Index (anchor-plugin-image-feature 1.0.0 API)

A B C D E F G H I K L M N O P Q R S T U V
All Classes and Interfaces|All Packages

A

AcquisitionTime - Class in org.anchoranalysis.plugin.image.feature.bean.metadata: The acquisition time of the image, if specified in the metadata.
AcquisitionTime() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.metadata.AcquisitionTime
aggregateResults(List<Double>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjectsSingleElement: Aggregates the results from individual intersecting object calculations.
aggregateResults(List<Double>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.MaxFeatureIntersectingObjects
aggregateResults(List<Double>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.MinFeatureIntersectingObjectsAboveThreshold
aggregateResults(List<Double>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.NumberIntersectingObjectsAboveThreshold
applyOperation(ObjectMask, Extent, boolean) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateIncrementalOperationMap: Applies the incremental operation to the input object.
applyOperation(ObjectMask, Extent, boolean) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateDilationMap
applyOperation(ObjectMask, Extent, boolean) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateErosionMap
ArbitraryInsidePoint - Class in org.anchoranalysis.plugin.image.feature.bean.object.single: Calculates deterministically a point that is definitely inside the object-mask and outputs a selected axis value.
ArbitraryInsidePoint() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.ArbitraryInsidePoint
ArbitraryInsidePoint(String) - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.ArbitraryInsidePoint: Creates an ArbitraryInsidePoint with a specified axis.
Area<T> - 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 org.anchoranalysis.plugin.image.feature.bean.dimensions.Area
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 org.anchoranalysis.plugin.image.feature.bean.stack.object.AsObjectMask
AtBorderBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.border: Base class for features that check if an object is at the border of an image.
AtBorderBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.border.AtBorderBase
AtBorderXY - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.border: Checks if an object's bounding box is at the border of the image in the XY plane.
AtBorderXY() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.border.AtBorderXY
AtBorderZ - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.border: Checks if an object's bounding box is at the border of the image in the Z dimension.
AtBorderZ() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.border.AtBorderZ

B

beforeCalc(FeatureInitialization) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjects
beforeCalc(FeatureInitialization) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.PairedWithMask
beforeCalc(FeatureInitialization) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.FeatureSingleObjectFromShared
beforeCalc(FeatureInitialization) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.ParamFromCollection
beforeCalcSetup(Histogram, int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevel
beforeCalcSetup(Histogram, int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevelBase: Performs setup operations before calculation.
beforeCalcSetup(Histogram, int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.DifferenceCalculateLevelStandardDeviation
beforeCalcWithInitialization(ImageInitialization) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.FeatureSingleObjectFromShared: Performs initialization before calculation with image-specific initialization.
beforeCalcWithInitialization(ImageInitialization) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.MaskAsSingleObject
beforeCalcWithInitialization(ImageInitialization) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.ObjectAggregationBase
BitDepthPerChannel - Class in org.anchoranalysis.plugin.image.feature.bean.metadata: The bit-depth of the image per channel.
BitDepthPerChannel() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.metadata.BitDepthPerChannel
BoundingBoxAlongAxisBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox: Base class for features that calculate a value along a specific axis of an object's bounding box.
BoundingBoxAlongAxisBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxAlongAxisBase
BoundingBoxExtentAlongAxis - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox: Calculates the extent of an object's bounding box along a specified axis.
BoundingBoxExtentAlongAxis() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxExtentAlongAxis
BoundingBoxMaximumAlongAxis - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox: Calculates the maximum coordinate of an object's bounding box along a specified axis.
BoundingBoxMaximumAlongAxis() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxMaximumAlongAxis
BoundingBoxMinimumAlongAxis - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox: Calculates the minimum coordinate of an object's bounding box along a specified axis.
BoundingBoxMinimumAlongAxis() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxMinimumAlongAxis
BoundingBoxNumberVoxels - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox: Calculates the number of voxels in the bounding box of an object.
BoundingBoxNumberVoxels() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxNumberVoxels
boundingBoxThatSpansInput(FeatureInputPairObjects) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
boundingBoxThatSpansInput(FeatureInputSingleObject) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.EachObjectIndependently
boundingBoxThatSpansInput(T) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.CombineObjectsForFeatures: Creates a bounding-box that tightly fits the input to a particular table row (could be for one or more objects).

C

cacheName() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.DerivedObject: Provides a unique name for caching the derived object.
cacheName() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.Erode: Provides a unique name for caching the eroded object.
cacheName() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.Shell
calc(CalculateForChild<T>, Feature<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.FeatureSingleObjectFromShared: Calculates the feature value for a single object.
calc(CalculateForChild<T>, Feature<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.MaskAsSingleObject
calc(CalculateForChild<T>, Feature<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.ObjectAggregationBase
calc(FeatureCalculationInput<T>, CalculationPart<U, T>, Function<ResolvedPart<U, T>, CalculateInputFromDelegateOption<S, T, U>>, Feature<S>, ChildCacheName, double) - Static method in class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegateOption: Calculates a feature using a cached-calculation as delegate.
calculate(int[]) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Difference
calculate(int[]) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Identity
calculate(int[]) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram
calculate(int[]) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.OutsideRange
calculate(int[]) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.RejectIfIntensityLessThan
calculate(int[]) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.SingleChannel
calculate(FeatureCalculationInput<FeatureInputHistogram>) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.LevelFromHistogram
calculate(FeatureCalculationInput<FeatureInputHistogram>) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.ThresholdHistogram
calculate(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.Intersection
calculate(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.CostOverlapWithinMidpointDistance
calculate(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.OverlapRelative
calculate(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.TouchingVoxels
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.ArbitraryInsidePoint
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.border.AtBorderBase
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxAlongAxisBase
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxNumberVoxels
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.SpecificEnergyChannelBase
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.FeatureEnergyChannel
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.GradientMagnitude
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.GradientMeanForAxis
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.ImageMomentsBase
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.DerivedObject
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.NumberRemovedVoxelsAfterClosing
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.OutlineKernelBase
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shape.ObjectRadiusStandardDeviation
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shape.ShapeRegularityCenterSlice
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shape.ShapeRegularityMaximumIntensityProjection
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjects
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.PairedWithMask
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.slice.MaximumNumberContourVoxelsOnSlice
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.slice.MaximumNumberVoxelsOnSlice
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.surface.SurfaceNumberVoxelsBase
calculate(FeatureCalculationInput<FeatureInputStack>) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.intensity.Intensity
calculate(FeatureCalculationInput<FeatureInputStack>) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.intensity.NumberChannels
calculate(FeatureCalculationInput<FeatureInputStack>) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.AsObjectMask
calculate(FeatureCalculationInput<FeatureInputStack>) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.QuantileAcrossConnectedComponents
calculate(FeatureCalculationInput<T>) - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.FromDimensionsBase
calculate(FeatureCalculationInput<T>) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.FeatureSingleObjectFromShared
calculate(FeatureCalculationInput<T>) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.ParamFromCollection
calculate(FeatureCalculationInput<T>) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.intensity.DataTypeMaxIntensity
calculate(ImageMetadata) - Method in class org.anchoranalysis.plugin.image.feature.bean.metadata.BitDepthPerChannel
calculate(ImageMetadata) - Method in class org.anchoranalysis.plugin.image.feature.bean.metadata.ExtractFromLocation
calculate(ImageMetadata) - Method in class org.anchoranalysis.plugin.image.feature.bean.metadata.ExtractTime
calculate(ImageMetadata) - Method in class org.anchoranalysis.plugin.image.feature.bean.metadata.NumberChannels
calculate(ImageMetadata) - Method in class org.anchoranalysis.plugin.image.feature.bean.metadata.NumberFrames
calculate(ImageMetadata) - Method in class org.anchoranalysis.plugin.image.feature.bean.metadata.NumberResolutionLevels
calculate(ImageMetadata) - Method in class org.anchoranalysis.plugin.image.feature.bean.metadata.NumberSeries
calculate(FeatureInputObjectCollection) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.collection.NumberObjects
calculateDenominator(FeatureInputPairObjects) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.OverlapRelative: Calculates the denominator for the overlap ratio.
calculateDenominator(FeatureInputPairObjects) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.OverlapRelativeToFirst
calculateDenominator(FeatureInputPairObjects) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.OverlapRelativeToMaxVolume
calculateDenominator(FeatureInputPairObjects) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.OverlapRelativeToMerged
calculateDenominator(FeatureInputPairObjects) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.OverlapRelativeToSecond
CalculateDeriveObjectInput - Class in org.anchoranalysis.plugin.image.feature.bean.stack.object: Derives a FeatureInputSingleObject from a FeatureInputStack by extracting an object mask from a specific energy channel.
CalculateDeriveObjectInput(int) - Constructor for class org.anchoranalysis.plugin.image.feature.bean.stack.object.CalculateDeriveObjectInput: Creates a new CalculateDeriveObjectInput instance.
CalculateDilation - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological: Calculates the dilation of an ObjectMask.
CalculateDilationMap - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological: Calculates a map of dilated ObjectMasks for different iteration counts.
CalculateDilationMap(boolean) - Constructor for class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateDilationMap: Creates a new CalculateDilationMap.
CalculateDilationMap(CalculateIncrementalOperationMap) - Constructor for class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateDilationMap: Copy constructor for CalculateDilationMap.
calculateEccentricity(double, double) - Static method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.PrincipalAxisEccentricity: Calculates the eccentricity from two eigenvalues.
CalculateErosion - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological: Calculates the erosion of an ObjectMask.
CalculateErosionMap - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological: Calculates a map of eroded ObjectMasks for different iteration counts.
CalculateErosionMap(boolean) - Constructor for class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateErosionMap: Creates a new CalculateErosionMap.
CalculateErosionMap(CalculateIncrementalOperationMap) - Constructor for class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateErosionMap: Copy constructor for CalculateErosionMap.
calculateForAxis(Dimensions, Axis) - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.Extent
calculateForAxis(Dimensions, Axis) - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.ForSpecificAxis: Calculates a feature value for a specific axis of the given dimensions.
calculateForAxis(Dimensions, Axis) - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.VoxelPhysicalSize
calculateForChannel(FeatureCalculationInput<FeatureInputSingleObject>, Channel) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.FeatureEnergyChannel: Calculates the feature value for a specific channel in the energy stack.
calculateForChannel(FeatureCalculationInput<FeatureInputSingleObject>, Channel) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.Intensity
calculateForChannel(FeatureCalculationInput<FeatureInputSingleObject>, Channel) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanMaxSlice: Calculates the maximum mean intensity across all slices of the object in the given channel.
calculateForChannel(FeatureCalculationInput<FeatureInputSingleObject>, Channel) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase
calculateForChannel(FeatureCalculationInput<FeatureInputSingleObject>, Channel) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.TextureScore
calculateForShell(ObjectMask, Channel) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShell
calculateForShell(ObjectMask, Channel) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase: Calculates the feature value for the given shell and channel.
calculateForShell(ObjectMask, Channel) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellMaxSlice
calculateForVoxel(int, int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevel
calculateForVoxel(int, int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevelBase: Calculates a score for a single voxel based on its intensity and the threshold level.
calculateForVoxel(int, int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.DifferenceCalculateLevelStandardDeviation
calculateFromAllMoments(ImageMoments) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.ImageMomentsBase: Calculates the feature value from the ImageMoments.
calculateFromAllMoments(ImageMoments) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.PrincipalAxisEccentricity
calculateFromAllMoments(ImageMoments) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.RatioPrincipalAxisLength
calculateFromAllMoments(ImageMoments) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.SpecificAxisBase
calculateFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.Area
calculateFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.ForSpecificAxis
calculateFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.FromDimensionsBase: Calculates a feature value from the given dimensions.
calculateFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.Volume
calculateFromSpecificMoment(EigenvalueAndVector) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.PrincipalAxisLength
calculateFromSpecificMoment(EigenvalueAndVector) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.PrincipalAxisOrientation
calculateFromSpecificMoment(EigenvalueAndVector) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.SpecificAxisBase: Calculates the result for the specific moment identified by index.
CalculateHistogram - Class in org.anchoranalysis.plugin.image.feature.stack.calculation: Calculates a Histogram from a specific channel in a FeatureInputStack.
CalculateHistogram(int) - Constructor for class org.anchoranalysis.plugin.image.feature.stack.calculation.CalculateHistogram: Creates a new CalculateHistogram instance.
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 org.anchoranalysis.plugin.image.feature.stack.calculation.CalculateHistogramMasked: Creates a new CalculateHistogramMasked instance.
CalculateIncrementalOperationMap - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single: Calculates incremental operations on ObjectMasks and stores the results in a map.
CalculateIncrementalOperationMap(boolean) - Constructor for class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateIncrementalOperationMap: Creates a new instance with the specified 3D flag.
CalculateIncrementalOperationMap(CalculateIncrementalOperationMap) - Constructor for class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateIncrementalOperationMap: Copy constructor.
CalculateInputFromDelegate<S,T,U> - Class in org.anchoranalysis.plugin.image.feature.object.calculation.delegate: A base class for CalculationParts that derive from an existing "delegate" calculation.
CalculateInputFromDelegate(ResolvedPart<U, T>) - Constructor for class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegate: Creates a new CalculateInputFromDelegate instance.
CalculateInputFromDelegate(CalculationPart<U, T>, CalculationPartResolver<T>) - Constructor for class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegate: Creates a new CalculateInputFromDelegate.
CalculateInputFromDelegateOption<S,T,U> - Class in org.anchoranalysis.plugin.image.feature.object.calculation.delegate: Like CalculateInputFromDelegate except assumes optional return value and no parameters.
CalculateInputFromDelegateOption(ResolvedPart<U, T>) - Constructor for class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegateOption: Creates with a delegate.
CalculateIntersecting - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting: Calculates a FeatureInputPairObjects from a FeatureInputSingleObject and an intersecting ObjectCollection.
CalculateIntersecting(ResolvedPart<ObjectCollection, FeatureInputSingleObject>, int) - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.CalculateIntersecting: Creates a new CalculateIntersecting instance.
CalculateLevel - Class in org.anchoranalysis.plugin.image.feature.bean.score: Calculates a level score based on voxel intensity and a given threshold.
CalculateLevel() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevel
CalculateLevelBase - Class in org.anchoranalysis.plugin.image.feature.bean.score: Base class for calculating a score based on a threshold level derived from a histogram.
CalculateLevelBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevelBase
CalculateObjectMask - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single: Calculates an ObjectMask based on a specified number of iterations.
CalculateObjectMask(int, ResolvedPartMap<ObjectMask, FeatureInputSingleObject, Integer>) - Constructor for class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateObjectMask: Creates a new CalculateObjectMask instance.
CalculateObjectMask(CalculateObjectMask) - Constructor for class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateObjectMask: Copy constructor.
CalculateShellObjectMask - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single: Calculates a shell ObjectMask by performing dilation and erosion operations.
CalculateShellObjectMask(ResolvedPart<ObjectMask, FeatureInputSingleObject>, ResolvedPart<ObjectMask, FeatureInputSingleObject>, int, boolean, boolean) - Constructor for class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateShellObjectMask: Creates a new CalculateShellObjectMask instance.
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.CoefficientOfVariation
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Count
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Kurtosis
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Maximum
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.MeanRaisedToPower
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Median
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Minimum
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Mode
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.NumberDistinctValues
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Quantile
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Range
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.RatioNonMode
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Skewness
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.StandardDeviation
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Sum
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.TotalCount
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Variance
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.RatioThreshold
calculateWithChannel(ObjectMask, Channel) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.CountEqual: Calculates the number of voxels in the object that have the specified intensity value in the channel.
calculateWithChannel(ObjectMask, Channel) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.SpecificEnergyChannelBase: Calculates the feature value for a specific object and channel.
calculateWithIntersection(ObjectMask, ObjectMask, BoundingBox) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.HasTouchingVoxels
calculateWithIntersection(ObjectMask, ObjectMask, BoundingBox) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.NumberTouchingVoxelFaces
calculateWithIntersection(ObjectMask, ObjectMask, BoundingBox) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.NumberTouchingVoxels
calculateWithIntersection(ObjectMask, ObjectMask, BoundingBox) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.TouchingVoxels: Calculates the feature value for the intersection of two objects.
calculateWithParameters(ObjectMask, KernelApplicationParameters, CheckedSupplier<EnergyStack, FeatureCalculationException>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.border.NumberVoxelsAtBorder
calculateWithParameters(ObjectMask, KernelApplicationParameters, CheckedSupplier<EnergyStack, FeatureCalculationException>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.NumberNeighboringVoxels
calculateWithParameters(ObjectMask, KernelApplicationParameters, CheckedSupplier<EnergyStack, FeatureCalculationException>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.OutlineKernelBase: Calculates the feature value using the specified parameters.
calculateWithResolution(double, Resolution) - Method in class org.anchoranalysis.plugin.image.feature.bean.physical.UnitsWithinRange
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.CalculateIntersecting
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.CalculateDeriveObjectInput
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegate
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegateOption
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateIncrementalOperationMap
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateObjectMask
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateShellObjectMask
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateDilation
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateDilationMap
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateErosion
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateErosionMap
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.stack.calculation.CalculateHistogram
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.stack.calculation.CalculateHistogramMasked
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeature
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureSequenceInteger
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.CombineObjectsForFeatures: Checks if the bean is misconfigured and saves the default instances for later use.
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.Intersection
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase
CoefficientOfVariation - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic: Calculates the coefficient of variation of all the values in the histogram.
CoefficientOfVariation() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.CoefficientOfVariation
CombineObjectsForFeatures<T> - Class in org.anchoranalysis.plugin.image.feature.bean.object.combine: A way to combine (or not combine) objects so that they provide a feature-table.
CombineObjectsForFeatures() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.combine.CombineObjectsForFeatures
CombineObjectsForFeatures(Interpolator) - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.combine.CombineObjectsForFeatures: Create with a specific interpolator.
configurePermuteProperty(PermutePropertySequenceInteger) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteDivideByParam
configurePermuteProperty(PermutePropertySequenceInteger) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureSequenceInteger: Configures the PermutePropertySequenceInteger for this permutation.
configurePermuteProperty(PermutePropertySequenceInteger) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFirstSecondOrder
copyChangeIterationsDilation(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations: Creates a copy of this bean with a new value for iterationsDilation.
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 org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.CostOverlapWithinMidpointDistance
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 org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Count
CountEqual - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.energy: Counts the number of voxels in an object that have a specific intensity value in a channel.
CountEqual() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.CountEqual
create() - Method in interface org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFirstSecondOrder.CreateFirstSecondOrder: Creates a new StatisticalBase instance.
createAggregateFeature(Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.FeatureListProviderAggregatePair: Creates an aggregate feature from individual features for first, second, and merged objects.
createAggregateFeature(Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.ReduceFirstAndSecond
createAggregateFeature(Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.ReduceRatioFirstAndSecond
createAggregateFeature(Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.SubtractReducedFromMerged
createCachedCalculationForDerived(CalculationPartResolver<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.DerivedObject: Creates a CalculationPart for deriving the object mask.
createCachedCalculationForDerived(CalculationPartResolver<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.Erode: Creates a CalculationPart for eroding the object mask.
createCachedCalculationForDerived(CalculationPartResolver<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.Shell
createCountKernelMask(ObjectMask) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.TouchingVoxels: Creates a CountKernel for the given object mask.
createDelegate(Feature<T>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteDivideByParam
createDelegate(Feature<T>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureSequenceInteger: Creates a delegate PermuteFeature for the given feature.
createDelegate(Feature<T>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFirstSecondOrder
createFeatures(List<NamedBean<FeatureListProvider<FeatureInputSingleObject>>>, NamedFeatureStoreFactory, boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.CombineObjectsForFeatures: Creates features that will be applied on the objects.
createFeatures(List<NamedBean<FeatureListProvider<FeatureInputSingleObject>>>, NamedFeatureStoreFactory, boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.EachObjectIndependently
createFeatures(List<NamedBean<FeatureListProvider<FeatureInputSingleObject>>>, NamedFeatureStoreFactory, boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
createFeatures(NamedFeatureStore<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.EachObjectIndependently: Creates a FeatureTableCalculator from a NamedFeatureStore.
createParam(String, boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureSequenceInteger: Creates a parameter feature for the permutation.
createParameters() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.TouchingVoxels: Creates KernelApplicationParameters based on the current configuration.
createParameters(boolean, boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.surface.SurfaceNumberVoxelFaces
createParameters(boolean, boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.surface.SurfaceNumberVoxels
createParameters(boolean, boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.surface.SurfaceNumberVoxelsBase: Creates the calculation parameters for the surface voxel count.
createPermutedFeaturesFor(Feature<T>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeature
createPermutedFeaturesFor(Feature<T>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureBase: Creates permuted features for the given feature.
createPermutedFeaturesFor(Feature<T>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureSequenceInteger
createReducedFeature(Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.FeatureListProviderAggregatePair: Creates a reduced feature from features for the first and second objects.
CreationTime - Class in org.anchoranalysis.plugin.image.feature.bean.metadata: The creation-time of the image, if specified on the image file.
CreationTime() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.metadata.CreationTime

D

DataTypeMaxIntensity<T> - Class in org.anchoranalysis.plugin.image.feature.bean.stack.intensity: The maximum-intensity allowed by the data-type of the stack.
DataTypeMaxIntensity() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.stack.intensity.DataTypeMaxIntensity
DerivedObject - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.morphological: A base class for features that operate on a derived object mask and calculate a feature on it.
DerivedObject() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.DerivedObject
deriveFromDelegate(FeatureInputSingleObject, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.CalculateIntersecting
deriveFromDelegate(T, U) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegate: Derives the result from the delegate calculation.
DeriveFromPair - Class in org.anchoranalysis.plugin.image.feature.bean.list.pair: Embeds each feature in a FeatureDeriveFromPair feature (first, second or merge) and prepends with a string.
DeriveFromPair() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.pair.DeriveFromPair
deriveInputsStartBatch(ObjectCollection, EnergyStack, boolean, OperationContext) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.CombineObjectsForFeatures: Derives a list of inputs (i.e.
deriveScoreFromVoxel(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevelBase
deriveScoreFromVoxel(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.NormalizeByConstant
deriveScoreFromVoxel(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.NormalizeByMax
deriveScoreFromVoxel(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.SingleChannel: Derives a score from a single voxel intensity.
deriveStatistic(DoubleArrayList) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.MeanAcrossObjects
deriveStatistic(DoubleArrayList) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.ObjectAggregationBase: Derives a statistic from the calculated feature values for all objects.
deriveStatistic(DoubleArrayList) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.QuantileAcrossObjects
describeParameters() - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.ForSpecificAxis
describeParameters() - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Count
describeParameters() - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.RatioThreshold
describeParameters() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxAlongAxisBase
describeParameters() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase
describeParameters() - Method in class org.anchoranalysis.plugin.image.feature.bean.physical.UnitsWithinRange
describePropertiesFriendly() - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations: Creates a string that uniquely identifies all properties in the bean, in a human-friendly format.
descriptionLong() - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.intensity.Intensity
Difference - Class in org.anchoranalysis.plugin.image.feature.bean.score
Difference() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.Difference
DifferenceCalculateLevelStandardDeviation - Class in org.anchoranalysis.plugin.image.feature.bean.score: Similar to Difference but calculates the width as the standard-deviation of the histogram
DifferenceCalculateLevelStandardDeviation() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.DifferenceCalculateLevelStandardDeviation

E

EachObjectIndependently - Class in org.anchoranalysis.plugin.image.feature.bean.object.combine: Selects features and objects directly from the input list, treating each object independently.
EachObjectIndependently() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.combine.EachObjectIndependently
EachObjectIndependently(Interpolator) - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.combine.EachObjectIndependently: Create with a specific interpolator.
equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations
equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.CalculateIntersecting
equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.CalculateDeriveObjectInput
equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegate
equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegateOption
equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateIncrementalOperationMap
equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateObjectMask
equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateShellObjectMask
equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateDilation
equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateDilationMap
equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateErosion
equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateErosionMap
equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.stack.calculation.CalculateHistogram
equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.stack.calculation.CalculateHistogramMasked
Erode - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.morphological: A feature that erodes an object mask and then calculates another feature on the eroded object.
Erode() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.Erode
errorMessageIfTooFewPixels() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.ImageMomentsBase: Generates an error message when there are too few pixels to calculate moments.
errorMessageIfTooFewPixels() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.PrincipalAxisEccentricity
errorMessageIfTooFewPixels() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.PrincipalAxisLength
errorMessageIfTooFewPixels() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.PrincipalAxisOrientation
errorMessageIfTooFewPixels() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.RatioPrincipalAxisLength
execute(FeatureInputSingleObject) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateObjectMask
execute(FeatureInputSingleObject) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateShellObjectMask
execute(FeatureInputSingleObject, Integer) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateIncrementalOperationMap
execute(FeatureInputStack) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.CalculateDeriveObjectInput
execute(FeatureInputStack) - Method in class org.anchoranalysis.plugin.image.feature.stack.calculation.CalculateHistogram
execute(FeatureInputStack) - Method in class org.anchoranalysis.plugin.image.feature.stack.calculation.CalculateHistogramMasked
execute(T) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegate
Extent<T> - Class in org.anchoranalysis.plugin.image.feature.bean.dimensions: Width/height/depth of energy-stack in pixels depending on axis.
Extent() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.dimensions.Extent
extractAsDouble(Dictionary, String) - Static method in class org.anchoranalysis.plugin.image.feature.bean.score.FromDictionaryBase: Extracts a double value from the dictionary for a given key.
ExtractFromLocation - Class in org.anchoranalysis.plugin.image.feature.bean.metadata: Extracts a double value from a ImageLocation if it exists in a ImageMetadata.
ExtractFromLocation() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.metadata.ExtractFromLocation
extractTime(ImageMetadata) - Method in class org.anchoranalysis.plugin.image.feature.bean.metadata.AcquisitionTime
extractTime(ImageMetadata) - Method in class org.anchoranalysis.plugin.image.feature.bean.metadata.CreationTime
extractTime(ImageMetadata) - Method in class org.anchoranalysis.plugin.image.feature.bean.metadata.ExtractTime: Extracts the time from the given metadata to return as the feature-value (if non-empty).
extractTime(ImageMetadata) - Method in class org.anchoranalysis.plugin.image.feature.bean.metadata.ModificationTime
ExtractTime - Class in org.anchoranalysis.plugin.image.feature.bean.metadata: Base class for extracting time information from an image's metadata.
ExtractTime() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.metadata.ExtractTime
extractTupleForBoundingBox(BoundingBox) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxAlongAxisBase: Extracts a ReadableTuple3i from the given BoundingBox.
extractTupleForBoundingBox(BoundingBox) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxExtentAlongAxis
extractTupleForBoundingBox(BoundingBox) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxMaximumAlongAxis
extractTupleForBoundingBox(BoundingBox) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxMinimumAlongAxis
extractValue(ImageLocation) - Method in class org.anchoranalysis.plugin.image.feature.bean.metadata.ExtractFromLocation: Extracts the value that is returned from the feature if an image-location is present.
extractValue(ImageLocation) - Method in class org.anchoranalysis.plugin.image.feature.bean.metadata.Latitude
extractValue(ImageLocation) - Method in class org.anchoranalysis.plugin.image.feature.bean.metadata.Longitude

F

FeatureEnergyChannel - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity: A feature that uses a channel from the energy-stack as identified by an index.
FeatureEnergyChannel() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.FeatureEnergyChannel
FeatureIntersectingObjects - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting: An abstract base class for features that calculate values based on intersecting objects.
FeatureIntersectingObjects() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjects
FeatureIntersectingObjectsSingleElement - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting: A feature that calculates a value based on intersecting objects, considering each intersecting object individually.
FeatureIntersectingObjectsSingleElement() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjectsSingleElement
FeatureIntersectingObjectsThreshold - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting: An abstract feature that calculates a value based on intersecting objects, considering each intersecting object individually and applying a threshold.
FeatureIntersectingObjectsThreshold() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjectsThreshold
FeatureListProviderAggregatePair - Class in org.anchoranalysis.plugin.image.feature.bean.list.pair: Calculates features on each part of a pair (first, second, merged etc.) and then reduces the calculation to a single number.
FeatureListProviderAggregatePair() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.pair.FeatureListProviderAggregatePair
FeatureSingleObjectFromShared<T> - Class in org.anchoranalysis.plugin.image.feature.bean.shared.object: Calculates object-masks from entities in shared, using the feature-input only for an energy-stack.
FeatureSingleObjectFromShared() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.shared.object.FeatureSingleObjectFromShared
ForSpecificAxis<T> - Class in org.anchoranalysis.plugin.image.feature.bean.dimensions: Dimensions-calculation for one specific axis only.
ForSpecificAxis() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.dimensions.ForSpecificAxis
FromDictionaryBase - Class in org.anchoranalysis.plugin.image.feature.bean.score: An abstract base class for features that require a Dictionary for initialization.
FromDictionaryBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.FromDictionaryBase
FromDimensionsBase<T> - Class in org.anchoranalysis.plugin.image.feature.bean.dimensions: Base class for features that are calculated from Dimensions.
FromDimensionsBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.dimensions.FromDimensionsBase

G

get() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.IntensityMoments
get() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.DeriveFromPair
get() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.FeatureListProviderAggregatePair
get() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureBase
get(int) - Method in class org.anchoranalysis.plugin.image.feature.object.ListWithThumbnails: Gets the item at the specified index in the list.
getAxis() - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.ForSpecificAxis: The axis to perform the calculation on.
getAxis() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.ArbitraryInsidePoint: The axis to output.
getAxis() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxAlongAxisBase: The axis along which to calculate the feature value ("x", "y", or "z").
getAxis() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.GradientMeanForAxis
getAxis() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.PrincipalAxisOrientation: Which axis to read from (x,y,z)
getCalculateLevel() - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.LevelFromHistogram
getCalculateLevel() - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.ThresholdHistogram
getCalculateLevel() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevelBase: The method to calculate the threshold level.
getChannelFirst() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Difference: Index of first channel
getChannelSecond() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Difference: Index of second channel
getDelegate() - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegate: Gets the delegate ResolvedPart.
getDictionary() - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.ParamFromCollection: The name of the Dictionary that will be retrieved from SharedObjects.
getDistanceMax() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevel: The maximum distance from the threshold level to consider.
getEmptyValue() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.Intersection
getEmptyValue() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.ArbitraryInsidePoint: The value to return if no point is found inside the object-mask.
getEmptyValue() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanMaxSlice: The value to return when the object has no voxels in any slice.
getEmptyValue() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase: The value to return when the resulting object is empty.
getEmptyValue() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.DerivedObject: The value to return when the derived object is empty.
getEnergyChannelIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Identity: The index of the energy channel to use for calculations.
getEnergyChannelIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.RejectIfIntensityLessThan: The index of the energy channel to check for intensity.
getEnergyChannelIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.SingleChannel: The index of the energy channel to use for score calculation.
getEnergyChannelIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.QuantileAcrossConnectedComponents
getEnergyChannelIndexCheck() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram: The index of the energy channel to check.
getEnergyChannelIndexFail() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram: The index of the energy channel to use if the relation check fails.
getEnergyIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.NumberNeighboringVoxels: Index of which channel in the energy-stack to select
getEnergyIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.SpecificEnergyChannelBase: Index of which channel in the energy-stack to select.
getEnergyIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.FeatureEnergyChannel: Index of channel to use in the energy-stack (0 is the first channel, 1 is second etc.)
getEnergyIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.OutsideRange: The index of the energy channel to use for intensity values.
getEnergyIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.intensity.Intensity: The channel that that forms the histogram.
getEnergyIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.AsObjectMask: The channel that that forms an object-mask with the bounding-box set to entire channel's dimensions
getEnergyIndexGradient() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.TextureScore
getEnergyIndexMask() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.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 org.anchoranalysis.plugin.image.feature.bean.stack.intensity.Intensity: Optionally, index of another channel that masks the histogram.
getEnergyIndexX() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.IntensityGradientBase: Index of the channel in the energy stack to use for the X-component of the gradient.
getEnergyIndexY() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.IntensityGradientBase: Index of the channel in the energy stack to use for the Y-component of the gradient.
getEnergyIndexZ() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.IntensityGradientBase: Index of the channel in the energy stack to use for the Z-component of the gradient.
getFactorHigh() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Identity: The factor to apply for values above 0.5 when normalizing.
getFactorLow() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Identity: The factor to apply for values below 0.5 when normalizing.
getFeature() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureBase: The feature to be permuted.
getFeaturesImage() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors: Additional features that only depend on the image, so do not need to be replicated for every object.
getFeaturesPair() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors: Additional features that are processed on the pair of images (i.e.
getHistogramChannelIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevelBase: The index of the histogram channel to use for calculations.
getHistogramIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram: The index of the histogram to use for comparison.
getId() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjects: ID for the particular object-collection
getIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.SpecificAxisBase: Specifies which principal-axis to use for calculations (0=largest eigenvalue, 1=second-largest eigenvalue etc.)
getInterpolator() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.CombineObjectsForFeatures: Interpolator used to resize images in thumbnail generation.
getItem() - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.ThresholdHistogram
getItem() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.DeriveFromPair
getItem() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.FeatureListProviderAggregatePair: For each feature in the list, a corresponding aggregate feature is created in the output list.
getItem() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.Intensity: Feature to apply to the histogram
getItem() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.DerivedObject: The feature to calculate on the derived object.
getItem() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjectsSingleElement: The feature to calculate for each intersecting object pair.
getItem() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.PairedWithMask
getItem() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.RejectIfIntensityLessThan: The VoxelScore to use for calculating the score if the intensity is not rejected.
getItem() - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.FeatureSingleObjectFromShared: The feature to be calculated on a single object.
getItem() - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.intensity.Intensity: Feature to apply to the histogram.
getItem() - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.AsObjectMask
getItem() - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.QuantileAcrossConnectedComponents
getIterations() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.Intersection: The number of dilations and erosions to apply to determine if two objects intersect
getIterations() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase: The number of dilations and erosions to apply and whether to do in the Z dimension.
getIterations() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.Erode: The number of iterations to perform the erosion operation.
getIterations() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.NumberRemovedVoxelsAfterClosing
getIterations() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.Shell: The number of dilations and erosions to apply and whether to do so in the Z dimension.
getIterationsDilation() - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations: Number of times to perform morphological dilation.
getIterationsErosion() - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations: Number of times to perform morphological erosion.
getKey() - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.ParamFromCollection: The name of the key in the dictionary, whose corresponding value will be returned.
getMask() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.PairedWithMask
getMask() - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.MaskAsSingleObject: The provider for the mask to be treated as a single object.
getMax() - Method in class org.anchoranalysis.plugin.image.feature.bean.physical.UnitsWithinRange: Maximum-boundary for acceptable range
getMax() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.OutsideRange: The maximum value of the range (exclusive).
getMaxDistance() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.CostOverlapWithinMidpointDistance
getMaximumNumberChannels() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.IntensityMoments: An upper limit on the number of channels in the energy-stack for which we create features.
getMin() - Method in class org.anchoranalysis.plugin.image.feature.bean.physical.UnitsWithinRange: Minimum-boundary for acceptable range
getMin() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.OutsideRange: The minimum value of the range (inclusive).
getMinDifference() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Difference: A minimum difference, below which 0.0 is returned
getMinDifference() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.DifferenceCalculateLevelStandardDeviation
getMinIntensity() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.RejectIfIntensityLessThan: The minimum intensity threshold.
getMinOverlap() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.CostOverlapWithinMidpointDistance
getObjects() - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.ObjectAggregationBase: The provider for the collection of objects to calculate features on.
getOutside() - Method in class org.anchoranalysis.plugin.image.feature.bean.physical.UnitsWithinRange: Returned as a constant if a value lies otside the range
getParamPrefix() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureSequenceInteger: Prefix for the parameter key.
getPermutation() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeature: A permutation to apply.
getPermutations() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeature: A list of permutations to apply.
getPermuteProperty() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureSequenceInteger: Defines how to permute the property with a sequence of integers.
getPower() - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.MeanRaisedToPower: The power to which the mean value is raised.
getPrefix() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.DeriveFromPair
getPrefix() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.FeatureListProviderAggregatePair: The string to prepend.
getQuantile() - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Quantile: The quantile to calculate from the histogram.
getQuantile() - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.QuantileAcrossObjects
getQuantile() - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.QuantileAcrossConnectedComponents
getQuantileHigh() - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Range
getQuantileLow() - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Range
getReduce() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.FeatureListProviderAggregatePair: Method for reducing all pairs into a single value e.g.
getReferencesFeatureListCreator() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeature: Makes sure a particular feature list creator is evaluated
getRelation() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram: The relation to test between the voxel value and the histogram value.
getSearchObjects() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjects: Gets the collection of objects to search for intersections.
getSelect() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.DeriveFromPair: Either "merged" or "first" or "second" indicating which feature to delegate from
getSubtractConstant() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.IntensityGradientBase: A constant value to subtract from each voxel intensity before calculating the gradient.
getThreshold() - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Count
getThreshold() - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.RatioThreshold: The threshold condition to be applied to the histogram values.
getThreshold() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjectsThreshold: The threshold value for considering intersecting objects.
getThumbnail() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.CombineObjectsForFeatures: Generates a thumbnail representation of one or more combined objects, as form a single input.
getThumbnailBatch() - Method in class org.anchoranalysis.plugin.image.feature.object.ListWithThumbnails: The optional thumbnail batch associated with the list.
getValue() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.CountEqual: The intensity value to count.
getValue() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram: The value to return if the relation test passes.
getValue() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.NormalizeByConstant: The constant value to divide the voxel intensity by.
getValueIfTooFewVoxels() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.ImageMomentsBase: A value to return if there are too few voxels (less than MIN_NUM_VOXELS) to calculate moments.
getValueNoObjects() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjects: The value to return when there are no objects in the search collection.
getWidth() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Difference: Width (what the difference is divided by)
getWidthFactor() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.DifferenceCalculateLevelStandardDeviation
getWithin() - Method in class org.anchoranalysis.plugin.image.feature.bean.physical.UnitsWithinRange: Returned as a constant if a value lies within the range
gradientCalculation() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.IntensityGradientBase: Creates a CalculationPart for calculating the gradient from the specified channels.
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 org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.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 org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.GradientMeanForAxis

H

hashCode() - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations
hashCode() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.CalculateIntersecting
hashCode() - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.CalculateDeriveObjectInput
hashCode() - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegate
hashCode() - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegateOption
hashCode() - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateIncrementalOperationMap
hashCode() - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateObjectMask
hashCode() - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateShellObjectMask
hashCode() - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateDilation
hashCode() - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateDilationMap
hashCode() - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateErosion
hashCode() - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateErosionMap
hashCode() - Method in class org.anchoranalysis.plugin.image.feature.stack.calculation.CalculateHistogram
hashCode() - Method in class org.anchoranalysis.plugin.image.feature.stack.calculation.CalculateHistogramMasked
HasTouchingVoxels - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.touching: A simple scheme for counting the touching voxels.
HasTouchingVoxels() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.HasTouchingVoxels

I

Identity - Class in org.anchoranalysis.plugin.image.feature.bean.score: A voxel score that can optionally normalize and adjust the intensity values.
Identity() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.Identity
IdentityImposeValueRelationToHistogram - Class in org.anchoranalysis.plugin.image.feature.bean.score: A voxel score that imposes a value relation to a histogram.
IdentityImposeValueRelationToHistogram() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram
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 org.anchoranalysis.plugin.image.feature.bean.object.single.moments.ImageMomentsBase
initialize(List<Histogram>, Optional<Dictionary>) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevelBase
initialize(List<Histogram>, Optional<Dictionary>) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.FromDictionaryBase: Initializes the feature with histograms and a dictionary.
initialize(List<Histogram>, Optional<Dictionary>) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram
initialize(List<Histogram>, Optional<Dictionary>) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.NormalizeByMax
inputType() - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.FromDimensionsBase
inputType() - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.FeatureSingleObjectFromShared
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 - 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 org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.Intensity
Intensity() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.stack.intensity.Intensity
IntensityGradientBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient: Base class for features that calculate intensity gradients from multiple channels.
IntensityGradientBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.IntensityGradientBase
IntensityMeanMaxSlice - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity: Calculates the maximum mean intensity across all slices of an object in a channel.
IntensityMeanMaxSlice() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.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 org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.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 org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.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 org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellMaxSlice
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 org.anchoranalysis.plugin.image.feature.bean.list.IntensityMoments
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 org.anchoranalysis.plugin.image.feature.bean.object.pair.Intersection
isAcceptMissingResolution() - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.VoxelPhysicalSize: Whether to throw an exception (if true) if image-resolution is missing, or return Double.Nan (if false).
isAtLeastOnePositive() - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations: Checks if at least one of iterationsDilation and iterationsErosion is more than 0.
isAvoidOverlappingObjects() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors: If true, no overlapping objects are treated as pairs
isBoundingBoxAtBorder(BoundingBox, Extent) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.border.AtBorderBase: Checks if the bounding box of an object is at the border of the image.
isBoundingBoxAtBorder(BoundingBox, Extent) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.border.AtBorderXY
isBoundingBoxAtBorder(BoundingBox, Extent) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.border.AtBorderZ
isCov() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shape.ObjectRadiusStandardDeviation: If true, returns the coefficient of variation (stdDev/mean) instead of standard deviation.
isDo3D() - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations: Whether to perform the morphological dimensions in 3D or 2D.
isDo3D() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
isDo3D() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.TouchingVoxels: Whether to perform calculations in 3D (true) or 2D (false).
isDo3D() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.Erode: If true, performs 3D erosion; if false, performs 2D erosion on each z-slice separately.
isDo3D() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.NumberRemovedVoxelsAfterClosing
isDo3D() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.OutlineKernelBase: If true, applies the kernel in 3D; otherwise, applies it in 2D.
isExcludeZero() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.Intensity: Iff true, zero-valued voxels are excluded from the histogram
isExcludeZero() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanMaxSlice: If true, zero-valued voxels are excluded from the mean intensity calculation.
isIgnoreAtThreshold() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.OutlineKernelBase: If true, ignores voxels at the threshold when applying the kernel.
isIgnoreZero() - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.RatioNonMode: Whether to ignore the zero value when calculating the ratio.
isIncludeFirst() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors: Include features for the First-object of the pair
isIncludeMerged() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors: Include features for the Merged-object of the pair
isIncludeSecond() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors: Include features for the Second-object of the pair
isInverse() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase: If true, calculates instead on the inverse of the object-mask (what's left when the shell is removed).
isInverseMask() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase: If true, uses the inverse of the passed mask.
isKeepExtremes() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Identity: Whether to keep extreme values (0 and 1) unchanged when normalizing.
isMax() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram: Whether to use the maximum (true) or minimum (false) value from the histogram.
isMip() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.surface.SurfaceNumberVoxelsBase: If true, calculates the surface on a maximum intensity projection rather than the 3D object.
isNormalize() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Identity: Whether to normalize the voxel intensity values.
isOutsideAtThreshold() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.OutlineKernelBase: If true, considers voxels outside the object at the threshold as part of the object.
isParamPrefixAppendNumber() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFirstSecondOrder: If true, the constant is appended to the param prefix (a dot and a number).
isSuppress3D() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.surface.SurfaceNumberVoxelsBase: If true, suppresses 3D calculations and treats the object as 2D.
isSuppressZ() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.CostOverlapWithinMidpointDistance
isSuppressZ() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.ImageMomentsBase: If true co-variance is suppressed in z-dimension.

K

Kurtosis - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic: Calculates the kurtosis of all the values in the histogram.
Kurtosis() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Kurtosis

L

Latitude - Class in org.anchoranalysis.plugin.image.feature.bean.metadata: Extracts the latitude from the image metadata.
Latitude() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.metadata.Latitude
LevelFromHistogram - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.threshold: Calculates a level (a threshold-value) from a histogram.
LevelFromHistogram() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.LevelFromHistogram
ListWithThumbnails<T,S> - Class in org.anchoranalysis.plugin.image.feature.object: A list of items with an associated thumbnail-batch.
ListWithThumbnails(List<T>) - Constructor for class org.anchoranalysis.plugin.image.feature.object.ListWithThumbnails: Creates a new instance without a thumbnail batch.
ListWithThumbnails(List<T>, ThumbnailBatch<S>) - Constructor for class org.anchoranalysis.plugin.image.feature.object.ListWithThumbnails: Creates a new instance with a thumbnail batch.
Longitude - Class in org.anchoranalysis.plugin.image.feature.bean.metadata: Extracts the longitude from the image metadata.
Longitude() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.metadata.Longitude

M

MaskAsSingleObject<T> - Class in org.anchoranalysis.plugin.image.feature.bean.shared.object: Calculates a feature, treating a mask as a single-object on the energy-stack.
MaskAsSingleObject() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.shared.object.MaskAsSingleObject
MaxFeatureIntersectingObjects - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting: 1.
MaxFeatureIntersectingObjects() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.MaxFeatureIntersectingObjects
Maximum - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic: Calculates the maximum value in a histogram.
Maximum() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Maximum
MaximumNumberContourVoxelsOnSlice - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.slice: Maximum number of voxels on any slice's contour (edge voxels) across all slices.
MaximumNumberContourVoxelsOnSlice() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.slice.MaximumNumberContourVoxelsOnSlice
MaximumNumberVoxelsOnSlice - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.slice: Maximum number of voxels in the object-mask across all slices.
MaximumNumberVoxelsOnSlice() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.slice.MaximumNumberVoxelsOnSlice
MeanAcrossObjects<T> - Class in org.anchoranalysis.plugin.image.feature.bean.shared.object: Calculates the mean of a feature applied to each connected component
MeanAcrossObjects() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.shared.object.MeanAcrossObjects
MeanRaisedToPower - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic: Calculates the mean value in a Histogram, and raises it to a power.
MeanRaisedToPower() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.MeanRaisedToPower
Median - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic: Calculates the median value in a Histogram.
Median() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Median
MinFeatureIntersectingObjectsAboveThreshold - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting: 1.
MinFeatureIntersectingObjectsAboveThreshold() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.MinFeatureIntersectingObjectsAboveThreshold
Minimum - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic: Calculates the minimum value in a Histogram.
Minimum() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Minimum
Mode - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic: Calculates the skewness of all the values in the histogram.
Mode() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Mode
ModificationTime - Class in org.anchoranalysis.plugin.image.feature.bean.metadata: The modification-time of the image, if specified on the image file.
ModificationTime() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.metadata.ModificationTime
MorphologicalIterations - Class in org.anchoranalysis.plugin.image.feature.bean.morphological: Specifies a certain number of iterations of the morphological operations of dilation and erosion.
MorphologicalIterations() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations

N

NormalizeByConstant - Class in org.anchoranalysis.plugin.image.feature.bean.score: Normalizes the voxel intensity by dividing it by a constant value.
NormalizeByConstant() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.NormalizeByConstant
NormalizeByMax - Class in org.anchoranalysis.plugin.image.feature.bean.score: This assumes the histograms correspond to the energy channels exactly (in terms of indexing)
NormalizeByMax() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.NormalizeByMax
numberBorderPixels(ObjectMask, KernelApplicationParameters) - Static method in class org.anchoranalysis.plugin.image.feature.bean.object.single.border.NumberVoxelsAtBorder: Calculates the number of border voxels for a given object.
NumberChannels - Class in org.anchoranalysis.plugin.image.feature.bean.metadata: The number of channels in an image.
NumberChannels - Class in org.anchoranalysis.plugin.image.feature.bean.stack.intensity: The number of channels in an image-stack.
NumberChannels() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.metadata.NumberChannels
NumberChannels() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.stack.intensity.NumberChannels
NumberDistinctValues - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic: Number of unique values in histogram.
NumberDistinctValues() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.NumberDistinctValues
NumberFrames - Class in org.anchoranalysis.plugin.image.feature.bean.metadata: The number of frames in an image.
NumberFrames() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.metadata.NumberFrames
NumberIntersectingObjects - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting: A feature that calculates the number of objects intersecting with the input object.
NumberIntersectingObjects() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.NumberIntersectingObjects
NumberIntersectingObjectsAboveThreshold - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting: 1.
NumberIntersectingObjectsAboveThreshold() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.NumberIntersectingObjectsAboveThreshold
NumberNeighboringVoxels - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.energy: Calculates the number of voxels on the object that have a neighbor.
NumberNeighboringVoxels() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.NumberNeighboringVoxels
NumberObjects - Class in org.anchoranalysis.plugin.image.feature.bean.object.collection: Calculates the number of objects in a FeatureInputObjectCollection.
NumberObjects() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.collection.NumberObjects
NumberRemovedVoxelsAfterClosing - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.morphological: How many pixels are removed after a morphological closing operation on the object-mask.
NumberRemovedVoxelsAfterClosing() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.NumberRemovedVoxelsAfterClosing
NumberResolutionLevels - Class in org.anchoranalysis.plugin.image.feature.bean.metadata: The number of resolution-levels in an image in a file.
NumberResolutionLevels() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.metadata.NumberResolutionLevels
NumberSeries - Class in org.anchoranalysis.plugin.image.feature.bean.metadata: The number of series in an image-file.
NumberSeries() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.metadata.NumberSeries
NumberTouchingVoxelFaces - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.touching: A scheme for counting the touching voxels by intersection of object-masks
NumberTouchingVoxelFaces() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.NumberTouchingVoxelFaces
NumberTouchingVoxels - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.touching: A scheme for counting touching voxels.
NumberTouchingVoxels() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.NumberTouchingVoxels
NumberVoxelsAtBorder - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.border: Calculates the number of voxels at the border of an object.
NumberVoxelsAtBorder() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.border.NumberVoxelsAtBorder

O

ObjectAggregationBase<T> - Class in org.anchoranalysis.plugin.image.feature.bean.shared.object: Calculates a feature for a set of objects using this stack as an energy-stack, and aggregates.
ObjectAggregationBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.shared.object.ObjectAggregationBase
ObjectRadiusStandardDeviation - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shape: Calculates the standard deviation of distances from surface voxels to the centroid of an ObjectMask.
ObjectRadiusStandardDeviation() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.shape.ObjectRadiusStandardDeviation
objectsForThumbnail(FeatureInputPairObjects) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
objectsForThumbnail(FeatureInputSingleObject) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.EachObjectIndependently
objectsForThumbnail(T) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.CombineObjectsForFeatures: Selects objects from an input that will be used for thumbnail generation.
of(CalculationPartResolver<FeatureInputSingleObject>, int, boolean) - Static method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateDilation: Creates a new ResolvedPart for calculating dilation.
of(CalculationPartResolver<FeatureInputSingleObject>, int, boolean) - Static method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateErosion: Creates a new CalculationPart for calculating erosion.
of(CalculationPartResolver<FeatureInputSingleObject>, MorphologicalIterations, int, boolean) - Static method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateShellObjectMask: Creates a new CalculateShellObjectMask instance.
ofResolved(CalculationPartResolver<FeatureInputSingleObject>, int, boolean) - Static method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateErosion: Creates a new ResolvedPart for calculating erosion.
onInitialization(FeatureRelatedInitialization) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeature
org.anchoranalysis.plugin.image.feature.bean.dimensions - package org.anchoranalysis.plugin.image.feature.bean.dimensions: Features that are calculated from Dimensions.
org.anchoranalysis.plugin.image.feature.bean.histogram.statistic - package org.anchoranalysis.plugin.image.feature.bean.histogram.statistic: Implementations of FeatureHistogram that calculate statistics.
org.anchoranalysis.plugin.image.feature.bean.histogram.threshold - package org.anchoranalysis.plugin.image.feature.bean.histogram.threshold: Implementations of FeatureHistogram that perform thresholding.
org.anchoranalysis.plugin.image.feature.bean.list - package org.anchoranalysis.plugin.image.feature.bean.list: Implementations of FeatureListProvider.
org.anchoranalysis.plugin.image.feature.bean.list.pair - package org.anchoranalysis.plugin.image.feature.bean.list.pair: Implementations of FeatureListProvider with input-type FeatureInputPairObjects.
org.anchoranalysis.plugin.image.feature.bean.list.permute - package org.anchoranalysis.plugin.image.feature.bean.list.permute: Implementations of FeatureListProvider that derive new features with permuted property-values.
org.anchoranalysis.plugin.image.feature.bean.metadata - package org.anchoranalysis.plugin.image.feature.bean.metadata: Implementations of FeatureImageMetadata.
org.anchoranalysis.plugin.image.feature.bean.morphological - package org.anchoranalysis.plugin.image.feature.bean.morphological: Beans that affects how morphological operations occur.
org.anchoranalysis.plugin.image.feature.bean.object.collection - package org.anchoranalysis.plugin.image.feature.bean.object.collection: Implementations of FeatureObjectCollection.
org.anchoranalysis.plugin.image.feature.bean.object.combine - package org.anchoranalysis.plugin.image.feature.bean.object.combine: Features from combinations of ObjectMasks.
org.anchoranalysis.plugin.image.feature.bean.object.pair - package org.anchoranalysis.plugin.image.feature.bean.object.pair: Features from pairs of ObjectMasks.
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 ObjectMasks.
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: Implementations of FeatureSingleObject.
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: Implementations of FeatureSingleObject that consider an object's bounding-box.
org.anchoranalysis.plugin.image.feature.bean.object.single.energy - package org.anchoranalysis.plugin.image.feature.bean.object.single.energy: Implementations of FeatureSingleObject that reference a particular Channel in the associated EnergyStack.
org.anchoranalysis.plugin.image.feature.bean.object.single.intensity - package org.anchoranalysis.plugin.image.feature.bean.object.single.intensity: Implementations of FeatureSingleObject that measure an object's intensity on a corresponding Channel.
org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient - package org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient: Implementations of FeatureSingleObject that measure an object's gradient from corresponding Channels storing the gradient.
org.anchoranalysis.plugin.image.feature.bean.object.single.moments - package org.anchoranalysis.plugin.image.feature.bean.object.single.moments: Implementations of FeatureSingleObject based on calculating image moments, with or without image intensity.
org.anchoranalysis.plugin.image.feature.bean.object.single.morphological - package org.anchoranalysis.plugin.image.feature.bean.object.single.morphological: Implementations of FeatureSingleObject that implement morphological operations.
org.anchoranalysis.plugin.image.feature.bean.object.single.shape - package org.anchoranalysis.plugin.image.feature.bean.object.single.shape: Implementations of FeatureSingleObject that measure the shape of the ObjectMask.
org.anchoranalysis.plugin.image.feature.bean.object.single.shared - package org.anchoranalysis.plugin.image.feature.bean.object.single.shared: Implementations of FeatureSingleObject that use SharedObjects for calculations.
org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting - package org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting: Implementations of FeatureSingleObject that use SharedObjects for calculations, and measure the degree of intersection between objects.
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: Implementations of FeatureSingleObject that measures aspects of the surface of an ObjectMask.
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: Implementations of VoxelScore.
org.anchoranalysis.plugin.image.feature.bean.shared - package org.anchoranalysis.plugin.image.feature.bean.shared: Beans involving SharedObjects.
org.anchoranalysis.plugin.image.feature.bean.shared.object - package org.anchoranalysis.plugin.image.feature.bean.shared.object: Beans involving SharedObjects and ObjectCollection.
org.anchoranalysis.plugin.image.feature.bean.stack.intensity - package org.anchoranalysis.plugin.image.feature.bean.stack.intensity: Implementations of FeatureStack or other features that involve processing a Stack.
org.anchoranalysis.plugin.image.feature.bean.stack.object - package org.anchoranalysis.plugin.image.feature.bean.stack.object: Implementations of FeatureStack that process an ObjectCollection.
org.anchoranalysis.plugin.image.feature.object - package org.anchoranalysis.plugin.image.feature.object: Non-bean classes that help calculate features from ObjectMasks.
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: Implementations of CalculationPart that that process a single ObjectMask.
org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological - package org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological: Implementations of CalculationPart that that process a single ObjectMask - with morphological operations.
org.anchoranalysis.plugin.image.feature.stack.calculation - package org.anchoranalysis.plugin.image.feature.stack.calculation: Implementations of CalculationPart that process Stacks as used by features elsewhere in this package.
OutlineKernelBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single: Base class for features that apply a kernel to the outline of an object.
OutlineKernelBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.OutlineKernelBase
OutsideRange - Class in org.anchoranalysis.plugin.image.feature.bean.score: Calculates a voxel score based on whether the voxel intensity is outside a specified range.
OutsideRange() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.OutsideRange
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 a denominator.
OverlapRelative() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.OverlapRelative
OverlapRelativeToFirst - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap: Calculates the overlap ratio between two objects relative to the size of the first object.
OverlapRelativeToFirst() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.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 org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.OverlapRelativeToMaxVolume
OverlapRelativeToMerged - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap: Calculates the overlap ratio between two objects relative to the size of the merged object.
OverlapRelativeToMerged() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.OverlapRelativeToMerged
OverlapRelativeToSecond - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap: Calculates the overlap ratio between two objects relative to the size of the second object.
OverlapRelativeToSecond() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.OverlapRelativeToSecond

P

PairedWithMask - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shared: Evaluates the object as a pair-feature together with the binary-mask from the shared objects.
PairedWithMask() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.PairedWithMask
PairNeighbors - Class in org.anchoranalysis.plugin.image.feature.bean.object.combine: Creates a set of features, that creates pairs of neighboring-objects and applies a mixture of single-object features and pair features.
PairNeighbors() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
ParamFromCollection<T> - Class in org.anchoranalysis.plugin.image.feature.bean.shared: Retrieves a parameter as stored in a Dictionary in SharedObjects.
ParamFromCollection() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.shared.ParamFromCollection
PermuteDivideByParam<T> - Class in org.anchoranalysis.plugin.image.feature.bean.list.permute: Similar to FeatureListProviderPermute but embeds the feature in a GaussianScore
PermuteDivideByParam() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteDivideByParam
PermuteFeature<S,T> - Class in org.anchoranalysis.plugin.image.feature.bean.list.permute: Permutes one or more properties of a Feature, so as to create a set of Features
PermuteFeature() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeature
PermuteFeatureBase<T> - Class in org.anchoranalysis.plugin.image.feature.bean.list.permute: Creates permutations of a feature by modifying a particular property of it in different ways.
PermuteFeatureBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureBase
PermuteFeatureSequenceInteger<T> - Class in org.anchoranalysis.plugin.image.feature.bean.list.permute: Permutes a property on a feature with a sequence of integers.
PermuteFeatureSequenceInteger() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureSequenceInteger
PermuteFirstSecondOrder<T> - Class in org.anchoranalysis.plugin.image.feature.bean.list.permute: Permutes a feature by applying first and second order statistical operations.
PermuteFirstSecondOrder(PermuteFirstSecondOrder.CreateFirstSecondOrder<T>, double, double) - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFirstSecondOrder: Creates a new PermuteFirstSecondOrder instance.
PermuteFirstSecondOrder.CreateFirstSecondOrder<T> - Interface in org.anchoranalysis.plugin.image.feature.bean.list.permute: Functional interface for creating first and second order statistical operations.
PermuteGaussianScore<T> - Class in org.anchoranalysis.plugin.image.feature.bean.list.permute: Permutes a feature by embedding it in a GaussianCumulative score.
PermuteGaussianScore() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteGaussianScore: Creates a new instance of PermuteGaussianScore.
PermuteZScore<T> - Class in org.anchoranalysis.plugin.image.feature.bean.list.permute: Permutes a feature by embedding it in a ZScore.
PermuteZScore() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteZScore: Creates a new instance of PermuteZScore.
PrincipalAxisEccentricity - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.moments: Calculates the eccentricity of the Principal Axes (as defined by Image Moments).
PrincipalAxisEccentricity() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.PrincipalAxisEccentricity
PrincipalAxisLength - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.moments: The length of a principal-axis (as defined by Image Moments).
PrincipalAxisLength() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.PrincipalAxisLength
PrincipalAxisOrientation - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.moments: An element from orientation of a principal-axis (as defined by Image Moments).
PrincipalAxisOrientation() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.PrincipalAxisOrientation

Q

Quantile - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic: Calculates a specified quantile value from a Histogram.
Quantile() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Quantile
QuantileAcrossConnectedComponents - Class in org.anchoranalysis.plugin.image.feature.bean.stack.object: Calculates the median of a feature applied to each connected component
QuantileAcrossConnectedComponents() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.stack.object.QuantileAcrossConnectedComponents
QuantileAcrossObjects<T> - Class in org.anchoranalysis.plugin.image.feature.bean.shared.object: Calculates the quantile of a feature applied to each connected component
QuantileAcrossObjects() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.shared.object.QuantileAcrossObjects

R

Range - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic: The range (difference in values) between two quantiles
Range() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Range
RatioNonMode - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic: Calculates the ratio of non-mode pixels to total pixels in a Histogram.
RatioNonMode() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.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 org.anchoranalysis.plugin.image.feature.bean.object.single.moments.RatioPrincipalAxisLength
RatioThreshold - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.threshold: Calculates the ratio of values in a Histogram that satisfy a specified threshold condition.
RatioThreshold() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.RatioThreshold
ReduceFirstAndSecond - Class in org.anchoranalysis.plugin.image.feature.bean.list.pair: Calculates the aggregate of a feature applied to both the first and second objects in a FeatureInputPairObjects.
ReduceFirstAndSecond() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.pair.ReduceFirstAndSecond
ReduceRatioFirstAndSecond - Class in org.anchoranalysis.plugin.image.feature.bean.list.pair: Calculates the aggregate of the ratio of first:second and second:first for a FeatureInputPairObjects
ReduceRatioFirstAndSecond() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.pair.ReduceRatioFirstAndSecond
RejectIfIntensityLessThan - Class in org.anchoranalysis.plugin.image.feature.bean.score: Rejects voxels with intensity less than a specified minimum, otherwise calculates a score using another VoxelScore.
RejectIfIntensityLessThan() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.RejectIfIntensityLessThan

S

setAcceptMissingResolution(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.VoxelPhysicalSize: Whether to throw an exception (if true) if image-resolution is missing, or return Double.Nan (if false).
setAvoidOverlappingObjects(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors: If true, no overlapping objects are treated as pairs
setAxis(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.ForSpecificAxis: The axis to perform the calculation on.
setAxis(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.ArbitraryInsidePoint: The axis to output.
setAxis(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxAlongAxisBase: The axis along which to calculate the feature value ("x", "y", or "z").
setAxis(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.GradientMeanForAxis
setAxis(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.PrincipalAxisOrientation: Which axis to read from (x,y,z)
setCalculateLevel(CalculateLevel) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.LevelFromHistogram
setCalculateLevel(CalculateLevel) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.ThresholdHistogram
setCalculateLevel(CalculateLevel) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevelBase: The method to calculate the threshold level.
setChannelFirst(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Difference: Index of first channel
setChannelSecond(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Difference: Index of second channel
setCov(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shape.ObjectRadiusStandardDeviation: If true, returns the coefficient of variation (stdDev/mean) instead of standard deviation.
setDictionary(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.ParamFromCollection: The name of the Dictionary that will be retrieved from SharedObjects.
setDistanceMax(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevel: The maximum distance from the threshold level to consider.
setDo3D(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations: Whether to perform the morphological dimensions in 3D or 2D.
setDo3D(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
setDo3D(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.TouchingVoxels: Whether to perform calculations in 3D (true) or 2D (false).
setDo3D(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.Erode: If true, performs 3D erosion; if false, performs 2D erosion on each z-slice separately.
setDo3D(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.NumberRemovedVoxelsAfterClosing
setDo3D(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.OutlineKernelBase: If true, applies the kernel in 3D; otherwise, applies it in 2D.
setEmptyValue(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.Intersection
setEmptyValue(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.ArbitraryInsidePoint: The value to return if no point is found inside the object-mask.
setEmptyValue(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase: The value to return when the resulting object is empty.
setEmptyValue(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.DerivedObject: The value to return when the derived object is empty.
setEmptyValue(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanMaxSlice: The value to return when the object has no voxels in any slice.
setEnergyChannelIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Identity: The index of the energy channel to use for calculations.
setEnergyChannelIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.RejectIfIntensityLessThan: The index of the energy channel to check for intensity.
setEnergyChannelIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.SingleChannel: The index of the energy channel to use for score calculation.
setEnergyChannelIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.QuantileAcrossConnectedComponents
setEnergyChannelIndexCheck(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram: The index of the energy channel to check.
setEnergyChannelIndexFail(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram: The index of the energy channel to use if the relation check fails.
setEnergyIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.NumberNeighboringVoxels: Index of which channel in the energy-stack to select
setEnergyIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.SpecificEnergyChannelBase: Index of which channel in the energy-stack to select.
setEnergyIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.FeatureEnergyChannel: Index of channel to use in the energy-stack (0 is the first channel, 1 is second etc.)
setEnergyIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.OutsideRange: The index of the energy channel to use for intensity values.
setEnergyIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.intensity.Intensity: The channel that that forms the histogram.
setEnergyIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.AsObjectMask: The channel that that forms an object-mask with the bounding-box set to entire channel's dimensions
setEnergyIndexGradient(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.TextureScore
setEnergyIndexMask(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.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 org.anchoranalysis.plugin.image.feature.bean.stack.intensity.Intensity: Optionally, index of another channel that masks the histogram.
setEnergyIndexX(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.IntensityGradientBase: Index of the channel in the energy stack to use for the X-component of the gradient.
setEnergyIndexY(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.IntensityGradientBase: Index of the channel in the energy stack to use for the Y-component of the gradient.
setEnergyIndexZ(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.IntensityGradientBase: Index of the channel in the energy stack to use for the Z-component of the gradient.
setExcludeZero(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.Intensity: Iff true, zero-valued voxels are excluded from the histogram
setExcludeZero(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanMaxSlice: If true, zero-valued voxels are excluded from the mean intensity calculation.
setFactorHigh(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Identity: The factor to apply for values above 0.5 when normalizing.
setFactorLow(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Identity: The factor to apply for values below 0.5 when normalizing.
setFeature(Feature<T>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureBase: The feature to be permuted.
setFeaturesImage(List<NamedBean<FeatureListProvider<FeatureInputStack>>>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.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 org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors: Additional features that are processed on the pair of images (i.e.
setHistogramChannelIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevelBase: The index of the histogram channel to use for calculations.
setHistogramIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram: The index of the histogram to use for comparison.
setId(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjects: ID for the particular object-collection
setIgnoreAtThreshold(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.OutlineKernelBase: If true, ignores voxels at the threshold when applying the kernel.
setIgnoreZero(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.RatioNonMode: Whether to ignore the zero value when calculating the ratio.
setIncludeFirst(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors: Include features for the First-object of the pair
setIncludeMerged(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors: Include features for the Merged-object of the pair
setIncludeSecond(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors: Include features for the Second-object of the pair
setIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.SpecificAxisBase: Specifies which principal-axis to use for calculations (0=largest eigenvalue, 1=second-largest eigenvalue etc.)
setInterpolator(Interpolator) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.CombineObjectsForFeatures: Interpolator used to resize images in thumbnail generation.
setInverse(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase: If true, calculates instead on the inverse of the object-mask (what's left when the shell is removed).
setInverseMask(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase: If true, uses the inverse of the passed mask.
setItem(Feature<FeatureInputHistogram>) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.ThresholdHistogram
setItem(Feature<FeatureInputHistogram>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.Intensity: Feature to apply to the histogram
setItem(Feature<FeatureInputHistogram>) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.intensity.Intensity: Feature to apply to the histogram.
setItem(Feature<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjectsSingleElement: The feature to calculate for each intersecting object pair.
setItem(Feature<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.DerivedObject: The feature to calculate on the derived object.
setItem(Feature<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.FeatureSingleObjectFromShared: The feature to be calculated on a single object.
setItem(Feature<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.AsObjectMask
setItem(Feature<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.QuantileAcrossConnectedComponents
setItem(FeatureListProvider<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.DeriveFromPair
setItem(FeatureListProvider<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.FeatureListProviderAggregatePair: For each feature in the list, a corresponding aggregate feature is created in the output list.
setItem(FeaturePairObjects) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.PairedWithMask
setItem(VoxelScore) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.RejectIfIntensityLessThan: The VoxelScore to use for calculating the score if the intensity is not rejected.
setIterations(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.Erode: The number of iterations to perform the erosion operation.
setIterations(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.NumberRemovedVoxelsAfterClosing
setIterations(MorphologicalIterations) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.Intersection: The number of dilations and erosions to apply to determine if two objects intersect
setIterations(MorphologicalIterations) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase: The number of dilations and erosions to apply and whether to do in the Z dimension.
setIterations(MorphologicalIterations) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.Shell: The number of dilations and erosions to apply and whether to do so in the Z dimension.
setIterationsDilation(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations: Number of times to perform morphological dilation.
setIterationsErosion(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations: Number of times to perform morphological erosion.
setKeepExtremes(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Identity: Whether to keep extreme values (0 and 1) unchanged when normalizing.
setKey(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.ParamFromCollection: The name of the key in the dictionary, whose corresponding value will be returned.
setMask(MaskProvider) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.PairedWithMask
setMask(MaskProvider) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.MaskAsSingleObject: The provider for the mask to be treated as a single object.
setMax(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram: Whether to use the maximum (true) or minimum (false) value from the histogram.
setMax(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.OutsideRange: The maximum value of the range (exclusive).
setMax(UnitValueExtent) - Method in class org.anchoranalysis.plugin.image.feature.bean.physical.UnitsWithinRange: Maximum-boundary for acceptable range
setMaxDistance(UnitValueDistance) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.CostOverlapWithinMidpointDistance
setMaximumNumberChannels(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.IntensityMoments: An upper limit on the number of channels in the energy-stack for which we create features.
setMin(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.OutsideRange: The minimum value of the range (inclusive).
setMin(UnitValueExtent) - Method in class org.anchoranalysis.plugin.image.feature.bean.physical.UnitsWithinRange: Minimum-boundary for acceptable range
setMinDifference(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Difference: A minimum difference, below which 0.0 is returned
setMinDifference(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.DifferenceCalculateLevelStandardDeviation
setMinIntensity(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.RejectIfIntensityLessThan: The minimum intensity threshold.
setMinOverlap(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.CostOverlapWithinMidpointDistance
setMip(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.surface.SurfaceNumberVoxelsBase: If true, calculates the surface on a maximum intensity projection rather than the 3D object.
setNormalize(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Identity: Whether to normalize the voxel intensity values.
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.ObjectAggregationBase: The provider for the collection of objects to calculate features on.
setOutside(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.physical.UnitsWithinRange: Returned as a constant if a value lies otside the range
setOutsideAtThreshold(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.OutlineKernelBase: If true, considers voxels outside the object at the threshold as part of the object.
setParamPrefix(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureSequenceInteger: Prefix for the parameter key.
setParamPrefixAppendNumber(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFirstSecondOrder: If true, the constant is appended to the param prefix (a dot and a number).
setPermutation(PermuteProperty<S>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeature: A permutation to apply.
setPermutations(List<PermuteProperty<S>>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeature: A list of permutations to apply.
setPermuteProperty(PermutePropertySequenceInteger) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureSequenceInteger: Defines how to permute the property with a sequence of integers.
setPower(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.MeanRaisedToPower: The power to which the mean value is raised.
setPrefix(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.DeriveFromPair
setPrefix(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.FeatureListProviderAggregatePair: The string to prepend.
setQuantile(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Quantile: The quantile to calculate from the histogram.
setQuantile(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.QuantileAcrossObjects
setQuantile(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.QuantileAcrossConnectedComponents
setQuantileHigh(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Range
setQuantileLow(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Range
setReduce(FeatureFromList<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.FeatureListProviderAggregatePair: Method for reducing all pairs into a single value e.g.
setReferencesFeatureListCreator(StringSet) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeature: Makes sure a particular feature list creator is evaluated
setRelation(RelationBean) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram: The relation to test between the voxel value and the histogram value.
setSelect(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.DeriveFromPair: Either "merged" or "first" or "second" indicating which feature to delegate from
setSubtractConstant(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.IntensityGradientBase: A constant value to subtract from each voxel intensity before calculating the gradient.
setSuppress3D(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.surface.SurfaceNumberVoxelsBase: If true, suppresses 3D calculations and treats the object as 2D.
setSuppressZ(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.CostOverlapWithinMidpointDistance
setSuppressZ(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.ImageMomentsBase: If true co-variance is suppressed in z-dimension.
setThreshold(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjectsThreshold: The threshold value for considering intersecting objects.
setThreshold(RelationToThreshold) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Count
setThreshold(RelationToThreshold) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.RatioThreshold: The threshold condition to be applied to the histogram values.
setThumbnail(ThumbnailFromObjects) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.CombineObjectsForFeatures: Generates a thumbnail representation of one or more combined objects, as form a single input.
setupDictionary(Dictionary) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.FromDictionaryBase: Sets up the feature using the provided dictionary.
setValue(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram: The value to return if the relation test passes.
setValue(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.NormalizeByConstant: The constant value to divide the voxel intensity by.
setValue(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.CountEqual: The intensity value to count.
setValueIfTooFewVoxels(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.ImageMomentsBase: A value to return if there are too few voxels (less than MIN_NUM_VOXELS) to calculate moments.
setValueNoObjects(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjects: The value to return when there are no objects in the search collection.
setWidth(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Difference: Width (what the difference is divided by)
setWidthFactor(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.DifferenceCalculateLevelStandardDeviation
setWithin(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.physical.UnitsWithinRange: Returned as a constant if a value lies within the range
ShapeRegularityCenterSlice - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shape: Calculates the shape regularity of the center slice of an ObjectMask.
ShapeRegularityCenterSlice() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.shape.ShapeRegularityCenterSlice
ShapeRegularityMaximumIntensityProjection - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shape: Calculates the shape regularity of the maximum intensity projection of an ObjectMask.
ShapeRegularityMaximumIntensityProjection() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.shape.ShapeRegularityMaximumIntensityProjection
Shell - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.morphological: Creates a shell around an ObjectMask by applying morphological operations.
Shell() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.Shell
SingleChannel - Class in org.anchoranalysis.plugin.image.feature.bean.score: A score that is calculated on a single channel only.
SingleChannel() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.SingleChannel
size() - Method in class org.anchoranalysis.plugin.image.feature.object.ListWithThumbnails: Gets the size of the list.
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 org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Skewness
SpecificAxisBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.moments: A feature based on one specific principal-axis as identified by image moments.
SpecificAxisBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.SpecificAxisBase
SpecificEnergyChannelBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.energy: A base class for features that operate on a specific channel from the energy stack.
SpecificEnergyChannelBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.SpecificEnergyChannelBase
StandardDeviation - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic: Calculates the standard deviation of values in a Histogram.
StandardDeviation() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.StandardDeviation
startBatchDeriveInputs(ObjectCollection, EnergyStack, Logger) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.CombineObjectsForFeatures: Derives a list of inputs from an object-collection.
startBatchDeriveInputs(ObjectCollection, EnergyStack, Logger) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.EachObjectIndependently
startBatchDeriveInputs(ObjectCollection, EnergyStack, Logger) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
SubtractReducedFromMerged - Class in org.anchoranalysis.plugin.image.feature.bean.list.pair: Calculates merged - reduce(first,second) for a FeatureInputPairObjects
SubtractReducedFromMerged() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.pair.SubtractReducedFromMerged
Sum - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic: Calculates the sum of all values in a Histogram.
Sum() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Sum
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 org.anchoranalysis.plugin.image.feature.bean.object.single.surface.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 org.anchoranalysis.plugin.image.feature.bean.object.single.surface.SurfaceNumberVoxels
SurfaceNumberVoxelsBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.surface: A base class for features that calculate the number of voxels on the surface of an object.
SurfaceNumberVoxelsBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.surface.SurfaceNumberVoxelsBase

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TextureScore - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity: From Page 727 from Lin et al (A Multi-Model Approach to Simultaneous Segmentation and Classification of Heterogeneous Populations of Cell Nuclei
TextureScore() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.TextureScore
ThresholdHistogram - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.threshold: Thresholds the histogram (using a weightedOtsu) and then applies a feature to the thresholded version.
ThresholdHistogram() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.ThresholdHistogram
toString() - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateObjectMask
toString() - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateShellObjectMask
TotalCount - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic: Calculates the total count of all entries in a Histogram.
TotalCount() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.TotalCount
TouchingVoxels - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.touching: Base class for features that calculate touching with a dilated bounding box intersection.
TouchingVoxels() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.TouchingVoxels

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uniqueIdentifierFor(FeatureInputPairObjects) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
uniqueIdentifierFor(FeatureInputSingleObject) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.EachObjectIndependently
uniqueIdentifierFor(T) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.CombineObjectsForFeatures: Generates a unique identifier for a particular input.
uniquelyIdentifyAllProperties() - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations: Creates a string that uniquely identifies all properties in the bean, in a compact format.
UnitsWithinRange<T> - Class in org.anchoranalysis.plugin.image.feature.bean.physical: Checks if a value lies within a range defined by units (a minimum and maximum boundary)
UnitsWithinRange() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.physical.UnitsWithinRange

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valueFor(FeatureCalculationInput<FeatureInputSingleObject>, ResolvedPart<ObjectCollection, FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjects: Calculates a value based on the input and the intersecting objects.
valueFor(FeatureCalculationInput<FeatureInputSingleObject>, ResolvedPart<ObjectCollection, FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjectsSingleElement
valueFor(FeatureCalculationInput<FeatureInputSingleObject>, ResolvedPart<ObjectCollection, FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.NumberIntersectingObjects
Variance - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic: Calculates the variance of all the values in the histogram.
Variance() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Variance
Volume<T> - Class in org.anchoranalysis.plugin.image.feature.bean.dimensions: Calculates the volume (x, y and z dimensions) of the scene from the dimensions
Volume() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.dimensions.Volume
VoxelPhysicalSize<T> - Class in org.anchoranalysis.plugin.image.feature.bean.dimensions: The physical size of a pixel in a specific dimension.
VoxelPhysicalSize() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.dimensions.VoxelPhysicalSize

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