate
-
- setList(List<Summarizer<T>>) - Method in class SummarizerAggregate
-
- setList(List<CheckMark>) - Method in class AndList
-
- setList(List<VisitScheduler>) - Method in class VisitSchedulerAnd
-
- setList(List<VisitScheduler>) - Method in class VisitSchedulerUniformSample
-
- setList(List<MarkProposer>) - Method in class MarkProposerFromList
-
- setListAdditionalChannelProviders(List<ChannelProvider>) - Method in class ScoreObjects
-
- setListAppend(List<NamedBean<DerivePath>>) - Method in class NamedChannelsAppend
-
- setListAppend(List<FilePathBaseAppendToManager>) - Method in class MultiInputManagerQuick
-
Additional entities that are appended to the multi-input
- setListFeatures(List<NamedBean<FeatureListProvider<FeatureInputStack>>>) - Method in class BinaryClassifierImageLabeller
-
- setListImageFeatures(List<NamedBean<FeatureListProvider<FeatureInputStack>>>) - Method in class EnergySchemeCreatorByElement
-
- setListPaths(StringList) - Method in class SpecificPathList
-
If specified, this forms the list of paths which is provided as input.
- setListReportFeatures(List<ReportFeature<ImageInitialization>>) - Method in class ExportReportFeatures
-
- setListStackProvider(List<NamedBean<StackProvider>>) - Method in class ExportObjectsAsCroppedImages
-
The channels we extract the object-masks from - all assumed to be of same dimension
- setListStackProviderMIP(List<NamedBean<StackProvider>>) - Method in class ExportObjectsAsCroppedImages
-
The channels we extract the object-masks from - all assumed to be of same dimension
- setLocalized(boolean) - Method in class FilesProviderWithDirectoryString
-
- setLog(LoggingDestination) - Method in class OnlyIf
-
The logger to use if conditions are fulfilled
- setLogExperiment(LoggingDestination) - Method in class OutputExperiment
-
Where log messages that do not pertain to a specific job (input) appear.
- setLogExperimentPath(String) - Method in class QuickMultiDatasetExperiment
-
Relative path to a logger for the experiment in gneeral
- setLoggerTaskCreator(LoggingDestination) - Method in class ParametersExperiment
-
This is a means to create new log-reporters for each task.
- setLogPath(boolean) - Method in class Rooted
-
if true, the pathIn and pathOut are logged.
- setLogTask(LoggingDestination) - Method in class InputOutputExperiment
-
Where log messages that do pertain to a specific job (input) appear.
- setLogTaskPath(String) - Method in class QuickMultiDatasetExperiment
-
Relative path to a logger for a specific task
- setMainChannelIndex(int) - Method in class NamedChannelsQuick
-
Index of the mainChannel
- setMainChannelName(String) - Method in class NamedChannelsQuick
-
The name of the channel provided by the rasters in file Provider
- setMap(StringMap) - Method in class ImageLabellerStringMap
-
- setMarkBounds(MarkBounds) - Method in class MarkBoundsDefine
-
- setMarkBounds(MarkBounds) - Method in class SegmentThresholdAboveMinBound
-
- setMarkEvaluator(NamedBean<MarkEvaluator>) - Method in class MarkProposerStrategy
-
A mark-evaluator that is added to the GUI to support this annotation
- setMarkFactory(MarkWithIdentifierFactory) - Method in class MarkEvaluator
-
- setMarkFactory(MarkWithIdentifierFactory) - Method in class SegmentWithMarkedPointProcess
-
Creates a new mark, before perhaps further manipulations by a kernel.
- setMarkFactory(MarkFactory) - Method in class FitPointsFromObjects
-
- setMarkFromMarksProposer(MarkFromCollectionProposer) - Method in class KernelSplit
-
- setMarkProposer(String) - Method in class MarkProposerStrategy
-
- setMarkProposer(MarkProposer) - Method in class FromMarkProposer
-
- setMarkProposer(MarkProposer) - Method in class MergeMarkEllipse
-
- setMarkProposer(MarkProposer) - Method in class KernelBirthAndKill
-
- setMarkProposer(MarkProposer) - Method in class KernelExchange
-
- setMarkProposer(MarkProposer) - Method in class KernelBirthVoxelized
-
- setMarkProposerAdditionalBirth(MarkProposer) - Method in class KernelBirthAndKill
-
- setMarkProvider(SingleMarkProvider) - Method in class CreateMarkFromPoints
-
- setMarkProvider(SingleMarkProvider) - Method in class ReportFeatureOnMark
-
- setMarkProvider(SingleMarkProvider) - Method in class FromSingleMark
-
- setMarkProvider(Provider<Optional<Mark>>) - Method in class RequireFeatureRelationThreshold
-
- setMarks(MarkCollection) - Method in class MarksWithTotalEnergy
-
The marks
- setMarks(MarkCollectionProvider) - Method in class ReportFeatureOnMarks
-
- setMarks(MarkCollection) - Method in class MarksWithDisplayStack
-
- setMarks(Point2d, Orientation) - Method in class Ellipse
-
- setMarks(MarkCollectionProvider) - Method in class FromMarks
-
- setMarks(MarkCollectionProvider) - Method in class ScaleXY
-
- setMarks(MarkCollectionProvider) - Method in class RetrieveSingleMarkOnly
-
- setMarks(MarkCollectionProvider) - Method in class ColoredMarks
-
- setMarksColored(ColoredMarks) - Method in class ColoredMarksWithDisplayStack
-
- setMarksExplicit(Point3d, Orientation, Point3d) - Method in class ConicBase
-
- setMarksExplicit(Point3d, Orientation) - Method in class ConicBase
-
- setMarksExplicit(Point3d) - Method in class ConicBase
-
- setMarksExplicit(Point3d, Orientation, Point2d) - Method in class Ellipse
-
- setMarksExplicit(Point3d) - Method in class Ellipse
-
- setMarksExplicit(Point3d, Orientation) - Method in class Ellipse
-
- setMarksExplicit(Point3d, Orientation, Point3d) - Method in class Ellipse
-
- setMarksExplicit(Point3d, Orientation, Point3d) - Method in class Ellipsoid
-
- setMarksExplicit(Point3d) - Method in class Ellipsoid
-
- setMarksExplicit(Point3d, Orientation) - Method in class Ellipsoid
-
- setMarksProposer(MarkCollectionProposer) - Method in class KernelInitialMarksFromPartition
-
- setMarksProposer(MarkCollectionProposer) - Method in class KernelInitialMarksProposed
-
- setMarksProposer(MarkCollectionProposer) - Method in class KernelInitialMarksVoxelized
-
- setMask(Provider<Mask>) - Method in class MaskProviderUnary
-
The delegate Provider<Mask>
that is called.
- setMask(MaskProvider) - Method in class FromMaskBase
-
- setMask(MaskProvider) - Method in class UnaryWithMaskBase
-
- setMask(MaskProvider) - Method in class ScoreVoxels
-
- setMask(MaskProvider) - Method in class FromChannel
-
- setMask(MaskProvider) - Method in class SegmentChannel
-
An optional mask which restricts the algorithm to only parts of the channel where the mask
has an on voxel
- setMask(Provider<Mask>) - Method in class ConnectedComponentsFromMask
-
- setMask(MaskProvider) - Method in class AndObjectsWithMasks
-
- setMask(Provider<Mask>) - Method in class FromMask
-
- setMask(MaskProvider) - Method in class SegmentChannel
-
- setMask(MaskProvider) - Method in class ColoredMask
-
- setMask(Provider<Mask>) - Method in class FromChannelOrMask
-
A mask that is provided to the stack.
- setMask(MaskProvider) - Method in class PairedWithMask
-
- setMask(MaskProvider) - Method in class MaskAsSingleObject
-
- setMask(MaskProvider) - Method in class FillHoles
-
- setMask(Provider<Mask>) - Method in class CheckMarkWithMask
-
- setMask(Provider<Mask>) - Method in class FindPointOnContourWalk
-
- setMask(Provider<Mask>) - Method in class XYOrientationExtendToZ
-
- setMaskContour(Provider<Mask>) - Method in class TraverseOuterContourOnImage
-
- setMaskElse(MaskProvider) - Method in class IfPredicateBase
-
Returned instead of mask
if the predicate is not satisfied
- setMaskFilled(Provider<Mask>) - Method in class TraverseOuterContourOnImage
-
- setMaskFilled(Provider<Mask>) - Method in class XYOrientationExtendToZ
-
- setMaskIndex(int) - Method in class SurfaceSizeMaskNonZero
-
- setMaskValue(int) - Method in class ExportImageHistograms
-
What voxel value to read as "On" in the mask above.
- setMaskValue(int) - Method in class OverlapMaskBase
-
- setMatch(String) - Method in class FilterCSVColumn
-
- setMatch(String) - Method in class MatchedAppendCsv
-
- setMatcher(FilePathMatcher) - Method in class SearchDirectory
-
- setMatcher(FilePathMatcher) - Method in class MatchExtensions
-
A secondary matcher, which is required additionally match (as well as the extension).
- setMatcher(ObjectMatcher) - Method in class RelationWithMatches
-
- setMatcher(ObjectMatcher) - Method in class ObjectWithMaximumFeatureFromEachMatchedCollection
-
- setMatcher(ObjectMatcher) - Method in class Match
-
- setMax(double) - Method in class BoundMinMax
-
- setMax(double) - Method in class ResolvedBound
-
- setMax(int) - Method in class ScaleByMinMaxValue
-
- setMax(int) - Method in class ClampHistogramMax
-
- setMax(UnitValueExtent) - Method in class UnitsWithinRange
-
Maximum-boundary for acceptable range
- setMax(boolean) - Method in class IdentityImposeValueRelationToHistogram
-
- setMax(int) - Method in class OutsideRange
-
- setMax(double) - Method in class MaxOverlapRatio
-
- setMax(double) - Method in class InvertedMax
-
- setMax(Feature<T>) - Method in class CompareWithRangeFeature
-
Calculates maximally-allowed range boundary
- setMax(double) - Method in class RangeCompareFromScalars
-
Boundary value indicating maximally-allowed range value
- setMaxCost(double) - Method in class MultipleComparer
-
The maximum cost (as calculated by featureEvaluator
) to accept when creating an
assignment between objects.
- setMaxCost(double) - Method in class FeatureCostAssigner
-
- setMaxDirectoryDepth(int) - Method in class SearchDirectory
-
If non-negative the max depth of directories.
- setMaxDirectoryDepth(int) - Method in class ExperimentResultsExperimentStructure
-
- setMaxDistance(UnitValueDistance) - Method in class MergeWithOptionalDistanceConstraint
-
An optional maximum distance
- setMaxDistance(UnitValueDistance) - Method in class CostOverlapWithinMidpointDistance
-
- setMaxDistance(UnitValueDistance) - Method in class FindPointOnContourWalk
-
- setMaxDistanceBetweenMinima(UnitValueDistance) - Method in class AddDistanceTransform
-
- setMaxDistanceCOG(UnitValueDistance) - Method in class MergeSpatialClusters
-
The maximum distance allowed between center-of-gravities of objects
- setMaxDistanceDeltaContour(double) - Method in class AddDistanceTransform
-
The maximum distance allowed between two seeds in terms of their values in the distance map
- setMaxDistanceDeltaContour(double) - Method in class MergeSpatialClusters
-
The maximum distance allowed between the 'distance from contour' values provided from the
distanceMap for each point.
- setMaxDistanceProposer(ScalarProposer) - Method in class VisitSchedulerMaxDistanceAlongContour
-
- setMaxDistanceZ(ScalarProposer) - Method in class XYOrientationExtendToZ
-
- setMaximumNumberChannels(int) - Method in class IntensityMoments
-
An upper limit on the number of channels in the energy-stack for which we create features.
- setMaxIter(int) - Method in class Repeat
-
- setMaxIter(int) - Method in class Repeat
-
- setMaxIter(int) - Method in class Repeat
-
- setMaxIter(int) - Method in class RadiiProposerRepeat
-
- setMaxNumberItems(int) - Method in class Limit
-
- setMaxNumberItems(int) - Method in class Limit
-
- setMaxNumberProcessors(int) - Method in class DebugDependentProcessor
-
An upper limit on the number of the processors that can be simultaneously used in parallel,
if they are available.
- setMaxNumberProcessors(int) - Method in class ParallelProcessor
-
Theoretical maximum number of (CPU) processors to use in parallel.
- setMaxNumberProcessors(int) - Method in class QuickMultiDatasetExperiment
-
An upper limit on the number of the processors that can be simultaneously used in parallel,
if they are available.
- setMaxNumberProcessors(int) - Method in class QuickMultiDatasetStructuredExperiment
-
- setMaxNumItems(int) - Method in class LimitWithDirectory
-
- setMaxPathWidth(int) - Method in class ExtractIdentifierAndPath
-
The maximum width permitted for an identifier, so that it is printed as one line.
- setMaxSize(long) - Method in class Mser
-
- setMaxSplitGroups(int) - Method in class CompareAnnotations
-
- setMaxValue(long) - Method in class ToUnsignedByteScaleByMaxValue
-
Assigns the maximum-value that will be represented in the scaled-values.
- setMaxVar(double) - Method in class Mser
-
- setMaxVolume(UnitValueExtent) - Method in class FillHoles
-
- setMaxX(int) - Method in class Box
-
Maximum X coordinate inclusive.
- setMaxY(int) - Method in class Box
-
Maximum Y coordinate inclusive.
- setMaxZ(int) - Method in class Box
-
Maximum Z coordinate inclusive.
- setMean(double) - Method in class MeanScale
-
The mean.
- setMedian(boolean) - Method in class AddEdgeFilters
-
If true, the median filter is included.
- setMedianRadiusMeters(double) - Method in class AddEdgeFilters
-
- setMerge(boolean) - Method in class CutBelowThreshold
-
- setMergedPosTolerance(double) - Method in class MergeMarkEllipse
-
- setMergeMarkProposer(MarkMergeProposer) - Method in class KernelMerge
-
- setMessage(String) - Method in class ReportFeatureWrapError
-
- setMessageNoInputs(String) - Method in class InputOutputExperiment
-
A message written to the logger if no inputs exist for the experiment, and it thus ends
early.
- setMethod(String) - Method in class AutoLocalThreshold
-
- setMethod(String) - Method in class ThresholderAutoIJ
-
One of the following strings to identify ImageJ's thresholding algorithms (or an empty string
for the default).
- setMethod(CopyFilesMethod) - Method in class CopyFiles
-
How the copying occurs from source to destination file.
- setMin(double) - Method in class BoundMinMax
-
- setMin(double) - Method in class ResolvedBound
-
- setMin(int) - Method in class ScaleByMinMaxValue
-
- setMin(UnitValueExtent) - Method in class UnitsWithinRange
-
Minimum-boundary for acceptable range
- setMin(int) - Method in class OutsideRange
-
- setMin(double) - Method in class RadiiMinRatio
-
- setMin(Feature<T>) - Method in class CompareWithRangeFeature
-
Calculates minimally-allowed range boundary
- setMin(double) - Method in class RangeCompareFromScalars
-
Boundary value indicating minimally-allowed range value
- setMinConfidence(double) - Method in class ThresholdConfidence
-
The minimum confidence of an element for its object-mask to be initially included for
consideration (before merging).
- setMinConfidence(float) - Method in class DecodeMaskRCNN
-
Only proposals outputted from the model with a score greater or equal to this threshold are
considered.
- setMinConfidence(double) - Method in class DecodeEAST
-
Proposed bounding boxes below this confidence interval are removed from consideration.
- setMinDiff(double) - Method in class MeanIntensityDifference
-
- setMinDifference(int) - Method in class Difference
-
A minimum difference, below which 0.0 is returned
- setMinDifference(int) - Method in class DifferenceCalculateLevelStandardDeviation
-
- setMinDiversity(double) - Method in class Mser
-
- setMinimaImposition(MinimaImposition) - Method in class ImposeMinima
-
- setMinimumBoundingBoxVolume(int) - Method in class FloodFillEachIntensityLevel
-
Only objects whose bounding-box volume is greater or equal to this threshold are included.
- setMinimumPerCluster(int) - Method in class ClusterByTimestamp
-
The minimum number of files that must exist for a cluster.
- setMinIntensity(int) - Method in class RejectIfIntensityLessThan
-
- setMinIntensity(int) - Method in class ThresholderSimpleFillHoles2D
-
Intensity for thresholding
- setMinIntensityValue(int) - Method in class MorphologicalOperatorBase
-
- setMinMaskValue(float) - Method in class DecodeMaskRCNN
-
Only voxels with a value greater or equal to this threshold are considered as part of the
mask.
- setMinMaxValues(long, long) - Method in class ToUnsignedByteScaleByMinMaxValue
-
Assigns the minimum- and maximum-values which existing values are scaled against.
- setMinNumberObjects(int) - Method in class DiscardOutliers
-
- setMinNumberPoints(int) - Method in class SplitContourAtSaddlePoints
-
If a contour has less than this number of points, we don't split it, and return it as-is
- setMinNumberVoxels(int) - Method in class SplitIntoSquares
-
Only includes squares that have at least this number of voxels.
- setMinNumberVoxels(int) - Method in class ConnectedComponentsFromBinarySegmentation
-
- setMinNumberVoxels(int) - Method in class ThresholdConfidence
-
The minimum number of voxels that must exist in a connected-component to be included.
- setMinNumPoints(int) - Method in class CreateMarkFromPoints
-
- setMinNumPoints(int) - Method in class PointsFitterToMark
-
If an object has fewer points than before being fitted, we ignore
- setMinNumSlices(int) - Method in class XYOrientationExtendToZ
-
- setMinNumZSlices(int) - Method in class AtLeastZSlices
-
- setMinOverlap(double) - Method in class CostOverlapWithinMidpointDistance
-
- setMinRadius(double) - Method in class LinearLeastSquaresEllipseFitter
-
- setMinRadius(double) - Method in class LinearLeastSquaresEllipsoidFitter
-
- setMinRatio(double) - Method in class DiscardOutliers
-
- setMinResolution(double) - Method in class MinimumXYResolution
-
- setMinSize(long) - Method in class Mser
-
- setMinVal(double) - Method in class FeatureValueCheckMark
-
- setMinVolume(UnitValueExtent) - Method in class ConnectedComponentsFromMask
-
- setMinVolume(UnitValueVolume) - Method in class VolumeMin
-
- setMinVolumeConnectedComponent(UnitValueVolume) - Method in class AddDistanceTransform
-
- setMinX(int) - Method in class Box
-
Minimum X coordinate inclusive.
- setMinY(int) - Method in class Box
-
Minimum Y coordinate inclusive.
- setMinZ(int) - Method in class Box
-
Minimum Z coordinate inclusive.
- setMip(boolean) - Method in class NumberVoxels
-
- setMip(boolean) - Method in class SurfaceNumberVoxelsBase
-
- setMip(boolean) - Method in class OverlapMIPBase
-
- setModelBinaryPath(String) - Method in class SegmentObjectsFromTensorFlowModel
-
Relative-path to the TensorFlow model file, likely with .pb
extension, relative
to the models/ directory in the Anchor distribution.
- setModelPath(String) - Method in class SegmentObjectsFromONNXModel
-
Relative-path to the model file in ONNX form, relative to the models/ directory in the
Anchor distribution.
- setModelTextGraphPath(String) - Method in class SegmentObjectsFromTensorFlowModel
-
Relative-path to the TensorFlow model file, likely with .pb.txt
extension,
relative to the models/ directory in the Anchor distribution.
- setMultipleComparer(MultipleComparer) - Method in class MarkProposerStrategy
-
- setMultipleOf(int) - Method in class FitTo
-
The eventual width and height of the image must be a multiple of this number.
- setMultiplyBy(float) - Method in class DistanceTransform3D
-
- setName(String) - Method in class FromXMLList
-
The name of the file in the current working directory WITHOUT THE .xml EXTENSION
- setName(String) - Method in class NamedBean
-
The name associated with item
.
- setName(String) - Method in class RootPath
-
The name of the root-path, which need not be unique in itself.
- setName(String) - Method in interface NameValue
-
Assigns the associated name.
- setName(String) - Method in class SimpleNameValue
-
- setName(String) - Method in class ExperimentIdentifierConstant
-
- setName(String) - Method in class IndexedChannel
-
The name of the
Channel
this entry represents.
- setName(String) - Method in class Kernel
-
- setName(String) - Method in class WeightedKernel
-
- setName(String) - Method in class AdjacentFile
-
A name to describe the adjacent file
- setName(String) - Method in class FilePathAppendBase
-
The name of the appended entity
- setNameLeft(String) - Method in class AnnotationComparisonInputManager
-
- setNamer(FileNamer) - Method in class GroupFiles
-
- setNamer(FileNamer) - Method in class RemoveExtension
-
- setNamer(FileNamer) - Method in class SubsetRangeIfRequested
-
The namer that is called to provide names that are subsetted.
- setNamer(FileNamer) - Method in class NamedFilesBase
-
- setNamer(FileNamer) - Method in class QuickBase
-
Assigns each input a unique compact name.
- setNameRight(String) - Method in class AnnotationComparisonInputManager
-
- setNaming(CopyFilesNaming<T>) - Method in class CopyFiles
-
How an output name (and path) is selected for an input file.
- setNavigateHigherDirectories(int) - Method in class MultiFileReader
-
Search x number directories higher than file.
- setNoBlack(boolean) - Method in class ThresholderAutoIJ
-
- setNormalize(boolean) - Method in class Identity
-
- setNormalize(boolean) - Method in class BoundingBoxZOverlapRatio
-
- setNormalizeFeatures(boolean) - Method in class FeatureListProviderSVMClassifier
-
Normalize features
- setNumberBins(int) - Method in class HOGParameters
-
The number of bins in each histogram for a cell.
- setNumberChannels(int) - Method in class ForceNumberChannels
-
- setNumberColumns(int) - Method in class Tile
-
The number of columns to use in the table produced when tiling.
- setNumberColumns(int) - Method in class CSVReader.OpenedCSVFile
-
Sets the number of columns, if it is already known from elsewhere.
- setNumberDecimalPlaces(int) - Method in class FeatureCostAssigner
-
- setNumberDigits(int) - Method in class IncrementingNumber
-
Number of digits in the number, with leading zeros as necessary.
- setNumberDilations(int) - Method in class LevelPerObjectIndependently
-
- setNumberFrames(int) - Method in class ForceNumberFrames
-
- setNumberGPUProcessors(int) - Method in class ParallelProcessor
-
How many GPU processors to use when this is possible as a substitute for a CPU processor
- setNumberLevelsGrouping(int) - Method in class CompareAnnotations
-
- setNumberLoopPoints(int) - Method in class SplitContourAtSaddlePoints
-
- setNumberRows(int) - Method in class Fill
-
The number of rows to use the montage, when sufficient images are available.
- setNumberRows(int) - Method in class Tile
-
The number of rows to use in the table produced when tiling.
- setNumberSubdirectories(int) - Method in class LastDirectories
-
How many directories to include in the name.
- setNumColumns(int) - Method in class TileWithLabels
-
- setNumMarks(int) - Method in class FromMarkProposer
-
- setObjectMatcher(ObjectMatcher) - Method in class Bridge
-
Used to match each intermediary-object to a final-object
- setObjects(Provider<ObjectCollection>) - Method in class ObjectCollectionProviderUnary
-
The delegate Provider<ObjectCollection>
that is called.
- setObjects(ObjectCollectionProvider) - Method in class OutputFeatureTable
-
The objects for which features are calculated.
- setObjects(ObjectCollectionProvider) - Method in class ReportFeatureOnObjectsBase
-
- setObjects(ObjectCollectionProvider) - Method in class DistanceTransformForEachObject3D
-
- setObjects(ObjectCollectionProvider) - Method in class LevelPerObjectBase
-
The objects for whom a level is calculated
- setObjects(ObjectCollectionProvider) - Method in class UnaryWithObjectsBase
-
- setObjects(ObjectCollectionProvider) - Method in class GenerateToMatchObjects
-
- setObjects(ObjectCollectionProvider) - Method in class FromObjects
-
- setObjects(ObjectCollectionProvider) - Method in class IntersectsWith
-
- setObjects(ObjectCollectionProvider) - Method in class Always
-
- setObjects(ObjectCollectionProvider) - Method in class Intersection
-
- setObjects(ObjectCollectionProvider) - Method in class Permute
-
- setObjects(ObjectCollectionProvider) - Method in class ColoredObjects
-
Objects to draw on a background
- setObjects(ObjectCollectionProvider) - Method in class ObjectAggregationBase
-
- setObjects(ObjectCollectionProvider) - Method in class FromObjects
-
- setObjects(ObjectCollectionProvider) - Method in class ObjectAsPoints
-
- setObjects(ObjectCollectionProvider) - Method in class IncludeRandomObjects
-
- setObjects(ObjectCollectionProvider) - Method in class PointsFromObjects
-
- setObjects(List<NamedBean<ObjectCollectionProvider>>) - Method in class FromObjects
-
- setObjects(ObjectCollectionProvider) - Method in class ExportObjectsBase
-
- setObjects(ObjectCollectionProvider) - Method in class PointsFitterToMark
-
- setObjects1(ObjectCollectionProvider) - Method in class MergeTwoCollectionsItemwise
-
First collection with items to be merged
- setObjects2(ObjectCollectionProvider) - Method in class MergeTwoCollectionsItemwise
-
Second collection with items to be merged
- setObjectsBlue(ObjectCollectionProvider) - Method in class ThreeColoredObjects
-
- setObjectsContainer(ObjectCollectionProvider) - Method in class WithContainerBase
-
- setObjectsElse(ObjectCollectionProvider) - Method in class ReferenceOrElse
-
- setObjectsGreater(ObjectCollectionProvider) - Method in class GreaterIntersectionWith
-
- setObjectsGreen(ObjectCollectionProvider) - Method in class ThreeColoredObjects
-
- setObjectsGrouped(ObjectCollectionProvider) - Method in class FilterByGroup
-
- setObjectsLesser(ObjectCollectionProvider) - Method in class GreaterIntersectionWith
-
- setObjectsRed(ObjectCollectionProvider) - Method in class ThreeColoredObjects
-
- setObjectsSeeds(ObjectCollectionProvider) - Method in class SegmentChannel
-
- setObjectsSeeds(ObjectCollectionProvider) - Method in class SegmentWithSeeds
-
- setObjectsSource(ObjectCollectionProvider) - Method in class AssignFromIntersectingObjects
-
- setObjectsSource(ObjectCollectionProvider) - Method in class SegmentWithSeeds
-
- setObjectsSplitBy(ObjectCollectionProvider) - Method in class SplitByObjects
-
- setObjectsTarget(ObjectCollectionProvider) - Method in class AssignFromIntersectingObjects
-
- setOfConnectedComponentIDs() - Method in class EncodedVoxels
-
- setOff(int, int, int) - Method in interface BinaryOnOffSetter
-
Assigns an off state to a voxel at a particular point.
- setOff(Point3i) - Method in interface BinaryOnOffSetter
-
Assigns an off state to a voxel at a particular point.
- setOn(int, int, int) - Method in interface BinaryOnOffSetter
-
Assigns an on state to a voxel at a particular point.
- setOn(Point3i) - Method in interface BinaryOnOffSetter
-
Assigns an on state to a voxel at a particular point.
- setOpenInDesktop(boolean) - Method in class ExperimentExecutor
-
Whether to open the output directory in the desktop GUI after execution (if supported on the
O/S).
- SetOperationFailedException - Exception in org.anchoranalysis.core.index
-
When a set operation fails for a particular key.
- SetOperationFailedException(String) - Constructor for exception SetOperationFailedException
-
Creates with only a message.
- SetOperationFailedException(Throwable) - Constructor for exception SetOperationFailedException
-
Creates with only a cause.
- setOptimization(OptimizationScheme<VoxelizedMarksWithEnergy, VoxelizedMarksWithEnergy, UpdatableMarksList>) - Method in class SegmentWithMarkedPointProcess
-
The optimization-scheme that determines which configurations are accepted/rejected from one
iteration to the next.
- setOptionList(List<KernelProposerOption<T, S>>) - Method in class KernelProposer
-
- setOptions(ReadOptions) - Method in class BioformatsReader
-
Options that influence how stack is read.
- setOptions(ReadOptions) - Method in class ReadOptionsDelegate
-
- setOrientationProposer(OrientationProposer) - Method in class OrientationAndRadiiProposer
-
- setOrientationXYProposer(OrientationProposer) - Method in class XYOrientationExtendToZ
-
- setOtherwise(FileNamer) - Method in class IfRelativeToDirectory
-
The namer to use if the relative-to-directory option is not selected.
- setOutline(boolean) - Method in class ColoredBase
-
If true, an outline is drawn around the entries.
- setOutlineAtBoundary(boolean) - Method in class ExteriorContour
-
- setOutlineColor(RGBColorBean) - Method in class SegmentInstanceWithModel
-
The color of the outline.
- setOutlinePixelsRetriever(TraverseOuterCounter) - Method in class TraversePointsOnContour
-
- setOutlinePixelsRetrieverReverse(TraverseOuterCounter) - Method in class TraversePointsOnContour
-
- setOutlineWidth(int) - Method in class Outline
-
The size of the outline, in terms of the number of voxels.
- setOutlineWidth(int) - Method in class CompareAnnotations
-
How many pixels should the outline be around objects.
- setOutlineWidth(int) - Method in class AtScale
-
- setOutlineWidth(int) - Method in class ColoredBase
-
The width of the outline (only relevant if outline==true
.
- setOutlineWidth(int) - Method in class OutlinePreserveRelativeSize
-
The width of the outline.
- setOutlineWidth(int) - Method in class SegmentInstanceWithModel
-
The width of the outline.
- setOutlineWidth(int) - Method in class VisualizeOnBackground
-
- setOutlineWidth(int) - Method in class ExportObjectsAsCroppedImages
-
- setOutPath(String) - Method in class InsertRegExGroups
-
Constructs a path as an output, replacing $1, $2 etc.
- setOutput(OutputManager) - Method in class OutputExperiment
-
The output-manager that specifies how/where/which elements occur duing outputting.
- setOutput(SelectParam<Optional<Path>>) - Method in class ExperimentExecutor
-
- setOutput(String) - Method in class QuickMultiDatasetExperiment
-
- setOutputName(String) - Method in class ToTextFileBase
-
The name to use (without extension) for the text-file log
- setOutputName(String) - Method in class OutputNameStyle
-
An identifier used in rules to determine if an output is enabled or not.
- setOutputName(String) - Method in class PeriodicSubdirectoryReporter
-
- setOutputName(String) - Method in class AggregateChannelTask
-
How to name the aggregated channel in the output.
- setOutputName(String) - Method in class MinimalExecutionTimeStatsReporter
-
- setOutputName(String) - Method in class VoxelizedMarksChangeReporter
-
- setOutputNameStyle(IndexableOutputNameStyle) - Method in class FromOutputName
-
- setOutputRGBOutline(StringSet) - Method in class ExportObjectsAsCroppedImages
-
- setOutputRGBOutlineFlattened(StringSet) - Method in class ExportObjectsAsCroppedImages
-
- setOutputsDisabled(StringSet) - Method in class SpecificDisabled
-
The names of the outputs that are disbled.
- setOutputsEnabled(StringSet) - Method in class SpecificEnabled
-
The names of the outputs that are enabled.
- setOutputsEnabled(OutputEnabledRules) - Method in class OutputManager
-
Which outputs are enabled or not enabled.
- setOutputShort(boolean) - Method in class GradientBase
-
Iff true, outputs a short channel, otherwise byte channel
- setOutputStackProvider(StackProvider) - Method in class ImageAssignLabel
-
If it's set, a stack is generated that is outputted into subdirectory corresponding to the
groupIdentifier.
- setOutputWriteSettings(OutputWriteSettings) - Method in class OutputManager
-
General settings (default file extensions, colors etc.) for outtping files.
- setOutputWriteSettings(OutputWriteSettings) - Method in class QuickExperiment
-
- setOutside(double) - Method in class UnitsWithinRange
-
Returned as a constant if a value lies otside the range
- setOutsideAtThreshold(boolean) - Method in class OutlineKernelBase
-
- setOverlappingObjects(boolean) - Method in class OutlinePreserveRelativeSize
-
Whether objects may overlap or not when unscaled.
- setOverlapRatioThreshold(double) - Method in class KernelBirthAndKill
-
- setPadding(Padding) - Method in class ExportObjectsBase
-
Padding placed on each side of the outputted image (if it's within the image)
- setPaddingXY(int) - Method in class Padding
-
Padding placed on each side of the outputted image (if it's within the image) in XY
directions
- setPaddingZ(int) - Method in class Padding
-
Padding placed on each side of the outputted image (if it's within the image) in Z direction
- setPairAddCriteria(AddCriteriaPair) - Method in class EnergySchemeCreatorByElement
-
- setPairCollection(RandomCollection<MarkPair<Mark>>) - Method in class KernelMerge
-
- setPairTypeClass(Class<?>) - Method in class RandomCollectionWithAddCriteria
-
- setParam(P) - Method in class BeanInitializer
-
Sets the current parameters used for propagation.
- setParameters(Dictionary) - Method in class EnergyStack
-
The associated parameters.
- setParameters(HOGParameters) - Method in class HOGDescriptor
-
Parameters used for calculating HOG
- setParameters(HOGParameters) - Method in class HOGFeature
-
Parameters used for calculating HOG.
- setParamPrefix(String) - Method in class PermuteFeatureSequenceInteger
-
- setParamPrefixAppendNumber(boolean) - Method in class PermuteFirstSecondOrder
-
If true the constant is appended to the param prefix (a dot and a number)
- setPath(String) - Method in class RootPath
-
A path on a file-system to the directory, that defines the root.
- setPath(String) - Method in class RootedFilePath
-
- setPath(String) - Method in class StaticFilePath
-
- setPathAnnotation(DerivePath) - Method in class SinglePathStrategy
-
Derives the path to the corresponding annotation files, given a path to the image to be
annotated.
- setPathDefaultMarks(DerivePath) - Method in class MarkProposerStrategy
-
- setPathDictionary(DerivePath) - Method in class MarkProposerStrategy
-
- setPathLabel(DerivePath) - Method in class ImageCSVLabeller
-
Path to a CSV label file (comma-separated, with header, no quotes)
- setPathParser(FilePathParser) - Method in class GroupFiles
-
- setPaths(StringSet) - Method in class FileSetFromStringSet
-
- setPaths(List<DerivePath>) - Method in class FilterForExistingFiles
-
All files need to be present
- setPenaltyValue(double) - Method in class MaxOverlapRatio
-
- setPeriodTriggerBank(PeriodTriggerBank<T>) - Method in class FeedbackBeginParameters
-
- setPermutation(PermuteProperty<S>) - Method in class PermuteFeature
-
A permutation to apply.
- setPermutations(List<PermuteProperty<S>>) - Method in class PermuteFeature
-
A list of permutations to apply.
- setPermuteProperty(PermuteProperty<?>) - Method in class Permute
-
- setPermuteProperty(PermutePropertySequenceInteger) - Method in class PermuteFeatureSequenceInteger
-
- setPhysical(boolean) - Method in class UnitConverter
-
- setPoint(Point3i, int) - Method in class EncodedVoxels
-
- setPointConnectedComponentID(Point3i, int) - Method in class EncodedVoxels
-
- setPointDirection(Point3i, int, int, int) - Method in class EncodedVoxels
-
- setPoints(Point3i, Point3i) - Method in class LineSegment
-
- setPoints(Point3d, Point3d) - Method in class LineSegment
-
- setPointsFitter(PointsFitter) - Method in class CreateMarkFromPoints
-
- setPointsFitter(String) - Method in class MarkProposerStrategy
-
- setPointsFitter(PointsFitter) - Method in class FitPoints
-
- setPointsFitter(PointsFitterToMark) - Method in class FitPointsFromObjects
-
- setPointsFitter(PointsFitter) - Method in class PointsFitterToMark
-
- setPointsFitter(PointsFitter) - Method in class ReflectInAxesWithinDistance
-
- setPointsFromOrientationProposer(PointsFromOrientationProposer) - Method in class MergeLists
-
- setPointsFromOrientationXYProposer(PointsFromOrientationProposer) - Method in class XYOrientationExtendToZ
-
- setPointsProposer(PointsProposer) - Method in class FitPoints
-
- setPosition(Point3d) - Method in class MarkWithPosition
-
- setPositionProposer(PositionProposer) - Method in class Position
-
- setPositionProposer(PositionProposer) - Method in class Repeat
-
- setPower(double) - Method in class MeanRaisedToPower
-
- setPrefix(String) - Method in class DefineAdderWithPrefixBean
-
A prefix that is placed before the name of every bean created.
- setPrefix(boolean) - Method in class FromXMLList
-
If true, a prefix is prepended to the name of each added bean.
- setPrefix(String) - Method in class PrependName
-
The string to prepend to the custom-name of each feature.
- setPrefix(String) - Method in class PathPrefixerAvoidResolve
-
A string prefixed to each output-path.
- setPrefix(String) - Method in class DirectoryWithPrefix
-
Always prepended to outputted filenames.
- setPrefix(String) - Method in class DeriveFromPair
-
- setPrefix(String) - Method in class FeatureListProviderAggregatePair
-
The string to prepend.
- setPrefix(String) - Method in class ExperimentStructure
-
- setPrefixer(PathPrefixer) - Method in class OutputManager
-
Determines a prefix to use when outputting a file based upon an input-path.
- setPrefixer(PathPrefixerAvoidResolve) - Method in class LastDirectoryAsPrefix
-
- setPrefixer(PathPrefixerAvoidResolve) - Method in class Rooted
-
- setPrefixerElse(PathPrefixerAvoidResolve) - Method in class IfIncrementingNumberRequested
-
Called if the requested condition is not true.
- setPrefixerIf(PathPrefixerAvoidResolve) - Method in class IfIncrementingNumberRequested
-
Called if the requested condition is true.
- setPrefixToRemove(String) - Method in class DirectoryStructure
-
- setPrependColor(RGBColorBean) - Method in class Prepend
-
The color to prepend.
- setPreserveAspectRatio(boolean) - Method in class Grow
-
Whether to preserve the aspect-ratio of the smaller image when growing.
- setPreserveAspectRatio(boolean) - Method in class FitTo
-
If true, the aspect-ratio is preserved between width and height.
- setPreserveAspectRatio(boolean) - Method in class ToDimensions
-
If true, the ratio between x and y is kept constant when scaling.
- setPreserveExtensionIfDuplicate(boolean) - Method in class RemoveExtension
-
Keeps the extension if the file-name (without the extension) becomes duplicated with another.
- setPreserveSubdirectories(boolean) - Method in class ClusterByTimestamp
-
If true, the entire relative-path is used when copying files into the cluster directory.
- setPrioritizeInputContext(boolean) - Method in class MatchExtensions
-
When true, any extensions available in the input-context are prioritized ahead of extensions
.
- setProbNeg(double) - Method in class KernelPosNeg
-
- setProbPos(double) - Method in class KernelPosNeg
-
- setProperty(String, T) - Method in class ObjectWithProperties
-
Assigns a value to a property with a particular name.
- setPropertyPath(String) - Method in class PermuteProperty
-
Either a direct property of a bean or a nested-property with the children separated by
full-stops.
- setProposal(boolean) - Method in class VoxelizedMarksPeriodicReporter
-
- setProposer(MarkFromCollectionProposer) - Method in class MarkFromCollectionProposerUnary
-
- setProposer(MarkProposer) - Method in class MarkProposerUnary
-
- setProvider(MarkCollectionProvider) - Method in class FromProvider
-
- setPxlPartMemo(EnergyMemoList) - Method in class FeatureInputAllMemo
-
- setPxlPartMemo(VoxelizedMarkMemo) - Method in class FeatureInputSingleMemo
-
- setQuantile(double) - Method in class Quantile
-
The quantile.
- setQuantile(double) - Method in class QuantileStretch
-
- setQuantile(double) - Method in class Quantile
-
- setQuantile(double) - Method in class DiscardOutliers
-
- setQuantile(double) - Method in class Quantile
-
- setQuantile(double) - Method in class QuantileAcrossObjects
-
- setQuantile(double) - Method in class QuantileAcrossConnectedComponents
-
- setQuantileHigh(double) - Method in class Range
-
- setQuantileLow(double) - Method in class Range
-
- setQuantileLower(double) - Method in class IntensityQuantiles
-
The lower quantile to use as the lower-limit for the intensity range to display.
- setQuantileLower(double) - Method in class ToByteUpperLowerQuantileIntensity
-
- setQuantileUpper(double) - Method in class IntensityQuantiles
-
The lower quantile to use as the upper-limit for the intensity range to display.
- setQuantileUpper(double) - Method in class ToByteUpperLowerQuantileIntensity
-
- setRadiiProposer(RadiiProposer) - Method in class OrientationAndRadiiProposer
-
- setRadiiProposer(RadiiProposer) - Method in class RadiiProposerRepeat
-
- setRadius(double) - Method in class MarkWithPositionAndSingleRadius
-
- setRadius(int) - Method in class AutoLocalThreshold
-
- setRadius(double) - Method in class WithRadiusBase
-
- setRadiusBound(Bound) - Method in class UniformRandomRadiiProposer
-
- setRadiusInMeters(boolean) - Method in class WithRadiusBase
-
- setRadiusX(double) - Method in class FitResult
-
- setRadiusY(double) - Method in class FitResult
-
- setRadiusZ(double) - Method in class FitResult
-
- setRate(double) - Method in class Geometry
-
- setRatioHeightForLabel(double) - Method in class Montage
-
When label==true
, this determines the height of the label.
- setRatioRowsToColumns(double) - Method in class Montage
-
An ideal approximate ratio of the number of rows to the number of columns.
- setReader(StackReaderOrientationCorrection) - Method in class RotateImageToMatchEXIFOrientation
-
Reads the image that is subsequently flattened.
- setReaderMatching(StackReader) - Method in class BranchExtension
-
The reader to use if the extension matches.
- setReaderNotMatching(StackReader) - Method in class BranchExtension
-
The reader to use if the extension does not match.
- setReadFromResources(boolean) - Method in class SegmentObjectsFromONNXModel
-
When true, rather than reading modelPath
from the file-system, it is read from Java
resources on the class-path.
- setReceive(MaskProvider) - Method in class CombineBase
-
- setRecurseSubfolders(boolean) - Method in class MultiFileReader
-
- setRecursive(boolean) - Method in class SearchDirectory
-
If true the search is applied recursively over sub-directories.
- setRecursive(boolean) - Method in class ExperimentResultsExperimentStructure
-
Whether to apply the search recursively or not
- setRed(int) - Method in class RGBColorBean
-
Sets the red component value.
- setRed(int) - Method in class RGBColor
-
Sets the red component value.
- setRed(ChannelProvider) - Method in class ThreeChannels
-
- setReduce(ReduceElements<ObjectMask>) - Method in class SuppressNonMaximum
-
The algorithm for reducing the number of object-masks.
- setReduce(FeatureFromList<FeatureInputPairObjects>) - Method in class FeatureListProviderAggregatePair
-
Method for reducing all pairs into a single value e.g.
- setReferencePoissonIntensity(double) - Method in class MarkWithIdentifierFactory
-
- setReferences(StringSet) - Method in class ReferencingFeatureListProvider
-
The names of other feature-lists, whose features may be referenced by this feature.
- setReferencesFeatureListCreator(StringSet) - Method in class PermuteFeature
-
Makes sure a particular feature list creator is evaluated
- setReferencesList(String) - Method in class FeatureProviderReference
-
The name of the list in which the feature referenced by id
resides.
- setRegex(String) - Method in class RegularExpressionBase
-
- setRegEx(RegEx) - Method in class RegExMatcher
-
- setRegEx(RegEx) - Method in class PathRegEx
-
Regular expression to use to match path with at least one group in it.
- setRegEx(RegEx) - Method in class RemoveMatching
-
If a path matches a regular expression it is removed.
- setRegEx(RegEx) - Method in class Exclude
-
A regular-expression to be matched against the identifiers of inputs.
- setRegEx(RegEx) - Method in class InsertRegExGroups
-
The regular-expression to use for matching groups.
- setRegEx(RegEx) - Method in class JoinRegExGroups
-
- setRegex(String) - Method in class Replace
-
Regular expression to match against string
- setRegex(String) - Method in class QuickBase
-
A regular-expression applied to the image file-path that matches three groups.
- setRegEx(RegEx) - Method in class ExperimentStructure
-
- setRegexAdjacent(String) - Method in class NamedChannelsQuick
-
This needs to be set if there is at least one adjacentChannel.
- setRegExDirectory(String) - Method in class MultiFileReader
-
If non-empty a regular-expression is applied to directories.
- setRegExFile(String) - Method in class MultiFileReader
-
If non-empty a regular-expression is applied to files.
- setRegExString(String) - Method in class InsertRegExGroups
-
The regular-expression to use for matching groups, overloaded to handle legacy situations
where a string is supplied.
- setRegion(MarkRegion) - Method in class Thresholded
-
- setRegion(MarkRegion) - Method in class Intensity
-
- setRegionID(int) - Method in class VolumeMin
-
- setRegionID(int) - Method in class FromMarks
-
- setRegionID(int) - Method in class IndexedRegionBase
-
- setRegionID(int) - Method in class ColoredMarks
-
- setRegionID(int) - Method in class FeatureMarkRegion
-
- setRegionID(int) - Method in class FeatureSingleMemoRegion
-
- setRegionID(int) - Method in class FeaturePairMemoSingleRegion
-
- setRegionID(int) - Method in class KernelBirthAndKill
-
- setRegionMap(RegionMap) - Method in class EnergySchemeCreatorByElement
-
- setRegionMap(RegionMap) - Method in class FromMarks
-
- setRegionMap(RegionMap) - Method in class AsObject
-
- setRegionMap(RegionMap) - Method in class SurfaceSizeMaskNonZero
-
- setRegularExpression(String) - Method in class TimestampPattern
-
The regular-expression that checks a match and specifies groups for the encoded date-time.
- setRejectIterationIfAllLow(boolean) - Method in class Erode
-
- setRejectIterationIfDisconnected(boolean) - Method in class Erode
-
- setRelation(RelationBean) - Method in class RelationToConstant
-
The relation to the threshold, where the threshold forms the second operand.
- setRelation(RelationBean) - Method in class ObjectFilterRelation
-
- setRelation(RelationBean) - Method in class MergePairs
-
Relation to threshold
- setRelation(RelationBean) - Method in class IdentityImposeValueRelationToHistogram
-
- setRelation(RelationToThreshold) - Method in class RejectIfConditionXYResolution
-
A predicate defined by the relationship of the XY-resolution to a constant threshold.
- setRelation(RelationBean) - Method in class AddCriteriaFeatureRelationThreshold
-
- setRelation(RelationBean) - Method in class RequireFeatureRelationThreshold
-
- setRelativeForIdentifier(boolean) - Method in class InputContextParameters
-
If true, the entire filename or relative path (excluding extension) is used to determine a
unique identifier.
- setRemoveExtension(boolean) - Method in class FilePathPattern
-
if true, the extension is removed from paths before finding the pattern.
- setRemoveExtensionInDescription(boolean) - Method in class LastDirectories
-
Whether to remove the file-extension from the filename.
- setRemoveNaNColumns(boolean) - Method in class ExportFeaturesStyle
-
When true, columns containing all
Double.NaN
values are removed before outputting.
- setRemoveTouchingBorderXY(boolean) - Method in class FeatureCostAssigner
-
- setRepeats(int) - Method in class KernelBirth
-
Total number of births
- setRepeatZProvider(Provider<Stack>) - Method in class WriteText
-
Repeats the generated (2D) string in z, so it's the same z-size as intensityProvider
- setReplaceMatchesWithSolids(boolean) - Method in class CompareAnnotations
-
- setReplacement(String) - Method in class SubstituteRegularExpression
-
- setReplacement(String) - Method in class Replace
-
What to replace in the path
- setReplacement(String) - Method in class AdjacentFile
-
The replacement string used to determine the file
- setReplaceWithMidpoint(boolean) - Method in class MergeGreedyToIncreaseObjectFeature
-
- setReportFitterErrors(boolean) - Method in class FitPoints
-
- setRequireAllFilesMatch(boolean) - Method in class GroupFiles
-
- setRequireArguments(RequireArguments) - Method in class OnlyIf
-
The conditions that must be fulfilled
- setRequireArguments(RequireArguments) - Method in class FeedbackReceiverRequireArguments
-
- setRequireBBoxNeighbors(boolean) - Method in class MergeWithFeature
-
Requires for any potential merge that the bounding-boxes of the two objects must intersect or
touch
- setRequireTouching(boolean) - Method in class MergeWithFeature
-
Requires the object-masks to touch.
- setResizeTo(SizeXY) - Method in class GroupedStackBase
-
If set, each channel is scaled to a specific size before aggregation (useful for combining
different sized images).
- setResizeTo(SizeXY) - Method in class HOGDescriptor
-
The input-image is rescaled to this width/height before calculating HOG descriptors
- setResizeTo(SizeXY) - Method in class HOGFeature
-
The input is rescaled to this width/height before calculating HOG descriptors.
- setRestrictTo(MaskProvider) - Method in class Invert
-
If set, the inversion only occurs on a particular region of the mask, as determined by this
mask
- setRewardHigherSide(boolean) - Method in class GaussianCumulative
-
Treat the higher side as if it's the the fill cdf
- setRewardLowerSide(boolean) - Method in class GaussianCumulative
-
- setRgb(boolean) - Method in class FromChannelOrMask
-
If true, the output contains three channels (the input and two duplicates) instead of one
- setRoot1(double) - Method in class QuadraticEquationSolver.QuadraticRoots
-
The first root.
- setRoot2(double) - Method in class QuadraticEquationSolver.QuadraticRoots
-
The second root.
- setRootInStructure(boolean) - Method in class ExperimentResultsExperimentStructure
-
If true the directory structure is
ROOT/experiments/${ROOT_NAME}/${DATASET_NAME}_${DATASET_SUFFIX} If false, the directory
structure is ROOT/experiments/${DATASET_NAME}_${DATASET_SUFFIX}
- setRootName(String) - Method in class Rooted
-
The name of the root-path to associate with this fileset.
- setRootName(String) - Method in class RootedFilePath
-
- setRootName(String) - Method in class Rooted
-
- setRootName(String) - Method in class Rooted
-
- setRootName(String) - Method in class QuickBase
-
If non-empty then a rooted filesystem is used with this root
- setRootName(String) - Method in class RootedExperiment
-
Root-name assuming multi-rooted structure.
- setRootNameForStructure(String) - Method in class ExperimentResultsExperimentStructure
-
If rootInStructure==true, the rootName is placed in the folder structure.
- setRotationAngle(Bound) - Method in class BoundRotation2D
-
- setRotationX(Bound) - Method in class BoundRotation3D
-
- setRotationY(Bound) - Method in class BoundRotation3D
-
- setRotationZ(Bound) - Method in class BoundRotation3D
-
- setRotMatrix(DoubleMatrix2D) - Method in class FitResult
-
The rotation matrix, which must be considered immutable to be used here.
- setRow(int) - Method in class Cell
-
The row in the table that the cell refers to (zero-indexed).
- setSampleEvery(int) - Method in class SampleWithDirectory
-
- setScalarProposer(ScalarProposer) - Method in class MaxWithConstant
-
- setScalarProposer(ScalarProposer) - Method in class Scale
-
- setScale(double) - Method in class MeanScale
-
The scale, typically the standard-deviation.
- setScale(double) - Method in class MontageSlices
-
Whether to increase or reduce the size of the images
- setScaleCalculator(ScaleCalculator) - Method in class ScaleXY
-
- setScaleCalculator(ScaleCalculator) - Method in class ScaleXY
-
Determines how much to scale by.
- setScaleCalculator(ScaleCalculator) - Method in class Scale
-
- setScaleCalculator(ScaleCalculator) - Method in class AtScale
-
- setScaleCalculator(ScaleCalculator) - Method in class Invert
-
- setScaleCalculator(ScaleCalculator) - Method in class ScaleImage
-
Calculates what scale-factor to apply on the image.
- setScaleCalculator(ScaleCalculator) - Method in class ScaleXY
-
- setScaleFactor(double) - Method in class GradientBase
-
- setScaleInput(ScaleCalculator) - Method in class SegmentStackIntoObjectsScaleDecode
-
Any scaling to be applied to the input-image before being input to the model for inference.
- setScaleLower(double) - Method in class ScaleByDictionary
-
- setScaleLower(double) - Method in class ToByteUpperLowerQuantileIntensity
-
Sets the min by multiplying the quantileLower by this constant.
- setScaleRadii(double) - Method in class ConicFitterBase
-
- setScaleUpper(double) - Method in class ScaleByDictionary
-
- setScaleUpper(double) - Method in class ToByteUpperLowerQuantileIntensity
-
Sets the max by multiplying the quantileUpper by this constant.
- setScore(VoxelScore) - Method in class ScoreVoxels
-
- setScoreProvider(FeatureListProvider<FeatureInputStack>) - Method in class ExtractSlice
-
- setScoreThreshold(double) - Method in class RemoveOverlappingObjects
-
Bounding boxes with scores above this threshold are removed.
- setSecond(boolean) - Method in class ExperimentIdentifierAuto
-
Only relevant if time==true.
- setSecond(List<NamedBean<StringSet>>) - Method in class OutputEnableRulesSpecify
-
Output-names in the second-level (for all first level output-names).
- setSecond(StateTransformerBean<U, T>) - Method in class Compose
-
Second transformation from U
to T
- setSecondary(boolean) - Method in class VoxelizedMarksPeriodicReporter
-
If proposal
is true, this toggles between the primary and secondary proposal
- setSecondary(StateTransformerBean<T, VoxelizedMarksWithEnergy>) - Method in class StateReporterToPixelized
-
- setSegment(BinarySegmentation) - Method in class BinarySegmentationUnary
-
- setSegment(SegmentChannelIntoObjects) - Method in class SegmentChannelIntoObjectsUnary
-
- setSegment(SegmentStackIntoObjectsPooled<T>) - Method in class SuppressNonMaximum
-
The segmentation algorithm that is applied as an input to non-maximum suppression.
- setSegment(BinarySegmentation) - Method in class SegmentChannel
-
Segmentation algorithm
- setSegment(SegmentChannelIntoObjects) - Method in class SegmentChannel
-
- setSegment(SegmentChannelIntoObjects) - Method in class SegmentChannelByObject
-
- setSegment(SegmentStackIntoObjectsPooled<T>) - Method in class SegmentStack
-
The segmentation procedure.
- setSegment(SegmentChannelIntoObjects) - Method in class SegmentWithSeeds
-
- setSegment(BinarySegmentation) - Method in class ConnectedComponentsFromBinarySegmentation
-
- setSegment(SegmentStackIntoObjectsPooled<T>) - Method in class SegmentInstanceWithModel
-
The segmentation algorithm.
- setSegment(SegmentIntoMarks) - Method in class SegmentMarksFromImage
-
How to perform the segmentation.
- setSegmentStack(BinarySegmentation) - Method in class SegmentOnMaximumIntensityAndExpandInZ
-
- setSelect(String) - Method in class DeriveFromPair
-
Either "merged" or "first" or "second" indicating which feature to delegate from
- setSelectChannels(FromStacks) - Method in class GroupedStackBase
-
Selects which channels are included, optionally renaming.
- setSeparateEachLabel(boolean) - Method in class SuppressNonMaximum
-
If true, each label is reduced separately.
- setSeperator(String) - Method in class CombineCSV
-
- setSequence(SequenceInteger) - Method in class PermutePropertySequence
-
A sequence of integers, with each element assigned assigned directly during the permutation,
or after further manipulation.
- setSequence(OutputSequenceIndexed<T, S>) - Method in class ChangeableOutputSequence
-
- setSeriesIndex(int) - Method in class FromStackReader
-
The series to open to the read the metadata (zero-indexed).
- setSharedState(S) - Method in class SharedStateRememberConverted
-
The shared state.
- setShell(double) - Method in class MarkEllipseFactory
-
- setShell(double) - Method in class MarkEllipsoidFactory
-
- setShell(double) - Method in class Ellipse
-
The size of the shell, expressed as a ratio of the radius.
- setShell(double) - Method in class Ellipsoid
-
- setShell(double) - Method in class FromObjects
-
- setShell(double) - Method in class CreateEllipse
-
- setShell(double) - Method in class ConicFitterBase
-
- setShowAgg(boolean) - Method in class MemoryUsageReporter
-
- setShowBest(boolean) - Method in class MemoryUsageReporter
-
- setShowOngoingJobsLessThan(int) - Method in class ParallelProcessor
-
When the number of ongoing jobs is less than this threshold, they are shown in event logs.
- setShuffle(boolean) - Method in class InputContextParameters
-
If true, the order of the inputs are shuffled (randomized).
- setSigma(double) - Method in class BlurStrategy
-
- setSigma(double) - Method in class GaussianBlur2D
-
- setSigmaInMeters(boolean) - Method in class BlurStrategy
-
- setSilentlyDeleteExisting(boolean) - Method in class OutputManager
-
Whether to silently first delete any existing output at the intended path, or rather throw an
error.
- setSimplePairCollectionID(String) - Method in class KernelMerge
-
- setSize(SizeXY) - Method in class WriteText
-
Explicit size of the image the string is draw on.
- setSize(double) - Method in class Aggregator
-
- setSize(SizeXY) - Method in class OutlinePreserveRelativeSize
-
Size of all created thumbnails
- setSize(SizeXY) - Method in class ScaleToSize
-
- setSizeXY(SizeXY) - Method in class SpecifyDimensions
-
Length of X and Y dimensions.
- setSizeZ(int) - Method in class SpecifyDimensions
-
Length of Z dimension.
- setSkipAtBorder(boolean) - Method in class FillHoles
-
If true we do not fill any objects that touch the border
- setSkipFileName(boolean) - Method in class LastDirectories
-
Iff true the filename is not considered, only the subdirectories.
- setSkipFileName(boolean) - Method in class FilePathAppendBase
-
- setSkipFirstTrim(int) - Method in class RemoveTrailingDirectory
-
- setSkipFirstTrim(int) - Method in class FilePathAppendBase
-
- setSkipMissingChannels(boolean) - Method in class NamedChannelsAppend
-
- setSkipNumberSubdirectories(int) - Method in class LastDirectories
-
Initially skip this number of directories before including them in the description.
- setSlice(ChannelProvider) - Method in class RepeatSlice
-
- setSliceFirst(int) - Method in class MontageSlices
-
First slice.
- setSliceID(int) - Method in class SelectSlicesBase
-
Index of slice to use, or -1 to use all slices
- setSliceIndex(int) - Method in class RepeatSlice
-
Which slice to use from mask
- setSliceLast(int) - Method in class MontageSlices
-
Last slice.
- setSlicesSeparately(boolean) - Method in class FitBoxToOnVoxels
-
- setSlicewise(boolean) - Method in class AggregateChannelTask
-
When true, a 3D image is added slice-by-slice to the aggregation, treating each slice as a
separate image.
- setSmoothingFactor(double) - Method in class SplitContourAtSaddlePoints
-
- setSortIfNotRequested(boolean) - Method in class ShuffleIfRequested
-
When true, the inputs are sorted alphabetically, if a shuffle is not requested.
- setSource(String) - Method in class StringMapItem
-
The origin of the mapping.
- setSource(FeatureSource<T, S, U>) - Method in class ExportFeatures
-
Source of feature-values to be exported.
- setSources(List<NamedBean<ComparableSource>>) - Method in class MultipleComparer
-
The other entities to compare with the annotation.
- setSplitIdentifierRegex(String) - Method in class CompareAnnotations
-
If non-empty, the string (a regular-expression) is used to split the file's identifier into
groups.
- setSplitProposer(MarkSplitProposer) - Method in class KernelSplit
-
- setSquareSize(int) - Method in class SplitIntoSquares
-
- setStack(Provider<Stack>) - Method in class StackProviderUnary
-
The delegate Provider<Stack>
that is called.
- setStack(Provider<Stack>) - Method in class StackProviderWithLabel
-
Provides the stack.
- setStack(DisplayStack) - Method in class ColoredMarksWithDisplayStack
-
- setStack(DisplayStack) - Method in class MarksWithDisplayStack
-
- setStack(ProviderAsStack) - Method in class FromStack
-
Provides a stack.
- setStack(ProviderAsStack) - Method in class SegmentStack
-
The stack to segment
- setStack(StackProvider) - Method in class ExportObjectsFromCSV
-
The stack that is the background for our objects
- setStackAsChannel(boolean) - Method in class MultiInputManagerQuick
-
If true, a raster-stack is treated as a single-channel, even if multiple exist (and no
additionalChannel is set)
- setStackBackground(boolean) - Method in class VisualizeOnBackground
-
- setStackEnergy(Provider<Stack>) - Method in class FeatureEvaluator
-
Optionally specifies an energy-stack to be associated with every calculation input.
- setStackEnergy(StackProvider) - Method in class FromImage
-
Optionally defines a energy-stack for feature calculation (if not set, the energy-stack is
considered to be the input stacks).
- setStackEnergy(StackProvider) - Method in class BinaryClassifierImageLabeller
-
- setStackEnergy(StackProvider) - Method in class ExtractSlice
-
- setStackEnergy(StackProvider) - Method in class DefineOutputterWithEnergy
-
- setStackID(String) - Method in class IfStackExists
-
- setStackName(String) - Method in class One
-
If defined, processing only occurs the stack with this specific name and index.
- setStackNameDefault(String) - Method in class AnnotationBackground
-
The name of the default stack from backgroundStackMap
to display as background when
annotating.
- setStackProviderID(String) - Method in class FromStack
-
Specifies the ID of an existing stack.
- setStackProviderID(String) - Method in class FromStackChannel
-
- setStackReader(StackReader) - Method in class AnnotatorStrategy
-
How to read raster
Stack
s from the file-system.
- setStackReader(StackReader) - Method in class FromStackReader
-
- setStackReader(StackReader) - Method in class InputManagerWithStackReader
-
How to read an image from the file-system.
- setStackReader(StackReader) - Method in class MaskAsObject
-
How to read the
Mask
from the file-system.
- setStackReader(StackReader) - Method in class Montage
-
Fallback for imageMetadataReader
to read image files without a directy metadata
reader.
- setStackReader(StackReader) - Method in class ScaleImageCommonSize
-
Fallback for imageMetadataReader
to read image files without a direct metadata
reader.
- setStackReader(StackReader) - Method in class FlattenAsChannel
-
Reads the image that is subsequently flattened.
- setStackReader(StackReader) - Method in class ImposeResolution
-
Reads an image before a resolution is imposed.
- setStackReader(StackReader) - Method in class MultiFileReader
-
- setStackReader(StackReader) - Method in class ReadVoxelExtentXml
-
Reads an image before a resolution is imposed.
- setStackReader(StackReader) - Method in class RejectIfConditionXYResolution
-
Reads an image before a resolution is imposed.
- setStackReaderAdjacent(StackReader) - Method in class NamedChannelsQuick
-
The raster-reader to use for opening any adjacent-channels
- setStackReaderAppend(StackReader) - Method in class QuickBase
-
The raster-reader for reading any appended files
- setStart(int) - Method in class SequenceInteger
-
The index to begin iteration from.
- setStartingIntensity(int) - Method in class FloodFillEachIntensityLevel
-
The first intensity-value to consider as a valid object (e.g.
- setStateReporter(StateReporter<T, S>) - Method in class TransformationAssignMode
-
- setStrategy(BlurStrategy) - Method in class Blur
-
- setStrongEdgeEnhancer(boolean) - Method in class AnisotropicDiffusion
-
If true uses, the strong-edge-enhancer diffusion function, otherwise the
wide-region-enhancer.
- setStyle(TextStyle) - Method in class WriteText
-
- setStyle(ExportFeaturesStyle) - Method in class ExportFeatures
-
Visual style for how feature export occurs.
- setStyle(ExportFeaturesStyle) - Method in class SegmentInstanceWithModel
-
Visual style for how feature export occurs.
- setSubdirectory(String) - Method in class AppendDictionary
-
- setSubdirectory(String) - Method in class ExperimentResultsExperimentStructure
-
If non-empty than an additional subdirectory is appended as a suffix
${DATASET_NAME}_${DATASET_SUFFIX}/${SUBDIRECTORY}/
- setSubtractConstant(int) - Method in class IntensityGradientBase
-
- setSubtractFromMaskOnly(boolean) - Method in class SubtractMean
-
- setSubtractMean(DoubleList) - Method in class SegmentStackIntoObjectsScaleDecode
-
A constant intensity for each respective channel to be subtracted before performing
inference.
- setSubtractRadii(double) - Method in class ConicFitterBase
-
- setSummarizer(Summarizer<S>) - Method in class SummarizerInputFromManager
-
- setSummarizer(Summarizer<S>) - Method in class SummarizeBase
-
- setSummarizerElse(Summarizer<T>) - Method in class SummarizerSplitMoreThan
-
Used for summary if count(elements) <= countThreshold
- setSummarizerGreaterThan(Summarizer<T>) - Method in class SummarizerSplitMoreThan
-
Used for summary if count(elements) > countThreshold
- setSuppress3D(boolean) - Method in class MorphologicalOperatorBase
-
- setSuppress3D(boolean) - Method in class SurfaceNumberVoxelsBase
-
- setSuppress3D(boolean) - Method in class SegmentThresholdAboveMinBound
-
- setSuppressDirectories(boolean) - Method in class FromDescriptiveName
-
If true, any directory separators in the identifier in a descriptive-name are replaced by
underscores.
- setSuppressErrors(boolean) - Method in class ExportFeaturesStyle
-
When false, an image is reported as errored, if any exception is thrown during calculation.
- setSuppressErrors(boolean) - Method in class FromObjects
-
When true, exceptions aren't thrown when feature-calculations fail, but rather a log error
message is written.
- setSuppressExceptions(boolean) - Method in class JobProcessor
-
When true, any exception thrown processing and input is caught and logged.
- setSuppressExceptions(boolean) - Method in class QuickMultiDatasetExperiment
-
- setSuppressExceptions(boolean) - Method in class QuickMultiDatasetStructuredExperiment
-
- setSuppressOutlineZ(boolean) - Method in class ColoredBase
-
if true, the outline is suppressed in the z-dimension i.e.
- setSuppressRes(boolean) - Method in class RadiiRatio
-
- setSuppressRootOut(boolean) - Method in class Rooted
-
if true, the root is not added to the outFilePath, and the path is instead localized against
the location of the BeanXML.
- setSuppressSeries(boolean) - Method in class ConvertImageFormat
-
If true, the series index is not included in the outputted file-names.
- setSuppressSubfolders(boolean) - Method in class DefineOutputter
-
- setSuppressZ(boolean) - Method in class BoundingBoxIntersection
-
- setSuppressZ(boolean) - Method in class DistanceTransform3D
-
- setSuppressZ(boolean) - Method in class DistanceTransformForEachObject3D
-
- setSuppressZ(boolean) - Method in class MergeWithOptionalDistanceConstraint
-
- setSuppressZ(boolean) - Method in class CostOverlapWithinMidpointDistance
-
- setSuppressZ(boolean) - Method in class ImageMomentsBase
-
If true co-voariance is suprpessed in z-dimension
- setSuppressZ(boolean) - Method in class CenterOnMask
-
- setSuppressZ(boolean) - Method in class UniformRandom
-
- setSuppressZ(boolean) - Method in class SurfaceSizeMaskNonZero
-
- setSuppressZ(boolean) - Method in class EllipsoidBase
-
Iff true, surpresses covariance in the z-direction.
- setSuppressZCovariance(boolean) - Method in class FromObjects
-
- setSuppressZCovariance(boolean) - Method in class LinearLeastSquaresEllipsoidFitter
-
- setTarget(String) - Method in class StringMapItem
-
The destination of the mapping.
- setTargetSize(SizeXY) - Method in class FitTo
-
The target size.
- setTask(Task<T, S>) - Method in class JobProcessor
-
The task to be applied to inputs.
- setTask(SelectParam<Optional<Path>>) - Method in class ExperimentExecutor
-
- setTask(Task<U, S>) - Method in class ConvertNamedChannels
-
The underlying task that will be called, perhaps with a different input-type.
- setTask(Task<MultiInput, S>) - Method in class QuickExperiment
-
- setTask(Task<T, S>) - Method in class QuickMultiDatasetExperiment
-
- setTask(Task<T, S>) - Method in class QuickMultiDatasetStructuredExperiment
-
- setTaskProcessor(JobProcessor<T, S>) - Method in class InputOutputExperiment
-
What task is associated with the experiment, and how it is processed.
- setTemperature(double) - Method in class OptimizationStep
-
- setTemplateMark(MarkFactory) - Method in class MarkWithIdentifierFactory
-
- setTermination(TerminationCondition) - Method in class SimulatedAnnealing
-
- setText(String) - Method in class WriteText
-
Text to draw on an image.
- setThreshold(double) - Method in class RelationToConstant
-
The constant threshold.
- setThreshold(int) - Method in class CutBelowThreshold
-
- setThreshold(int) - Method in class CalculateLevelRelativeToThreshold
-
- setThreshold(UnitValueDistance) - Method in class IntensityGreaterEqualThan
-
- setThreshold(double) - Method in class ThresholdedFeature
-
- setThreshold(UnitValueVolume) - Method in class ThresholdedVolume
-
- setThreshold(RelationToThreshold) - Method in class Count
-
- setThreshold(RelationToThreshold) - Method in class RatioThreshold
-
- setThreshold(double) - Method in class FeatureIntersectingObjectsThreshold
-
Only considers values greater or equal to the threshold
- setThreshold(double) - Method in class AddCriteriaFeatureRelationThreshold
-
- setThreshold(double) - Method in class RequireFeatureRelationThreshold
-
- setThreshold(RelationToThreshold) - Method in class GreatestAreaSlice
-
- setThreshold(RelationToThreshold) - Method in class Thresholded
-
- setThreshold(RelationToThreshold) - Method in class IfCondition
-
- setThresholder(Thresholder) - Method in class BinarySegmentationThreshold
-
Performs the global thresholding.
- setThresholder(Thresholder) - Method in class Threshold
-
The thresholder that will convert a channel into a binary-channel
- setThresholdHours(double) - Method in class ClusterByTimestamp
-
Files whose creation-time differs <=
this parameter are joined into the same cluster.
- setThresholdNumberObjectsGlobal(int) - Method in class ThresholdConfidence
-
When the number of objects is greater or equal than this, they are reduced globally, without
separation.
- setThrowExceptionForInsufficientPoints(boolean) - Method in class CreateMarkFromPoints
-
- setThumbnail(ThumbnailFromObjects) - Method in class CombineObjectsForFeatures
-
Generates a thumbnail representation of one or more combined objects, as form a single input.
- setThumbnail(ThumbnailFromStack) - Method in class FromImage
-
Method to generate a thumbnail for images.
- setTime(boolean) - Method in class ExperimentIdentifierAuto
-
If true, the current time (HH.mm.ss) is included in the output.
- setTimeIndex(int) - Method in class ConvertNamedChannelsToStack
-
- setTimeIndexGroupID(int) - Method in class RegularExpression
-
- setTimes(int) - Method in class Repeat
-
How many times to duplicate the list.
- setTimestampPatterns(List<TimestampPattern>) - Method in class ClusterByTimestamp
-
The patterns which can be used to extract a date-time from a filename.
- setTimeZoneOffset(int) - Method in class ClusterByTimestamp
-
If >= 0
, sets a specific time-offset in hours.
- setTitle(String) - Method in class ReportFeatureEvaluator
-
- setTolerance(int) - Method in class UnchangedScore
-
An exponent of 10 which determines a tolerance, less than which a score will be deemed
unchanged compared to another.
- setTransformer(StateTransformerBean<MarkCollection, T>) - Method in class RemovePartitionAndThen
-
- setTransformer(StateTransformerBean<T, VoxelizedMarksWithEnergy>) - Method in class VoxelizeWithTransform
-
- setTransformer(StateTransformerBean<T, VoxelizedMarksWithEnergy>) - Method in class KernelStateBridgePixelize
-
- setTransformerKernelToState(StateTransformerBean<U, T>) - Method in class KernelStateBridgeTransformer
-
- setTransformerMarks(StateTransformerBean<MarkCollection, VoxelizedMarksWithEnergy>) - Method in class AddDualTransformer
-
- setTransformerPrimary(StateTransformerBean<T, S>) - Method in class StateReporterTransformer
-
- setTransformerSecondary(StateTransformerBean<T, S>) - Method in class StateReporterTransformer
-
- setTransformerStateToKernel(StateTransformerBean<T, U>) - Method in class KernelStateBridgeTransformer
-
- setTransposed(boolean) - Method in class CombineCSV
-
- setTrimTrailingDirectory(int) - Method in class RemoveTrailingDirectory
-
- setTrimTrailingDirectory(int) - Method in class FilePathAppendBase
-
- setUniqueLabel(String) - Method in class AnnotationLabel
-
Label that uniquely identifies the ID (for machine purposes)
- setUnit(UnitConverter) - Method in class BoundingBoxExtent
-
- setUnit(UnitConverter) - Method in class FeatureSingleMemoRegion
-
- setUnitType(String) - Method in class DistancePhysical
-
A string indicating type of units to use, as per
SpatialUnits
.
- setUnitType(String) - Method in class AreaPhysical
-
How much each value represents e.g.
- setUnitType(String) - Method in class VolumePhysical
-
How much each value represents e.g.
- setUnitType(String) - Method in class FeatureConvertUnits
-
- setUnitType(String) - Method in class UnitConverter
-
- setUnitTypeFrom(String) - Method in class ConvertUnits
-
- setUnitTypeTo(String) - Method in class ConvertUnits
-
- setUnitValueDistance(UnitValueDistance) - Method in class FromUnitValueDistance
-
- setupBefore(Dimensions, ImageFileEncoding) - Method in class ConvertTo
-
- setupBefore(Dimensions, ImageFileEncoding) - Method in class FloatFromUnsignedByte
-
- setupDictionary(Dictionary) - Method in class FromDictionaryBase
-
- setUseLastSeriesIndexOnly(boolean) - Method in class NamedChannels
-
- setUseLastSeriesIndexOnly(boolean) - Method in class Stacks
-
- setUseMax(boolean) - Method in class OverlapRatio
-
- setUseMax(boolean) - Method in class OverlapRatioMask
-
- setUserFriendlyLabel(String) - Method in class AnnotationLabel
-
Descriptive user-friendly label displayed via GUI
- setUseZ(boolean) - Method in class RemoveTouchingBorder
-
- setUseZ(boolean) - Method in class TraverseOuterContourOnImage
-
- setValue(T) - Method in class NamedBean
-
- setValue(T) - Method in interface NameValue
-
Assigns the associated value.
- setValue(V) - Method in class SimpleNameValue
-
- setValue(double) - Method in class Constant
-
The constant value.
- setValue(double) - Method in class DistancePhysical
-
The value in units of type unitType
.
- setValue(double) - Method in class DistanceVoxels
-
The distance in units of voxels.
- setValue(double) - Method in class AreaPhysical
-
The volume in units of meters, with the unit described by unitType
.
- setValue(double) - Method in class AreaPixels
-
The volume in pixels.
- setValue(double) - Method in class VolumePhysical
-
The volume in units of meters, with the unit described by unitType
.
- setValue(double) - Method in class VolumeVoxels
-
The volume in voxels.
- setValue(double) - Method in class AssignValue
-
- setValue(int) - Method in class CreateNew
-
- setValue(double) - Method in class UnaryWithValueBase
-
- setValue(String) - Method in class DictionaryCondition
-
The value the key should have in the dictionary, in order for the condition to be fulfilled.
- setValue(int) - Method in class EmptyHistogramConstant
-
- setValue(String) - Method in class IfParamEqual
-
- setValue(double) - Method in class ConstantScaleFactor
-
The constant floating-point value to scale each dimension by.
- setValue(int) - Method in class CountEqual
-
- setValue(double) - Method in class IdentityImposeValueRelationToHistogram
-
- setValue(double) - Method in class NormalizeByConstant
-
- setValue(String) - Method in class Constant
-
- setValue(double) - Method in class Constant
-
- setValue(double) - Method in class WithValueBase
-
- setValueByDimension(int, double) - Method in class Tuple3d
-
Assigns a value to a component of the tuple corresponding to a particular dimension by index.
- setValueByDimension(int, float) - Method in class Tuple3f
-
Assigns a value to a component of a tuple corresponding to a particular dimension by index.
- setValueIfEmpty(double) - Method in class FeatureHistogramStatistic
-
The value to return iff exceptionifEmpty
is false.
- setValueIfTooFewVoxels(double) - Method in class ImageMomentsBase
-
A value to return if there are too few voxels (less than MIN_NUM_VOXELS
to calculate
moments
- setValueNoObject(int) - Method in class ScoreObjects
-
- setValueNoObjects(double) - Method in class FeatureIntersectingObjects
-
- setValues(DoubleSet) - Method in class PermutePropertyDoubleSet
-
The respect double values to assign during the permutation.
- setValues(StringSet) - Method in class PermutePropertyStringSet
-
The respect string values to assign during the permutation.
- setVaryColors(boolean) - Method in class SegmentInstanceWithModel
-
When true, the colors change for different objects in the image (using a default color set).
- setVaryImageLocation(boolean) - Method in class Montage
-
When true, the location of an image in the grid, as well as the number of images in each row
are both allowed to vary to fill space.
- setVaryImageSize(boolean) - Method in class Montage
-
When true, the images may vary in width/height in their respective rows to fill space, while
preserving the aspect-ratio of each image.
- setVaryingSizeWidth(int) - Method in class Montage
-
If no specific width or scaling-factor is suggested, this determines the default width that
the combined-montage should have, when varyImageSize==true
.
- setVaryingSizeWidthRatio(double) - Method in class Montage
-
If no specific width or scaling-factor is suggested, this determines the default percentage
of the existing size, the combined-montage should have, when varyImageSize==true
.
- setVaryNumberImagesPerRow(boolean) - Method in class Fill
-
When true the number of
Extent
s per row is allowed vary, to sensibly fill space.
- setVersion(String) - Method in class ExperimentIdentifierConstant
-
- setVisitScheduler(VisitScheduler) - Method in class TraverseOuterContourOnImage
-
- setVisuallyShortenDecimals(boolean) - Method in class ExportFeaturesStyle
-
When true, feature-values are shown as visually compressed as possible, including suppressing
decimal places.
- setWeight(double) - Method in class KernelProposerOptionSingle
-
- setWeightBackground(double) - Method in class OtsuWeighted
-
- setWeightForeground(double) - Method in class OtsuWeighted
-
- setWeightItem1Greater(double) - Method in class Range
-
- setWeightItem2Greater(double) - Method in class Range
-
- setWeightNegative(double) - Method in class KernelProposerOptionDual
-
- setWeightPositive(double) - Method in class KernelProposerOptionDual
-
- setWeightWidthDescription(int) - Method in class ImageLabelStrategy
-
- setWhenBinaryChannel(StackWriter) - Method in class BranchChannels
-
Writer employed if a stack is a single-channeled binary image.
- setWhenDetailed(LoggingDestination) - Method in class SwitchDetailedLogging
-
Logger to use when detailed-logging is on
- setWhenEqual(ObjectCollectionProvider) - Method in class IfParamEqual
-
- setWhenFalse(DrawObject) - Method in class IfElse
-
The
DrawObject
that is used when
condition==false
.
- setWhenNot(LoggingDestination) - Method in class SwitchDetailedLogging
-
Logger to use when detailed-logging is off
- setWhenNotEightBit(StackWriter) - Method in class BranchChannels
-
Writer employed if a stack contains channels that are not 8-bit.
- setWhenNotEqual(ObjectCollectionProvider) - Method in class IfParamEqual
-
- setWhenRelative(FileNamer) - Method in class IfRelativeToDirectory
-
The namer to use if the relative-to-directory option is selected.
- setWhenRGB(StackWriter) - Method in class BranchChannels
-
Writer employed if a stack is a three-channeled RGB image.
- setWhenRGBAlpha(StackWriter) - Method in class BranchChannels
-
Writer employed if a stack is a four-channeled RGBA image.
- setWhenSingleChannel(StackWriter) - Method in class BranchChannels
-
Writer employed if a stack is a single-channeled image, not guaranteed to be binary.
- setWhenThreeChannels(StackWriter) - Method in class BranchChannels
-
Writer employed if a stack is a three-channeled non-RGB image.
- setWhenTrue(DrawObject) - Method in class IfElse
-
- setWidth(int) - Method in class Fill
-
The width of the combined image in pixels.
- setWidth(int) - Method in class SizeXY
-
Size in X dimension.
- setWidth(double) - Method in class Difference
-
Width (what the difference is divided by)
- setWidth(double) - Method in class ImposeResolution
-
Physical pixel size of a voxel in x-dimension.
- setWidthFactor(double) - Method in class DifferenceCalculateLevelStandardDeviation
-
- setWidthRatio(double) - Method in class Fill
-
What fraction of the natural width of the elements should be used to determine the final
width.
- setWindowSize(int) - Method in class CenterSliceWindow
-
- setWindowSize(SizeXY) - Method in class HOGParameters
-
The window-size as per OpenCV implementation.
- setWithin(double) - Method in class UnitsWithinRange
-
Returned as a constant if a value lies within the range
- setWithinValue(double) - Method in class CompareWithRange
-
Constant to return if value lies within the range
- setWithinValue(double) - Method in class CompareWithRangeFeature
-
Constant to return if value lies within the range
- setWriter(DrawObject) - Method in class Flatten
-
- setWriter(StackWriter) - Method in class BranchChannels
-
Default writer, if a more specific writer is not specified for a condition.
- setWriter(StackWriter) - Method in class WriteResolutionXml
-
- setWriterAlways2D(StackWriter) - Method in class BranchStack
-
Writer to use if it is guaranteed that the image will always be 2D.
- setWriterElse(StackWriter) - Method in class BranchStack
-
Otherwise the writer to use.
- setWriterIfNoSuggestion(StackWriter) - Method in class BranchSuggestedFormat
-
The writer to use if there is no suggested file-format.
- setWriters(List<NamedBean<?>>) - Method in class OutputWriteSettings
-
Specifies a writer bean instance for a particular type of writer (identified by the writer
bean class)
- setWritersIfSuggested(List<StackWriter>) - Method in class BranchSuggestedFormat
-
A list of writers to select if a given format is used
- setX(double) - Method in class SpecifyVector
-
Component of the vector along the x-axis.
- setX(int) - Method in class Point2i
-
X-axis component of point.
- setX(int) - Method in class Tuple3d
-
X-axis component of the tuple.
- setX(double) - Method in class Tuple3d
-
X-axis component of the tuple.
- setX(int) - Method in class Tuple3i
-
X-axis component of the tuple.
- setY(double) - Method in class SpecifyVector
-
Component of the vector along the y-axis.
- setY(int) - Method in class Point2i
-
Y-axis component of point.
- setY(int) - Method in class Tuple3d
-
Y-axis component of the tuple.
- setY(double) - Method in class Tuple3d
-
Y-axis component of the tuple.
- setY(int) - Method in class Tuple3i
-
Y-axis component of the tuple.
- setZ(double) - Method in class SpecifyVector
-
Component of the vector along the z-axis.
- setZ(int) - Method in class Tuple3d
-
Z-axis component of the tuple.
- setZ(double) - Method in class Tuple3d
-
Z-axis component of the tuple.
- setZ(int) - Method in class Tuple3i
-
Z-axis component of the tuple.
- setZSliceGroupID(int) - Method in class RegularExpression
-
- setZSliceNum(int) - Method in class SortedSetSlice
-
- shallowCopy() - Method in class ColorList
-
Creates a new list, containing the same elements as the current list.
- shallowCopy() - Method in class GraphWithPayload
-
Creates a new graph with identical elements and structure, reusing the existing vertice and
edge data objects.
- shallowCopy() - Method in class RandomCollectionWithAddCriteria
-
- shallowCopy() - Method in class MarksWithEnergyBreakdown
-
- shallowCopy() - Method in class MarksWithTotalEnergy
-
Make a shallow copy
- shallowCopy() - Method in class VoxelizedMarksWithEnergy
-
Creates a shallow-copy of the marks
- shallowCopy() - Method in class EnergySavedAll
-
- shallowCopy() - Method in class EnergySavedInd
-
- shallowCopy() - Method in class EnergySavedPairs
-
- shallowCopy() - Method in class ColoredMarks
-
- shallowCopy() - Method in class MarkCollection
-
- shallowDuplicate() - Method in class FeatureList
-
Creates a new feature-list which contains identical elements.
- ShapeRegularityCenterSlice - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shape
-
- ShapeRegularityCenterSlice() - Constructor for class ShapeRegularityCenterSlice
-
- ShapeRegularityMIP - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shape
-
- ShapeRegularityMIP() - Constructor for class ShapeRegularityMIP
-
- SharedFeatures - Class in org.anchoranalysis.feature.shared
-
A group of features made available to other features to reference.
- SharedFeatures() - Constructor for class SharedFeatures
-
Create empty, without any features.
- SharedFeaturesSubset<T extends FeatureInput> - Class in org.anchoranalysis.feature.shared
-
A subset of features from
SharedFeatures
that share a common feature input-type.
- SharedFeaturesSubset(NameValueMap<Feature<T>>) - Constructor for class SharedFeaturesSubset
-
- SharedObjects - Class in org.anchoranalysis.core.identifier.provider.store
-
Objects shared between different components.
- SharedObjects(CommonContext) - Constructor for class SharedObjects
-
- sharedObjects() - Method in class ImageInitialization
-
Objects shared between different components, a form of shared memory between them.
- sharedObjectsRequired() - Method in class FeatureInitialization
-
Retrieves the shared-objects associated with the initialization, or throws an an exception if
they do not exist.
- SharedStateFilteredImageOutput<T> - Class in org.anchoranalysis.plugin.image.task.labeller
-
- SharedStateFilteredImageOutput(Outputter, ImageLabeller<T>, String, String) - Constructor for class SharedStateFilteredImageOutput
-
- SharedStateRememberConverted<U extends InputFromManager,S> - Class in org.anchoranalysis.plugin.mpp.experiment.shared
-
Shared-state that remembers converted inputs for corresponding unconverted inputs.
- SharedStateRememberConverted() - Constructor for class SharedStateRememberConverted
-
- SharedStateSegmentInstance<T extends InferenceModel> - Class in org.anchoranalysis.plugin.image.task.segment
-
Shared-state for instance segmentation
- SharedStateSegmentInstance(ConcurrentModelPool<T>, FeatureTableCalculator<FeatureInputSingleObject>, LabelHeaders, String, FeatureExporterContext) - Constructor for class SharedStateSegmentInstance
-
- SharedStateSelectedSlice - Class in org.anchoranalysis.plugin.image.task.stack
-
- SharedStateSelectedSlice(Outputter) - Constructor for class SharedStateSelectedSlice
-
- Shell - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.morphological
-
- Shell() - Constructor for class Shell
-
- shift() - Method in class SlidingBuffer
-
Increments the slice number by one.
- shiftBackBy(VoxelsAssigner, ReadableTuple3i) - Static method in class VoxelsAssignerFactory
-
Shifts all coordinates
backwards before passing to another
VoxelsAssigner
.
- shiftBackBy(ReadableTuple3i) - Method in class ObjectMask
-
Shifts the object-mask by moving its bounding-box backwards.
- shiftBackBy(ReadableTuple3i) - Method in class BoundingBox
-
Shifts the bounding-box backwards.
- shiftBy(T, ReadableTuple3i) - Method in interface AccessObjectMask
-
Positionally-shifts an element by a given quantity in the positive direction.
- shiftBy(ObjectMask, ReadableTuple3i) - Method in class AccessObjectMaskSimple
-
- shiftBy(ReadableTuple3i) - Method in class ObjectCollection
-
Shifts the bounding-box of each object by adding to it.
- shiftBy(ReadableTuple3i) - Method in class ObjectMask
-
Shifts the object-mask by moving its bounding-box forwards.
- shiftBy(ReadableTuple3i) - Method in class BoundingBox
-
Shifts the bounding-box forwards.
- shiftTo(ReadableTuple3i) - Method in class BoundingBox
-
Assigns a new corner-location to the bounding-box.
- shiftToOrigin() - Method in class ObjectMask
-
Creates a new object-mask with identical voxels but with the bounding-box beginning at the
origin (0,0,0).
- shiftToOrigin() - Method in class BoundingBox
-
Moves the bounding-box to the origin (0,0,0) but preserves the extent.
- shiftToZ(int) - Method in class BoundingBox
-
Assigns a new z-slice corner-location to the bounding-box.
- SHORT_OPTION_DEBUG - Static variable in class CommandLineOptions
-
Enables debug-mode: runs only the first available input [whose name contains string].
- SHORT_OPTION_GROUP - Static variable in class CommandLineOptions
-
Activates grouping from a subset of the identifier's elements.
- SHORT_OPTION_HELP - Static variable in class CommandLineOptions
-
Displays help message with all command-line options.
- SHORT_OPTION_INPUT - Static variable in class CommandLineOptions
-
Changes inputs.
- SHORT_OPTION_INPUT_COPY_NON_INPUTS - Static variable in class CommandLineOptions
-
Additionally copies any files in the input directory, unused as inputs.
- SHORT_OPTION_INPUT_LIMIT - Static variable in class CommandLineOptions
-
Imposes an upper limit on the number of inputs.
- SHORT_OPTION_INPUT_RANDOM_SAMPLE - Static variable in class CommandLineOptions
-
Randomly samples a number of inputs.
- SHORT_OPTION_INPUT_RELATIVE_PATH - Static variable in class CommandLineOptions
-
Derives the unique identifier from the **entire relative filename or path** (excluding file
extension).
- SHORT_OPTION_INPUT_SHUFFLE - Static variable in class CommandLineOptions
-
Shuffles the order of the inputs.
- SHORT_OPTION_INPUT_SUBSET_IDENTIFIER - Static variable in class CommandLineOptions
-
Subsets the identifier.
- SHORT_OPTION_LOG_ERROR - Static variable in class CommandLineOptions
-
Logs initial BeanXML errors in greater detail to a file-path.
- SHORT_OPTION_OUTPUT - Static variable in class CommandLineOptions
-
Changes output manager.
- SHORT_OPTION_OUTPUT_CONSOLE_ONLY - Static variable in class CommandLineOptions
-
Output console only.
- SHORT_OPTION_OUTPUT_DISABLE_ADDITIONAL - Static variable in class CommandLineOptions
-
Disables specific output(s).
- SHORT_OPTION_OUTPUT_ENABLE_ADDITIONAL - Static variable in class CommandLineOptions
-
Enables specific output(s).
- SHORT_OPTION_OUTPUT_ENABLE_ALL - Static variable in class CommandLineOptions
-
Enables all outputs.
- SHORT_OPTION_OUTPUT_IMAGE_FILE_FORMAT - Static variable in class CommandLineOptions
-
Suggests an output image file format: e.g -of jpg or -of ome.xml.
- SHORT_OPTION_OUTPUT_INCREMENTING_NUMBER - Static variable in class CommandLineOptions
-
Outputs with an incrementing number instead of the input identifier.
- SHORT_OPTION_OUTPUT_OMIT_EXPERIMENT_IDENTIFIER - Static variable in class CommandLineOptions
-
Ignores the experiment identifier, when forming an output-path.
- SHORT_OPTION_OUTPUT_SUPPRESS_DIRECTORIES - Static variable in class CommandLineOptions
-
Suppressed the subdirectory structure when outputting file identifiers.
- SHORT_OPTION_SHOW_EXPERIMENT_ARGUMENTS - Static variable in class CommandLineOptions
-
Shows additional argument information, otherwise executes as normal.
- SHORT_OPTION_SHOW_TASKS - Static variable in class CommandLineOptions
-
Prints the names of predefined tasks that can be easily used with -t.
- SHORT_OPTION_TASK - Static variable in class CommandLineOptions
-
Changes task.
- SHORT_OPTION_TASK_NUMBER_PROCESSORS - Static variable in class CommandLineOptions
-
Suggests a maximum number of processors to use for the task.
- SHORT_OPTION_TASK_SIZE - Static variable in class CommandLineOptions
-
Suggests dimensions or a scaling factor for certain tasks.
- SHORT_OPTION_VERSION - Static variable in class CommandLineOptions
-
Displays version and authorship information.
- shouldObjectsBeProcessed(ObjectMask, ObjectMask) - Method in class ReduceElementsGreedy
-
Whether to include another (possibly-overlapping with source
) element in processing?
- shouldObjectsBeProcessed(ObjectMask, ObjectMask) - Method in class RemoveOverlappingObjects
-
- shouldOverwriteVoxelWithConstant(int, int) - Method in class ArithmeticWithConstantConditionallyWriteBase
-
Whether to overwrite the current voxel-value with the constant?
- shouldOverwriteVoxelWithConstant(int, int) - Method in class MaxWithConstant
-
- shouldOverwriteVoxelWithConstant(int, int) - Method in class MinWithConstant
-
- shouldVisitPoint(Point3i, int) - Method in interface ConsiderVisit
-
Determines whether to visit a point or not.
- shrinkBy(ReadableTuple3i) - Method in class Extent
-
Creates a new
Extent
with
toSubtract
size
subtracted from each
respective dimension.
- Shuffle - Class in org.anchoranalysis.bean.shared.color.scheme
-
Randomizes the order of colors in a list created by another
ColorScheme
.
- Shuffle(ColorScheme) - Constructor for class Shuffle
-
- Shuffle() - Constructor for class Shuffle
-
- shuffle() - Method in class ColorList
-
Randomize the order of the colors in the list.
- Shuffle<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input
-
Randomly shuffles the order of the inputs.
- Shuffle() - Constructor for class Shuffle
-
- ShuffleIfRequested<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input
-
- ShuffleIfRequested() - Constructor for class ShuffleIfRequested
-
- SignedShortVoxelType - Class in org.anchoranalysis.image.voxel.datatype
-
A 16-bit voxel data-type representing signed-short numbers.
- SignedVoxelType - Class in org.anchoranalysis.image.voxel.datatype
-
Base class for voxel-data-types that are signed and integral.
- SignedVoxelType(int, String, long, long) - Constructor for class SignedVoxelType
-
Construct for a particular number of bits, with a unique identifier, and with bounds on the
values.
- SimpleAnnotationDeleter - Class in org.anchoranalysis.annotation.io
-
Deletes any annotation when it is represented by a single file.
- SimpleAnnotationDeleter() - Constructor for class SimpleAnnotationDeleter
-
- SimpleName - Class in org.anchoranalysis.feature.io.name
-
A name with only one part, and is always unique.
- SimpleName(String) - Constructor for class SimpleName
-
- SimpleNameValue<V> - Class in org.anchoranalysis.core.identifier.name
-
A simple container expressing a name-value pair.
- SimpleNameValue(String, V) - Constructor for class SimpleNameValue
-
- SimpleOutputNameStyle - Class in org.anchoranalysis.io.output.namestyle
-
- SimpleOutputNameStyle(String) - Constructor for class SimpleOutputNameStyle
-
- SimulatedAnnealing<S,T,U> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme
-
Finds an optima using a simulated-annealing approach
- SimulatedAnnealing() - Constructor for class SimulatedAnnealing
-
- Single - Class in org.anchoranalysis.image.bean.spatial.arrange
-
A single
Stack
arranged as-is.
- Single() - Constructor for class Single
-
- Single - Class in org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition
-
- Single() - Constructor for class Single
-
- SingleChannel - Class in org.anchoranalysis.plugin.image.feature.bean.score
-
A score that is calculated on a single channel only
- SingleChannel() - Constructor for class SingleChannel
-
- SingleChannel - Class in org.anchoranalysis.plugin.io.bean.channel.map
-
For an image with a single channel
- SingleChannel() - Constructor for class SingleChannel
-
- SingleChannel(String) - Constructor for class SingleChannel
-
- singleChannelMaybe3D(boolean) - Static method in class StackWriteAttributesFactory
-
A
StackWriteAttributes
which is
always a single-channel, and depending on a
flag, may be guaranteed to be 2D.
- SingleColor - Class in org.anchoranalysis.core.color
-
An index that always uses the same single color
- SingleColor(Color) - Constructor for class SingleColor
-
Creates with a particular color.
- SingleColor(RGBColor) - Constructor for class SingleColor
-
- singleCPUProcessor() - Static method in class ConcurrencyPlan
-
Creates a plan for a single-CPU processor with the default number of GPUs.
- singleCPUProcessor(int) - Static method in class ConcurrencyPlan
-
Creates a plan for a single-CPU processor - with a maximum number of GPUs.
- SingleFile - Class in org.anchoranalysis.io.input.bean.files
-
Provides a single file only.
- SingleFile(String) - Constructor for class SingleFile
-
Creates with a path for the single-file.
- SingleFile() - Constructor for class SingleFile
-
- SingleFileInputBase - Class in org.anchoranalysis.io.input.file
-
A base class for inputs that refer to a single file.
- SingleFileInputBase(NamedFile) - Constructor for class SingleFileInputBase
-
Creates for a particular file.
- SingleFileTypeGenerator<T,S> - Class in org.anchoranalysis.io.generator
-
A
Generator
that eventually writes only a single file to the filesystem.
- SingleFileTypeGenerator() - Constructor for class SingleFileTypeGenerator
-
- SingleFileTypeGeneratorBridge<S,T,V> - Class in org.anchoranalysis.io.generator
-
Allows us to call an SingleFileTypeGenerator<V,S>
as if it was an SingleFileTypeGenerator<T,S>
using an function to connect the two.
- SingleFileTypeGeneratorBridge(SingleFileTypeGenerator<V, S>, CheckedFunction<T, V, ? extends Throwable>) - Constructor for class SingleFileTypeGeneratorBridge
-
- SingleLevelAnd - Class in org.anchoranalysis.io.output.enabled.single
-
- SingleLevelAnd(SingleLevelOutputEnabled, SingleLevelOutputEnabled) - Constructor for class SingleLevelAnd
-
- SingleLevelBinary - Class in org.anchoranalysis.io.output.enabled.single
-
- SingleLevelBinary(SingleLevelOutputEnabled, SingleLevelOutputEnabled) - Constructor for class SingleLevelBinary
-
- SingleLevelInSet - Class in org.anchoranalysis.io.output.enabled.single
-
Outputs are enabled if they are contained in a set.
- SingleLevelInSet(Set<String>) - Constructor for class SingleLevelInSet
-
- SingleLevelNot - Class in org.anchoranalysis.io.output.enabled.single
-
- SingleLevelNot(SingleLevelOutputEnabled) - Constructor for class SingleLevelNot
-
- SingleLevelOr - Class in org.anchoranalysis.io.output.enabled.single
-
- SingleLevelOr(SingleLevelOutputEnabled, SingleLevelOutputEnabled) - Constructor for class SingleLevelOr
-
- SingleLevelOutputEnabled - Interface in org.anchoranalysis.io.output.enabled.single
-
- SingleMarkProvider - Class in org.anchoranalysis.mpp.bean.provider
-
Provides (maybe) a single mark
- SingleMarkProvider() - Constructor for class SingleMarkProvider
-
- SinglePathStrategy - Class in org.anchoranalysis.plugin.annotation.bean.strategy
-
A base class for implementations of
AnnotatorStrategy
where a single unique path exists
for every annotation.
- SinglePathStrategy() - Constructor for class SinglePathStrategy
-
- SingleRowPerInput<T extends InputFromManager,S extends FeatureInput> - Class in org.anchoranalysis.plugin.image.task.bean.feature.source
-
Base class for exporting features, where features are calculated per-image using a
NamedFeatureStore
.
- SingleRowPerInput(String) - Constructor for class SingleRowPerInput
-
Creates with a single non-group header that should be describe an identifier.
- SingleRowPerInput(String[]) - Constructor for class SingleRowPerInput
-
- SingleTableCalculator - Class in org.anchoranalysis.image.feature.calculator
-
- SingleTableCalculator(NamedFeatureStore<FeatureInputSingleObject>) - Constructor for class SingleTableCalculator
-
- size() - Method in class ColorList
-
The number of elements (colors) in the list.
- size() - Method in class NameValueMap
-
The number of elements in the set.
- size() - Method in class FeatureList
-
Returns the number of elements in this list.
- size() - Method in class LabelledResultsVector
-
The number of calculations stored in the vector.
- size() - Method in class FeatureNameList
-
The number of names in the list.
- size() - Method in class ResultsVector
-
The number of calculations stored in the vector.
- size() - Method in class ResultsVectorList
-
- size() - Method in class NamedFeatureStore
-
The total number of
Feature
s in the store.
- size() - Method in class ObjectCollectionWithProperties
-
Number of objects in the collection.
- size() - Method in class ScaledElements
-
Number of scaled-elements.
- size() - Method in class NamedStacks
-
Number of stacks.
- size() - Method in class SegmentedObjects
-
The total number of segmented objects.
- size() - Method in class SegmentedObjectsAtScale
-
A count of the total number of elements in each representation.
- size() - Method in class TimeSeries
-
The number of frames in the time-series.
- size() - Method in class IntersectingObjects
-
Number of items in the r-tree.
- size() - Method in class ObjectCollection
-
The number of objects in the collection.
- size() - Method in interface VoxelStatistics
-
The total count.
- size() - Method in class VoxelStatisticsCombined
-
- size() - Method in class VoxelStatisticsFromHistogram
-
- size() - Method in class Histogram
-
The size of the range of values in the histogram.
- size() - Method in class BoundUnitless
-
- size() - Method in class MarksWithEnergyBreakdown
-
- size() - Method in class MarksWithTotalEnergy
-
- size() - Method in class VoxelizedMarksWithEnergy
-
- size() - Method in class EnergySavedInd
-
- size() - Method in class EnergyMemoList
-
- size() - Method in class MemoList
-
- size() - Method in class UpdatableMarksList
-
- size() - Method in class IndexByChannel
-
- size() - Method in class ColoredMarks
-
- size() - Method in class MarkCollection
-
- size() - Method in interface MemoForIndex
-
- size() - Method in class TerminationConditionListOr
-
- size() - Method in class WeightedKernelList
-
- size() - Method in class ColoredOverlayCollection
-
The total number of elements in the list.
- size() - Method in class OverlayCollection
-
The total number of elements in the list.
- size() - Method in class ListWithThumbnails
-
- size() - Method in class ParsedFilePathBag
-
- size() - Method in class ContiguousVoxelPath
-
- size() - Method in class LoopablePoints
-
- Size - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
-
- Size() - Constructor for class Size
-
- size() - Method in class BoundedList
-
The number of elements.
- size() - Method in class RTree
-
The total number of items stored in the tree.
- sizeAfter() - Method in class ReductionOutcome
-
The total number of elements after reduction.
- sizeAfterAnyScaling() - Method in class ScaleableBackground
-
The size of the background after any scaling has occurred.
- sizeC(IFormatReader) - Method in class Default
-
- sizeC(IFormatReader) - Method in class ForceNumberChannels
-
- sizeC(IFormatReader) - Method in class ReadOptions
-
Number of channels.
- sizeC(IFormatReader) - Method in class ReadOptionsDelegate
-
- sizeCurrentLoad() - Method in class LRUCache
-
Number of items currently in the cache.
- sizeDescriptor(Extent) - Method in class HOGParameters
-
Calculates the size of the descriptor will be for a given image.
- SizeExtents - Class in org.anchoranalysis.plugin.io.multifile
-
Remembers the different sizes among the files
- SizeExtents(ParsedFilePathBag) - Constructor for class SizeExtents
-
- sizeFeatures() - Method in interface FeatureCalculatorMulti
-
- sizeFeatures() - Method in class FeatureCalculatorMultiChangeInput
-
- sizeFeatures() - Method in class SequentialSession
-
- sizeFeatures() - Method in class PairsTableCalculator
-
- sizeFeatures() - Method in class SingleTableCalculator
-
- sizeFirst() - Method in class CostMatrix
-
The number of elements in the first list.
- SizeMapping - Class in org.anchoranalysis.plugin.image.task.size
-
Maps a
Path
to a particular image-size and orientation-change.
- SizeMapping(Path, Extent) - Constructor for class SizeMapping
-
- sizeSecond() - Method in class CostMatrix
-
The number of elements in the second list.
- sizeT(Logger) - Method in class NamedChannelsConcatenate
-
- sizeT(Logger) - Method in interface NamedChannelsMap
-
The number of frames along the time-axis.
- sizeT(Logger) - Method in class OpenedNamedChannels
-
- sizeT(IFormatReader) - Method in class Default
-
- sizeT(IFormatReader) - Method in class ForceNumberFrames
-
- sizeT(IFormatReader) - Method in class ForceTimeSeriesToStack
-
- sizeT(IFormatReader) - Method in class ReadOptions
-
Number of time-points (frames in a time series).
- sizeT(IFormatReader) - Method in class ReadOptionsDelegate
-
- SizeXY - Class in org.anchoranalysis.image.bean.spatial
-
The size of an entity in the X and Y dimensions.
- SizeXY(Extent) - Constructor for class SizeXY
-
- SizeXY() - Constructor for class SizeXY
-
- SizeXY(int, int) - Constructor for class SizeXY
-
- sizeZ(IFormatReader) - Method in class Default
-
- sizeZ(IFormatReader) - Method in class ForceTimeSeriesToStack
-
- sizeZ(IFormatReader) - Method in class ReadOptions
-
Number of z-slices (slices in a 3D image).
- sizeZ(IFormatReader) - Method in class ReadOptionsDelegate
-
- skewness(Histogram) - Static method in class HistogramStatistics
-
Calculates the skewness of a distribution of values, represented by their histogram.
- Skewness - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
-
Calculates the
skewness of all the values in
the histogram.
- Skewness() - Constructor for class Skewness
-
- SkipInit - Annotation Type in org.anchoranalysis.bean.annotation
-
Indicates that this particular bean-field should be ignored during (recursive) initialization.
- slice(int) - Method in class BinaryVoxels
-
- slice(int) - Method in class FromByte
-
- slice(int) - Method in class FromFloat
-
- slice(int) - Method in class FromInt
-
- slice(int) - Method in class FromShort
-
- slice(int) - Method in interface SliceBufferIndex
-
- slice(int) - Method in interface VoxelsExtracter
-
Creates a new
Voxels
with only particular slice.
- slice(int) - Method in class Voxels
-
- slice(int) - Method in class VoxelsUntyped
-
- SliceAt - Class in org.anchoranalysis.plugin.image.bean.object.provider.slice
-
- SliceAt() - Constructor for class SliceAt
-
- sliceBinary(int) - Method in class BinaryVoxels
-
- sliceBuffer(int) - Method in class Mask
-
A buffer corresponding to a particular z-slice.
- sliceBuffer(int, int) - Method in class RGBStack
-
A buffer corresponding to a particular z-slice of a particular channel.
- sliceBuffer(int) - Method in class BinaryVoxels
-
A buffer corresponding to a particular z-slice.
- sliceBuffer(int) - Method in interface SliceBufferIndex
-
The underlying buffer corresponding to a particular z-slice.
- sliceBuffer(int) - Method in class Voxels
-
A buffer corresponding to a particular z-slice.
- sliceBufferGlobal(int) - Method in class BoundedVoxels
-
A slice buffer with global coordinates.
- sliceBufferGlobal(int) - Method in class ObjectMask
-
A slice buffer with global coordinates.
- SliceBufferIndex<T> - Interface in org.anchoranalysis.image.voxel.buffer.slice
-
A container with voxel-buffers for each z-slice.
- sliceBufferLocal(int) - Method in class ObjectWithProperties
-
A slice buffer with local coordinates.
- sliceBufferLocal(int) - Method in class BoundedVoxels
-
A slice buffer with local coordinates.
- sliceBufferLocal(int) - Method in class ObjectMask
-
A slice buffer with local coordinates.
- slices() - Method in class BinaryVoxels
-
An index mapping slice of voxels (in the z dimension) to a particular buffer with the
corresponding voxel intensities.
- slices() - Method in class Voxels
-
An index mapping slice of voxels (in the z dimension) to a particular buffer with the
corresponding voxel intensities.
- sliceStatisticsForRegion(VoxelizedMark, int) - Method in class IndexedRegionBase
-
- SliceThresholder - Class in org.anchoranalysis.plugin.image.segment.thresholder.slice
-
Segmenting a z-
Stack
slice-by-slice.
- SliceThresholder(BinaryValuesByte) - Constructor for class SliceThresholder
-
- SliceThresholderMask - Class in org.anchoranalysis.plugin.image.segment.thresholder.slice
-
- SliceThresholderMask(boolean, ObjectMask, BinaryValuesByte) - Constructor for class SliceThresholderMask
-
- SliceThresholderWithoutMask - Class in org.anchoranalysis.plugin.image.segment.thresholder.slice
-
- SliceThresholderWithoutMask(BinaryValuesByte) - Constructor for class SliceThresholderWithoutMask
-
- SlidingBuffer<T> - Class in org.anchoranalysis.image.voxel.buffer
-
An index that places a particular z-slice in local context.
- SlidingBuffer(Voxels<T>) - Constructor for class SlidingBuffer
-
Create for particular voxels.
- SMALL_2D - Static variable in class ChannelFixture
-
- SMALL_3D - Static variable in class ChannelFixture
-
- Sobel - Class in org.anchoranalysis.plugin.image.bean.channel.provider.gradient
-
3x3 Sobel Filter
- Sobel() - Constructor for class Sobel
-
- solveQuadraticEquation(double, double, double) - Static method in class QuadraticEquationSolver
-
Solves a quadratic equation in form x^2 + b^x + c = 0
.
- sort(Comparator<Feature<T>>) - Method in class FeatureList
-
Creates a new feature-list sorted in a particular order.
- SortAlphabetically - Class in org.anchoranalysis.plugin.io.bean.file.provider
-
- SortAlphabetically() - Constructor for class SortAlphabetically
-
- SortAlphabetically<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input
-
Sorts the input-items in alphabetical order of their input-name.
- SortAlphabetically() - Constructor for class SortAlphabetically
-
- SortAlphabeticallyWithDirectory - Class in org.anchoranalysis.plugin.io.bean.file.provider
-
- SortAlphabeticallyWithDirectory() - Constructor for class SortAlphabeticallyWithDirectory
-
- SortByFeature - Class in org.anchoranalysis.plugin.image.bean.object.provider.feature
-
Creates a new object-collection with objects sorted by a derived feature-value (in ascending
order)
- SortByFeature() - Constructor for class SortByFeature
-
- SortedSetChannel - Class in org.anchoranalysis.plugin.io.multifile
-
- SortedSetChannel() - Constructor for class SortedSetChannel
-
- SortedSetSlice - Class in org.anchoranalysis.plugin.io.multifile
-
- SortedSetSlice(String, int) - Constructor for class SortedSetSlice
-
- sourceIncrement - Variable in class ConvertTo
-
The number of elements (bytes) to increment by, when iterating through the source buffer.
- sourceSize - Variable in class ConvertTo
-
The total number of elements (always bytes) in the source buffer.
- sourceValue - Variable in class ProcessVoxelNeighborAbsoluteWithSlidingBuffer
-
The intensity value of the source voxel.
- spatiallySeparate() - Method in class IntersectingObjects
-
Splits the collection of objects into spatially separate clusters.
- SpatiallySeparate<T> - Class in org.anchoranalysis.spatial.rtree
-
Splits a collection of elements into spatially separate clusters.
- SpatiallySeparate(Function<T, BoundingBox>) - Constructor for class SpatiallySeparate
-
- SpatialUnits - Class in org.anchoranalysis.image.core.dimensions
-
Units to describe spatial quantities.
- SpatialUnits.UnitSuffix - Enum in org.anchoranalysis.image.core.dimensions
-
Suffix that describes a particular quantity of units (micron, nano, square microns etc.)
- Specific - Class in org.anchoranalysis.plugin.mpp.bean.region
-
- Specific() - Constructor for class Specific
-
- SpecificAndRename - Class in org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels
-
Selects a specific set of channels from stacks, each identified by a stack-name and channel index
- SpecificAndRename() - Constructor for class SpecificAndRename
-
- SpecificAxisBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.moments
-
A feature based one one-specific principal-axis as identified by image moments.
- SpecificAxisBase() - Constructor for class SpecificAxisBase
-
- SpecificDisabled - Class in org.anchoranalysis.io.output.bean.enabled
-
Only specific outputs, identified by a textual name, are disabled, and all others are enabled.
- SpecificDisabled() - Constructor for class SpecificDisabled
-
- SpecificDisabled(StringSet) - Constructor for class SpecificDisabled
-
- SpecificEnabled - Class in org.anchoranalysis.io.output.bean.enabled
-
Only specific outputs, identified by a textual name, are enabled.
- SpecificEnabled(String) - Constructor for class SpecificEnabled
-
Create with a single output-enabled.
- SpecificEnabled() - Constructor for class SpecificEnabled
-
- SpecificEnabled(StringSet) - Constructor for class SpecificEnabled
-
- SpecificEnergyChannelBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.energy
-
- SpecificEnergyChannelBase() - Constructor for class SpecificEnergyChannelBase
-
- SpecificPathList - Class in org.anchoranalysis.io.input.bean.files
-
A specific list of paths which form the input.
- SpecificPathList(List<String>) - Constructor for class SpecificPathList
-
Creates by reusing an existing list.
- SpecificPathList(StringList) - Constructor for class SpecificPathList
-
Creates by reusing an existing list.
- SpecificPathList() - Constructor for class SpecificPathList
-
- SpecifyDimensions - Class in org.anchoranalysis.plugin.image.bean.dimensions.provider
-
Specifies dimensions explicitly via bean properties.
- SpecifyDimensions(int, int) - Constructor for class SpecifyDimensions
-
Create with specific lengths for X and Y dimensions.
- SpecifyDimensions(SizeXY) - Constructor for class SpecifyDimensions
-
Create with specific lengths for X and Y dimensions.
- SpecifyDimensions() - Constructor for class SpecifyDimensions
-
- SpecifyVector - Class in org.anchoranalysis.image.bean.spatial.direction
-
Specifies each axis-component of a vector in a particular direction.
- SpecifyVector(DirectionVector) - Constructor for class SpecifyVector
-
- SpecifyVector() - Constructor for class SpecifyVector
-
- SpecifyVector(double, double, double) - Constructor for class SpecifyVector
-
- Sphere - Class in org.anchoranalysis.mpp.mark.conic
-
A sphere
- Sphere(Bound) - Constructor for class Sphere
-
Creates with a radius within particular bounds.
- Sphere(Sphere) - Constructor for class Sphere
-
Copy Constructor
- Sphere() - Constructor for class Sphere
-
- split(Path) - Method in class RootPath
-
It splits the root portion of a path from the remainder.
- split(Path, String, boolean) - Method in class RootPathMap
-
Given a path, it splits the *root* portion of the path from the remainder, trying a root
identified by the rootName and debugMode (and if this fails, also trying with
debugMode==false)
- SplitByObjects - Class in org.anchoranalysis.plugin.image.bean.object.provider.split
-
- SplitByObjects() - Constructor for class SplitByObjects
-
- SplitContourAtSaddlePoints - Class in org.anchoranalysis.plugin.points.bean
-
Splits a 2D contour represented by an object-mask into several contours, splitting at "turn"
points.
- SplitContourAtSaddlePoints() - Constructor for class SplitContourAtSaddlePoints
-
- splitFilename(String) - Static method in class ExtensionUtilities
-
Splits the file-name of a path into a base part and an extension part.
- SplitIntoSquares - Class in org.anchoranalysis.plugin.image.bean.object.provider.split
-
Splits objects into sub-objects by cutting by an orthogonal square lattice (like a chessboard).
- SplitIntoSquares() - Constructor for class SplitIntoSquares
-
- SplitPath - Class in org.anchoranalysis.core.system.path
-
A path that has been split into two components: a root and a remainder.
- SplitPath(Path, Path) - Constructor for class SplitPath
-
- Stack - Class in org.anchoranalysis.image.core.stack
-
One or more single-channel images that all have the same dimensions.
- Stack() - Constructor for class Stack
-
Creates a new empty
Stack
that will not become an RGB image after adding channels.
- Stack(boolean) - Constructor for class Stack
-
Creates a new empty
Stack
and whether it will become an RGB image or not.
- Stack(Channel) - Constructor for class Stack
-
Creates a
Stack
with a single channel.
- Stack(Extent) - Constructor for class Stack
-
Creates a
Stack
with a single
unsigned-byte channel of size
channel
.
- Stack(Dimensions, ChannelFactorySingleType, int, boolean) - Constructor for class Stack
-
Create with a particular number of empty
Channel
s.
- Stack(boolean, Channel...) - Constructor for class Stack
-
Creates from a varying number of channels, and a flag to indicate if they represent an RGB
image or not.
- Stack(Stream<Channel>) - Constructor for class Stack
-
- Stack(boolean, Stream<Channel>) - Constructor for class Stack
-
Like
Stack(Stream)
but allows explicitly setting whether it should be interpreted as
RGB or not.
- stack() - Method in class MultiInput
-
- stack(String) - Static method in class ReferenceFactory
-
- StackArrangement - Class in org.anchoranalysis.image.bean.nonbean.spatial.arrange
-
A list of
BoundingBox
es that indicate where to locate corresponding
Stack
s on a
unified larger image.
- StackArrangement(Extent) - Constructor for class StackArrangement
-
Create with the overall
Extent
and no boxes.
- StackArrangement(Extent, BoundingBox) - Constructor for class StackArrangement
-
- StackArrangement(Extent, List<BoundingBoxEnclosed>) - Constructor for class StackArrangement
-
- StackArranger - Class in org.anchoranalysis.image.bean.spatial.arrange
-
Base class for a method that determines positions for
RGBStack
s when combined onto a
single plane.
- StackArranger() - Constructor for class StackArranger
-
- StackCopierAtBox - Class in org.anchoranalysis.image.bean.nonbean.spatial.arrange
-
Copies a
source
stack into a
destination
stack at a particular
BoundingBox
.
- StackDisplayer - Class in org.anchoranalysis.image.bean.displayer
-
- StackDisplayer() - Constructor for class StackDisplayer
-
- StackFixture - Class in org.anchoranalysis.test.image
-
- StackFixture(Optional<VoxelDataType>) - Constructor for class StackFixture
-
Create with a voxel-type for the first channel.
- StackFixture() - Constructor for class StackFixture
-
- StackGenerator - Class in org.anchoranalysis.image.io.stack.output.generator
-
Writes a stack to the filesystem.
- StackGenerator(boolean) - Constructor for class StackGenerator
-
Creates a generator that performs no padding.
- StackGenerator(boolean, boolean) - Constructor for class StackGenerator
-
Creates the generator from a stack, inferring whether all stacks will be 2D from this stack's
dimensions.
- StackGenerator(boolean, StackWriteAttributes) - Constructor for class StackGenerator
-
- stackGrayscale() - Method in class InstanceSegmentationTestBase
-
The grayscale stack that is tested.
- StackIdentifiers - Class in org.anchoranalysis.image.io.stack
-
Common identifiers used for storing particular types of images.
- StackNotUniformSized - Class in org.anchoranalysis.image.core.stack
-
A list of
Channel
s that are permitted to vary in size.
- StackNotUniformSized() - Constructor for class StackNotUniformSized
-
Creates an empty with no channels.
- StackNotUniformSized(Stream<Channel>) - Constructor for class StackNotUniformSized
-
- StackNotUniformSized(Channel) - Constructor for class StackNotUniformSized
-
- StackProvider - Class in org.anchoranalysis.image.bean.provider.stack
-
- StackProvider() - Constructor for class StackProvider
-
- StackProviderUnary - Class in org.anchoranalysis.image.bean.provider.stack
-
Implementation of
StackProvider
that calls a single delegate
Provider<Stack>
.
- StackProviderUnary() - Constructor for class StackProviderUnary
-
- StackProviderWithLabel - Class in org.anchoranalysis.image.io.bean.stack.combine
-
Combines a Provider<Stack>
with a label.
- StackProviderWithLabel(Stack, String) - Constructor for class StackProviderWithLabel
-
Create for a particular
Stack
and label.
- StackProviderWithLabel() - Constructor for class StackProviderWithLabel
-
- StackReader - Class in org.anchoranalysis.image.io.bean.stack.reader
-
Reads an image-
Stack
from the file-system.
- StackReader() - Constructor for class StackReader
-
- StackReaderOrientationCorrection - Class in org.anchoranalysis.image.io.bean.stack.reader
-
A
StackReader
that supports the correction of orientation as images are read from the
file-system.
- StackReaderOrientationCorrection() - Constructor for class StackReaderOrientationCorrection
-
- stackRGB() - Method in class InstanceSegmentationTestBase
-
The RGB stack that is tested.
- StackRGBState - Enum in org.anchoranalysis.image.io.stack.output
-
Whether a stack is RGB or RGBA or neither.
- stacks(Logger) - Method in class AnnotationWithStrategy
-
All stacks associated with the input, lazily evaluated.
- stacks() - Method in class ImageInitialization
-
A collection of
Stack
s, indexed by name.
- STACKS - Static variable in class OutputterDirectories
-
Where stacks are typically placed in a define-experiment output
- Stacks - Class in org.anchoranalysis.plugin.io.bean.input.stack
-
- Stacks(InputManager<FileInput>) - Constructor for class Stacks
-
- Stacks() - Constructor for class Stacks
-
- StackSequenceInput - Interface in org.anchoranalysis.image.io.stack.input
-
Provides a single stack (or a time series of such stacks) as an input
- StackTester - Class in org.anchoranalysis.test.image.stackwriter
-
- StackTester(StackWriter, Path, String, boolean) - Constructor for class StackTester
-
- stackTrace() - Method in exception AnchorFriendlyCheckedException
-
Prints a stack trace of the current exception to a string.
- StackWithMap - Class in org.anchoranalysis.mpp.io.input
-
Combines a Stack with a map of other stacks
- StackWithMap(String, ProvidesStackInput) - Constructor for class StackWithMap
-
- StackWriteAttributes - Class in org.anchoranalysis.image.io.stack.output
-
Attributes describing stack which may determine which writer is used.
- StackWriteAttributes(boolean, boolean, boolean, StackRGBState, boolean) - Constructor for class StackWriteAttributes
-
Alternative constructor that assumes each channel is 8-bits.
- StackWriteAttributesFactory - Class in org.anchoranalysis.image.io.stack.output
-
- StackWriteOptions - Class in org.anchoranalysis.image.io.stack.output
-
A combination of attributions describing how to write a particular stack and any suggestions from
the user.
- StackWriteOptions(StackWriteAttributes, Optional<ImageFileFormat>) - Constructor for class StackWriteOptions
-
- StackWriter - Class in org.anchoranalysis.image.io.bean.stack.writer
-
Writes a stack (i.e.
- StackWriter() - Constructor for class StackWriter
-
- StackWriterDelegateBase - Class in org.anchoranalysis.plugin.io.bean.stack.writer
-
- StackWriterDelegateBase() - Constructor for class StackWriterDelegateBase
-
- StackWriterTestBase - Class in org.anchoranalysis.test.image.stackwriter
-
Base class for testing various implementations of
StackWriter
.
- StackWriterTestBase(ImageFileFormat, boolean, ComparisonPlan) - Constructor for class StackWriterTestBase
-
- StandardDeviation - Class in org.anchoranalysis.feature.bean.results
-
The standard-deviation of the results from a particular feature.
- StandardDeviation() - Constructor for class StandardDeviation
-
- standardDeviation() - Method in class Histogram
-
Calculates the standard-deviation of the distribution represented by the histogram.
- StandardDeviation - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
-
- StandardDeviation() - Constructor for class StandardDeviation
-
- StandardDeviationIntensityProjection - Class in org.anchoranalysis.image.voxel.projection
-
Creates buffers for projecting the standard-deviation.
- StandardDeviationProjection<T> - Class in org.anchoranalysis.plugin.image.bean.channel.aggregator
-
Projection of the standard-deviation of voxels values across all inputs.
- StandardDeviationProjection() - Constructor for class StandardDeviationProjection
-
- start() - Method in class StatefulNullMessageLogger
-
- start() - Method in class ConsoleMessageLogger
-
- start() - Method in class FailureOnlyMessageLogger
-
- start() - Method in class MultipleLoggers
-
- start() - Method in interface StatefulMessageLogger
-
Starts logging.
- start() - Method in class TextFileMessageLogger
-
- start() - Method in class LabelledResultsCSVWriter
-
Starts writing the CSV file.
- start(FeatureInitialization, SharedFeatures, Logger) - Method in class SequentialSession
-
Starts the session.
- start(ImageInitialization, Optional<EnergyStack>, Logger) - Method in interface FeatureTableCalculator
-
Initializes a feature store that has the same structure as that previously created by
createFeatures() from the same object
- start(ImageInitialization, Optional<EnergyStack>, Logger) - Method in class PairsTableCalculator
-
- start(ImageInitialization, Optional<EnergyStack>, Logger) - Method in class SingleTableCalculator
-
- start() - Method in class TextFileOutput
-
- start(EnergyStack) - Method in class CheckMark
-
- start(FeedbackBeginParameters<T>) - Method in class AggregateTriggerBank
-
- start(Optional<Dimensions>, ObjectCollection) - Method in class DiscardOutliers
-
- start(Optional<Dimensions>, ObjectCollection) - Method in class RelationWithMatches
-
- start(Optional<Dimensions>, ObjectCollection) - Method in class GreaterIntersectionWith
-
- start(Optional<Dimensions>, ObjectCollection) - Method in class IntensityGreaterEqualThan
-
- start(Optional<Dimensions>, ObjectCollection) - Method in class IntersectsWith
-
- start(Optional<Dimensions>, ObjectCollection) - Method in class ThresholdedFeature
-
- start(Optional<Dimensions>, ObjectCollection) - Method in class ThresholdedVolume
-
- start(Optional<Dimensions>, ObjectCollection) - Method in class ObjectFilterPredicate
-
- start(Optional<Dimensions>, ObjectCollection) - Method in class ObjectFilterRelation
-
- start(ObjectCollection, StreamableCollection<BoundingBox>, Optional<Stack>, ExecutionTimeRecorder) - Method in class OutlinePreserveRelativeSize
-
- start(ObjectCollection, StreamableCollection<BoundingBox>, Optional<Stack>, ExecutionTimeRecorder) - Method in class ThumbnailFromObjects
-
Initializes a batch to create thumbnails.
- start() - Method in class ScaleToSize
-
- start() - Method in class ThumbnailFromStack
-
- start(EnergyStack) - Method in class AndList
-
- start(EnergyStack) - Method in class FeatureValueCheckMark
-
- startBatchDeriveInputs(ObjectCollection, EnergyStack, Logger) - Method in class CombineObjectsForFeatures
-
Derives a list of inputs from an object-collection.
- startBatchDeriveInputs(ObjectCollection, EnergyStack, Logger) - Method in class EachObjectIndependently
-
- startBatchDeriveInputs(ObjectCollection, EnergyStack, Logger) - Method in class PairNeighbors
-
- startSeries(NoSharedState, OutputSequenceIndexed<Stack, String>, InputOutputContext) - Method in class ConvertImageFormat
-
- startSeries(S, U, InputOutputContext) - Method in class RasterTask
-
Starts processing of a series.
- StatefulMessageLogger - Interface in org.anchoranalysis.experiment.log
-
A
MessageLogger
that can be started and stopped, and is aware of this state.
- StatefulNullMessageLogger - Class in org.anchoranalysis.experiment.bean.log
-
Does nothing (i.e.
- StatefulNullMessageLogger() - Constructor for class StatefulNullMessageLogger
-
- StateReporter<T,S> - Class in org.anchoranalysis.mpp.segment.bean.optimization.feedback
-
Converts the optimization state to a form that the reporter needs
- StateReporter() - Constructor for class StateReporter
-
- stateReporter() - Method in class AssignMode
-
- stateReporter() - Method in class DirectAssignMode
-
- stateReporter() - Method in class TransformationAssignMode
-
- StateReporterIdentity<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter
-
Assumes the state is reported without any transformation
- StateReporterIdentity() - Constructor for class StateReporterIdentity
-
- StateReporterToPixelized<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter
-
Assumes we are interested in
VoxelizedMarksWithEnergy
as reporting type, and our
optimization-state is in the form
ToPixelized<T>
- StateReporterToPixelized() - Constructor for class StateReporterToPixelized
-
- StateReporterTransformer<T,S> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter
-
- StateReporterTransformer() - Constructor for class StateReporterTransformer
-
- stateToKernel() - Method in class KernelStateBridge
-
- stateToKernel() - Method in class KernelStateBridgeIdentity
-
- stateToKernel() - Method in class KernelStateBridgePixelize
-
- stateToKernel() - Method in class KernelStateBridgeTransformer
-
- StateTransformer<W,X> - Interface in org.anchoranalysis.mpp.segment.transformer
-
- StateTransformerBean<S,T> - Class in org.anchoranalysis.mpp.segment.transformer
-
Transforms one type into another.
- StateTransformerBean() - Constructor for class StateTransformerBean
-
- StaticFilePath - Class in org.anchoranalysis.plugin.io.bean.file.path
-
- StaticFilePath() - Constructor for class StaticFilePath
-
- StatisticalBase<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.statistics
-
Calculates a score based upon the statistical mean and std-deviation.
- StatisticalBase() - Constructor for class StatisticalBase
-
- statisticFromFeatureValue(DoubleArrayList) - Method in class FeatureResultsStatistic
-
Calculates the statistic for a given list of result-value.
- statisticFromFeatureValue(DoubleArrayList) - Method in class Maximum
-
- statisticFromFeatureValue(DoubleArrayList) - Method in class Mean
-
- statisticFromFeatureValue(DoubleArrayList) - Method in class Minimum
-
- statisticFromFeatureValue(DoubleArrayList) - Method in class Quantile
-
- statisticFromFeatureValue(DoubleArrayList) - Method in class StandardDeviation
-
- statisticFromFeatureValue(DoubleArrayList) - Method in class Sum
-
- statistics() - Method in interface Assignment
-
The statistics associated with the assignment.
- statistics() - Method in class ObjectVoxelIntersection
-
- statistics() - Method in class OverlappingObjects
-
- statisticsFor(int, int, int) - Method in interface VoxelizedMark
-
- statisticsForAllGroups() - Method in class ComparisonSharedState
-
- statisticsForAllSlices(int, int) - Method in interface VoxelizedMark
-
- statisticsForAllSlices(VoxelizedMark, boolean) - Method in class SelectSlicesWithIndexBase
-
- statisticsForAllSlicesMaskSlice(int, int, int) - Method in interface VoxelizedMark
-
- StatisticsToExport - Class in org.anchoranalysis.annotation.io.comparer
-
Statistics to be exported, comprised of name-value pairs.
- StatisticsToExport() - Constructor for class StatisticsToExport
-
- stdDev() - Method in interface VoxelStatistics
-
The standard-deviation of all voxel values.
- Steepest - Class in org.anchoranalysis.plugin.image.segment.watershed.encoding
-
- Steepest(SlidingBuffer<?>, WatershedEncoding, boolean, boolean, Optional<ObjectMask>) - Constructor for class Steepest
-
Create for a specific buffer.
- steepestDescent(Point3i, int, int) - Method in class Steepest
-
- StoreSupplier<T> - Interface in org.anchoranalysis.core.identifier.provider.store
-
Supplier of an object for a store.
- stream() - Method in class DoubleSet
-
Creates a stream of elements in the set.
- stream() - Method in class IntegerSet
-
Creates a stream of elements in the set.
- stream() - Method in class StringSet
-
Creates a stream of elements in the set.
- stream() - Method in class StreamableCollection
-
A single instance of the stream from the supplier.
- stream() - Method in class NameValueMap
-
Exposes the elements in the set as a stream.
- stream() - Method in class ResultsVectorList
-
- stream() - Method in class ObjectCollection
-
Provides various functional-programming operations on the object-collection.
- stream() - Method in class ImageCounterList
-
- stream() - Method in class BoundedList
-
A stream of elements in the list.
- StreamableCollection<T> - Class in org.anchoranalysis.core.functional
-
As a stream can only be used once, this data-structure allows for repeatedly getting streams from
a collection.
- StreamableCollection(Collection<T>) - Constructor for class StreamableCollection
-
Create for a particular collection
- StreamableCollection(Supplier<Stream<T>>) - Constructor for class StreamableCollection
-
- streamIndices(Collection<Integer>) - Method in class ObjectCollection
-
Streams only objects at specific indices.
- streamObjectWithProperties() - Method in class ColoredObjectCollection
-
- streamOverZ() - Method in class Extent
-
Streams over the range of z values.
- streamStandardJava() - Method in class ObjectCollection
-
A stream of object-masks as per Java's standard collections interface.
- StringGenerator - Class in org.anchoranalysis.io.generator.text
-
- StringGenerator() - Constructor for class StringGenerator
-
- StringList - Class in org.anchoranalysis.bean.primitive
-
A bean defining a list of
String
s.
- StringList() - Constructor for class StringList
-
Constructs with an empty list.
- StringList(String...) - Constructor for class StringList
-
Constructs, populated with one or more values.
- StringList(List<String>) - Constructor for class StringList
-
Constructs, populated with a list of strings.
- StringListFactory - Class in org.anchoranalysis.bean.xml.factory.primitive
-
- StringListFactory() - Constructor for class StringListFactory
-
- StringMap - Class in org.anchoranalysis.bean.shared
-
A bean that defines a mapping between a set of
String
s to another set of
String
s.
- StringMap() - Constructor for class StringMap
-
- StringMapItem - Class in org.anchoranalysis.bean.shared
-
A bean with a pair of strings, representing a mapping from one string to the other.
- StringMapItem() - Constructor for class StringMapItem
-
- StringSet - Class in org.anchoranalysis.bean.primitive
-
A bean defining a set of
String
s.
- StringSet(String...) - Constructor for class StringSet
-
Constructs with one or more values added to the list.
- StringSet() - Constructor for class StringSet
-
- StringSet(Set<String>) - Constructor for class StringSet
-
- StringSetFactory - Class in org.anchoranalysis.bean.xml.factory.primitive
-
- StringSetFactory() - Constructor for class StringSetFactory
-
- StringSetTrie - Class in org.anchoranalysis.core.collection
-
- StringSetTrie() - Constructor for class StringSetTrie
-
Create with no elements.
- StringSetTrie(Collection<String>) - Constructor for class StringSetTrie
-
Create from existing collection.
- StringSetTrie(Stream<String>) - Constructor for class StringSetTrie
-
Create from existing collection.
- StringSuffixOutputNameStyle - Class in org.anchoranalysis.io.output.namestyle
-
- StringSuffixOutputNameStyle() - Constructor for class StringSuffixOutputNameStyle
-
- StringSuffixOutputNameStyle(String, Optional<String>) - Constructor for class StringSuffixOutputNameStyle
-
- StringUtilities - Class in org.anchoranalysis.core.value
-
Utility functions for manipualting strings.
- strMarks() - Method in class MarkWithPositionAndSingleRadius
-
- strPos() - Method in class MarkWithPosition
-
- subdirectory(String, boolean) - Method in interface InputOutputContext
-
Creates a new context that writes instead to a subdirectory.
- subdirectoryForGroupOutputs() - Method in class AggregateChannelTask
-
- subdirectoryForGroupOutputs() - Method in class GroupedStackBase
-
An optional subdirectory where the group outputs are placed.
- subdirectoryForGroupOutputs() - Method in class ExportImageHistograms
-
- subList(int, int) - Method in class UpdatableMarksList
-
- SUBMARK_CORE - Static variable in class GlobalRegionIdentifiers
-
- SUBMARK_CORE_INNER - Static variable in class GlobalRegionIdentifiers
-
- SUBMARK_INSIDE - Static variable in class GlobalRegionIdentifiers
-
- SUBMARK_OUTSIDE - Static variable in class GlobalRegionIdentifiers
-
- SUBMARK_SHELL - Static variable in class GlobalRegionIdentifiers
-
- SUBMARK_SHELL_OUTSIDE - Static variable in class GlobalRegionIdentifiers
-
- SubmittedJob - Class in org.anchoranalysis.experiment.task.processor
-
A job that has been submitted for execution.
- SubmittedJob(JobDescription, JobStateMonitor) - Constructor for class SubmittedJob
-
- subset(StringSet) - Method in class NamedStacks
-
Creates a new collection containing only items whose keys exist in a particular set.
- subsetCompatibleWith(Class<? extends FeatureInput>) - Method in class SharedFeatures
-
Extracts the subset of inputs that are compatible with a particular input-type.
- SubsetRangeIfRequested - Class in org.anchoranalysis.plugin.io.bean.file.namer
-
If specified in the context, the existing name if subsetted according to an index range.
- SubsetRangeIfRequested() - Constructor for class SubsetRangeIfRequested
-
- subsetWhereBBoxIntersects(Dimensions, int, List<BoundingBox>) - Method in class ColoredMarks
-
- subsetWhereBoxIntersects(Dimensions, DrawOverlay, List<BoundingBox>) - Method in class ColoredOverlayCollection
-
Find overlays whose bounding-boxes intersect with any of the boxes in toIntersectWith
.
- SubstituteRegularExpression - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming
-
A regular expression substitution (replaceAll) is applied to the relative-path
- SubstituteRegularExpression() - Constructor for class SubstituteRegularExpression
-
- subtract(VarianceCalculatorDouble) - Method in class VarianceCalculatorDouble
-
- subtract(VarianceCalculatorLong) - Method in class VarianceCalculatorLong
-
- subtract(Tuple3d) - Method in class Tuple3d
-
Arithmetically subtract a
Tuple3d
's values across each dimension.
- subtract(int) - Method in class Tuple3i
-
Arithmetically subtracts a value across each dimension.
- subtract(ReadableTuple3i) - Method in class Tuple3i
-
Arithmetically subtracts a value across each dimension.
- subtractFrom(int) - Method in interface VoxelsArithmetic
-
Subtracts all current voxel-values from a constant-value.
- SubtractFrom<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic
-
- SubtractFrom() - Constructor for class SubtractFrom
-
- SubtractFromConstant - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
-
- SubtractFromConstant() - Constructor for class SubtractFromConstant
-
- subtractFromMaxValue() - Method in class VoxelsUntyped
-
Subtracts all voxel-values from the maximum value associated with the data-type.
- SubtractMean - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
-
Subtract the mean (of the entire channel or a masked portion thereof) from every voxel
- SubtractMean() - Constructor for class SubtractMean
-
- SubtractReducedFromMerged - Class in org.anchoranalysis.plugin.image.feature.bean.list.pair
-
- SubtractReducedFromMerged() - Constructor for class SubtractReducedFromMerged
-
- SubtractSecondFromFirst - Class in org.anchoranalysis.image.feature.bean.object.pair
-
Subtract second-object from first-object in a pair.
- SubtractSecondFromFirst() - Constructor for class SubtractSecondFromFirst
-
- SubtractTwoChannels - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
-
- SubtractTwoChannels() - Constructor for class SubtractTwoChannels
-
- successiveCircles(int, Point2d, int, Point2d, double) - Static method in class CircleObjectFixture
-
Creates several successive circles whose center is incrementally shifted.
- suffixStringForMeters(SpatialUnits.UnitSuffix) - Static method in class SpatialUnits
-
A string that describes the suffix for meters.
- suggestedSize() - Method in class ImageInitialization
-
A suggested input on how to resize an image, if one is provided.
- SuggestionFormatException - Exception in org.anchoranalysis.image.core.dimensions.size.suggestion
-
- SuggestionFormatException(String) - Constructor for exception SuggestionFormatException
-
Create with a message only.
- Sum<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.operator
-
Sums the results after calculating a list of
Feature
s.
- Sum(FeatureList<T>) - Constructor for class Sum
-
Create with a list of
Feature
s which become summed.
- Sum() - Constructor for class Sum
-
- Sum - Class in org.anchoranalysis.feature.bean.results
-
The sum of the results from a particular feature.
- Sum() - Constructor for class Sum
-
- sum() - Method in interface VoxelStatistics
-
The sum of all voxel values.
- sum() - Method in class VoxelStatisticsCombined
-
- sum() - Method in class VoxelStatisticsFromHistogram
-
- sum() - Method in class AggIDCounter
-
- Sum - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
-
- Sum() - Constructor for class Sum
-
- sumExecutionTimeSeconds() - Method in class RecordedExecutionTimes.RecordedOperation
-
The total summed execution time in seconds for the operation.
- summarize() - Method in exception BeanMisconfiguredXMLException
-
This summarize() option just looks for the most deep exception that can be 'combined' and
takes its message
- summarize() - Method in exception LocalisedBeanException
-
- summarize() - Method in exception AnchorCombinableException
-
Creates a new {link Throwable} that summarizes this exception and any nested causes of the
exception.
- summarize() - Method in exception NamedProviderGetException
-
- SummarizeBase<T extends InputFromManager,S> - Class in org.anchoranalysis.plugin.io.bean.task
-
- SummarizeBase() - Constructor for class SummarizeBase
-
- summarizeDisabled() - Method in class RecordedOutputs
-
A comma-separated string of all output-names that were not enabled.
- summarizeEnabled() - Method in class RecordedOutputs
-
A comma-separated string of all output-names that were enabled.
- summarizeIgnoreIdenticalFilePath(Path) - Method in exception LocalisedBeanException
-
If there is no nested-set of combinable exceptions, and the
message
related to this
current exception is identical as the passed parameter, then we simply ignore the current
exception and promote its
Throwable.getCause()
.
- SummarizeInputs<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.task
-
- SummarizeInputs() - Constructor for class SummarizeInputs
-
- summarizeMultiplex(boolean) - Method in class RecordedOutputs
-
- Summarizer<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer
-
Summarizes a set of elements by outputting a descriptive string.
- Summarizer() - Constructor for class Summarizer
-
- SummarizerAggregate<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer
-
Collects summary data about a set of input files that will eventually be outputted to the user
- SummarizerAggregate() - Constructor for class SummarizerAggregate
-
- SummarizerCount<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer
-
A count of the number of inputs.
- SummarizerCount() - Constructor for class SummarizerCount
-
- SummarizerImageMetadata<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer.image
-
- SummarizerImageMetadata() - Constructor for class SummarizerImageMetadata
-
- SummarizerImageMetadataSimple<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer.image
-
A simple summarizer, where there's one summary-item per image.
- SummarizerImageMetadataSimple() - Constructor for class SummarizerImageMetadataSimple
-
- SummarizerInputFromManager<T extends InputFromManager,S> - Class in org.anchoranalysis.plugin.io.bean.summarizer.input
-
Extracts a particular item from an
InputFromManager
for further summarization downstream.
- SummarizerInputFromManager() - Constructor for class SummarizerInputFromManager
-
- SummarizerListMultiline<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer
-
Creates a string where each line is an element.
- SummarizerListMultiline() - Constructor for class SummarizerListMultiline
-
- SummarizerPath - Class in org.anchoranalysis.plugin.io.bean.summarizer.path
-
Base class for
Summarizer
s that operate on the
Path
associated with inputs.
- SummarizerPath() - Constructor for class SummarizerPath
-
- SummarizerSplitMoreThan<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer
-
Multiplexes between two summarizers depending on the total number of count.
- SummarizerSplitMoreThan() - Constructor for class SummarizerSplitMoreThan
-
- SummaryException - Exception in org.anchoranalysis.core.exception.combinable
-
A special kind of exception that represents a summary of an existing set of exceptions.
- SummaryException(String, Throwable) - Constructor for exception SummaryException
-
Creates with a message and a cause.
- sumModulo(int, int, int) - Static method in class ChannelFixture
-
- sumOfSquares() - Method in interface VoxelStatistics
-
The sum of the square of all voxel values.
- sumOfSquares() - Method in class VoxelStatisticsCombined
-
- sumOfSquares() - Method in class VoxelStatisticsFromHistogram
-
- sumOverlapFromPaired() - Method in class OverlappingObjects
-
Sums the overlap-ratio across all assigned pairs.
- supportsMultipleChannelsPerSourceBuffer() - Method in class ConvertTo
-
Whether the source buffer can encode more than one channel?
- supportsMultipleChannelsPerSourceBuffer() - Method in class ToUnsignedByteWithScaling
-
- supportsMultipleChannelsPerSourceBuffer() - Method in class UnsignedByteFromFloat
-
- supportsMultipleChannelsPerSourceBuffer() - Method in class UnsignedByteFromUnsignedByte
-
- supportsMultipleChannelsPerSourceBuffer() - Method in class ToFloat
-
- supportsMultipleChannelsPerSourceBuffer() - Method in class UnsignedIntFromUnsignedInt
-
- supportsMultipleChannelsPerSourceBuffer() - Method in class ToUnsignedShort
-
- suppressedLogger() - Static method in class LoggerFixture
-
A
Logger
that doesn't output anything.
- suppressedMessageLogger() - Static method in class LoggerFixture
-
- suppressedOperationContext() - Static method in class LoggerFixture
-
- SuppressNonMaximum<T extends InferenceModel> - Class in org.anchoranalysis.image.inference.bean.segment.instance
-
Applies a segmentation procedure followed by non-maximum suppression.
- SuppressNonMaximum(SegmentStackIntoObjectsPooled<T>) - Constructor for class SuppressNonMaximum
-
Creates with a particular segmentation algorithm as an input.
- SuppressNonMaximum() - Constructor for class SuppressNonMaximum
-
- SuppressNonMaximum(SegmentStackIntoObjectsPooled<T>, ReduceElements<ObjectMask>, boolean) - Constructor for class SuppressNonMaximum
-
- SurfaceNumberVoxelFaces - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.surface
-
The number of voxel-faces along the surface (the faces of each voxel that touch outside)
- SurfaceNumberVoxelFaces() - Constructor for class SurfaceNumberVoxelFaces
-
- SurfaceNumberVoxels - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.surface
-
The number of voxels on the surface (all voxels on the exterior of the object)
- SurfaceNumberVoxels() - Constructor for class SurfaceNumberVoxels
-
- SurfaceNumberVoxelsBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.surface
-
- SurfaceNumberVoxelsBase() - Constructor for class SurfaceNumberVoxelsBase
-
- SurfaceSizeMaskNonZero - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
-
- SurfaceSizeMaskNonZero() - Constructor for class SurfaceSizeMaskNonZero
-
- SwitchChannelTime - Class in org.anchoranalysis.io.bioformats.bean.options
-
Treats the channel index as if it's time, and vice versa
- SwitchChannelTime() - Constructor for class SwitchChannelTime
-
- SwitchDetailedLogging - Class in org.anchoranalysis.experiment.bean.log
-
Switches between two log-reporters depending on whether detailed logging is switched on or not
- SwitchDetailedLogging() - Constructor for class SwitchDetailedLogging
-