Index (anchor-plugin-image 1.0.0 API)

A B C D E F G H I L M N O P Q R S T U V W X Y Z
All Classes and Interfaces|All Packages|Constant Field Values

A

accept(ObjectMask) - Method in class org.anchoranalysis.plugin.image.object.merge.condition.AndCondition
accept(ObjectMask) - Method in class org.anchoranalysis.plugin.image.object.merge.condition.NeighborhoodCondition
accept(ObjectMask) - Method in interface org.anchoranalysis.plugin.image.object.merge.condition.UpdatableBeforeCondition: Checks if the destination object should be merged with the previously set source object.
accept(ObjectMask) - Method in class org.anchoranalysis.plugin.image.object.merge.condition.WrapAsUpdatable
accept(ObjectMask, ObjectMask, Optional<UnitConverter>) - Method in interface org.anchoranalysis.plugin.image.object.merge.condition.BeforeCondition: Checks if the source and destination objects satisfy the condition for merging.
accept(ObjectMask, ObjectMask, Optional<UnitConverter>) - Method in class org.anchoranalysis.plugin.image.object.merge.condition.DistanceCondition
accept(ObjectMask, ObjectMask, ObjectMask) - Method in interface org.anchoranalysis.plugin.image.object.merge.condition.AfterCondition: Checks if the merged object satisfies the condition.
accept(ObjectMask, ObjectMask, ObjectMask) - Method in class org.anchoranalysis.plugin.image.object.merge.condition.IncreaseFeatureCondition
add(LevelResult) - Method in class org.anchoranalysis.plugin.image.intensity.level.LevelResultCollection: Adds a LevelResult to the collection.
addChannelAfterCheck(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.aggregator.ProjectableBufferAggregator
AddConstant - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic: Adds a constant value to each voxel in a channel.
AddConstant() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.AddConstant
addObjectsToGraph(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.object.merge.MergeGraph: Adds objects to the graph.
addObjectsWithColor(ObjectCollectionProvider, RGBColor) - Method in class org.anchoranalysis.plugin.image.object.ColoredObjectCollection: Adds objects from a ObjectCollectionProvider all with one specific color
AfterCondition - Interface in org.anchoranalysis.plugin.image.object.merge.condition: A condition to be checked after merging two ObjectMasks.
AllValuesOff - Class in org.anchoranalysis.plugin.image.bean.mask.provider: Creates a new mask of particular dimensionality where all values are off.
AllValuesOff() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.AllValuesOff
AllValuesOn - Class in org.anchoranalysis.plugin.image.bean.mask.provider: Creates a new mask of particular dimensionality where all values are on.
AllValuesOn() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.AllValuesOn
Always - Class in org.anchoranalysis.plugin.image.bean.object.match: Specifies a single object that will always be the "match" for whatever source object.
Always() - Constructor for class org.anchoranalysis.plugin.image.bean.object.match.Always
And - Class in org.anchoranalysis.plugin.image.bean.mask.provider.combine: Outputs the logical operation and voxelwise on both masks, modifying {mask} with the result.
And - Class in org.anchoranalysis.plugin.image.bean.object.filter.combine: Applies multiples filter with logical AND i.e.
And() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.combine.And
And() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.combine.And
AndCondition - Class in org.anchoranalysis.plugin.image.object.merge.condition: Combines two UpdatableBeforeConditions as LOGICAL ANDs
AndCondition(UpdatableBeforeCondition, UpdatableBeforeCondition) - Constructor for class org.anchoranalysis.plugin.image.object.merge.condition.AndCondition
AndObjectsWithMasks - Class in org.anchoranalysis.plugin.image.bean.object.provider.mask: Reduce the size of individual objects (if neccessary, and minimally) to fit within a binary-mask.
AndObjectsWithMasks() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.mask.AndObjectsWithMasks
applyMorphologicalOperation(Mask, boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Dilate
applyMorphologicalOperation(Mask, boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Erode
applyMorphologicalOperation(Mask, boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.MorphologicalOperatorBase: Applies the morphological operation to the source mask.
applyMorphologicalOperation(ObjectMask, Optional<Extent>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Dilate
applyMorphologicalOperation(ObjectMask, Optional<Extent>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Erode
applyMorphologicalOperation(ObjectMask, Optional<Extent>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.ObjectCollectionProviderMorphological: Applies the morphological operation to a single ObjectMask.
ArithmeticWithConstantBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic: Base-class for operations that perform a binary arithmetic operation with each voxel-value and a constant.
ArithmeticWithConstantBase() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.ArithmeticWithConstantBase
ArithmeticWithConstantConditionallyWriteBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic: Base class for arithmetic operations that conditionally overwrite voxel values with a constant.
ArithmeticWithConstantConditionallyWriteBase() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.ArithmeticWithConstantConditionallyWriteBase
AssignFromChannel - Class in org.anchoranalysis.plugin.image.bean.channel.provider.assign: Copies the pixels from channelAssignFrom to channel (possibly masking).
AssignFromChannel() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromChannel
AssignFromDictionary - Class in org.anchoranalysis.plugin.image.bean.channel.provider.assign: Assigns a value from a dictionary to all voxels in a channel.
AssignFromDictionary() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromDictionary
AssignFromIntersectingObjects - Class in org.anchoranalysis.plugin.image.bean.channel.provider.assign: Matches source-objects to target objects, based upon intersection, and assigns the value in the respective source object to the target object
AssignFromIntersectingObjects() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromIntersectingObjects
assignPriority(ObjectVertex, ObjectVertex, GraphLogger) - Method in class org.anchoranalysis.plugin.image.object.merge.priority.AssignPriority: Assigns a priority to a potential merge between two objects.
AssignPriority - Class in org.anchoranalysis.plugin.image.object.merge.priority: Abstract class for assigning priorities to potential object merges.
AssignPriority() - Constructor for class org.anchoranalysis.plugin.image.object.merge.priority.AssignPriority
AssignPriorityFromImprovement - Class in org.anchoranalysis.plugin.image.object.merge.priority: Allows merges if there is an increase in the payload i.e.
AssignPriorityFromImprovement(PayloadCalculator) - Constructor for class org.anchoranalysis.plugin.image.object.merge.priority.AssignPriorityFromImprovement
AssignPriorityFromPair - Class in org.anchoranalysis.plugin.image.object.merge.priority: Calculates pair-feature on each potential merge, and this value determines priority..
AssignPriorityFromPair(FeatureCalculatorSingle<FeatureInputPairObjects>, double, DoubleBiPredicate) - Constructor for class org.anchoranalysis.plugin.image.object.merge.priority.AssignPriorityFromPair
assignPriorityToEdge(ObjectVertex, ObjectVertex, ObjectMask, ErrorReporter) - Method in class org.anchoranalysis.plugin.image.object.merge.priority.AssignPriority: Assigns a priority to an edge between two objects.
assignPriorityToEdge(ObjectVertex, ObjectVertex, ObjectMask, ErrorReporter) - Method in class org.anchoranalysis.plugin.image.object.merge.priority.AssignPriorityFromImprovement
assignPriorityToEdge(ObjectVertex, ObjectVertex, ObjectMask, ErrorReporter) - Method in class org.anchoranalysis.plugin.image.object.merge.priority.AssignPriorityFromPair
AssignValue - Class in org.anchoranalysis.plugin.image.bean.channel.provider.assign: Assigns a constant (scalar) value to the portion of the image covered by a mask
AssignValue() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignValue
AtIndex - Class in org.anchoranalysis.plugin.image.bean.object.provider: Extract a single ObjectMask into a new collection.
AtIndex() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.AtIndex
AtScale - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel: Perform a segmentation at a different scale, and then fit the results back to the original scale.
AtScale() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.channel.AtScale

B

BeforeCondition - Interface in org.anchoranalysis.plugin.image.object.merge.condition: A condition to be checked before merging two ObjectMasks.
BinarySegmentByObject - Class in org.anchoranalysis.plugin.image.bean.object.provider.segment: Performs a binary-segmentation using the upstream objects as masks.
BinarySegmentByObject() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.segment.BinarySegmentByObject
blur(VoxelsUntyped, Dimensions, MessageLogger) - Method in class org.anchoranalysis.plugin.image.bean.blur.BlurGaussian3D
blur(VoxelsUntyped, Dimensions, MessageLogger) - Method in class org.anchoranalysis.plugin.image.bean.blur.BlurGaussianEachSlice2D
blur(VoxelsUntyped, Dimensions, MessageLogger) - Method in class org.anchoranalysis.plugin.image.bean.blur.BlurStrategy: Applies the blur operation to the given voxels.
Blur - Class in org.anchoranalysis.plugin.image.bean.channel.provider.intensity: Blurs an image using a particular strategy (defaults to a gaussian blur in each slice)
Blur() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.Blur
BlurGaussian3D - Class in org.anchoranalysis.plugin.image.bean.blur: Performs a Gaussian Blur in 3D
BlurGaussian3D() - Constructor for class org.anchoranalysis.plugin.image.bean.blur.BlurGaussian3D
BlurGaussianEachSlice2D - Class in org.anchoranalysis.plugin.image.bean.blur: Performs a Gaussian-blur in 2D on each slice independently
BlurGaussianEachSlice2D() - Constructor for class org.anchoranalysis.plugin.image.bean.blur.BlurGaussianEachSlice2D
BlurStrategy - Class in org.anchoranalysis.plugin.image.bean.blur: A method for applying blurring to an image.
BlurStrategy() - Constructor for class org.anchoranalysis.plugin.image.bean.blur.BlurStrategy
Box - Class in org.anchoranalysis.plugin.image.bean.mask.provider.morphological: Creates a Mask where all pixels are on within a box region.
Box() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Box
Bridge - Class in org.anchoranalysis.plugin.image.bean.object.match: Matches to another object, and then uses that object to bridge to another
Bridge() - Constructor for class org.anchoranalysis.plugin.image.bean.object.match.Bridge

C

calculate(Optional<Dimensions>, Optional<ImageSizeSuggestion>) - Method in class org.anchoranalysis.plugin.image.bean.scale.ConstantScaleFactor
calculate(Optional<Dimensions>, Optional<ImageSizeSuggestion>) - Method in class org.anchoranalysis.plugin.image.bean.scale.FitTo
calculate(Optional<Dimensions>, Optional<ImageSizeSuggestion>) - Method in class org.anchoranalysis.plugin.image.bean.scale.Invert
calculate(Optional<Dimensions>, Optional<ImageSizeSuggestion>) - Method in class org.anchoranalysis.plugin.image.bean.scale.MinimumXYResolution
calculate(Optional<Dimensions>, Optional<ImageSizeSuggestion>) - Method in class org.anchoranalysis.plugin.image.bean.scale.ToDimensions
calculate(Optional<Dimensions>, Optional<ImageSizeSuggestion>) - Method in class org.anchoranalysis.plugin.image.bean.scale.ToSuggested
calculate(ObjectMask) - Method in interface org.anchoranalysis.plugin.image.object.merge.PayloadCalculator: Calculates the payload value for a given object mask.
calculateConnectedComponentID(Point3i, int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels: Calculates the connected component ID for a given point and initial chain code.
calculateLevel(Histogram) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelRelativeToThreshold
calculateLevel(Histogram) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.ClampHistogramMax
calculateLevel(Histogram) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Constant
calculateLevel(Histogram) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.EmptyHistogramConstant
calculateLevel(Histogram) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Maximum
calculateLevel(Histogram) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Minimum
calculateLevel(Histogram) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Otsu
calculateLevel(Histogram) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.OtsuWeighted
calculateLevel(Histogram) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Quantile
CalculateLevelListBase - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold: Base class for CalculateLevel implementations that operate on a list of other CalculateLevel objects.
CalculateLevelListBase() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelListBase
CalculateLevelRelativeToThreshold - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold: A CalculateLevelUnary that calculates a level relative to a threshold, with an alternative calculation method.
CalculateLevelRelativeToThreshold() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelRelativeToThreshold
calculateMeanIntensityObject(Channel, ObjectMask) - Static method in class org.anchoranalysis.plugin.image.intensity.IntensityMeanCalculator: Calculates the mean intensity of an object in a channel.
calculateMeanIntensityObject(Channel, ObjectMask, boolean) - Static method in class org.anchoranalysis.plugin.image.intensity.IntensityMeanCalculator: Calculates the mean intensity of an object in a channel, with an option to exclude zero values.
calculateSigma(Dimensions, MessageLogger) - Method in class org.anchoranalysis.plugin.image.bean.blur.BlurStrategy: Calculates the sigma value to use for blurring, considering the dimensions and whether sigma is in meters.
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelListBase
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelRelativeToThreshold
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.ClampHistogramMax
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Constant
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.EmptyHistogramConstant
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.IfGreaterThan
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.IfLessThan
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Maximum
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Minimum
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Otsu
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.OtsuWeighted
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Quantile
chainCode(int, int, int) - Static method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.ChainCodesDirection: Encodes a direction into a chain code.
chainCodes(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.WatershedEncoding: Decodes a chain-code into a point.
ChainCodesDirection - Class in org.anchoranalysis.plugin.image.segment.watershed.encoding: Maps directions to chain codes and vice versa.
channel(String) - Static method in class org.anchoranalysis.plugin.image.provider.ReferenceFactory: Creates a reference to a channel.
check(Channel, String, Dimensions) - Static method in class org.anchoranalysis.plugin.image.channel.DimensionsChecker: Checks a channel to make sure it's the same size as an existing channel.
check(Channel, Mask) - Static method in class org.anchoranalysis.plugin.image.channel.DimensionsChecker: Checks if a channel and a mask have the same dimensions.
check(Mask, String, Dimensions) - Static method in class org.anchoranalysis.plugin.image.channel.DimensionsChecker: Checks a mask to make sure it's the same size as an existing channel.
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromStack
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.slice.ExtractSliceRange
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Erode
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.Sequence
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeChannels
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeColoredObjects
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.FromChannelOrMask
ClampHistogramMax - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold: Clamps the input-histogram to a certain maximum value, and then delegates the calculate-level.
ClampHistogramMax() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.ClampHistogramMax
CODE_MINIMA - Static variable in class org.anchoranalysis.plugin.image.segment.watershed.encoding.WatershedEncoding: Code representing a minima voxel.
CODE_PLATEAU - Static variable in class org.anchoranalysis.plugin.image.segment.watershed.encoding.WatershedEncoding: Code representing a plateau voxel.
CODE_TEMPORARY - Static variable in class org.anchoranalysis.plugin.image.segment.watershed.encoding.WatershedEncoding: Code representing a temporary voxel.
CODE_UNVISITED - Static variable in class org.anchoranalysis.plugin.image.segment.watershed.encoding.WatershedEncoding: Code representing an unvisited voxel.
ColoredBase - Class in org.anchoranalysis.plugin.image.bean.stack.provider.color: Base class for providers that draw entities (an outline or filled) on a background.
ColoredBase() - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase
ColoredBaseWithGenerator - Class in org.anchoranalysis.plugin.image.bean.stack.provider.color: Like ColoredBase but uses a generator to determine the colors for the objects.
ColoredBaseWithGenerator() - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBaseWithGenerator
ColoredMask - Class in org.anchoranalysis.plugin.image.bean.stack.provider.color: Draws a colored representation (outline or filled) of a ObjectMask on a background
ColoredMask() - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredMask
ColoredObject - Class in org.anchoranalysis.plugin.image.object: An ObjectMask with an associated color.
ColoredObject(ObjectMask, RGBColor) - Constructor for class org.anchoranalysis.plugin.image.object.ColoredObject: Creates a new ColoredObject instance.
ColoredObjectCollection - Class in org.anchoranalysis.plugin.image.object: Associates a ColorList with a ObjectCollection
ColoredObjectCollection() - Constructor for class org.anchoranalysis.plugin.image.object.ColoredObjectCollection: Create with an empty collection.
ColoredObjectCollection(Stream<ColoredObject>) - Constructor for class org.anchoranalysis.plugin.image.object.ColoredObjectCollection: Create from a stream of ColoredObjects.
ColoredObjectCollection(ObjectCollection, ColorList) - Constructor for class org.anchoranalysis.plugin.image.object.ColoredObjectCollection: Create with an existing object and color list.
ColoredObjectCollection(ObjectMask, RGBColor) - Constructor for class org.anchoranalysis.plugin.image.object.ColoredObjectCollection: Create with a single object and color.
ColoredObjects - Class in org.anchoranalysis.plugin.image.bean.stack.provider.color: Draws a colored representation (outline or filled) of an ObjectCollection on a background
ColoredObjects() - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredObjects
coloredObjectsToDraw(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase: Creates colored-objects to be drawn.
coloredObjectsToDraw(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBaseWithGenerator
coloredObjectsToDraw(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredMask
coloredObjectsToDraw(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeColoredObjects
CombineBase - Class in org.anchoranalysis.plugin.image.bean.mask.provider.combine: Base class for combining two masks.
CombineBase() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.combine.CombineBase
Concatenate - Class in org.anchoranalysis.plugin.image.bean.color.provider: Combines one or more ColorProviders into a unitary ColorProvider.
Concatenate - Class in org.anchoranalysis.plugin.image.bean.object.provider: An ObjectCollectionProvider that concatenates multiple ObjectCollections from a list of providers.
Concatenate - Class in org.anchoranalysis.plugin.image.bean.stack.provider: Combines all the channels from one or more sources (stacks, channels etc.)
Concatenate() - Constructor for class org.anchoranalysis.plugin.image.bean.color.provider.Concatenate
Concatenate() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.Concatenate
Concatenate() - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.Concatenate
ConnectedComponentsFromBinarySegmentation - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel: Performs a binary-segmentation of the channel and converts its connected-components into objects
ConnectedComponentsFromBinarySegmentation() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.channel.ConnectedComponentsFromBinarySegmentation
ConnectedComponentsFromMask - Class in org.anchoranalysis.plugin.image.bean.object.provider.connected: Converts a binary-mask into its connected components
ConnectedComponentsFromMask() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.connected.ConnectedComponentsFromMask
Constant - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold: A constant value for thresholding.
Constant() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.Constant
Constant(int) - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.Constant
ConstantScaleFactor - Class in org.anchoranalysis.plugin.image.bean.scale: Scale X and Y dimension by a constant floating-point number.
ConstantScaleFactor() - Constructor for class org.anchoranalysis.plugin.image.bean.scale.ConstantScaleFactor
ConstantScaleFactor(double) - Constructor for class org.anchoranalysis.plugin.image.bean.scale.ConstantScaleFactor: Creates a new ConstantScaleFactor instance.
containerOptional() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithContainerBase: Retrieves the optional container of objects.
containerRequired() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithContainerBase: Retrieves the required container of objects.
Convert<T> - Class in org.anchoranalysis.plugin.image.bean.channel.provider.convert: Converts a channel by applying a converter (no histogram is involved in the conversion).
Convert() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.convert.Convert
ConvertBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider.convert: Base class for channel providers that perform conversions on a single input channel.
ConvertBase() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.convert.ConvertBase
convertCode(int, int, EncodedVoxels, Point3i) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedIntBuffer: Converts the code at the given index to a connected component ID.
convertToOutputType(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientBase: Converts the input channel to the output type specified by GradientBase.outputShort.
ConvertWithHistogram<T> - Class in org.anchoranalysis.plugin.image.bean.channel.provider.convert: Converts a channel to a different voxel data-type by applying a converter with an associated histogram.
ConvertWithHistogram() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.convert.ConvertWithHistogram
create(VoxelDataType, Extent) - Method in class org.anchoranalysis.plugin.image.bean.channel.aggregator.MaxProjection
create(VoxelDataType, Extent) - Method in class org.anchoranalysis.plugin.image.bean.channel.aggregator.MeanProjection
create(VoxelDataType, Extent) - Method in class org.anchoranalysis.plugin.image.bean.channel.aggregator.MinProjection
create(VoxelDataType, Extent) - Method in class org.anchoranalysis.plugin.image.bean.channel.aggregator.ProjectableBufferAggregator: Creates the ProjectableBuffer used for aggregation.
create(VoxelDataType, Extent) - Method in class org.anchoranalysis.plugin.image.bean.channel.aggregator.StandardDeviationProjection
createAxisArray() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientBaseAddSum: Creates an array of booleans indicating which axes to calculate the gradient for.
createAxisArray() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientForAxis
createAxisArray() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientXY
createCollection(Channel, ObjectCollection, CalculateLevel, int, MessageLogger) - Static method in class org.anchoranalysis.plugin.image.intensity.level.LevelResultCollectionFactory: Creates a LevelResultCollection from a channel and object collection.
createConverter() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByDictionary
createConverter() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByMinMaxValue
createConverter() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByTypeToByte
createConverter() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ToByte
createConverter() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ToByteUpperLowerQuantileIntensity
createDimensions() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithDimensionsBase: Creates the dimensions using the specified DimensionsProvider.
createDims() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithOptionalDimensionsBase: Creates the dimensions if a DimensionsProvider is specified.
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.Invert
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromDictionary
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromIntersectingObjects
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.convert.Convert
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.convert.ConvertWithHistogram
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.Duplicate
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientBaseAddSum
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.Sobel
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.IfParamEquals
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.Blur
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.IfVoxelZero
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.Median
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.QuantileStretch
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.ScaleXY
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.mask.UnaryWithMaskBase
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectBase
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.slice.ExtractCenterSlice
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.slice.ExtractSliceRange
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.slice.MaximumIntensityProjection
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.slice.MeanIntensityProjection
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.UnaryWithObjectsBase
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.UnaryWithValueBase
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentChannel
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentWithSeeds
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithChannelBase: Creates an ObjectCollection from a source Channel.
createFromChannel(Channel, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.NormalizeDifferenceToMedian
createFromChannel(Channel, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.NormalizeObjectIntensity
createFromChannel(Channel, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.IdentifyObjects
createFromChannel(Channel, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreObjects
createFromChannel(Channel, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.UnaryWithObjectsBase: Creates a new channel from an existing channel and a collection of objects.
createFromChannelWithConstant(Channel, double) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.ArithmeticWithConstantBase
createFromChannelWithConstant(Channel, double) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.ArithmeticWithConstantConditionallyWriteBase
createFromChannelWithConstant(Channel, double) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.UnaryWithValueBase: Creates a new channel from an existing channel and a scalar value.
createFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.CreateNew
createFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromDimensionsBase: Creates a channel from the given dimensions.
createFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.slice.RepeatSlice
createFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.AllValuesOff
createFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.AllValuesOn
createFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromObjects
createFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.FromDimensionsBase: Creates a Mask from the given Dimensions.
createFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Box
createFromHistogram(Histogram) - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.CutBelowThreshold
createFromHistogram(Histogram) - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.GreaterThanThreshold
createFromMask(Mask) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.mask.FromMask
createFromMask(Mask) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.mask.FromMaskBase: Creates a Channel from the provided Mask.
createFromMask(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.combine.CombineBase
createFromMask(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.Duplicate
createFromMask(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.Invert
createFromMask(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.ExteriorContour
createFromMask(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.FitBoxToOnVoxels
createFromMask(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.MorphologicalOperatorBase
createFromMask(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfPredicateBase
createFromMask(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.ScaleXY
createFromMask(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.slice.FlattenZ
createFromMask(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.slice.RepeatSlice
createFromMaskedChannel(Channel, Mask) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.SubtractMean
createFromMaskedChannel(Channel, Mask) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromChannel
createFromMaskedChannel(Channel, Mask) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignValue
createFromMaskedChannel(Channel, Mask) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.mask.UnaryWithMaskBase: Creates a new Channel from the input channel and mask.
createFromMaskedChannel(Channel, Mask) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.mask.ZeroOutsideMask
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.AtIndex
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.DecomposeIntoConnectedComponents
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.RejectIfNotConnected
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Duplicate
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.feature.ObjectWithMaximumFeature
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.feature.ObjectWithMaximumFeatureFromEachMatchedCollection
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.feature.SortByFeature
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.IntersectsWithContainer
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.Match
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.NotInContainer
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.ObjectCollectionProviderFilterBase
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.RemoveTouchingBorder
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.mask.AndObjectsWithMasks
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeGreedyToIncreaseObjectFeature
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithFeature
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.ObjectCollectionProviderMorphological
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Scale
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.slice.ExtendInZ
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.slice.ExtendInZWithinContainer
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.slice.FlattenZ
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.slice.SliceAt
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.split.RemoveIntersectingVoxels
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.split.SplitByObjects
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.split.SplitIntoSquares
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.UnaryWithChannelBase
createFromObjects(ObjectCollection, Optional<List<ObjectMask>>, Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.Filter
createFromObjects(ObjectCollection, Optional<List<ObjectMask>>, Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.FilterByGroup
createFromObjects(ObjectCollection, Optional<List<ObjectMask>>, Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.ObjectCollectionProviderFilterBase: Creates an ObjectCollection from the given objects, potentially applying a filter and considering dimensions.
createFromObjects(ObjectCollection, Channel) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.BinarySegmentByObject
createFromObjects(ObjectCollection, Channel) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentChannelByObject
createFromObjects(ObjectCollection, Channel) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.UnaryWithChannelBase: Creates objects from a source collection and a channel.
createFromSource(Channel) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromChannel
createFromSource(Channel) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.FromChannelBase: Creates a Mask from the source Channel.
createFromSource(Channel) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.segment.SegmentChannel
createFromSource(Channel) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.segment.Threshold
createFromTwoMasks(Mask, Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.combine.And
createFromTwoMasks(Mask, Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.combine.CombineBase: Creates a mask from some combination of two masks.
createFromTwoMasks(Mask, Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.combine.IfHighLow
createFromTwoMasks(Mask, Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.combine.Or
createFromTwoMasks(Mask, Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.combine.Xor
CreateNew - Class in org.anchoranalysis.plugin.image.bean.channel.provider: Creates a new channel with all values initialized to a constant (by default zero)
CreateNew() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.CreateNew
createPayloadCalculator() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergePairs
createPayloadCalculator() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeToIncreaseObjectFeature
createPayloadCalculator() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithFeature: Determines the payload for any given or potential vertex.
createPolicy() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.convert.ConvertBase: Creates a ConversionPolicy based on the changeExisting property.
createPrioritizer() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergePairs
createPrioritizer() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeToIncreaseObjectFeature
createPrioritizer() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithFeature: Determines the priority (and selection criteria) used to allow merges between neighbors.
createPriority(ObjectVertex, ObjectVertex, Logger) - Method in interface org.anchoranalysis.plugin.image.object.merge.priority.Prioritizer: Creates a prioritized vertex based on the source and destination vertices.
createRGBStack(Channel, Channel, Channel, VoxelDataType) - Static method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeChannels: Creates an RGB stack from up to three channels.
createSameSize(ChannelProvider, String, Channel) - Static method in class org.anchoranalysis.plugin.image.channel.DimensionsChecker: Creates a new channel from a provider, making sure it's the same size as an existing channel.
createSameSize(MaskProvider, String, Channel) - Static method in class org.anchoranalysis.plugin.image.channel.DimensionsChecker: Creates a new mask from a provider, making sure it's the same size as an existing channel.
createSession() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.feature.ObjectCollectionProviderWithFeature: Creates a feature calculation session for single objects.
createToColorUnselectedObjects(Interpolator) - Static method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize: Alternative constructor that switches on the coloring of unselected objects by default.
CutBelowThreshold - Class in org.anchoranalysis.plugin.image.bean.histogram.provider: This cuts a Histogram below a threshold BUT TRANSFERS ALL THE COUNT greater than equal to the threshold into the bin just below the threshold value
CutBelowThreshold() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.provider.CutBelowThreshold

D

decode(int) - Static method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.ChainCodesDirection: Decodes a chain-code into a point.
decodeConnectedComponentID(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.WatershedEncoding: Decodes a connected component ID from its encoded form.
DecomposeIntoConnectedComponents - Class in org.anchoranalysis.plugin.image.bean.object.provider.connected: Ensures each object in a collection is a connected-component, decomposing it if necessary into multiple objects.
DecomposeIntoConnectedComponents() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.connected.DecomposeIntoConnectedComponents
DEFAULT_COLOR_SET_GENERATOR - Static variable in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase: The default ColorScheme used for generating colors.
deriveColorList() - Method in class org.anchoranalysis.plugin.image.object.ColoredObjectCollection: Derives a ColorList from the collection.
deriveExtent() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.ObjectCollectionProviderMorphological: Derives the extent from the dimensions, if available.
describe() - Method in class org.anchoranalysis.plugin.image.object.merge.DescribeGraph: Generates a string describing the entire graph (vertices and edges).
describeEdge(ObjectVertex, ObjectVertex, ObjectVertex, double, boolean) - Method in class org.anchoranalysis.plugin.image.object.merge.DescribeGraph: Generates a string to describe a potential merge.
describeEdge(ObjectVertex, ObjectVertex, ObjectVertex, double, boolean) - Method in class org.anchoranalysis.plugin.image.object.merge.GraphLogger: Logs a description of a potential edge merge.
DescribeGraph - Class in org.anchoranalysis.plugin.image.object.merge: Builds string-descriptions of a NeighborGraph.
DescribeGraph(NeighborGraph, boolean) - Constructor for class org.anchoranalysis.plugin.image.object.merge.DescribeGraph: Creates a new DescribeGraph instance.
describeMerge(ObjectVertex, TypedEdge<ObjectVertex, PrioritisedVertex>) - Method in class org.anchoranalysis.plugin.image.object.merge.DescribeGraph: Describes a merge operation that has been decided upon.
describeMerge(ObjectVertex, TypedEdge<ObjectVertex, PrioritisedVertex>) - Method in class org.anchoranalysis.plugin.image.object.merge.GraphLogger: Logs a description of a merge operation that has been decided upon.
DictionaryCondition - Class in org.anchoranalysis.plugin.image.bean.dictionary: Checks if a value in a Dictionary is equal to an expected value.
DictionaryCondition() - Constructor for class org.anchoranalysis.plugin.image.bean.dictionary.DictionaryCondition
Dilate - Class in org.anchoranalysis.plugin.image.bean.mask.provider.morphological: Performs a dilation morphological operation on BinaryVoxels.
Dilate - Class in org.anchoranalysis.plugin.image.bean.object.provider.morphological: Dilates each object in the collection, growing bounding-boxes as necessary in relevant dimensions.
Dilate() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Dilate
Dilate() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Dilate
DimensionsChecker - Class in org.anchoranalysis.plugin.image.channel: Utility class for checking and ensuring consistency of dimensions across channels and masks.
DiscardOutliers - Class in org.anchoranalysis.plugin.image.bean.object.filter.collective: Calculates features values for all objects, and discards any object less than quantile - (minRatio * stdDev)
DiscardOutliers() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.collective.DiscardOutliers
DistanceCondition - Class in org.anchoranalysis.plugin.image.object.merge.condition: A BeforeCondition that checks if two ObjectMasks are within a specified maximum distance.
DistanceCondition(Optional<UnitValueDistance>, boolean, MessageLogger) - Constructor for class org.anchoranalysis.plugin.image.object.merge.condition.DistanceCondition: Creates a new DistanceCondition instance.
distanceSquaredTo(Point3i) - Method in class org.anchoranalysis.plugin.image.intensity.level.LevelResult: Calculates the squared distance from the midpoint of this level's object to a given point.
Duplicate - Class in org.anchoranalysis.plugin.image.bean.channel.provider: Creates a duplicate of the input channel.
Duplicate - Class in org.anchoranalysis.plugin.image.bean.mask.provider: A provider that creates a duplicate of a given Mask.
Duplicate - Class in org.anchoranalysis.plugin.image.bean.object.provider: Duplicates (deep copy) an object-collection.
Duplicate() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.Duplicate
Duplicate() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.Duplicate
Duplicate() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.Duplicate

E

Empty - Class in org.anchoranalysis.plugin.image.bean.object.provider: Creates an empty object-collection.
Empty() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.Empty
EmptyHistogramConstant - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold: Specifies a constant if a histogram is empty, otherwise delegates to another {#link org.anchoranalysis.image.bean.threshold.CalculateLevel}
EmptyHistogramConstant() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.EmptyHistogramConstant
encodeConnectedComponentID(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.WatershedEncoding: Encodes a connected component ID.
EncodedIntBuffer - Class in org.anchoranalysis.plugin.image.segment.watershed.encoding: A wrapper around UnsignedIntBuffer that provides methods for encoding and decoding watershed-related information.
EncodedIntBuffer(UnsignedIntBuffer, WatershedEncoding) - Constructor for class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedIntBuffer
encodeDirection(int, int, int) - Method in interface org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodeDirection: Encodes a 3D direction into an integer representation.
encodeDirection(int, int, int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.WatershedEncoding: Encodes a 3D direction into an integer representation.
EncodeDirection - Interface in org.anchoranalysis.plugin.image.segment.watershed.encoding: An interface for encoding a 3D direction into an integer representation.
EncodedVoxels - Class in org.anchoranalysis.plugin.image.segment.watershed.encoding: Represents voxels encoded with watershed-related information.
EncodedVoxels(Voxels<UnsignedIntBuffer>) - Constructor for class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels: Creates a new EncodedVoxels instance.
ENCODING - Static variable in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels: The encoding used for the direction-vectors.
end() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.collective.DiscardOutliers
end() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.collective.RelationWithMatches
end() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.GreaterIntersectionWith
end() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntensityGreaterEqualThan
end() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntersectsWith
end() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.NotTouchingSceneBorder
end() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedFeature
end() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterPredicate: Performs any necessary cleanup after filtering is complete.
end() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterRelation
equals(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelListBase
equals(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelRelativeToThreshold
equals(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.ClampHistogramMax
equals(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Constant
equals(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.EmptyHistogramConstant
equals(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.IfGreaterThan
equals(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.IfLessThan
equals(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Maximum
equals(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Minimum
equals(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Otsu
equals(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.OtsuWeighted
equals(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Quantile
equals(Object) - Method in class org.anchoranalysis.plugin.image.object.ColoredObject
Erode - Class in org.anchoranalysis.plugin.image.bean.mask.provider.morphological: Performs an erosion morphological operation on BinaryVoxels.
Erode - Class in org.anchoranalysis.plugin.image.bean.object.provider.morphological: Erodes each object in the collection, growing bounding-boxes as necessary in relevant dimensions.
Erode() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Erode
Erode() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Erode
existingDimensions() - Method in class org.anchoranalysis.plugin.image.bean.channel.aggregator.ProjectableBufferAggregator
ExtendInZ - Class in org.anchoranalysis.plugin.image.bean.object.provider.slice: Creates a 3D version of an object by replicating each input-object across the z-dimension to meet (3D) dimensions.
ExtendInZ() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.slice.ExtendInZ
ExtendInZWithinContainer - Class in org.anchoranalysis.plugin.image.bean.object.provider.slice: Extends an object (2D/3D) as much as it can within the z-slices of a containing object
ExtendInZWithinContainer() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.slice.ExtendInZWithinContainer
extent() - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels: Gets the extent of the voxels.
ExteriorContour - Class in org.anchoranalysis.plugin.image.bean.mask.provider.morphological: Finds the exterior outer contour for a Mask that forms its outline.
ExteriorContour() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.ExteriorContour
ExtractCenterSlice - Class in org.anchoranalysis.plugin.image.bean.channel.provider.slice: Extracts the slice at the center (rounding down) of the range of z-stacks.
ExtractCenterSlice() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.slice.ExtractCenterSlice
ExtractSliceRange - Class in org.anchoranalysis.plugin.image.bean.channel.provider.slice: Extracts slices from sliceStart (inclusive) to sliceEnd (inclusive).
ExtractSliceRange() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.slice.ExtractSliceRange

F

filter(ObjectCollection, Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.combine.And
filter(ObjectCollection, Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.combine.Or
filter(ObjectCollection, Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterPredicate
filter(ObjectCollection, Optional<Dimensions>, Optional<List<ObjectMask>>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.ObjectCollectionProviderFilterBase: Filters the given object collection using the specified filter.
Filter - Class in org.anchoranalysis.plugin.image.bean.object.provider.filter: Filters an ObjectCollection using the specified ObjectFilter.
Filter - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel: Applies an object-filter to the results of an upstream segmentation.
Filter() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.filter.Filter
Filter() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.channel.Filter
FilterByGroup - Class in org.anchoranalysis.plugin.image.bean.object.provider.filter: Filters an ObjectCollection by grouping objects and then applying a filter to each group.
FilterByGroup() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.filter.FilterByGroup
findClosestResult(Point3i) - Method in class org.anchoranalysis.plugin.image.intensity.level.LevelResultCollection: Finds the LevelResult closest to a given point.
findMatch(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.match.Always
findMatch(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.match.Bridge
findMatch(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.match.Intersection
findMaxPriority() - Method in class org.anchoranalysis.plugin.image.object.merge.MergeGraph: Finds the edge with the maximum priority for merging.
FitBoxToOnVoxels - Class in org.anchoranalysis.plugin.image.bean.mask.provider.morphological: Fits a box around the on voxels.
FitBoxToOnVoxels() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.FitBoxToOnVoxels
FitTo - Class in org.anchoranalysis.plugin.image.bean.scale: Scales an image to approximately similar in size to a SizeXY.
FitTo() - Constructor for class org.anchoranalysis.plugin.image.bean.scale.FitTo
flattenZ() - Method in class org.anchoranalysis.plugin.image.object.ColoredObject: A maximum-intensity projection.
flattenZ() - Method in class org.anchoranalysis.plugin.image.object.ColoredObjectCollection: A maximum-intensity projection.
FlattenZ - Class in org.anchoranalysis.plugin.image.bean.mask.provider.slice: Flattens a mask in the z-dimension, so it is 2D instead of 3D (like a maximum intensity projection).
FlattenZ - Class in org.anchoranalysis.plugin.image.bean.object.provider.slice: Flattens all object-masks in the z-dimension, so it is 2D instead of 3D (like a maximum intensity projection).
FlattenZ() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.slice.FlattenZ
FlattenZ() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.slice.FlattenZ
FromChannel - Class in org.anchoranalysis.plugin.image.bean.dimensions.provider: Creates image-dimensions by referencing them from a ChannelProvider.
FromChannel - Class in org.anchoranalysis.plugin.image.bean.histogram.provider: Creates a Histogram from a Channel, optionally using a mask.
FromChannel - Class in org.anchoranalysis.plugin.image.bean.mask.provider.convert: Creates a mask from an existing channel, reusing the channel's buffer and considering all 0 values as off, and 255 values as on.
FromChannel() - Constructor for class org.anchoranalysis.plugin.image.bean.dimensions.provider.FromChannel
FromChannel() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.provider.FromChannel
FromChannel() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromChannel
FromChannelBase - Class in org.anchoranalysis.plugin.image.bean.mask.provider: Base-class for MaskProviders that accept a Channel as input.
FromChannelBase() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.FromChannelBase
FromChannelOrMask - Class in org.anchoranalysis.plugin.image.bean.stack.provider: Creates a Stack from a Channel or Mask (reusing the voxel buffers).
FromChannelOrMask() - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.FromChannelOrMask
FromChannelOrMask(ChannelProvider) - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.FromChannelOrMask: Creates a new instance with a specified channel provider.
FromDimensionsBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider: An abstract base class for creating a channel from specified dimensions.
FromDimensionsBase - Class in org.anchoranalysis.plugin.image.bean.mask.provider: Base class for MaskProviders that create a mask based on given dimensions.
FromDimensionsBase() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.FromDimensionsBase
FromDimensionsBase() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.FromDimensionsBase
FromInput - Class in org.anchoranalysis.plugin.image.bean.channel.provider: Finds the input-stack using a conventional name of input_image - and extracts the first channel
FromInput - Class in org.anchoranalysis.plugin.image.bean.stack.provider: Finds the input-stack using a conventional name of input_image
FromInput() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.FromInput
FromInput() - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.FromInput
FromMask - Class in org.anchoranalysis.plugin.image.bean.channel.provider.mask: Creates a Channel directly from a Mask without any modification.
FromMask - Class in org.anchoranalysis.plugin.image.bean.object.provider.mask: Converts a binary-mask to an object-collection (containing a single object)
FromMask() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.mask.FromMask
FromMask() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.mask.FromMask
FromMaskBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider.mask: A base class for a ChannelProvider which also uses a binary-mask, but which doesn't use any other ChannelProvider as an input.
FromMaskBase() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.mask.FromMaskBase
FromObjects - Class in org.anchoranalysis.plugin.image.bean.mask.provider.convert: Creates a Mask from a collection of object-masks.
FromObjects() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromObjects
FromStack - Class in org.anchoranalysis.plugin.image.bean.channel.provider: Extracts a channel from a provider of a stack.
FromStack() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.FromStack
FromStack(ProviderAsStack) - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.FromStack: Creates a new instance with a specified stack provider.
FromStackChannel - Class in org.anchoranalysis.plugin.image.bean.mask.provider.convert: Creates a Mask from a specific channel in a stack.
FromStackChannel() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromStackChannel

G

GenerateToMatchObjects - Class in org.anchoranalysis.plugin.image.bean.color.provider: Generates colors to match the size of an object-collection.
GenerateToMatchObjects() - Constructor for class org.anchoranalysis.plugin.image.bean.color.provider.GenerateToMatchObjects
get() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromDimensionsBase
get() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromInput
get() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromStack
get() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.mask.FromMaskBase
get() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.Reference
get() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
get() - Method in class org.anchoranalysis.plugin.image.bean.color.provider.Concatenate
get() - Method in class org.anchoranalysis.plugin.image.bean.color.provider.GenerateToMatchObjects
get() - Method in class org.anchoranalysis.plugin.image.bean.dimensions.provider.FromChannel
get() - Method in class org.anchoranalysis.plugin.image.bean.dimensions.provider.GuessDimensions
get() - Method in class org.anchoranalysis.plugin.image.bean.dimensions.provider.SpecifyDimensions
get() - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.FromChannel
get() - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.Reference
get() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromStackChannel
get() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.FromChannelBase
get() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.FromDimensionsBase
get() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.Reference
get() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Concatenate
get() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.ConnectedComponentsFromMask
get() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Empty
get() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.IfParamEqual
get() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.mask.FromMask
get() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeTwoCollectionsItemwise
get() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Permute
get() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Reference
get() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.ReferenceOrElse
get() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentStack
get() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithChannelBase
get() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase
get() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeChannels
get() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.Concatenate
get() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.FromChannelOrMask
get() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.FromInput
get() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.Reference
get() - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.PriorityQueueIndexRangeDownhill: Retrieves and removes the next item from the queue.
getAddSum() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientBaseAddSum: Added to all gradients (so we can store negative gradients).
getAxis() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientForAxis: Which axis? X=0, Y=1, Z=2
getBackground() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase: The background.
getBackgroundChannelIndex() - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize: Uses only this channel (identified by an index in the stack) as the background, -1 disables.
getBackgroundChannelProvider() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.MorphologicalOperatorBase: Optional provider for a background channel to use in intensity-based conditions.
getBinarySgmn() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.BinarySegmentByObject
getBlue() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeChannels: Provider for the blue channel.
getBridgeMatcher() - Method in class org.anchoranalysis.plugin.image.bean.object.match.Bridge: Used to match each input-object to an intermediary-object
getCacheSize() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.collective.RelationWithMatches: Size of feature evaluation cache for featureEvaluatorMatch
getCalculateLevel() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectBase: Method to calculate the level for a particular object.
getCalculateLevel() - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.GreaterThanThreshold: Calculates the level for the threshold
getCalculateLevelElse() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelRelativeToThreshold: Alternative CalculateLevel to use when the condition in CalculateLevelRelativeToThreshold.useElseInstead(int, int) is met.
getChannel() - Method in class org.anchoranalysis.plugin.image.bean.dimensions.provider.FromChannel: The ChannelProvider to use for dimensions.
getChannel() - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.FromChannel: The provider for the channel from which to create the histogram.
getChannel() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.FromChannelBase: The provider for the channel from which to create the mask.
getChannel() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntensityGreaterEqualThan
getChannel() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.UnaryWithChannelBase: Provider for the channel to be used in object creation.
getChannel() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithChannelBase: Provider for the channel from which objects will be created.
getChannel() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.FromChannelOrMask: A channel that is provided to the stack.
getChannelAssignFrom() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromChannel: The channel provider from which pixels will be assigned.
getChannelConverter() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.convert.Convert
getChannelElse() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.IfParamEquals: The channel provider to use if the condition is false.
getChannelIfVoxelZero() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.IfVoxelZero: If a pixel is zero in the input-channel, the output is formed from the corresponding pixel in this channel instead
getChannelIndex() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromStack: The index of the channel to extract from the stack.
getChannelIndex() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromStackChannel: The index of the channel to use from the stack.
getChannelLookup() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.NormalizeDifferenceToMedian
getChannelsExtra() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
getChannelThreshold() - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.ThresholdAgainstChannel
getCode(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedIntBuffer: Gets the encoded value at the given index.
getColor() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredMask
getColor() - Method in class org.anchoranalysis.plugin.image.object.ColoredObject: The RGB color.
getColors() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBaseWithGenerator: Colors to use for drawing objects.
getColorScheme() - Method in class org.anchoranalysis.plugin.image.bean.color.provider.GenerateToMatchObjects
getColorUnselectedObjects() - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize: Optionally outline the other (unselected for the thumbnail) objects in this particular color.
getCondition() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.IfParamEquals: The condition to evaluate from the dictionary.
getCondition() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfKeyValueCondition
getConvert() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.convert.ConvertWithHistogram
getDelta() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Mser
getDictionary() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByDictionary
getDictionary() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromDictionary: The dictionary from which an assignment will occur.
getDictionary() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
getDictionary() - Method in class org.anchoranalysis.plugin.image.bean.dictionary.DictionaryCondition: The dictionary to provide a value to check.
getDictionary() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.IfParamEqual
getDimensions() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromDimensionsBase: The provider for the dimensions of the channel to be created.
getDimensions() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.FromDimensionsBase: Provider for the dimensions used to create the mask.
getDimensions() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.slice.RepeatSlice: Dimensions to create new mask
getDimensions() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeBase: Provider for image dimensions.
getDimensions() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithDimensionsBase: Provider for the dimensions to be used.
getDimensions() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithOptionalDimensionsBase: Optional provider for dimensions.
getDimensions() - Method in class org.anchoranalysis.plugin.image.bean.scale.ToDimensions: The dimensions the source image/entity is desired to be scaled to.
getDimensionsSourceFallback() - Method in class org.anchoranalysis.plugin.image.bean.scale.ToDimensions: Source dimensions used as a fallback, if they are not passed as parameter to ToDimensions.calculate(java.util.Optional<org.anchoranalysis.image.core.dimensions.Dimensions>, java.util.Optional<org.anchoranalysis.image.core.dimensions.size.suggestion.ImageSizeSuggestion>).
getDisplayer() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase: How to convert an image to be displayed to the user.
getDisplayer() - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize: How to convert an image so that it can be displayed.
getDisplayer() - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.stack.ScaleToSize: How to convert an image to be displayed to the user.
getDistance() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectNeighbors: How many neighbors to include by distance (distance==1 implies all directly touching neighbors, distance==2 implies those touching the directly touching etc.)
getErrorReporter() - Method in class org.anchoranalysis.plugin.image.object.merge.GraphLogger: Gets the error reporter associated with the logger.
getFactor() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreObjects: Factor to multiply the feature value by before assigning it to the output channel.
getFallback() - Method in class org.anchoranalysis.plugin.image.bean.scale.ToSuggested: Used as a delegate to calculate the scale if suggestedSize is empty when passed to ToSuggested.calculate(java.util.Optional<org.anchoranalysis.image.core.dimensions.Dimensions>, java.util.Optional<org.anchoranalysis.image.core.dimensions.size.suggestion.ImageSizeSuggestion>).
getFeature() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreObjects: Feature that calculates the score for an object.
getFeatureEvaluator() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.collective.DiscardOutliers
getFeatureEvaluator() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.collective.RelationWithMatches
getFeatureEvaluator() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedFeature
getFeatureEvaluator() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.feature.ObjectCollectionProviderWithFeature: The feature evaluator used to calculate features for single objects.
getFeatureEvaluator() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeGreedyToIncreaseObjectFeature
getFeatureEvaluator() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeToIncreaseObjectFeature
getFeatureEvaluatorMatch() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.collective.RelationWithMatches
getFeatureEvaluatorMerge() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergePairs
getFeatureEvaluatorThreshold() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergePairs: Allows merge only if the feature-value satisfies a relation to this threshold
getFilter() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfObjectFilter
getFilter() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.ObjectCollectionProviderFilterBase: The filter to apply to the object collection.
getFilter() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Filter
getGradient() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
getGrayscaleReconstruction() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.MinimaImpositionGrayscaleReconstruction: The grayscale reconstruction algorithm to be used.
getGreen() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeChannels: Provider for the green channel.
getHistogram() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.convert.ConvertWithHistogram: If set, a histogram used in conversion to describe input intensities (across perhaps multiple images).
getHistogram() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.segment.SegmentChannel: An optional histogram of voxel intensity values which can be used by segment
getHistogram() - Method in class org.anchoranalysis.plugin.image.intensity.level.LevelResult: The Histogram of intensity values for this level.
getHistogramsExtra() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
getId() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.Reference: The ID of the channel to retrieve from the named-provider.
getId() - Method in class org.anchoranalysis.plugin.image.bean.dimensions.provider.FromChannel: An shared-objects identifier for a ChannelProvider to use for dimensions.
getId() - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.Reference: The identifier of the histogram to reference.
getId() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.Reference: The identifier of the mask to reference.
getId() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Reference: The identifier of the object collection to reference.
getId() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.ReferenceOrElse
getId() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.Reference: The identifier of the stack to retrieve.
getIndex() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.AtIndex
getIndex() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.slice.SliceAt: Index in z-dimension of slice to extract.
getIndexEnd() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.slice.ExtractSliceRange: Slice index to end extracting from (inclusive).
getIndexStart() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.slice.ExtractSliceRange: Slice index to start extracting from (inclusive).
getIntensity() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
getInterpolator() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.ScaleXY: The interpolator to use for scaling images.
getInterpolator() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.AtScale: The interpolator to use.
getInterpolator() - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize: Interpolator used when scaling the background
getInterpolator() - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.stack.ScaleToSize
getIterations() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.MorphologicalOperatorBase: Number of iterations to apply the morphological operation.
getIterations() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.ObjectCollectionProviderMorphological: The number of iterations to apply the morphological operation.
getIterations() - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.Repeat: The maximum number of iterations.
getKernelHalfWidth() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.Median: Kernel will be a square kernel of size (2*kernelHalfWidth+1)x(2*kernelHalfWidth+1)
getKey() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromDictionary: The key of the value in the dictionary that will be assigned.
getKey() - Method in class org.anchoranalysis.plugin.image.bean.dictionary.DictionaryCondition: The key in the dictionary whose value is checked.
getKey() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.IfParamEqual
getKeyLower() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByDictionary
getKeyUpper() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByDictionary
getLevel() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Constant
getLevel() - Method in class org.anchoranalysis.plugin.image.intensity.level.LevelResult: The level value.
getList() - Method in class org.anchoranalysis.plugin.image.bean.color.provider.Concatenate: A list of ColorProvider to be concatenated.
getList() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelListBase: List of CalculateLevel objects to be used in the calculation.
getList() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.combine.ObjectFilterCombine: A list of other filters from which the sub-classes implement filtering behaviour.
getList() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Concatenate: List of ObjectCollectionProviders whose ObjectCollections will be concatenated.
getList() - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.Sequence: A list of binary-segmentations that are applied successively (the output of the predecessor becomes the input of the sucecssor)
getList() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.Concatenate
getListAdditionalChannelProviders() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreObjects: Additional channels to be included in the EnergyStack for feature calculation.
getMask() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.mask.FromMaskBase: The MaskProvider used to create the binary mask.
getMask() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.mask.UnaryWithMaskBase: The MaskProvider used to create the binary mask.
getMask() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
getMask() - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.FromChannel: An optional mask provider to restrict the histogram creation to specific areas.
getMask() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.segment.SegmentChannel: An optional mask which restricts the algorithm to only parts of the channel where the mask has an on voxel
getMask() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.ConnectedComponentsFromMask
getMask() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.mask.AndObjectsWithMasks
getMask() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.mask.FromMask
getMask() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentChannel: Optional mask to restrict the segmentation area.
getMask() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredMask
getMask() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.FromChannelOrMask: A mask that is provided to the stack.
getMaskElse() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfPredicateBase: Returned instead of mask if the predicate is not satisfied.
getMatcher() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.collective.RelationWithMatches
getMatcher() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.feature.ObjectWithMaximumFeatureFromEachMatchedCollection
getMatcher() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.Match: The ObjectMatcher used to find matches in the input object collection.
getMax() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByMinMaxValue
getMax() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.ClampHistogramMax
getMaxDistance() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithOptionalDistanceConstraint: An optional maximum distance between objects that can be merged.
getMaxSize() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Mser
getMaxVar() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Mser
getMaxX() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Box: Maximum X coordinate inclusive.
getMaxY() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Box: Maximum Y coordinate inclusive.
getMaxZ() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Box: Maximum Z coordinate inclusive.
getMin() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByMinMaxValue
getMinConfidence() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ThresholdConfidence: The minimum confidence of an element for its object-mask to be initially included for consideration (before merging).
getMinDiversity() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Mser
getMinimaImposition() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.ImposeMinima
getMinIntensityValue() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.MorphologicalOperatorBase: Minimum intensity value for voxels to be considered in the operation.
getMinNumberObjects() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.collective.DiscardOutliers
getMinNumberVoxels() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.split.SplitIntoSquares: Only includes squares that have at least this number of voxels.
getMinNumberVoxels() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.ConnectedComponentsFromBinarySegmentation
getMinNumberVoxels() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ThresholdConfidence: The minimum number of voxels that must exist in a connected-component to be included.
getMinRatio() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.collective.DiscardOutliers
getMinResolution() - Method in class org.anchoranalysis.plugin.image.bean.scale.MinimumXYResolution: The minimum resolution to achieve in meters.
getMinSize() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Mser
getMinVolume() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.ConnectedComponentsFromMask
getMinX() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Box: Minimum X coordinate inclusive.
getMinY() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Box: Minimum Y coordinate inclusive.
getMinZ() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Box: Minimum Z coordinate inclusive.
getMultipleOf() - Method in class org.anchoranalysis.plugin.image.bean.scale.FitTo: The eventual width and height of the image must be a multiple of this number.
getNumberDilations() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectIndependently
getObject() - Method in class org.anchoranalysis.plugin.image.intensity.level.LevelResult: The ObjectMask associated with this level.
getObject() - Method in class org.anchoranalysis.plugin.image.object.ColoredObject: The object-mask.
getObject() - Method in class org.anchoranalysis.plugin.image.object.merge.ObjectVertex: The ObjectMask represented by this vertex.
getObjectMatcher() - Method in class org.anchoranalysis.plugin.image.bean.object.match.Bridge: Used to match each intermediary-object to a final-object
getObjects() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectBase: The objects for whom a level is calculated.
getObjects() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.UnaryWithObjectsBase: The provider for the collection of objects to be used in channel creation.
getObjects() - Method in class org.anchoranalysis.plugin.image.bean.color.provider.GenerateToMatchObjects
getObjects() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromObjects
getObjects() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntersectsWith
getObjects() - Method in class org.anchoranalysis.plugin.image.bean.object.match.Always
getObjects() - Method in class org.anchoranalysis.plugin.image.bean.object.match.Intersection: Provider for the objects to intersect with the source objects.
getObjects() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Permute
getObjects() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredObjects: Objects to draw on a background
getObjects1() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeTwoCollectionsItemwise: First collection with items to be merged
getObjects2() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeTwoCollectionsItemwise: Second collection with items to be merged
getObjectsBlue() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeColoredObjects
getObjectsContainer() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithContainerBase: Optional provider for a container of objects.
getObjectsElse() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.ReferenceOrElse
getObjectsGreater() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.GreaterIntersectionWith
getObjectsGreen() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeColoredObjects
getObjectsGrouped() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.FilterByGroup: Provides the ObjectCollection used for grouping the objects to be filtered.
getObjectsLesser() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.GreaterIntersectionWith
getObjectsRed() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeColoredObjects
getObjectsSeeds() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentChannel: Optional provider for seed objects to guide the segmentation.
getObjectsSeeds() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentWithSeeds
getObjectsSource() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromIntersectingObjects
getObjectsSource() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentWithSeeds
getObjectsSplitBy() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.split.SplitByObjects: Provider for the collection of objects used to split the input objects.
getObjectsTarget() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromIntersectingObjects
getOutlineWidth() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.AtScale
getOutlineWidth() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase: The width of the outline (only relevant if outline==true).
getOutlineWidth() - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize: The width of the outline.
getPayload() - Method in class org.anchoranalysis.plugin.image.object.merge.ObjectVertex: The payload associated with this vertex.
getPermuteProperty() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Permute
getPixelsForPlane(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels: Gets the encoded int buffer for a specific plane.
getPriority() - Method in class org.anchoranalysis.plugin.image.object.merge.priority.PrioritisedVertex
getQuantile() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.QuantileStretch
getQuantile() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Quantile
getQuantile() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.collective.DiscardOutliers
getQuantileLower() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ToByteUpperLowerQuantileIntensity: The lower quantile value for intensity scaling.
getQuantileUpper() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ToByteUpperLowerQuantileIntensity: The upper quantile value for intensity scaling.
getReceive() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.combine.CombineBase: The MaskProvider for the second mask to be combined.
getRed() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeChannels: Provider for the red channel.
getRelation() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterRelation: The relation to be used in the filter predicate.
getRelation() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergePairs: Relation to threshold
getRestrictTo() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.Invert: If set, the inversion only occurs on a particular region of the mask, as determined by this mask
getScaleCalculator() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.ScaleXY
getScaleCalculator() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.ScaleXY: Determines how much to scale by.
getScaleCalculator() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Scale
getScaleCalculator() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.AtScale
getScaleCalculator() - Method in class org.anchoranalysis.plugin.image.bean.scale.Invert: The delegate ScaleCalculator whose calculation will be inverted.
getScaleFactor() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientBase: Scale factor applied to the gradient values.
getScaleLower() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByDictionary
getScaleLower() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ToByteUpperLowerQuantileIntensity: Sets the min by multiplying the quantileLower by this constant.
getScaleUpper() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByDictionary
getScaleUpper() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ToByteUpperLowerQuantileIntensity: Sets the max by multiplying the quantileUpper by this constant.
getScore() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
getSegment() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.segment.SegmentChannel: Segmentation algorithm
getSegment() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentChannel: The segmentation algorithm to use.
getSegment() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentChannelByObject
getSegment() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentStack: The segmentation procedure.
getSegment() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentWithSeeds
getSegment() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.ConnectedComponentsFromBinarySegmentation
getSegmentStack() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.SegmentOnMaximumIntensityAndExpandInZ
getSigma() - Method in class org.anchoranalysis.plugin.image.bean.blur.BlurStrategy: The sigma value for the blur operation.
getSize() - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize: Size of all created thumbnails
getSize() - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.stack.ScaleToSize
getSizeXY() - Method in class org.anchoranalysis.plugin.image.bean.dimensions.provider.SpecifyDimensions: Length of X and Y dimensions.
getSizeZ() - Method in class org.anchoranalysis.plugin.image.bean.dimensions.provider.SpecifyDimensions: Length of Z dimension.
getSlice() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.slice.RepeatSlice
getSliceIndex() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.slice.RepeatSlice: Which slice to use from mask
getSquareSize() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.split.SplitIntoSquares
getStack() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromStack: Provides a stack.
getStack() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentStack: The stack to segment
getStackID() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfStackExists
getStackProviderID() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromStack: Specifies the ID of an existing stack.
getStackProviderID() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromStackChannel: The identifier of the stack provider to retrieve the stack from.
getStrategy() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.Blur
getTargetSize() - Method in class org.anchoranalysis.plugin.image.bean.scale.FitTo: The target size.
getTemporary() - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels: Gets a list of points with temporary encoded values.
getThreshold() - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.CutBelowThreshold
getThreshold() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelRelativeToThreshold: Threshold value to compare against when deciding whether to use the alternative calculation.
getThreshold() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntensityGreaterEqualThan
getThreshold() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedFeature
getThreshold() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedVolume
getThresholder() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.segment.Threshold: The thresholder that will convert a channel into a binary-channel
getThresholdNumberObjectsGlobal() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ThresholdConfidence: When the number of objects is greater or equal than this, they are reduced globally, without separation.
getValue() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignValue
getValue() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.CreateNew
getValue() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.UnaryWithValueBase: The scalar value to be used in channel creation.
getValue() - Method in class org.anchoranalysis.plugin.image.bean.dictionary.DictionaryCondition: The value the key should have in the dictionary, in order for the condition to be fulfilled.
getValue() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.EmptyHistogramConstant
getValue() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.IfParamEqual
getValue() - Method in class org.anchoranalysis.plugin.image.bean.scale.ConstantScaleFactor: The constant floating-point value to scale each dimension by.
getValueNoObject() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreObjects: The value assigned to voxels that do not belong to any object.
getVertex() - Method in class org.anchoranalysis.plugin.image.object.merge.priority.PrioritisedVertex
getWeightBackground() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.OtsuWeighted
getWeightForeground() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.OtsuWeighted
getWhenEqual() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.IfParamEqual
getWhenNotEqual() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.IfParamEqual
GradientBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider.gradient: Base class to calculate the gradient of the voxels in a Channel.
GradientBase() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientBase
GradientBaseAddSum - Class in org.anchoranalysis.plugin.image.bean.channel.provider.gradient: Like GradientBase but allows an arbitrary constant to be added to voxels storing the gradient.
GradientBaseAddSum() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientBaseAddSum
GradientForAxis - Class in org.anchoranalysis.plugin.image.bean.channel.provider.gradient: Extracts the gradient in the direction of a particular axis (identified by an index)
GradientForAxis() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientForAxis
GradientXY - Class in org.anchoranalysis.plugin.image.bean.channel.provider.gradient: Calculates a Channel's gradient along the x and y axes.
GradientXY() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientXY
GraphLogger - Class in org.anchoranalysis.plugin.image.object.merge: A logger for graph operations, using a DescribeGraph to generate descriptions.
GraphLogger(DescribeGraph, Logger) - Constructor for class org.anchoranalysis.plugin.image.object.merge.GraphLogger: Creates a new GraphLogger instance.
GrayscaleReconstructionByErosion - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction: Abstract base class for performing grayscale reconstruction by erosion.
GrayscaleReconstructionByErosion() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction.GrayscaleReconstructionByErosion
GrayscaleReconstructionRobinson - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction: Implements grayscale reconstruction using Robinson's algorithm.
GrayscaleReconstructionRobinson() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction.GrayscaleReconstructionRobinson
GreaterIntersectionWith - Class in org.anchoranalysis.plugin.image.bean.object.filter.independent: Only accepts an object if it has greater (or EQUAL) intersection with objectsGreater than objectsLesser
GreaterIntersectionWith() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.independent.GreaterIntersectionWith
GreaterThanThreshold - Class in org.anchoranalysis.plugin.image.bean.histogram.provider: Thresholds a histogram using a CalculateLevel keeping only the values greater equal than the threshold
GreaterThanThreshold() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.provider.GreaterThanThreshold
GuessDimensions - Class in org.anchoranalysis.plugin.image.bean.dimensions.provider: Guesses dimensions from an input-image if it exists.
GuessDimensions() - Constructor for class org.anchoranalysis.plugin.image.bean.dimensions.provider.GuessDimensions

H

hashCode() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelListBase
hashCode() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelRelativeToThreshold
hashCode() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.ClampHistogramMax
hashCode() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Constant
hashCode() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.EmptyHistogramConstant
hashCode() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.IfGreaterThan
hashCode() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.IfLessThan
hashCode() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Maximum
hashCode() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Minimum
hashCode() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Otsu
hashCode() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.OtsuWeighted
hashCode() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Quantile
hashCode() - Method in class org.anchoranalysis.plugin.image.object.ColoredObject
hasNext() - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.PriorityQueueIndexRangeDownhill: Checks if there are any items left in the queue.
hasTemporary() - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels: Checks if there are any temporary encoded values in the voxels.
histogram(String) - Static method in class org.anchoranalysis.plugin.image.provider.ReferenceFactory: Creates a reference to a histogram.
HistogramThresholder - Class in org.anchoranalysis.plugin.image.intensity: Utility class for thresholding histograms.

I

IdentifyObjects - Class in org.anchoranalysis.plugin.image.bean.channel.provider.score: Assigns a unique id number to each object.
IdentifyObjects() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.score.IdentifyObjects
IfGreaterThan - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold: Calculates a level from the first delegate and if greater than a threshold, recalculates from a second delegate.
IfGreaterThan() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.IfGreaterThan
IfHighLow - Class in org.anchoranalysis.plugin.image.bean.mask.provider.combine: Outputs the logical operation iff first==HIGH and second==LOW then LOW voxelwise on both masks, modifying {mask} with the result.
IfHighLow() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.combine.IfHighLow
IfKeyValueCondition - Class in org.anchoranalysis.plugin.image.bean.mask.provider.predicate: The current mask is returned if a condition on key-values is satisfied otherwise maskElse is returned.
IfKeyValueCondition() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfKeyValueCondition
IfLessThan - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold: Calculates a level from the first delegate and if less than a threshold, recalculates from a second delegate.
IfLessThan() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.IfLessThan
IfNotEmpty - Class in org.anchoranalysis.plugin.image.bean.mask.provider.predicate: The current mask is returned if it's non-empty (at least one on voxel) otherwise maskElse is returned.
IfNotEmpty() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfNotEmpty
IfObjectFilter - Class in org.anchoranalysis.plugin.image.bean.mask.provider.predicate: The current mask is returned if the mask (treated as an object) passed an object-filter, otherwise maskElse is returned.
IfObjectFilter() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfObjectFilter
IfParamEqual - Class in org.anchoranalysis.plugin.image.bean.object.provider: Multiplexes between two object-collection-providers depending on whether a parameter value equals a particular string
IfParamEqual() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.IfParamEqual
IfParamEquals - Class in org.anchoranalysis.plugin.image.bean.channel.provider: Provides a channel based on a condition from a dictionary.
IfParamEquals() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.IfParamEquals
IfPredicateBase - Class in org.anchoranalysis.plugin.image.bean.mask.provider.predicate: Base class which multiplexes between the current mask and an alternative depending if a condition is met.
IfPredicateBase() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfPredicateBase
IfStackExists - Class in org.anchoranalysis.plugin.image.bean.mask.provider.predicate: The current mask is a particular stack exists (at least one on voxel) otherwise maskElse is returned.
IfStackExists() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfStackExists
IfVoxelZero - Class in org.anchoranalysis.plugin.image.bean.channel.provider.intensity: Creates a new channel which is a merged version of two input channels according to rules.
IfVoxelZero() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.IfVoxelZero
imposeMinima(Channel, ObjectCollection, Optional<ObjectMask>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.MinimaImposition: Imposes minima on a channel based on seed objects and an optional containing mask.
imposeMinima(Channel, ObjectCollection, Optional<ObjectMask>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.MinimaImpositionGrayscaleReconstruction
ImposeMinima - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel: Imposes minima in seed locations on the input-channel before performing the segmentation
ImposeMinima() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.channel.ImposeMinima
IncreaseFeatureCondition - Class in org.anchoranalysis.plugin.image.object.merge.condition: An AfterCondition that checks if merging two ObjectMasks increases a specific feature value.
IncreaseFeatureCondition(FeatureEvaluator<FeatureInputSingleObject>) - Constructor for class org.anchoranalysis.plugin.image.object.merge.condition.IncreaseFeatureCondition: Creates a new IncreaseFeatureCondition instance.
initialize(Logger) - Method in interface org.anchoranalysis.plugin.image.object.merge.condition.AfterCondition: Initializes the condition with a logger.
initialize(Logger) - Method in class org.anchoranalysis.plugin.image.object.merge.condition.IncreaseFeatureCondition
IntensityGreaterEqualThan - Class in org.anchoranalysis.plugin.image.bean.object.filter.independent: Only keep objects where at least one voxel (on a particular channel) has intensity greater or equal to a threshold.
IntensityGreaterEqualThan() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntensityGreaterEqualThan
IntensityMeanCalculator - Class in org.anchoranalysis.plugin.image.intensity: Utility class for calculating mean intensity of objects in a channel.
Intersection - Class in org.anchoranalysis.plugin.image.bean.object.match: An ObjectMatcher that matches objects based on their intersection with a provided set of objects.
Intersection() - Constructor for class org.anchoranalysis.plugin.image.bean.object.match.Intersection
IntersectsWith - Class in org.anchoranalysis.plugin.image.bean.object.filter.independent: Keeps objects which intersects with ANY ONE of a collection of other objects.
IntersectsWith() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntersectsWith
IntersectsWithContainer - Class in org.anchoranalysis.plugin.image.bean.object.provider.filter: Returns only the objects that intersect with at least one object in the container
IntersectsWithContainer() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.filter.IntersectsWithContainer
Invert - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic: Inverts the intensity values of a Channel by subtracting each voxel from the maximum value for the channel's data type.
Invert - Class in org.anchoranalysis.plugin.image.bean.mask.provider: Switches on voxels to off and vice-versa.
Invert - Class in org.anchoranalysis.plugin.image.bean.scale: Invert the ScaleFactor calculated by the scaleCalculator delegate.
Invert - Class in org.anchoranalysis.plugin.image.bean.segment.binary: Performs a segmentation and inverts and on and off bytes
Invert() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.Invert
Invert() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.Invert
Invert() - Constructor for class org.anchoranalysis.plugin.image.bean.scale.Invert
Invert() - Constructor for class org.anchoranalysis.plugin.image.bean.segment.binary.Invert
isAddOne() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Quantile
isBigNeighborhood() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Dilate
isBigNeighborhood() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.ConnectedComponentsFromMask: If true uses 8 neighborhood rather than 4 neighborhood etc.
isBigNeighborhood() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.DecomposeIntoConnectedComponents: if true, uses 8 neighborhood instead of 4, and similarly in 3d
isBigNeighborhood() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Dilate
isBySlices() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.ConnectedComponentsFromMask
isChangeExisting() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.convert.ConvertBase: If true, the existing channel can be changed.
isClearOutsideMask() - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.ThresholdAgainstChannel
isConditionTrue() - Method in class org.anchoranalysis.plugin.image.bean.dictionary.DictionaryCondition: Checks if the condition is true by comparing the value in the dictionary with the expected value.
isConnectedComponentID(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedIntBuffer: Checks if the value at the given offset is a connected component ID.
isConnectedComponentIDCode(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels: Checks if the given code represents a connected component ID.
isConnectedComponentIDCode(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.WatershedEncoding: Checks if the given code represents a connected component ID.
isConsiderForMerge() - Method in class org.anchoranalysis.plugin.image.object.merge.priority.PrioritisedVertex
isCreateShort() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.CreateNew: If True creates an unsigned short-image
isDebug() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedFeature
isDirectionChainCode(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels: Checks if the given code represents a direction chain code.
isDirectionChainCode(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.WatershedEncoding: Checks if the given code represents a direction chain code.
isDo3D() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.ObjectCollectionProviderMorphological: Whether to perform the operation in 3D (true) or 2D (false).
isDuplicate() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.Reference: If true, the channel is duplicated after it is retrieved, to prevent overwriting existing data.
isDuplicate() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.Reference: If true, the mask is duplicated after it is retrieved, to prevent overwriting existing data.
isErrorDisconnectedObjects() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.split.RemoveIntersectingVoxels: If true, throws an error if there is a disconnected object after the erosion
isExitWithMinima() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong.WatershedYeong: If true, exits early and just returns the minima, without any further segmentation
isFlatten() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.ExteriorContour: If true, any 3D mask is flattened in the z-dimension (maximum intensity projection) to make it 2D
isFlatten() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase: If true, objects and the background are flattened in the z dimension (via maximum intensity projection), so that a 2D image is produced.
isForceChangeBytes() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.Invert: If true, rather than modifying the binary-values (an index) bytes are modified in the buffer to reflect the existing binary-values.
isIncludeZ() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.NotTouchingSceneBorder
isInverse() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.IntersectsWithContainer
isInvert() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromObjects
isMerge() - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.CutBelowThreshold
isMinima(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedIntBuffer: Checks if the value at the given offset is a minima.
isMinima(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels: Checks if the given code represents a minima.
isOutline() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase: If true, an outline is drawn around the entries.
isOutlineAtBoundary() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.ExteriorContour
isOutputShort() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientBase: If true, outputs a short channel, otherwise byte channel.
isOverlappingObjects() - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize: Whether objects may overlap or not when unscaled.
isPlateau(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels: Checks if the given code represents a plateau.
isPlayloadUsed() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergePairs
isPlayloadUsed() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeToIncreaseObjectFeature
isPlayloadUsed() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithFeature: Checks if the payload is considered in making decisions.
isPreserveAspectRatio() - Method in class org.anchoranalysis.plugin.image.bean.scale.FitTo: If true, the aspect-ratio is preserved between width and height.
isPreserveAspectRatio() - Method in class org.anchoranalysis.plugin.image.bean.scale.ToDimensions: If true, the ratio between x and y is kept constant when scaling.
isRejectIterationIfAllLow() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Erode
isRejectIterationIfDisconnected() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Erode
isReplaceWithMidpoint() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeGreedyToIncreaseObjectFeature
isRequireBBoxNeighbors() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithFeature: Requires for any potential merge that the bounding-boxes of the two objects must intersect or touch.
isRequireTouching() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithFeature: Requires the object-masks to touch.
isRgb() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.FromChannelOrMask: If true, the output contains three channels (the input and two duplicates) instead of one.
isSigmaInMeters() - Method in class org.anchoranalysis.plugin.image.bean.blur.BlurStrategy: If true, treats sigma as if it's in meters (physical units).
isSlicesSeparately() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.FitBoxToOnVoxels
isSubtractFromMaskOnly() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.SubtractMean: Whether to subtract the mean only from voxels within the mask.
isSuppress3D() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.MorphologicalOperatorBase: Whether to suppress 3D operations and only perform 2D operations.
isSuppressOutlineZ() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase: If true, the outline is suppressed in the z-dimension i.e.
isSuppressZ() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithOptionalDistanceConstraint: If true, suppresses the Z-dimension when calculating distances between objects.
isTemporary(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedIntBuffer: Checks if the value at the given offset is temporary.
isTemporary(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels: Checks if the given code represents a temporary value.
isUnvisited(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedIntBuffer: Checks if the value at the given offset is unvisited.
isUnvisited(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels: Checks if the given code represents an unvisited value.
isUseZ() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.RemoveTouchingBorder
iterator() - Method in class org.anchoranalysis.plugin.image.intensity.level.LevelResultCollection

L

LevelPerObjectBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider.object: Creates a channel with a level calculated for each object using various methods.
LevelPerObjectBase() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectBase
LevelPerObjectIndependently - Class in org.anchoranalysis.plugin.image.bean.channel.provider.object: Creates a channel with different threshold-levels for each object, calculating the level only from the histogram of the particular object.
LevelPerObjectIndependently() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectIndependently
LevelPerObjectNeighbors - Class in org.anchoranalysis.plugin.image.bean.channel.provider.object: Calculates a threshold-level for each object collectively based on other objects
LevelPerObjectNeighbors() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectNeighbors
LevelResult - Class in org.anchoranalysis.plugin.image.intensity.level: Represents the result of a level operation, containing the level value, object mask, and histogram.
LevelResult(int, ObjectMask, Histogram) - Constructor for class org.anchoranalysis.plugin.image.intensity.level.LevelResult: Creates a new LevelResult instance.
LevelResultCollection - Class in org.anchoranalysis.plugin.image.intensity.level: A collection of LevelResult objects that can be iterated over and searched.
LevelResultCollection() - Constructor for class org.anchoranalysis.plugin.image.intensity.level.LevelResultCollection
LevelResultCollectionFactory - Class in org.anchoranalysis.plugin.image.intensity.level: Factory for creating LevelResultCollection objects.
logDescription() - Method in class org.anchoranalysis.plugin.image.object.merge.GraphLogger: Logs a description of the entire graph.
logGraphDescription() - Method in class org.anchoranalysis.plugin.image.object.merge.MergeGraph: Logs a description of the current graph state.

M

markAsTemporary(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedIntBuffer: Marks the value at the given offset as temporary.
mask(String) - Static method in class org.anchoranalysis.plugin.image.provider.ReferenceFactory: Creates a reference to a mask.
match(ObjectMask, Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.collective.DiscardOutliers
match(ObjectMask, Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.GreaterIntersectionWith
match(ObjectMask, Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntensityGreaterEqualThan
match(ObjectMask, Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntersectsWith
match(ObjectMask, Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.NotTouchingSceneBorder
match(ObjectMask, Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterPredicate: A predicate condition for an object to be kept in the collection.
match(ObjectMask, Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterRelation
match(ObjectMask, Optional<Dimensions>, DoubleBiPredicate) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.collective.RelationWithMatches
match(ObjectMask, Optional<Dimensions>, DoubleBiPredicate) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedFeature
match(ObjectMask, Optional<Dimensions>, DoubleBiPredicate) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedVolume
match(ObjectMask, Optional<Dimensions>, DoubleBiPredicate) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterRelation: Performs the matching operation using the resolved relation.
Match - Class in org.anchoranalysis.plugin.image.bean.object.provider.filter: Provides an ObjectCollection by matching objects using a specified ObjectMatcher.
Match() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.filter.Match
MatcherIntersectionHelper - Class in org.anchoranalysis.plugin.image.bean.object.match: Helper class for matching objects based on intersection.
matchIntersectingObjects(ObjectCollection, ObjectCollection) - Static method in class org.anchoranalysis.plugin.image.bean.object.match.MatcherIntersectionHelper: Matches objects from the source collection with intersecting objects from the search collection.
MAX_VALUE - Static variable in class org.anchoranalysis.plugin.image.segment.watershed.encoding.ChainCodesDirection: The maximum value for a chain code, corresponding to code 0.
Maximum - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold: The maximum value of one or more {#link org.anchoranalysis.image.bean.threshold.CalculateLevel}
Maximum() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.Maximum
MaximumIntensityProjection - Class in org.anchoranalysis.plugin.image.bean.channel.provider.slice: Creates a maximum intensity projection of a 3D Channel.
MaximumIntensityProjection() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.slice.MaximumIntensityProjection
MaxProjection<T> - Class in org.anchoranalysis.plugin.image.bean.channel.aggregator: Maximum-intensity-projection across Channels.
MaxProjection() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.aggregator.MaxProjection
MaxTwoChannels - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic: Creates a new channel by taking the maximum value of corresponding voxels from two input channels.
MaxTwoChannels() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.MaxTwoChannels: Constructs a new MaxTwoChannels instance.
MaxWithConstant - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic: Replaces voxel values with a constant value if the constant is greater than the original voxel value.
MaxWithConstant() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.MaxWithConstant
maybeDistanceCondition() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithOptionalDistanceConstraint: Creates a BeforeCondition that checks the distance between objects before merging.
MeanIntensityProjection - Class in org.anchoranalysis.plugin.image.bean.channel.provider.slice: Creates a mean intensity projection of a 3D Channel.
MeanIntensityProjection() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.slice.MeanIntensityProjection
MeanProjection<T> - Class in org.anchoranalysis.plugin.image.bean.channel.aggregator: Mean-intensity-projection across Channels.
MeanProjection() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.aggregator.MeanProjection
MeanThreeChannels - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic: Creates a new channel that is the mean of three input channels.
MeanThreeChannels() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.MeanThreeChannels
Median - Class in org.anchoranalysis.plugin.image.bean.channel.provider.intensity: Applies a median-filter with square kernel
Median() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.Median
merge(TypedEdge<ObjectVertex, PrioritisedVertex>) - Method in class org.anchoranalysis.plugin.image.object.merge.MergeGraph: Merges two vertices in the graph.
MergeBase - Class in org.anchoranalysis.plugin.image.bean.object.provider.merge: A base class for algorithms that merge object-masks.
MergeBase() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeBase
MergeBase.MergeObjects - Interface in org.anchoranalysis.plugin.image.bean.object.provider.merge: Functional interface for merging objects.
MergeGraph - Class in org.anchoranalysis.plugin.image.object.merge: A graph that stores each object as a vertex, where edges represent a neighborhood relation.
MergeGraph(PayloadCalculator, UpdatableBeforeCondition, Optional<UnitConverter>, AssignPriority, Logger, boolean) - Constructor for class org.anchoranalysis.plugin.image.object.merge.MergeGraph: Constructor.
MergeGreedyToIncreaseObjectFeature - Class in org.anchoranalysis.plugin.image.bean.object.provider.merge: Naive greedy merge strategy when any two neighboring objects are merged if it increases a feature.
MergeGreedyToIncreaseObjectFeature() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeGreedyToIncreaseObjectFeature
mergeMultiplex(ObjectCollection, MergeBase.MergeObjects) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeBase: Merges objects either in a container or altogether.
mergeObjects(ObjectCollection) - Method in interface org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeBase.MergeObjects: Merges a collection of objects.
MergePairs - Class in org.anchoranalysis.plugin.image.bean.object.provider.merge: Merges objects if a pair feature value satisfies a condition.
MergePairs() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergePairs
MergeToIncreaseObjectFeature - Class in org.anchoranalysis.plugin.image.bean.object.provider.merge: Merges neighboring objects if it results in an increase in the average feature-value calculated on each single object.
MergeToIncreaseObjectFeature() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeToIncreaseObjectFeature
MergeTwoCollectionsItemwise - Class in org.anchoranalysis.plugin.image.bean.object.provider.merge: Merges itemwise objects from two collections.
MergeTwoCollectionsItemwise() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeTwoCollectionsItemwise
mergeViaZeroCheck(Channel, Channel, VoxelDataType, double) - Static method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.IfVoxelZero: Creates a new channel which is a merged version of two input channels according to rules.
MergeWithFeature - Class in org.anchoranalysis.plugin.image.bean.object.provider.merge: Base class for object-merging strategies that involve calculating a feature.
MergeWithFeature() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithFeature
MergeWithOptionalDistanceConstraint - Class in org.anchoranalysis.plugin.image.bean.object.provider.merge: Expands MergeBase by optionally imposing a maximum-distance requirement between objects that are possibly merged.
MergeWithOptionalDistanceConstraint() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithOptionalDistanceConstraint
MinimaImposition - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima: Abstract base class for imposing minima on a channel for watershed segmentation.
MinimaImposition() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.MinimaImposition
MinimaImpositionGrayscaleReconstruction - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima: Imposes minima on a channel using grayscale reconstruction by erosion.
MinimaImpositionGrayscaleReconstruction() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.MinimaImpositionGrayscaleReconstruction
Minimum - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold: The minimum value of one or more {#link org.anchoranalysis.image.bean.threshold.CalculateLevel}
Minimum() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.Minimum
MinimumXYResolution - Class in org.anchoranalysis.plugin.image.bean.scale: Calculates a scale factor to ensure a minimum XY resolution is achieved.
MinimumXYResolution() - Constructor for class org.anchoranalysis.plugin.image.bean.scale.MinimumXYResolution
MinProjection<T> - Class in org.anchoranalysis.plugin.image.bean.channel.aggregator: Minimum-intensity-projection across Channels.
MinProjection() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.aggregator.MinProjection
MinTwoChannels - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic: Creates a new channel by taking the minimum value of corresponding voxels from two input channels.
MinTwoChannels() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.MinTwoChannels: Constructs a new MinTwoChannels instance.
MinWithConstant - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic: Replaces voxel values with a constant value if the constant is less than the original voxel value.
MinWithConstant() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.MinWithConstant
MorphologicalOperatorBase - Class in org.anchoranalysis.plugin.image.bean.mask.provider.morphological: Base class for performing morphological operations on BinaryVoxels.
MorphologicalOperatorBase() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.MorphologicalOperatorBase
Mser - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel: Applies the MSER algorithm from imglib2
Mser() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.channel.Mser
MultiplyConstant - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic: Multiplies each voxel value in a channel by a constant value.
MultiplyConstant() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.MultiplyConstant
MultiplyTwoChannels - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic: Creates a new channel by multiplying corresponding voxels from two input channels.
MultiplyTwoChannels() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.MultiplyTwoChannels: Constructs a new MultiplyTwoChannels instance.

N

NeighborhoodCondition - Class in org.anchoranalysis.plugin.image.object.merge.condition: A condition to determine if two objects are potential neighbors and candidates for merging.
NeighborhoodCondition(boolean, boolean) - Constructor for class org.anchoranalysis.plugin.image.object.merge.condition.NeighborhoodCondition: Creates a new NeighborhoodCondition.
nextValue() - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.PriorityQueueIndexRangeDownhill: Returns the index value of the next item to be retrieved.
NormalizeDifferenceToMedian - Class in org.anchoranalysis.plugin.image.bean.channel.provider.intensity: Corrects a channel in the following way
NormalizeDifferenceToMedian() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.NormalizeDifferenceToMedian
NormalizeObjectIntensity - Class in org.anchoranalysis.plugin.image.bean.channel.provider.intensity: Rewrites the intensity for each object-mask (assume no overlap) so that its mean is 128
NormalizeObjectIntensity() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.NormalizeObjectIntensity
NotInContainer - Class in org.anchoranalysis.plugin.image.bean.object.provider.filter: Filters objects to keep only those which are NOT in the container.
NotInContainer() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.filter.NotInContainer
NotTouchingSceneBorder - Class in org.anchoranalysis.plugin.image.bean.object.filter.independent: Keeps only objects that are not adjacent to the scene-border (i.e.
NotTouchingSceneBorder() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.independent.NotTouchingSceneBorder
numberVoxels() - Method in class org.anchoranalysis.plugin.image.object.merge.ObjectVertex: Gets the number of voxels in the object.

O

ObjectCollectionProviderFilterBase - Class in org.anchoranalysis.plugin.image.bean.object.provider.filter: Base class for object collection providers that apply a filter to the objects.
ObjectCollectionProviderFilterBase() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.filter.ObjectCollectionProviderFilterBase
ObjectCollectionProviderMorphological - Class in org.anchoranalysis.plugin.image.bean.object.provider.morphological: Base class for providers that apply morphological operations to an ObjectCollection.
ObjectCollectionProviderMorphological() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.morphological.ObjectCollectionProviderMorphological
ObjectCollectionProviderWithFeature - Class in org.anchoranalysis.plugin.image.bean.object.provider.feature: An abstract base class for object collection providers that use a feature evaluator.
ObjectCollectionProviderWithFeature() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.feature.ObjectCollectionProviderWithFeature
ObjectFilterCombine - Class in org.anchoranalysis.plugin.image.bean.object.filter.combine: A filter that combines other filters (in a list)
ObjectFilterCombine() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.combine.ObjectFilterCombine
ObjectFilterPredicate - Class in org.anchoranalysis.plugin.image.bean.object.filter: Uses a predicate to make a decision whether to keep objects or not.
ObjectFilterPredicate() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterPredicate
ObjectFilterRelation - Class in org.anchoranalysis.plugin.image.bean.object.filter: An independent object-filter that uses a relation in its predicate.
ObjectFilterRelation() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterRelation
ObjectIntersectionRemover - Class in org.anchoranalysis.plugin.image.object: Utility class for removing intersecting voxels between objects in a collection.
objects(String) - Static method in class org.anchoranalysis.plugin.image.provider.ReferenceFactory: Creates a reference to objects.
objectsToDraw(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBaseWithGenerator: The objects to draw (without any colors) on the background.
objectsToDraw(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredObjects
ObjectVertex - Class in org.anchoranalysis.plugin.image.object.merge: A vertex in a merge graph representing an object (and an associated payload).
ObjectVertex(ObjectMask, double) - Constructor for class org.anchoranalysis.plugin.image.object.merge.ObjectVertex: Creates a new ObjectVertex instance.
ObjectWithMaximumFeature - Class in org.anchoranalysis.plugin.image.bean.object.provider.feature: Finds the object with the maximum feature-value from a collection.
ObjectWithMaximumFeature() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.feature.ObjectWithMaximumFeature
ObjectWithMaximumFeatureFromEachMatchedCollection - Class in org.anchoranalysis.plugin.image.bean.object.provider.feature: Finds the object with the maximum feature among a group of matches for each object.
ObjectWithMaximumFeatureFromEachMatchedCollection() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.feature.ObjectWithMaximumFeatureFromEachMatchedCollection
onInitialization(ImageInitialization) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromInput
onInitialization(ImageInitialization) - Method in class org.anchoranalysis.plugin.image.bean.dimensions.provider.FromChannel
onInitialization(ImageInitialization) - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.Reference
onInitialization(ImageInitialization) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromStackChannel
onInitialization(ImageInitialization) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.ReferenceOrElse
onInitialization(ImageInitialization) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.FromInput
Or - Class in org.anchoranalysis.plugin.image.bean.mask.provider.combine: Outputs the logical operation or voxelwise on both masks, modifying {mask} with the result.
Or - Class in org.anchoranalysis.plugin.image.bean.object.filter.combine: Applies multiples filter with logical OR i.e.
Or() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.combine.Or
Or() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.combine.Or
org.anchoranalysis.plugin.image.bean.blur - package org.anchoranalysis.plugin.image.bean.blur: Filters that perform blurring.
org.anchoranalysis.plugin.image.bean.channel.aggregator - package org.anchoranalysis.plugin.image.bean.channel.aggregator: Implementations of ConvertChannelTo and ConvertChannelToWithHistogram.
org.anchoranalysis.plugin.image.bean.channel.convert - package org.anchoranalysis.plugin.image.bean.channel.convert: Implementations of ConvertChannelTo and ConvertChannelToWithHistogram.
org.anchoranalysis.plugin.image.bean.channel.provider - package org.anchoranalysis.plugin.image.bean.channel.provider: Implementations of ChannelProvider that are generic base-classes or otherwise abstract or general.
org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic - package org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic: Implementations of ChannelProvider that perform arithmetic on voxels in one or more Channels.
org.anchoranalysis.plugin.image.bean.channel.provider.assign - package org.anchoranalysis.plugin.image.bean.channel.provider.assign: Implementations of ChannelProvider that sets the values of the voxels in a Channel.
org.anchoranalysis.plugin.image.bean.channel.provider.convert - package org.anchoranalysis.plugin.image.bean.channel.provider.convert: Implementations of ChannelProvider that converts a Channel from one voxel-type to another.
org.anchoranalysis.plugin.image.bean.channel.provider.gradient - package org.anchoranalysis.plugin.image.bean.channel.provider.gradient: Implementations of ChannelProvider that calculate the gradient of a Channel's voxels in one or more dimensions.
org.anchoranalysis.plugin.image.bean.channel.provider.intensity - package org.anchoranalysis.plugin.image.bean.channel.provider.intensity: Implementations of ChannelProvider that manipulate the intensity-values of the voxels of a Channel's voxels.
org.anchoranalysis.plugin.image.bean.channel.provider.mask - package org.anchoranalysis.plugin.image.bean.channel.provider.mask: Implementations of ChannelProvider that involve conversion from or application of Masks.
org.anchoranalysis.plugin.image.bean.channel.provider.object - package org.anchoranalysis.plugin.image.bean.channel.provider.object: Implementations of ChannelProvider that involve conversion from or application of ObjectMasks.
org.anchoranalysis.plugin.image.bean.channel.provider.score - package org.anchoranalysis.plugin.image.bean.channel.provider.score: Implementations of ChannelProvider that assign a score to particular subregions of a channel.
org.anchoranalysis.plugin.image.bean.channel.provider.slice - package org.anchoranalysis.plugin.image.bean.channel.provider.slice: Implementations of ChannelProvider that process 3D channels slice-by-slice.
org.anchoranalysis.plugin.image.bean.color.provider - package org.anchoranalysis.plugin.image.bean.color.provider: Implementations of ColorProvider.
org.anchoranalysis.plugin.image.bean.dictionary - package org.anchoranalysis.plugin.image.bean.dictionary: Beans pertaining to Dictionary.
org.anchoranalysis.plugin.image.bean.dimensions.provider - package org.anchoranalysis.plugin.image.bean.dimensions.provider: Implementations of DimensionsProvider.
org.anchoranalysis.plugin.image.bean.histogram.provider - package org.anchoranalysis.plugin.image.bean.histogram.provider: Implementations of HistogramProvider.
org.anchoranalysis.plugin.image.bean.histogram.threshold - package org.anchoranalysis.plugin.image.bean.histogram.threshold: Thresholding of intensity values represented in at Histogram.
org.anchoranalysis.plugin.image.bean.mask.provider - package org.anchoranalysis.plugin.image.bean.mask.provider: Implementations of MaskProvider.
org.anchoranalysis.plugin.image.bean.mask.provider.combine - package org.anchoranalysis.plugin.image.bean.mask.provider.combine: Implementations of MaskProvider that combine existing providers.
org.anchoranalysis.plugin.image.bean.mask.provider.convert - package org.anchoranalysis.plugin.image.bean.mask.provider.convert: Implementations of MaskProvider that convert providers of other types to ObjectMasks.
org.anchoranalysis.plugin.image.bean.mask.provider.morphological - package org.anchoranalysis.plugin.image.bean.mask.provider.morphological: Implementations of MaskProvider that implement morphological operations.
org.anchoranalysis.plugin.image.bean.mask.provider.predicate - package org.anchoranalysis.plugin.image.bean.mask.provider.predicate: Provides if-else conditions to a MaskProvider.
org.anchoranalysis.plugin.image.bean.mask.provider.segment - package org.anchoranalysis.plugin.image.bean.mask.provider.segment: Implementations of MaskProvider where an ObjectCollection is created by segmenting a Channel.
org.anchoranalysis.plugin.image.bean.mask.provider.slice - package org.anchoranalysis.plugin.image.bean.mask.provider.slice: Implementations of MaskProvider that process 3D masks slice-by-slice.
org.anchoranalysis.plugin.image.bean.object.filter - package org.anchoranalysis.plugin.image.bean.object.filter: Implementations of ObjectFilter.
org.anchoranalysis.plugin.image.bean.object.filter.collective - package org.anchoranalysis.plugin.image.bean.object.filter.collective: Implementations of ObjectFilter that assess each element in a collection collectively.
org.anchoranalysis.plugin.image.bean.object.filter.combine - package org.anchoranalysis.plugin.image.bean.object.filter.combine: Implementations of ObjectFilter that combine two or more other ObjectFilters.
org.anchoranalysis.plugin.image.bean.object.filter.independent - package org.anchoranalysis.plugin.image.bean.object.filter.independent: Implementations of ObjectFilter that independently assess each element in a collection.
org.anchoranalysis.plugin.image.bean.object.match - package org.anchoranalysis.plugin.image.bean.object.match: Implementations of ObjectMatcher.
org.anchoranalysis.plugin.image.bean.object.provider - package org.anchoranalysis.plugin.image.bean.object.provider: Implementations of ObjectCollectionProvider.
org.anchoranalysis.plugin.image.bean.object.provider.connected - package org.anchoranalysis.plugin.image.bean.object.provider.connected: Implementations of ObjectCollectionProvider involving connected-components.
org.anchoranalysis.plugin.image.bean.object.provider.feature - package org.anchoranalysis.plugin.image.bean.object.provider.feature: Implementations of ObjectCollectionProvider involving feature calculation.
org.anchoranalysis.plugin.image.bean.object.provider.filter - package org.anchoranalysis.plugin.image.bean.object.provider.filter: Implementations of ObjectCollectionProvider that filter objects.
org.anchoranalysis.plugin.image.bean.object.provider.mask - package org.anchoranalysis.plugin.image.bean.object.provider.mask: Implementations of ObjectCollectionProvider involving a Mask.
org.anchoranalysis.plugin.image.bean.object.provider.merge - package org.anchoranalysis.plugin.image.bean.object.provider.merge: Implementations of ObjectCollectionProvider involving merging objects together.
org.anchoranalysis.plugin.image.bean.object.provider.morphological - package org.anchoranalysis.plugin.image.bean.object.provider.morphological: Implementations of ObjectCollectionProvider involving morphological operations.
org.anchoranalysis.plugin.image.bean.object.provider.segment - package org.anchoranalysis.plugin.image.bean.object.provider.segment: Implementations of ObjectCollectionProvider involving segmentation.
org.anchoranalysis.plugin.image.bean.object.provider.slice - package org.anchoranalysis.plugin.image.bean.object.provider.slice: Implementations of ObjectCollectionProvider involving z-slice processing.
org.anchoranalysis.plugin.image.bean.object.provider.split - package org.anchoranalysis.plugin.image.bean.object.provider.split: Implementations of ObjectCollectionProvider involving splitting objects into smaller objects.
org.anchoranalysis.plugin.image.bean.object.segment.channel - package org.anchoranalysis.plugin.image.bean.object.segment.channel: Implementations of SegmentChannelIntoObjects.
org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima - package org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima: Minima imposition for a Watershed transformation.
org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction - package org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction: Grayscale reconstruction to support the Watershed transformation.
org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong - package org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong: Implementation of a Watershed transformation based on Yeong et al.
org.anchoranalysis.plugin.image.bean.object.segment.reduce - package org.anchoranalysis.plugin.image.bean.object.segment.reduce: Strategies for reducing the number of elements with a list by merging/removing lower-confidence elements that overlap.
org.anchoranalysis.plugin.image.bean.scale - package org.anchoranalysis.plugin.image.bean.scale: Implementations of ScaleCalculator for calculating a scaling-factor from dimensions.
org.anchoranalysis.plugin.image.bean.segment.binary - package org.anchoranalysis.plugin.image.bean.segment.binary: Implementations of BinarySegmentation.
org.anchoranalysis.plugin.image.bean.stack.provider - package org.anchoranalysis.plugin.image.bean.stack.provider: Implementations of StackProvider.
org.anchoranalysis.plugin.image.bean.stack.provider.color - package org.anchoranalysis.plugin.image.bean.stack.provider.color: Implementations of StackProvider that color portions of an image.
org.anchoranalysis.plugin.image.bean.thumbnail.object - package org.anchoranalysis.plugin.image.bean.thumbnail.object: Implementations of ThumbnailFromObjects.
org.anchoranalysis.plugin.image.bean.thumbnail.stack - package org.anchoranalysis.plugin.image.bean.thumbnail.stack: Implementations of ThumbnailFromStack.
org.anchoranalysis.plugin.image.channel - package org.anchoranalysis.plugin.image.channel: Non-beans for operations or calculations relating to Channels.
org.anchoranalysis.plugin.image.intensity - package org.anchoranalysis.plugin.image.intensity: Non-bean for operations or calculations relating to intensity.
org.anchoranalysis.plugin.image.intensity.level - package org.anchoranalysis.plugin.image.intensity.level: Non-beans for calculating a thresholding level from itensity values.
org.anchoranalysis.plugin.image.object - package org.anchoranalysis.plugin.image.object: Non-beans pertaining to ObjectMasks.
org.anchoranalysis.plugin.image.object.merge - package org.anchoranalysis.plugin.image.object.merge: Merging ObjectMasks.
org.anchoranalysis.plugin.image.object.merge.condition - package org.anchoranalysis.plugin.image.object.merge.condition: Conditions for merging ObjectMasks.
org.anchoranalysis.plugin.image.object.merge.priority - package org.anchoranalysis.plugin.image.object.merge.priority: Assigning priority when merging ObjectMasks.
org.anchoranalysis.plugin.image.provider - package org.anchoranalysis.plugin.image.provider: Non-bean classes pertaining to Providers.
org.anchoranalysis.plugin.image.segment.thresholder.slice - package org.anchoranalysis.plugin.image.segment.thresholder.slice: Non-beans pertaining to segmenting a z-stack slice-by-slice.
org.anchoranalysis.plugin.image.segment.watershed.encoding - package org.anchoranalysis.plugin.image.segment.watershed.encoding: Encoding voxels in a watershed-transformation implementation.
org.anchoranalysis.plugin.image.thumbnail - package org.anchoranalysis.plugin.image.thumbnail: Non-bean classes for thumbnail creation.
Otsu - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold: Performs auto-thresholding using Otsu's method.
Otsu() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.Otsu
OtsuWeighted - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold: Similar to Otsu, but weighs the variances differently of background and foreground.
OtsuWeighted() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.OtsuWeighted
OtsuWeighted(double, double) - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.OtsuWeighted
OutlinePreserveRelativeSize - Class in org.anchoranalysis.plugin.image.bean.thumbnail.object: Create a thumbnail by drawing an outline of an object at a particular-scale, and placing it centered in a window of a certain size.
OutlinePreserveRelativeSize() - Constructor for class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize

P

PayloadCalculator - Interface in org.anchoranalysis.plugin.image.object.merge: Calculates a payload value for an ObjectMask.
performBinaryOperation(int, int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.AddConstant
performBinaryOperation(int, int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.ArithmeticWithConstantBase: The binary arithmetic operation that combines the voxel-value and the constant-value.
performBinaryOperation(int, int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.MultiplyConstant
performBinaryOperation(int, int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.SubtractFromConstant
Permute - Class in org.anchoranalysis.plugin.image.bean.object.provider: Permutes some changes over an ObjectCollectionProvider and collects all the results in an ObjectCollection
Permute() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.Permute
pointListAtFirstPoint(List<Point3i>) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels: Sets all points in a list to point at the first point (the root point) in the list.
precondition() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.MorphologicalOperatorBase: Creates a precondition for the morphological operation based on intensity values.
precondition(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.collective.DiscardOutliers
precondition(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.GreaterIntersectionWith
precondition(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntensityGreaterEqualThan
precondition(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntersectsWith
precondition(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.NotTouchingSceneBorder
precondition(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterPredicate: A precondition, which if evaluates to false, cancels the filter i.e.
precondition(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterRelation
predicate(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfKeyValueCondition
predicate(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfNotEmpty
predicate(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfObjectFilter
predicate(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfPredicateBase: Evaluates a predicate condition on the input mask.
predicate(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfStackExists
PrioritisedVertex - Class in org.anchoranalysis.plugin.image.object.merge.priority: A vertex with a priority attached, and a boolean flag as to whether it can be merged or not
PrioritisedVertex(ObjectMask, double, double, boolean) - Constructor for class org.anchoranalysis.plugin.image.object.merge.priority.PrioritisedVertex: Constructor
Prioritizer - Interface in org.anchoranalysis.plugin.image.object.merge.priority: Creates a priority between two vertices for object merging.
PriorityQueueIndexRangeDownhill<T> - Class in org.anchoranalysis.plugin.image.segment.watershed.encoding: Implements a priority queue based upon a range of values from 0 to maxValue.
PriorityQueueIndexRangeDownhill(int) - Constructor for class org.anchoranalysis.plugin.image.segment.watershed.encoding.PriorityQueueIndexRangeDownhill: Creates a new priority queue with a specified maximum value.
process(Channel, Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.TwoVoxelMappingBase
process(Channel, Channel, Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.MeanThreeChannels
ProjectableBufferAggregator<T> - Class in org.anchoranalysis.plugin.image.bean.channel.aggregator: An aggregator that calculates the aggregation of every voxel across successive channels via a ProjectableBuffer.
ProjectableBufferAggregator() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.aggregator.ProjectableBufferAggregator
put(T, int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.PriorityQueueIndexRangeDownhill: Adds an item to the priority queue with a specified index value.
putCode(int, int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedIntBuffer: Puts an encoded value at the given index.

Q

Quantile - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold: Calculates the threshold value from a quantile of a histogram.
Quantile() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.Quantile
QuantileStretch - Class in org.anchoranalysis.plugin.image.bean.channel.provider.intensity: Changes the voxel values to map the range of 0th quantile to xth quantile across the entire voxel data range
QuantileStretch() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.QuantileStretch

R

reconstruction(VoxelsUntyped, VoxelsUntyped, Optional<ObjectMask>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction.GrayscaleReconstructionByErosion: Performs grayscale reconstruction of a mask image from a marker image.
reconstruction(VoxelsUntyped, VoxelsUntyped, Optional<ObjectMask>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction.GrayscaleReconstructionRobinson
reduce(List<LabelledWithConfidence<ObjectMask>>, Extent, ExecutionTimeRecorder) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ThresholdConfidence
Reference - Class in org.anchoranalysis.plugin.image.bean.channel.provider: Provides a channel by referencing it from a a set of named-channels.
Reference - Class in org.anchoranalysis.plugin.image.bean.histogram.provider: A provider that references an existing Histogram by its identifier.
Reference - Class in org.anchoranalysis.plugin.image.bean.mask.provider: A provider that references an existing Mask by its identifier.
Reference - Class in org.anchoranalysis.plugin.image.bean.object.provider: An ObjectCollectionProvider that references an existing ObjectCollection by its identifier.
Reference - Class in org.anchoranalysis.plugin.image.bean.stack.provider: Retrieves an existing stack.
Reference() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.Reference
Reference() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.provider.Reference
Reference() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.Reference
Reference() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.Reference
Reference() - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.Reference
Reference(String) - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.Reference: Creates a new instance with a specified channel ID.
Reference(String) - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.provider.Reference: Creates a new Reference with the specified identifier.
Reference(String) - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.Reference: Creates a new Reference with the specified identifier.
Reference(String) - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.Reference: Creates a new Reference with the specified identifier.
Reference(String) - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.Reference: Creates a new Reference with a specified identifier.
ReferenceFactory - Class in org.anchoranalysis.plugin.image.provider: Creates reference (i.e.
ReferenceOrElse - Class in org.anchoranalysis.plugin.image.bean.object.provider: Returns a object-collection by name if it exists, or else calls objectsElse if it doesn't exist.
ReferenceOrElse() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.ReferenceOrElse
RejectIfNotConnected - Class in org.anchoranalysis.plugin.image.bean.object.provider.connected: Rejects a set of objects, if any object is not fully connected (pixels form two or more separate connected components)
RejectIfNotConnected() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.connected.RejectIfNotConnected
RelationWithMatches - Class in org.anchoranalysis.plugin.image.bean.object.filter.collective: Matches each object with others, and keeps only those where a relation holds true for all matches (in terms of features)
RelationWithMatches() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.collective.RelationWithMatches
removeIntersectingVoxels(ObjectCollection, Dimensions, boolean) - Static method in class org.anchoranalysis.plugin.image.object.ObjectIntersectionRemover: Removes intersecting voxels from a collection of objects.
RemoveIntersectingVoxels - Class in org.anchoranalysis.plugin.image.bean.object.provider.split: Considers all possible pairs of objects in a provider, and removes any intersecting pixels
RemoveIntersectingVoxels() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.split.RemoveIntersectingVoxels
RemoveTouchingBorder - Class in org.anchoranalysis.plugin.image.bean.object.provider.filter: Considers all possible pairs of objects in a provider, and removes those that touch the border.
RemoveTouchingBorder() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.filter.RemoveTouchingBorder
Repeat - Class in org.anchoranalysis.plugin.image.bean.segment.binary: Repeats a binary segmentation operation for a specified number of iterations.
Repeat() - Constructor for class org.anchoranalysis.plugin.image.bean.segment.binary.Repeat
RepeatSlice - Class in org.anchoranalysis.plugin.image.bean.channel.provider.slice: Creates a new channel with specific dimensions that repeatedly duplicates a slice from an existing channel
RepeatSlice - Class in org.anchoranalysis.plugin.image.bean.mask.provider.slice: Creates a new mask with specific dimensions that repeatedly duplicates a slice from an existing mask
RepeatSlice() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.slice.RepeatSlice
RepeatSlice() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.slice.RepeatSlice
resolutionRequired() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeBase: Gets the required Resolution.
retrieveCreateAggregatedChannel() - Method in class org.anchoranalysis.plugin.image.bean.channel.aggregator.ProjectableBufferAggregator

S

Scale - Class in org.anchoranalysis.plugin.image.bean.object.provider: Scales all the objects in the collection by a particular scale-factor.
Scale() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.Scale
ScaleByDictionary - Class in org.anchoranalysis.plugin.image.bean.channel.convert: Scales by compressing a certain range of values into the 8-bit signal.
ScaleByDictionary() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByDictionary
ScaleByMinMaxValue - Class in org.anchoranalysis.plugin.image.bean.channel.convert: Scales by compressing a certain range of values into the 8-bit signal
ScaleByMinMaxValue() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByMinMaxValue
ScaleByTypeToByte - Class in org.anchoranalysis.plugin.image.bean.channel.convert: Converts a channel to unsigned byte format, scaling the values based on the original voxel type.
ScaleByTypeToByte() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByTypeToByte
ScaleToSize - Class in org.anchoranalysis.plugin.image.bean.thumbnail.stack: Create a thumbnail by scales an image to a particular size.
ScaleToSize() - Constructor for class org.anchoranalysis.plugin.image.bean.thumbnail.stack.ScaleToSize
ScaleXY - Class in org.anchoranalysis.plugin.image.bean.channel.provider.intensity: Scales the channel in the X and Y dimensions.
ScaleXY - Class in org.anchoranalysis.plugin.image.bean.mask.provider: Scales the mask in XY dimensions, but not in Z dimension.
ScaleXY() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.ScaleXY
ScaleXY() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.ScaleXY
ScoreObjects - Class in org.anchoranalysis.plugin.image.bean.channel.provider.score: Creates a channel by scoring objects based on a feature calculation.
ScoreObjects() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreObjects
ScoreVoxels - Class in org.anchoranalysis.plugin.image.bean.channel.provider.score: Assigns a score (a value indicating how probable something is) to each voxel
ScoreVoxels() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
segment(Channel, Optional<ObjectMask>, Optional<ObjectCollection>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.ConnectedComponentsFromBinarySegmentation
segment(Channel, Optional<ObjectMask>, Optional<ObjectCollection>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Mser
segment(Channel, Optional<ObjectMask>, Optional<ObjectCollection>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong.WatershedYeong
segment(Channel, Optional<ObjectMask>, Optional<ObjectCollection>, SegmentChannelIntoObjects) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.AtScale
segment(Channel, Optional<ObjectMask>, Optional<ObjectCollection>, SegmentChannelIntoObjects) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Filter
segment(Channel, Optional<ObjectMask>, Optional<ObjectCollection>, SegmentChannelIntoObjects) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.ImposeMinima
segment(Channel, Optional<ObjectMask>, Optional<ObjectCollection>, SegmentChannelIntoObjects) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.SegmentOnMaximumIntensityAndExpandInZ
segment(VoxelsUntyped, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.Sequence
segment(VoxelsUntyped, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.ThresholdAgainstChannel
segmentAll(Voxels<?>, Voxels<?>, Voxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.plugin.image.segment.thresholder.slice.SliceThresholder: Segments all slices in the input voxels.
segmentAll(Voxels<?>, Voxels<?>, Voxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.plugin.image.segment.thresholder.slice.SliceThresholderMask
segmentAll(Voxels<?>, Voxels<?>, Voxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.plugin.image.segment.thresholder.slice.SliceThresholderWithoutMask
SegmentChannel - Class in org.anchoranalysis.plugin.image.bean.mask.provider.segment: Applies a BinarySegmentation algorithm to derive a mask from a channel
SegmentChannel - Class in org.anchoranalysis.plugin.image.bean.object.provider.segment: Segments a channel into objects using a specified segmentation algorithm.
SegmentChannel() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.segment.SegmentChannel
SegmentChannel() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentChannel
SegmentChannelByObject - Class in org.anchoranalysis.plugin.image.bean.object.provider.segment: Performs segmentation of a channel using each object in the upstream collection as a mask.
SegmentChannelByObject() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentChannelByObject
segmentFromExistingSegmentation(VoxelsUntyped, BinarySegmentationParameters, Optional<ObjectMask>, BinarySegmentation) - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.Invert
segmentFromExistingSegmentation(VoxelsUntyped, BinarySegmentationParameters, Optional<ObjectMask>, BinarySegmentation) - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.Repeat
SegmentOnMaximumIntensityAndExpandInZ - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel: Perform a segmentation in a MIP instead of z-stacks, and fits the result back into a 3D segmentation.
SegmentOnMaximumIntensityAndExpandInZ() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.channel.SegmentOnMaximumIntensityAndExpandInZ
SegmentStack<T> - Class in org.anchoranalysis.plugin.image.bean.object.provider.segment: Segments a stack into objects.
SegmentStack() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentStack
SegmentWithSeeds - Class in org.anchoranalysis.plugin.image.bean.object.provider.segment: Takes each object one-by-one from objectsSource, and finds matching seeds from objectsSeeds
SegmentWithSeeds() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentWithSeeds
Sequence - Class in org.anchoranalysis.plugin.image.bean.segment.binary: Performs a sequence of succesive segmentations
Sequence() - Constructor for class org.anchoranalysis.plugin.image.bean.segment.binary.Sequence
setAddOne(boolean) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Quantile
setAddSum(int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientBaseAddSum: Added to all gradients (so we can store negative gradients).
setAxis(String) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientForAxis: Which axis? X=0, Y=1, Z=2
setBackground(ProviderAsStack) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase: The background.
setBackgroundChannelIndex(int) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize: Uses only this channel (identified by an index in the stack) as the background, -1 disables.
setBackgroundChannelProvider(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.MorphologicalOperatorBase: Optional provider for a background channel to use in intensity-based conditions.
setBigNeighborhood(boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Dilate
setBigNeighborhood(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.ConnectedComponentsFromMask: If true uses 8 neighborhood rather than 4 neighborhood etc.
setBigNeighborhood(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.DecomposeIntoConnectedComponents: if true, uses 8 neighborhood instead of 4, and similarly in 3d
setBigNeighborhood(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Dilate
setBinarySgmn(BinarySegmentation) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.BinarySegmentByObject
setBlue(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeChannels: Provider for the blue channel.
setBridgeMatcher(ObjectMatcher) - Method in class org.anchoranalysis.plugin.image.bean.object.match.Bridge: Used to match each input-object to an intermediary-object
setBySlices(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.ConnectedComponentsFromMask
setCacheSize(int) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.collective.RelationWithMatches: Size of feature evaluation cache for featureEvaluatorMatch
setCalculateLevel(CalculateLevel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectBase: Method to calculate the level for a particular object.
setCalculateLevel(CalculateLevel) - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.GreaterThanThreshold: Calculates the level for the threshold
setCalculateLevelElse(CalculateLevel) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelRelativeToThreshold: Alternative CalculateLevel to use when the condition in CalculateLevelRelativeToThreshold.useElseInstead(int, int) is met.
setChangeExisting(boolean) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.convert.ConvertBase: If true, the existing channel can be changed.
setChannel(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.dimensions.provider.FromChannel: The ChannelProvider to use for dimensions.
setChannel(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.FromChannel: The provider for the channel from which to create the histogram.
setChannel(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.FromChannelBase: The provider for the channel from which to create the mask.
setChannel(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntensityGreaterEqualThan
setChannel(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.UnaryWithChannelBase: Provider for the channel to be used in object creation.
setChannel(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithChannelBase: Provider for the channel from which objects will be created.
setChannel(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.FromChannelOrMask: A channel that is provided to the stack.
setChannelAssignFrom(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromChannel: The channel provider from which pixels will be assigned.
setChannelConverter(ConvertChannelTo<T>) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.convert.Convert
setChannelElse(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.IfParamEquals: The channel provider to use if the condition is false.
setChannelIfVoxelZero(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.IfVoxelZero: If a pixel is zero in the input-channel, the output is formed from the corresponding pixel in this channel instead
setChannelIndex(int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromStack: The index of the channel to extract from the stack.
setChannelIndex(int) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromStackChannel: The index of the channel to use from the stack.
setChannelLookup(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.NormalizeDifferenceToMedian
setChannelsExtra(List<ChannelProvider>) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
setChannelThreshold(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.ThresholdAgainstChannel
setClearOutsideMask(boolean) - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.ThresholdAgainstChannel
setColor(RGBColorBean) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredMask
setColors(ColorScheme) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBaseWithGenerator: Colors to use for drawing objects.
setColorScheme(ColorScheme) - Method in class org.anchoranalysis.plugin.image.bean.color.provider.GenerateToMatchObjects
setColorUnselectedObjects(RGBColorBean) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize: Optionally outline the other (unselected for the thumbnail) objects in this particular color.
setCondition(DictionaryCondition) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.IfParamEquals: The condition to evaluate from the dictionary.
setCondition(DictionaryCondition) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfKeyValueCondition
setConvert(ConvertChannelToWithHistogram<T>) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.convert.ConvertWithHistogram
setCreateShort(boolean) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.CreateNew: If True creates an unsigned short-image
setDebug(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedFeature
setDelta(double) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Mser
setDictionary(DictionaryProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByDictionary
setDictionary(DictionaryProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromDictionary: The dictionary from which an assignment will occur.
setDictionary(DictionaryProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
setDictionary(DictionaryProvider) - Method in class org.anchoranalysis.plugin.image.bean.dictionary.DictionaryCondition: The dictionary to provide a value to check.
setDictionary(DictionaryProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.IfParamEqual
setDimensions(DimensionsProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromDimensionsBase: The provider for the dimensions of the channel to be created.
setDimensions(DimensionsProvider) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.FromDimensionsBase: Provider for the dimensions used to create the mask.
setDimensions(DimensionsProvider) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.slice.RepeatSlice: Dimensions to create new mask
setDimensions(DimensionsProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeBase: Provider for image dimensions.
setDimensions(DimensionsProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithDimensionsBase: Provider for the dimensions to be used.
setDimensions(DimensionsProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithOptionalDimensionsBase: Optional provider for dimensions.
setDimensions(DimensionsProvider) - Method in class org.anchoranalysis.plugin.image.bean.scale.ToDimensions: The dimensions the source image/entity is desired to be scaled to.
setDimensionsSourceFallback(DimensionsProvider) - Method in class org.anchoranalysis.plugin.image.bean.scale.ToDimensions: Source dimensions used as a fallback, if they are not passed as parameter to ToDimensions.calculate(java.util.Optional<org.anchoranalysis.image.core.dimensions.Dimensions>, java.util.Optional<org.anchoranalysis.image.core.dimensions.size.suggestion.ImageSizeSuggestion>).
setDisplayer(StackDisplayer) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase: How to convert an image to be displayed to the user.
setDisplayer(StackDisplayer) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize: How to convert an image so that it can be displayed.
setDisplayer(StackDisplayer) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.stack.ScaleToSize: How to convert an image to be displayed to the user.
setDistance(int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectNeighbors: How many neighbors to include by distance (distance==1 implies all directly touching neighbors, distance==2 implies those touching the directly touching etc.)
setDo3D(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.ObjectCollectionProviderMorphological: Whether to perform the operation in 3D (true) or 2D (false).
setDuplicate(boolean) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.Reference: If true, the channel is duplicated after it is retrieved, to prevent overwriting existing data.
setDuplicate(boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.Reference: If true, the mask is duplicated after it is retrieved, to prevent overwriting existing data.
setErrorDisconnectedObjects(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.split.RemoveIntersectingVoxels: If true, throws an error if there is a disconnected object after the erosion
setExitWithMinima(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong.WatershedYeong: If true, exits early and just returns the minima, without any further segmentation
setFactor(double) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreObjects: Factor to multiply the feature value by before assigning it to the output channel.
setFallback(ScaleCalculator) - Method in class org.anchoranalysis.plugin.image.bean.scale.ToSuggested: Used as a delegate to calculate the scale if suggestedSize is empty when passed to ToSuggested.calculate(java.util.Optional<org.anchoranalysis.image.core.dimensions.Dimensions>, java.util.Optional<org.anchoranalysis.image.core.dimensions.size.suggestion.ImageSizeSuggestion>).
setFeature(Feature<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreObjects: Feature that calculates the score for an object.
setFeatureEvaluator(FeatureEvaluator<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.collective.DiscardOutliers
setFeatureEvaluator(FeatureEvaluator<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.collective.RelationWithMatches
setFeatureEvaluator(FeatureEvaluator<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedFeature
setFeatureEvaluator(FeatureEvaluator<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.feature.ObjectCollectionProviderWithFeature: The feature evaluator used to calculate features for single objects.
setFeatureEvaluator(FeatureEvaluator<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeGreedyToIncreaseObjectFeature
setFeatureEvaluator(FeatureEvaluator<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeToIncreaseObjectFeature
setFeatureEvaluatorMatch(FeatureEvaluator<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.collective.RelationWithMatches
setFeatureEvaluatorMerge(FeatureEvaluator<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergePairs
setFeatureEvaluatorThreshold(FeatureEvaluator<FeatureInputNull>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergePairs: Allows merge only if the feature-value satisfies a relation to this threshold
setFilter(ObjectFilter) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfObjectFilter
setFilter(ObjectFilter) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.ObjectCollectionProviderFilterBase: The filter to apply to the object collection.
setFilter(ObjectFilter) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Filter
setFlatten(boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.ExteriorContour: If true, any 3D mask is flattened in the z-dimension (maximum intensity projection) to make it 2D
setFlatten(boolean) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase: If true, objects and the background are flattened in the z dimension (via maximum intensity projection), so that a 2D image is produced.
setForceChangeBytes(boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.Invert: If true, rather than modifying the binary-values (an index) bytes are modified in the buffer to reflect the existing binary-values.
setGradient(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
setGrayscaleReconstruction(GrayscaleReconstructionByErosion) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.MinimaImpositionGrayscaleReconstruction: The grayscale reconstruction algorithm to be used.
setGreen(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeChannels: Provider for the green channel.
setHistogram(HistogramProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.convert.ConvertWithHistogram: If set, a histogram used in conversion to describe input intensities (across perhaps multiple images).
setHistogram(HistogramProvider) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.segment.SegmentChannel: An optional histogram of voxel intensity values which can be used by segment
setHistogramsExtra(List<HistogramProvider>) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
setId(String) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.Reference: The ID of the channel to retrieve from the named-provider.
setId(String) - Method in class org.anchoranalysis.plugin.image.bean.dimensions.provider.FromChannel: An shared-objects identifier for a ChannelProvider to use for dimensions.
setId(String) - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.Reference: The identifier of the histogram to reference.
setId(String) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.Reference: The identifier of the mask to reference.
setId(String) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Reference: The identifier of the object collection to reference.
setId(String) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.ReferenceOrElse
setId(String) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.Reference: The identifier of the stack to retrieve.
setIncludeZ(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.NotTouchingSceneBorder
setIndex(int) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.AtIndex
setIndex(int) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.slice.SliceAt: Index in z-dimension of slice to extract.
setIndexEnd(int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.slice.ExtractSliceRange: Slice index to end extracting from (inclusive).
setIndexStart(int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.slice.ExtractSliceRange: Slice index to start extracting from (inclusive).
setIntensity(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
setInterpolator(Interpolator) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.ScaleXY: The interpolator to use for scaling images.
setInterpolator(Interpolator) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.AtScale: The interpolator to use.
setInterpolator(Interpolator) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize: Interpolator used when scaling the background
setInterpolator(Interpolator) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.stack.ScaleToSize
setInverse(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.IntersectsWithContainer
setInvert(boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromObjects
setIterations(int) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.MorphologicalOperatorBase: Number of iterations to apply the morphological operation.
setIterations(int) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.ObjectCollectionProviderMorphological: The number of iterations to apply the morphological operation.
setIterations(int) - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.Repeat: The maximum number of iterations.
setKernelHalfWidth(int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.Median: Kernel will be a square kernel of size (2*kernelHalfWidth+1)x(2*kernelHalfWidth+1)
setKey(String) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromDictionary: The key of the value in the dictionary that will be assigned.
setKey(String) - Method in class org.anchoranalysis.plugin.image.bean.dictionary.DictionaryCondition: The key in the dictionary whose value is checked.
setKey(String) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.IfParamEqual
setKeyLower(String) - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByDictionary
setKeyUpper(String) - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByDictionary
setLevel(int) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Constant
setList(List<ObjectFilter>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.combine.ObjectFilterCombine: A list of other filters from which the sub-classes implement filtering behaviour.
setList(List<ColorProvider>) - Method in class org.anchoranalysis.plugin.image.bean.color.provider.Concatenate: A list of ColorProvider to be concatenated.
setList(List<ObjectCollectionProvider>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Concatenate: List of ObjectCollectionProviders whose ObjectCollections will be concatenated.
setList(List<BinarySegmentation>) - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.Sequence: A list of binary-segmentations that are applied successively (the output of the predecessor becomes the input of the sucecssor)
setList(List<CalculateLevel>) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelListBase: List of CalculateLevel objects to be used in the calculation.
setList(List<ProviderAsStack>) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.Concatenate
setListAdditionalChannelProviders(List<ChannelProvider>) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreObjects: Additional channels to be included in the EnergyStack for feature calculation.
setMask(Provider<Mask>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.ConnectedComponentsFromMask
setMask(Provider<Mask>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.mask.FromMask
setMask(Provider<Mask>) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.FromChannelOrMask: A mask that is provided to the stack.
setMask(MaskProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.mask.FromMaskBase: The MaskProvider used to create the binary mask.
setMask(MaskProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.mask.UnaryWithMaskBase: The MaskProvider used to create the binary mask.
setMask(MaskProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
setMask(MaskProvider) - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.FromChannel: An optional mask provider to restrict the histogram creation to specific areas.
setMask(MaskProvider) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.segment.SegmentChannel: An optional mask which restricts the algorithm to only parts of the channel where the mask has an on voxel
setMask(MaskProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.mask.AndObjectsWithMasks
setMask(MaskProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentChannel: Optional mask to restrict the segmentation area.
setMask(MaskProvider) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredMask
setMaskElse(MaskProvider) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfPredicateBase: Returned instead of mask if the predicate is not satisfied.
setMatcher(ObjectMatcher) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.collective.RelationWithMatches
setMatcher(ObjectMatcher) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.feature.ObjectWithMaximumFeatureFromEachMatchedCollection
setMatcher(ObjectMatcher) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.Match: The ObjectMatcher used to find matches in the input object collection.
setMax(int) - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByMinMaxValue
setMax(int) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.ClampHistogramMax
setMaxDistance(UnitValueDistance) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithOptionalDistanceConstraint: An optional maximum distance between objects that can be merged.
setMaxSize(long) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Mser
setMaxVar(double) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Mser
setMaxX(int) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Box: Maximum X coordinate inclusive.
setMaxY(int) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Box: Maximum Y coordinate inclusive.
setMaxZ(int) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Box: Maximum Z coordinate inclusive.
setMerge(boolean) - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.CutBelowThreshold
setMin(int) - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByMinMaxValue
setMinConfidence(double) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ThresholdConfidence: The minimum confidence of an element for its object-mask to be initially included for consideration (before merging).
setMinDiversity(double) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Mser
setMinimaImposition(MinimaImposition) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.ImposeMinima
setMinIntensityValue(int) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.MorphologicalOperatorBase: Minimum intensity value for voxels to be considered in the operation.
setMinNumberObjects(int) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.collective.DiscardOutliers
setMinNumberVoxels(int) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.split.SplitIntoSquares: Only includes squares that have at least this number of voxels.
setMinNumberVoxels(int) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.ConnectedComponentsFromBinarySegmentation
setMinNumberVoxels(int) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ThresholdConfidence: The minimum number of voxels that must exist in a connected-component to be included.
setMinRatio(double) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.collective.DiscardOutliers
setMinResolution(double) - Method in class org.anchoranalysis.plugin.image.bean.scale.MinimumXYResolution: The minimum resolution to achieve in meters.
setMinSize(long) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Mser
setMinVolume(UnitValueExtent) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.ConnectedComponentsFromMask
setMinX(int) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Box: Minimum X coordinate inclusive.
setMinY(int) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Box: Minimum Y coordinate inclusive.
setMinZ(int) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Box: Minimum Z coordinate inclusive.
setMultipleOf(int) - Method in class org.anchoranalysis.plugin.image.bean.scale.FitTo: The eventual width and height of the image must be a multiple of this number.
setNumberDilations(int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectIndependently
setObjectMatcher(ObjectMatcher) - Method in class org.anchoranalysis.plugin.image.bean.object.match.Bridge: Used to match each intermediary-object to a final-object
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectBase: The objects for whom a level is calculated.
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.UnaryWithObjectsBase: The provider for the collection of objects to be used in channel creation.
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.color.provider.GenerateToMatchObjects
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromObjects
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntersectsWith
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.match.Always
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.match.Intersection: Provider for the objects to intersect with the source objects.
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Permute
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredObjects: Objects to draw on a background
setObjects1(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeTwoCollectionsItemwise: First collection with items to be merged
setObjects2(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeTwoCollectionsItemwise: Second collection with items to be merged
setObjectsBlue(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeColoredObjects
setObjectsContainer(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithContainerBase: Optional provider for a container of objects.
setObjectsElse(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.ReferenceOrElse
setObjectsGreater(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.GreaterIntersectionWith
setObjectsGreen(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeColoredObjects
setObjectsGrouped(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.FilterByGroup: Provides the ObjectCollection used for grouping the objects to be filtered.
setObjectsLesser(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.GreaterIntersectionWith
setObjectsRed(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeColoredObjects
setObjectsSeeds(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentChannel: Optional provider for seed objects to guide the segmentation.
setObjectsSeeds(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentWithSeeds
setObjectsSource(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromIntersectingObjects
setObjectsSource(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentWithSeeds
setObjectsSplitBy(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.split.SplitByObjects: Provider for the collection of objects used to split the input objects.
setObjectsTarget(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromIntersectingObjects
setOfConnectedComponentIDs() - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels: Gets a set of all connected component IDs in the voxels.
setOutline(boolean) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase: If true, an outline is drawn around the entries.
setOutlineAtBoundary(boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.ExteriorContour
setOutlineWidth(int) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.AtScale
setOutlineWidth(int) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase: The width of the outline (only relevant if outline==true).
setOutlineWidth(int) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize: The width of the outline.
setOutputShort(boolean) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientBase: If true, outputs a short channel, otherwise byte channel.
setOverlappingObjects(boolean) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize: Whether objects may overlap or not when unscaled.
setPermuteProperty(PermuteProperty<?>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Permute
setPoint(Point3i, int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels: Sets the encoded value for a specific point.
setPointConnectedComponentID(Point3i, int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels: Sets the connected component ID for a specific point.
setPointDirection(Point3i, int, int, int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels: Sets the direction for a specific point.
setPreserveAspectRatio(boolean) - Method in class org.anchoranalysis.plugin.image.bean.scale.FitTo: If true, the aspect-ratio is preserved between width and height.
setPreserveAspectRatio(boolean) - Method in class org.anchoranalysis.plugin.image.bean.scale.ToDimensions: If true, the ratio between x and y is kept constant when scaling.
setQuantile(double) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.QuantileStretch
setQuantile(double) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Quantile
setQuantile(double) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.collective.DiscardOutliers
setQuantileLower(double) - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ToByteUpperLowerQuantileIntensity: The lower quantile value for intensity scaling.
setQuantileUpper(double) - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ToByteUpperLowerQuantileIntensity: The upper quantile value for intensity scaling.
setReceive(MaskProvider) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.combine.CombineBase: The MaskProvider for the second mask to be combined.
setRed(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeChannels: Provider for the red channel.
setRejectIterationIfAllLow(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Erode
setRejectIterationIfDisconnected(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Erode
setRelation(RelationBean) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterRelation: The relation to be used in the filter predicate.
setRelation(RelationBean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergePairs: Relation to threshold
setReplaceWithMidpoint(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeGreedyToIncreaseObjectFeature
setRequireBBoxNeighbors(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithFeature: Requires for any potential merge that the bounding-boxes of the two objects must intersect or touch.
setRequireTouching(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithFeature: Requires the object-masks to touch.
setRestrictTo(MaskProvider) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.Invert: If set, the inversion only occurs on a particular region of the mask, as determined by this mask
setRgb(boolean) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.FromChannelOrMask: If true, the output contains three channels (the input and two duplicates) instead of one.
setScaleCalculator(ScaleCalculator) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.ScaleXY
setScaleCalculator(ScaleCalculator) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.ScaleXY: Determines how much to scale by.
setScaleCalculator(ScaleCalculator) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Scale
setScaleCalculator(ScaleCalculator) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.AtScale
setScaleCalculator(ScaleCalculator) - Method in class org.anchoranalysis.plugin.image.bean.scale.Invert: The delegate ScaleCalculator whose calculation will be inverted.
setScaleFactor(double) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientBase: Scale factor applied to the gradient values.
setScaleLower(double) - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByDictionary
setScaleLower(double) - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ToByteUpperLowerQuantileIntensity: Sets the min by multiplying the quantileLower by this constant.
setScaleUpper(double) - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByDictionary
setScaleUpper(double) - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ToByteUpperLowerQuantileIntensity: Sets the max by multiplying the quantileUpper by this constant.
setScore(VoxelScore) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
setSegment(BinarySegmentation) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.segment.SegmentChannel: Segmentation algorithm
setSegment(BinarySegmentation) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.ConnectedComponentsFromBinarySegmentation
setSegment(SegmentChannelIntoObjects) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentChannel: The segmentation algorithm to use.
setSegment(SegmentChannelIntoObjects) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentChannelByObject
setSegment(SegmentChannelIntoObjects) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentWithSeeds
setSegment(SegmentStackIntoObjectsPooled<T>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentStack: The segmentation procedure.
setSegmentStack(BinarySegmentation) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.SegmentOnMaximumIntensityAndExpandInZ
setSigma(double) - Method in class org.anchoranalysis.plugin.image.bean.blur.BlurStrategy: The sigma value for the blur operation.
setSigmaInMeters(boolean) - Method in class org.anchoranalysis.plugin.image.bean.blur.BlurStrategy: If true, treats sigma as if it's in meters (physical units).
setSize(SizeXY) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize: Size of all created thumbnails
setSize(SizeXY) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.stack.ScaleToSize
setSizeXY(SizeXY) - Method in class org.anchoranalysis.plugin.image.bean.dimensions.provider.SpecifyDimensions: Length of X and Y dimensions.
setSizeZ(int) - Method in class org.anchoranalysis.plugin.image.bean.dimensions.provider.SpecifyDimensions: Length of Z dimension.
setSlice(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.slice.RepeatSlice
setSliceIndex(int) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.slice.RepeatSlice: Which slice to use from mask
setSlicesSeparately(boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.FitBoxToOnVoxels
setSquareSize(int) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.split.SplitIntoSquares
setStack(ProviderAsStack) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromStack: Provides a stack.
setStack(ProviderAsStack) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentStack: The stack to segment
setStackID(String) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfStackExists
setStackProviderID(String) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromStack: Specifies the ID of an existing stack.
setStackProviderID(String) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromStackChannel: The identifier of the stack provider to retrieve the stack from.
setStrategy(BlurStrategy) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.Blur
setSubtractFromMaskOnly(boolean) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.SubtractMean: Whether to subtract the mean only from voxels within the mask.
setSuppress3D(boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.MorphologicalOperatorBase: Whether to suppress 3D operations and only perform 2D operations.
setSuppressOutlineZ(boolean) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase: If true, the outline is suppressed in the z-dimension i.e.
setSuppressZ(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithOptionalDistanceConstraint: If true, suppresses the Z-dimension when calculating distances between objects.
setTargetSize(SizeXY) - Method in class org.anchoranalysis.plugin.image.bean.scale.FitTo: The target size.
setThreshold(double) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedFeature
setThreshold(int) - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.CutBelowThreshold
setThreshold(int) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelRelativeToThreshold: Threshold value to compare against when deciding whether to use the alternative calculation.
setThreshold(UnitValueDistance) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntensityGreaterEqualThan
setThreshold(UnitValueVolume) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedVolume
setThresholder(Thresholder) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.segment.Threshold: The thresholder that will convert a channel into a binary-channel
setThresholdNumberObjectsGlobal(int) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ThresholdConfidence: When the number of objects is greater or equal than this, they are reduced globally, without separation.
setUseZ(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.RemoveTouchingBorder
setValue(double) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignValue
setValue(double) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.UnaryWithValueBase: The scalar value to be used in channel creation.
setValue(double) - Method in class org.anchoranalysis.plugin.image.bean.scale.ConstantScaleFactor: The constant floating-point value to scale each dimension by.
setValue(int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.CreateNew
setValue(int) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.EmptyHistogramConstant
setValue(String) - Method in class org.anchoranalysis.plugin.image.bean.dictionary.DictionaryCondition: The value the key should have in the dictionary, in order for the condition to be fulfilled.
setValue(String) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.IfParamEqual
setValueNoObject(int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreObjects: The value assigned to voxels that do not belong to any object.
setWeightBackground(double) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.OtsuWeighted
setWeightForeground(double) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.OtsuWeighted
setWhenEqual(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.IfParamEqual
setWhenNotEqual(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.IfParamEqual
shouldOverwriteVoxelWithConstant(int, int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.ArithmeticWithConstantConditionallyWriteBase: Determines whether to overwrite the current voxel value with the constant.
shouldOverwriteVoxelWithConstant(int, int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.MaxWithConstant
shouldOverwriteVoxelWithConstant(int, int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.MinWithConstant
SliceAt - Class in org.anchoranalysis.plugin.image.bean.object.provider.slice: Extracts a specific slice from a collection of 3D objects.
SliceAt() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.slice.SliceAt
SliceThresholder - Class in org.anchoranalysis.plugin.image.segment.thresholder.slice: Segmenting a z-Stack slice-by-slice.
SliceThresholder(BinaryValuesByte) - Constructor for class org.anchoranalysis.plugin.image.segment.thresholder.slice.SliceThresholder: Creates a new SliceThresholder instance.
SliceThresholderMask - Class in org.anchoranalysis.plugin.image.segment.thresholder.slice: A slice thresholder that applies thresholding within a mask region.
SliceThresholderMask(boolean, ObjectMask, BinaryValuesByte) - Constructor for class org.anchoranalysis.plugin.image.segment.thresholder.slice.SliceThresholderMask: Creates a new SliceThresholderMask.
SliceThresholderWithoutMask - Class in org.anchoranalysis.plugin.image.segment.thresholder.slice: A slice thresholder that applies thresholding to the entire image without using a mask.
SliceThresholderWithoutMask(BinaryValuesByte) - Constructor for class org.anchoranalysis.plugin.image.segment.thresholder.slice.SliceThresholderWithoutMask: Creates a new SliceThresholderWithoutMask.
Sobel - Class in org.anchoranalysis.plugin.image.bean.channel.provider.gradient: 3x3 Sobel Filter
Sobel() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.Sobel
SortByFeature - Class in org.anchoranalysis.plugin.image.bean.object.provider.feature: Creates a new object-collection with objects sorted by a derived feature-value (in ascending order)
SortByFeature() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.feature.SortByFeature
SpecifyDimensions - Class in org.anchoranalysis.plugin.image.bean.dimensions.provider: Specifies dimensions explicitly via bean properties.
SpecifyDimensions() - Constructor for class org.anchoranalysis.plugin.image.bean.dimensions.provider.SpecifyDimensions
SpecifyDimensions(int, int) - Constructor for class org.anchoranalysis.plugin.image.bean.dimensions.provider.SpecifyDimensions: Create with specific lengths for X and Y dimensions.
SpecifyDimensions(SizeXY) - Constructor for class org.anchoranalysis.plugin.image.bean.dimensions.provider.SpecifyDimensions: Create with specific lengths for X and Y dimensions.
SplitByObjects - Class in org.anchoranalysis.plugin.image.bean.object.provider.split: Splits objects in a collection based on intersections with another set of objects.
SplitByObjects() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.split.SplitByObjects
SplitIntoSquares - Class in org.anchoranalysis.plugin.image.bean.object.provider.split: Splits objects into sub-objects by cutting by an orthogonal square lattice (like a chessboard).
SplitIntoSquares() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.split.SplitIntoSquares
stack(String) - Static method in class org.anchoranalysis.plugin.image.provider.ReferenceFactory: Creates a reference to a stack.
StandardDeviationProjection<T> - Class in org.anchoranalysis.plugin.image.bean.channel.aggregator: Projection of the standard-deviation of voxels values across all inputs.
StandardDeviationProjection() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.aggregator.StandardDeviationProjection
start() - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.stack.ScaleToSize
start() - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.stack.ThumbnailFromStack: Initializes the thumbnail creation process.
start(Optional<Dimensions>, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.collective.DiscardOutliers
start(Optional<Dimensions>, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.collective.RelationWithMatches
start(Optional<Dimensions>, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.GreaterIntersectionWith
start(Optional<Dimensions>, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntensityGreaterEqualThan
start(Optional<Dimensions>, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntersectsWith
start(Optional<Dimensions>, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedFeature
start(Optional<Dimensions>, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedVolume
start(Optional<Dimensions>, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterPredicate: Performs any necessary initialization before filtering begins.
start(Optional<Dimensions>, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterRelation
start(ObjectCollection, StreamableCollection<BoundingBox>, Optional<Stack>, ExecutionTimeRecorder) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize
start(ObjectCollection, StreamableCollection<BoundingBox>, Optional<Stack>, ExecutionTimeRecorder) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.ThumbnailFromObjects: Initializes a batch to create thumbnails.
Steepest - Class in org.anchoranalysis.plugin.image.segment.watershed.encoding: Calculates the steepest descent direction for voxels in a watershed segmentation.
Steepest(SlidingBuffer<?>, WatershedEncoding, boolean, boolean, Optional<ObjectMask>) - Constructor for class org.anchoranalysis.plugin.image.segment.watershed.encoding.Steepest: Creates a Steepest instance for a specific buffer.
steepestDescent(Point3i, int, int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.Steepest: Calculates the steepest descent direction for a given point.
streamObjectWithProperties() - Method in class org.anchoranalysis.plugin.image.object.ColoredObjectCollection: Creates a stream of ObjectWithProperties derived from the collection.
SubtractFromConstant - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic: Subtracts each voxel value in a channel from a constant value.
SubtractFromConstant() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.SubtractFromConstant
SubtractMean - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic: Subtracts the mean intensity (of the entire channel or a masked portion thereof) from every voxel.
SubtractMean() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.SubtractMean
SubtractTwoChannels - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic: Creates a new channel by subtracting corresponding voxels of the second channel from the first channel.
SubtractTwoChannels() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.SubtractTwoChannels: Constructs a new SubtractTwoChannels instance.

T

ThreeChannels - Class in org.anchoranalysis.plugin.image.bean.stack.provider.color: Provides a Stack by combining up to three channels (red, green, blue) into an RGB image.
ThreeChannels() - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeChannels
ThreeColoredObjects - Class in org.anchoranalysis.plugin.image.bean.stack.provider.color: Colors three collections of objects in RED, GREEN, BLUE channels on top of a background.
ThreeColoredObjects() - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeColoredObjects
Threshold - Class in org.anchoranalysis.plugin.image.bean.mask.provider.segment: Thresholds a channel to produce a mask, reusing (and modifying) the input-buffers of the channel if possible.
Threshold() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.segment.Threshold
ThresholdAgainstChannel - Class in org.anchoranalysis.plugin.image.bean.segment.binary: Thresholds each voxels by comparing against another channel that has per-voxel thresholds
ThresholdAgainstChannel() - Constructor for class org.anchoranalysis.plugin.image.bean.segment.binary.ThresholdAgainstChannel
ThresholdConfidence - Class in org.anchoranalysis.plugin.image.bean.object.segment.reduce: Combines object-masks by projecting the maximum confidence-level for each voxel and thresholding.
ThresholdConfidence() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ThresholdConfidence
ThresholdConfidence(double) - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ThresholdConfidence: Creates with a minimum-confidence level.
ThresholdedFeature - Class in org.anchoranalysis.plugin.image.bean.object.filter.independent: Only keeps objects whose feature-value satisfies a condition relative to a threshold.
ThresholdedFeature() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedFeature
ThresholdedVolume - Class in org.anchoranalysis.plugin.image.bean.object.filter.independent: Only keeps objects whose feature-value satisfies a condition relative to a threshold.
ThresholdedVolume() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedVolume
ThumbnailBatch<T> - Interface in org.anchoranalysis.plugin.image.thumbnail: Creates thumbnails for a particular batch of objects that can be calibrated to have similar properties (identical scale etc.)
thumbnailFor(Stack) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.stack.ScaleToSize
thumbnailFor(Stack) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.stack.ThumbnailFromStack: Creates a thumbnail for a stack.
thumbnailFor(T) - Method in interface org.anchoranalysis.plugin.image.thumbnail.ThumbnailBatch: Creates a thumbnail for an element in the batch.
ThumbnailFromObjects - Class in org.anchoranalysis.plugin.image.bean.thumbnail.object: Creates a thumbnail of one or more objects on a stack by drawing the outline of the objects.
ThumbnailFromObjects() - Constructor for class org.anchoranalysis.plugin.image.bean.thumbnail.object.ThumbnailFromObjects
ThumbnailFromStack - Class in org.anchoranalysis.plugin.image.bean.thumbnail.stack: Creates a thumbnail from a stack.
ThumbnailFromStack() - Constructor for class org.anchoranalysis.plugin.image.bean.thumbnail.stack.ThumbnailFromStack
ToByte - Class in org.anchoranalysis.plugin.image.bean.channel.convert: Converts a channel to unsigned byte format without any scaling.
ToByte() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.convert.ToByte
ToByteUpperLowerQuantileIntensity - Class in org.anchoranalysis.plugin.image.bean.channel.convert: Converts a channel to unsigned byte format using upper and lower quantile intensities from a histogram.
ToByteUpperLowerQuantileIntensity() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.convert.ToByteUpperLowerQuantileIntensity
ToDimensions - Class in org.anchoranalysis.plugin.image.bean.scale: Calculates a scaling-factor to make the source image have identical dimensions as dimensionsTarget.
ToDimensions() - Constructor for class org.anchoranalysis.plugin.image.bean.scale.ToDimensions
ToDimensions(int, int) - Constructor for class org.anchoranalysis.plugin.image.bean.scale.ToDimensions: Create with specific lengths for X and Y dimensions.
ToDimensions(int, int, boolean) - Constructor for class org.anchoranalysis.plugin.image.bean.scale.ToDimensions: Create with specific lengths for X and Y dimensions and preserveAspectRatio.
ToDimensions(DimensionsProvider) - Constructor for class org.anchoranalysis.plugin.image.bean.scale.ToDimensions: Create with specific dimensions.
ToDimensions(DimensionsProvider, boolean) - Constructor for class org.anchoranalysis.plugin.image.bean.scale.ToDimensions: Create with specific dimensions and preserveAspectRatio.
toString() - Method in class org.anchoranalysis.plugin.image.object.ColoredObject
toString() - Method in class org.anchoranalysis.plugin.image.object.merge.ObjectVertex
ToSuggested - Class in org.anchoranalysis.plugin.image.bean.scale: Scales to the suggested-size if one is provided, otherwise calls fallback.
ToSuggested() - Constructor for class org.anchoranalysis.plugin.image.bean.scale.ToSuggested
ToSuggested(ScaleCalculator) - Constructor for class org.anchoranalysis.plugin.image.bean.scale.ToSuggested: Creates a new ToSuggested instance.
TwoVoxelMappingBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider: Takes the two channels and creates a NEW third channel whose pixels are a function of the two channels
TwoVoxelMappingBase(IntBinaryOperator) - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.TwoVoxelMappingBase: Creates a new TwoVoxelMappingBase instance.

U

UnaryWithChannelBase - Class in org.anchoranalysis.plugin.image.bean.object.provider: Base class for ObjectCollectionProviderUnary that also requires a Channel.
UnaryWithChannelBase() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.UnaryWithChannelBase
UnaryWithMaskBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider.mask: A base class for a ChannelProviderUnary which also uses a binary mask.
UnaryWithMaskBase() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.mask.UnaryWithMaskBase
UnaryWithObjectsBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider: An abstract base class for creating a channel from an existing channel and a collection of objects.
UnaryWithObjectsBase() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.UnaryWithObjectsBase
UnaryWithValueBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider: A ChannelProviderUnary which has a scalar value field.
UnaryWithValueBase() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.UnaryWithValueBase
unitConvertOptional() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeBase: Gets an optional UnitConverter based on the image resolution.
UpdatableBeforeCondition - Interface in org.anchoranalysis.plugin.image.object.merge.condition: A two-stage process for checking if two ObjectMasks should be merged.
updateSourceObject(ObjectMask, Optional<UnitConverter>) - Method in class org.anchoranalysis.plugin.image.object.merge.condition.AndCondition
updateSourceObject(ObjectMask, Optional<UnitConverter>) - Method in class org.anchoranalysis.plugin.image.object.merge.condition.NeighborhoodCondition
updateSourceObject(ObjectMask, Optional<UnitConverter>) - Method in interface org.anchoranalysis.plugin.image.object.merge.condition.UpdatableBeforeCondition: Updates the source object and performs any necessary pre-computations.
updateSourceObject(ObjectMask, Optional<UnitConverter>) - Method in class org.anchoranalysis.plugin.image.object.merge.condition.WrapAsUpdatable
useElseInstead(int, int) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelRelativeToThreshold: Determines whether to use the alternative calculation method.
useElseInstead(int, int) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.IfGreaterThan
useElseInstead(int, int) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.IfLessThan

V

verticesAsObjects() - Method in class org.anchoranalysis.plugin.image.object.merge.MergeGraph: Retrieves all vertices in the graph as an ObjectCollection.
voxels() - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels: The voxels containing encoded information.

W

WatershedEncoding - Class in org.anchoranalysis.plugin.image.segment.watershed.encoding: Encodes watershed-related information in an integer range.
WatershedEncoding() - Constructor for class org.anchoranalysis.plugin.image.segment.watershed.encoding.WatershedEncoding
WatershedYeong - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong: A 'rainfall' watershed algorithm
WatershedYeong() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong.WatershedYeong
withCalculateLevel(Histogram, CalculateLevel) - Static method in class org.anchoranalysis.plugin.image.intensity.HistogramThresholder: Retains the portion of the histogram greater or equal to the calculated-level.
WithChannelBase - Class in org.anchoranalysis.plugin.image.bean.object.provider: Base class for ObjectCollectionProviders that create objects from a Channel.
WithChannelBase() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.WithChannelBase
WithContainerBase - Class in org.anchoranalysis.plugin.image.bean.object.provider: Base class for ObjectCollectionProviderUnary that take an optional objectsContainer bean-field.
WithContainerBase() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.WithContainerBase
WithDimensionsBase - Class in org.anchoranalysis.plugin.image.bean.object.provider: Base class for ObjectCollectionProviderUnary classes that require dimensions to be specified.
WithDimensionsBase() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.WithDimensionsBase
WithOptionalDimensionsBase - Class in org.anchoranalysis.plugin.image.bean.object.provider: Base class for ObjectCollectionProviderUnary classes that offer an optional means to specify dimensions.
WithOptionalDimensionsBase() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.WithOptionalDimensionsBase
WrapAsUpdatable - Class in org.anchoranalysis.plugin.image.object.merge.condition: Wraps a BeforeCondition as an UpdatableBefoerCondition
WrapAsUpdatable(BeforeCondition) - Constructor for class org.anchoranalysis.plugin.image.object.merge.condition.WrapAsUpdatable
writeLevelsForObjects(Channel, ObjectCollection, Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectBase: Creates a channel with the levels for a set of objects.
writeLevelsForObjects(Channel, ObjectCollection, Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectIndependently
writeLevelsForObjects(Channel, ObjectCollection, Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectNeighbors
writeOffByte(int, UnsignedByteBuffer) - Method in class org.anchoranalysis.plugin.image.segment.thresholder.slice.SliceThresholder: Writes the 'off' binary value to the output buffer at the specified offset.
writeThresholdedByte(int, UnsignedByteBuffer, VoxelBuffer<?>, VoxelBuffer<?>) - Method in class org.anchoranalysis.plugin.image.segment.thresholder.slice.SliceThresholder: Writes a thresholded value to the output buffer based on the input and threshold buffers.

X

xFromChainCode(int) - Static method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.ChainCodesDirection: Extracts the x-component from a chain code.
Xor - Class in org.anchoranalysis.plugin.image.bean.mask.provider.combine: Outputs the logical operation xor (exclusive or) voxelwise on both masks, modifying {mask} with the result.
Xor() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.combine.Xor

Y

yFromChainCode(int) - Static method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.ChainCodesDirection: Extracts the y-component from a chain code.

Z

ZeroOutsideMask - Class in org.anchoranalysis.plugin.image.bean.channel.provider.mask: Set pixels NOT IN the mask to 0, but keep pixels IN the mask identical.
ZeroOutsideMask() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.mask.ZeroOutsideMask
zFromChainCode(int) - Static method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.ChainCodesDirection: Extracts the z-component from a chain code.

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