Uses of Class
org.anchoranalysis.image.voxel.object.ObjectMask

Packages that use ObjectMask

Package	Description
org.anchoranalysis.annotation.io.assignment	A pairing of objects from two collections (bipartite matching).
org.anchoranalysis.annotation.io.assignment.generator	Generates output images to illustrate a Assignment between annotations.
org.anchoranalysis.image.bean.segment.binary	Base classes to perform binary-segmentation.
org.anchoranalysis.image.bean.segment.object	Base classes to segment a channel into objects.
org.anchoranalysis.image.core.channel	The Channel core data-class and related operations and converters.
org.anchoranalysis.image.core.contour	Finds outline voxels, the pixels on the contour/edge of the object.
org.anchoranalysis.image.core.mask	An image with only two permissible states.
org.anchoranalysis.image.core.merge	Merges two or more entities.
org.anchoranalysis.image.core.object	The key data entity org.anchoranalysis.image.voxel.object and related-classes and operations.
org.anchoranalysis.image.core.object.label	Labelling elements (object-masks or similar) with unique successive integers in a channel.
org.anchoranalysis.image.core.object.properties	An ObjectCollection with associated key-value pairs.
org.anchoranalysis.image.core.object.scale	Scaling object-collections, or lists of elements with object-representations.
org.anchoranalysis.image.core.points	Operations that extract points from image data entities or vice versa.
org.anchoranalysis.image.core.stack	Defines the key data object, Stack, and related classes.
org.anchoranalysis.image.feature.input	Image-related implementations of FeatureInput.
org.anchoranalysis.image.inference.bean.reduce	Beans to reduce the number of results that are returned from inference, by removing overlaping entities etc.
org.anchoranalysis.image.inference.bean.segment.instance	Instance-segmentation of a Stack.
org.anchoranalysis.image.inference.segment	Non-beans pertaining to segmentation of images via model inference.
org.anchoranalysis.image.io.object.output.mask	Writing an ObjectCollection to the filesystem as multiple binary singled-channeled images.
org.anchoranalysis.image.io.stack.output.box	Base classes for generators that ultimately write only a bounding-box portion of a Stack to the filesystem.
org.anchoranalysis.image.voxel	Data-structures to store and manipulate image raster-data or voxels.
org.anchoranalysis.image.voxel.arithmetic	Arithmetic operations for Voxels.
org.anchoranalysis.image.voxel.assigner	Assigns values to some or all voxels.
org.anchoranalysis.image.voxel.extracter	Methods to read/copy/duplicate portions of voxels.
org.anchoranalysis.image.voxel.extracter.predicate	Methods to find or count voxels that satisfy a predicate.
org.anchoranalysis.image.voxel.iterator	Utilities to iterate over voxel-locations in images and sub-regions of images.
org.anchoranalysis.image.voxel.iterator.intersecting	Like org.anchoranalysis.image.voxel.iterator but refers to iterators that operation over the intersecting regions of two entities.
org.anchoranalysis.image.voxel.iterator.neighbor	Iterating over a point's neighboring voxels.
org.anchoranalysis.image.voxel.kernel.count	Kernels to count the number of voxels that are equal to a particular value.
org.anchoranalysis.image.voxel.neighborhood	A region in proximity to a voxel, encompassing this voxel as well as others.
org.anchoranalysis.image.voxel.object	The fundamental data class that is an ObjectMask and related structures.
org.anchoranalysis.image.voxel.object.morphological	Morphological operations applied to ObjectMasks.
org.anchoranalysis.image.voxel.thresholder	Thresholding operations on voxels.
org.anchoranalysis.mpp.mark	Non-bean classes related to Marks.
org.anchoranalysis.overlay.object	An implementation of an Overlay that draws an ObjectMask on an image.
org.anchoranalysis.plugin.annotation.bean.comparison	Task to compare a set of annotations to a segmentation or another set of annotations.
org.anchoranalysis.plugin.annotation.bean.comparison.assigner	Pairs annotations from two different sets, creating an assignment of some type.
org.anchoranalysis.plugin.annotation.counter	Utility classes for counting images incrementally.
org.anchoranalysis.plugin.fiji.bean.channel.grayscalereconstruction	Morphological grayscale-reconstruction algorithm.
org.anchoranalysis.plugin.image.bean.object.filter	Implementations of ObjectFilter.
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.independent	Implementations of ObjectFilter that independently assess each element in a collection.
org.anchoranalysis.plugin.image.bean.object.provider.filter	Implementations of ObjectCollectionProvider that filter objects.
org.anchoranalysis.plugin.image.bean.object.provider.morphological	Implementations of ObjectCollectionProvider involving morphological operations.
org.anchoranalysis.plugin.image.bean.object.segment.channel	Implementations of SegmentChannelIntoObjects.
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	Grayscale reconstruction to support the Watershed transformation.
org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong	Implementation of a Watershed transformation based on Yeong et al. 2009.
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.segment.binary	Implementations of BinarySegmentation.
org.anchoranalysis.plugin.image.feature.bean.object.pair.touching	Features that calculate how many other objects an ObjectMask directly neighbors.
org.anchoranalysis.plugin.image.feature.bean.object.single	Implementations of FeatureSingleObject.
org.anchoranalysis.plugin.image.feature.bean.object.single.border	Implementations of FeatureSingleObject that determine if an object lies at the border of an image.
org.anchoranalysis.plugin.image.feature.bean.object.single.energy	Implementations of FeatureSingleObject that reference a particular Channel in the associated EnergyStack.
org.anchoranalysis.plugin.image.feature.bean.object.single.intensity	Implementations of FeatureSingleObject that measure an object's intensity on a corresponding Channel.
org.anchoranalysis.plugin.image.feature.bean.object.single.morphological	Implementations of FeatureSingleObject that implement morphological operations.
org.anchoranalysis.plugin.image.feature.object.calculation.single	Implementations of CalculationPart that that process a single ObjectMask.
org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological	Implementations of CalculationPart that that process a single ObjectMask - with morphological operations.
org.anchoranalysis.plugin.image.intensity	Non-bean for operations or calculations relating to intensity.
org.anchoranalysis.plugin.image.intensity.level	Non-beans for calculating a thresholding level from itensity values.
org.anchoranalysis.plugin.image.object	Non-beans pertaining to ObjectMasks.
org.anchoranalysis.plugin.image.object.merge	Merging ObjectMasks.
org.anchoranalysis.plugin.image.object.merge.condition	Conditions for merging ObjectMasks.
org.anchoranalysis.plugin.image.object.merge.priority	Assigning priority when merging ObjectMasks.
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	Encoding voxels in a watershed-transformation implementation.
org.anchoranalysis.plugin.imagej.bean.object.segment	Implementations of ObjectCollectionProvider that call ImageJ to perform segmentation.
org.anchoranalysis.plugin.opencv	Plugins that call OpenCV.
org.anchoranalysis.plugin.opencv.convert	Conversion to/from OpenCV data-structures.
org.anchoranalysis.plugin.points.calculate.ellipse	CalculationPart related to fitting ellipses to points by least-squares.
org.anchoranalysis.plugin.points.calculate.ellipsoid	CalculationPart related to fitting ellipsoids to points by least-squares.
org.anchoranalysis.plugin.points.convexhull	Non-bean convex hull operations.
org.anchoranalysis.test.feature.plugins.objects	Fixtures for creating object-masks and related feature-inputs.
org.anchoranalysis.test.image	Testing utilities and fixtures with no greater downstream dependency than anchor-image-io or anchor-io-bioformats or anchor-imagej.
org.anchoranalysis.test.image.object	Fixtures for creating object-masks.

Uses of ObjectMask in org.anchoranalysis.annotation.io.assignment

Methods in org.anchoranalysis.annotation.io.assignment that return types with arguments of type ObjectMask

Modifier and Type	Method	Description
CostMatrix<ObjectMask>	AssignOverlappingObjects.getCosts()	A matrix linking the overlap between each ObjectMask to each other, respectively as rows and columns.
List<ObjectMask>	OverlappingObjects.getLeftUnassigned()	The unassigned objects in the left set.
List<ObjectMask>	OverlappingObjects.getRightUnassigned()	The unassigned objects in the right set.
List<ObjectMask>	ObjectVoxelIntersection.paired(boolean left)
List<ObjectMask>	OverlappingObjects.paired(boolean left)
List<ObjectMask>	ObjectVoxelIntersection.unassigned(boolean left)
List<ObjectMask>	OverlappingObjects.unassigned(boolean left)

Methods in org.anchoranalysis.annotation.io.assignment with parameters of type ObjectMask

Modifier and Type	Method	Description
void	OverlappingObjects.addAssignedPair(ObjectMask object1, ObjectMask object2, double overlapRatio)	Adds an assigned pair of objects with a particular overlap-ratio.
void	OverlappingObjects.addUnassignedLeft(ObjectMask object)	Add an unassigned object to the left set.
void	OverlappingObjects.addUnassignedRight(ObjectMask object)	Add an unassigned object to the right set.

Constructors in org.anchoranalysis.annotation.io.assignment with parameters of type ObjectMask

Modifier	Constructor	Description
	ObjectVoxelIntersection(ObjectMask left, ObjectMask right)	Determines a voxel-assignment between two objects.

Uses of ObjectMask in org.anchoranalysis.annotation.io.assignment.generator

Method parameters in org.anchoranalysis.annotation.io.assignment.generator with type arguments of type ObjectMask

Modifier and Type	Method	Description
Stack	DrawColoredObjects.createObjectsImage(Assignment<ObjectMask> assignment, boolean left, AssignmentColorPool colorPool)	Creates an image with the objects colored, as indicated in the class description.
Stack	AssignmentGenerator.transform(Assignment<ObjectMask> element)

Uses of ObjectMask in org.anchoranalysis.image.bean.segment.binary

Method parameters in org.anchoranalysis.image.bean.segment.binary with type arguments of type ObjectMask

Modifier and Type	Method	Description
abstract BinaryVoxels<UnsignedByteBuffer>	BinarySegmentation.segment(VoxelsUntyped voxels, BinarySegmentationParameters parameters, Optional<ObjectMask> objectMask)	Performs a segmentation on voxels so that each voxel has an on or off state after the operation.
BinaryVoxels<UnsignedByteBuffer>	BinarySegmentationReference.segment(VoxelsUntyped voxels, BinarySegmentationParameters parameters, Optional<ObjectMask> objectMask)
BinaryVoxels<UnsignedByteBuffer>	BinarySegmentationThreshold.segment(VoxelsUntyped voxels, BinarySegmentationParameters parameters, Optional<ObjectMask> objectMask)
BinaryVoxels<UnsignedByteBuffer>	BinarySegmentationUnary.segment(VoxelsUntyped voxels, BinarySegmentationParameters parameters, Optional<ObjectMask> objectMask)
protected abstract BinaryVoxels<UnsignedByteBuffer>	BinarySegmentationUnary.segmentFromExistingSegmentation(VoxelsUntyped voxels, BinarySegmentationParameters parameters, Optional<ObjectMask> objectMask, BinarySegmentation segment)	Performs a binary-segmentation, in a similar manner to BinarySegmentation.segment(org.anchoranalysis.image.voxel.VoxelsUntyped, org.anchoranalysis.image.bean.nonbean.segment.BinarySegmentationParameters, java.util.Optional<org.anchoranalysis.image.voxel.object.ObjectMask>) but with the delegate as additional argument.

Uses of ObjectMask in org.anchoranalysis.image.bean.segment.object

Method parameters in org.anchoranalysis.image.bean.segment.object with type arguments of type ObjectMask

Modifier and Type	Method	Description
protected static void	SegmentChannelIntoObjects.checkUnsupportedObjectMask(Optional<ObjectMask> objectMask)	Throws an exception if object is present, as it is unsupported by the implementation.
abstract ObjectCollection	SegmentChannelIntoObjects.segment(Channel channel, Optional<ObjectMask> objectMask, Optional<ObjectCollection> seeds)	Segments a channel to produce an object-collection.
ObjectCollection	SegmentChannelIntoObjectsUnary.segment(Channel channel, Optional<ObjectMask> objectMask, Optional<ObjectCollection> seeds)
protected abstract ObjectCollection	SegmentChannelIntoObjectsUnary.segment(Channel channel, Optional<ObjectMask> object, Optional<ObjectCollection> seeds, SegmentChannelIntoObjects upstreamSegmenter)	Creates an ObjectCollection given the segmentation-results provided by the delegate.

Uses of ObjectMask in org.anchoranalysis.image.core.channel

Methods in org.anchoranalysis.image.core.channel that return ObjectMask

Modifier and Type	Method	Description
ObjectMask	Channel.equalMask(BoundingBox box, int equalValue)	Creates a ObjectMask representing all the voxels in box equal to equalValue.

Uses of ObjectMask in org.anchoranalysis.image.core.contour

Methods in org.anchoranalysis.image.core.contour that return ObjectMask

Modifier and Type	Method	Description
static ObjectMask	FindContour.createFrom(ObjectMask object, int numberErosions, boolean do3D, boolean atImageBoundary)	Creates an contour from a ObjectMask.

Methods in org.anchoranalysis.image.core.contour with parameters of type ObjectMask

Modifier and Type	Method	Description
static ObjectMask	FindContour.createFrom(ObjectMask object, int numberErosions, boolean do3D, boolean atImageBoundary)	Creates an contour from a ObjectMask.

Uses of ObjectMask in org.anchoranalysis.image.core.mask

Methods in org.anchoranalysis.image.core.mask that return ObjectMask

Modifier and Type	Method	Description
static ObjectMask	MaskInverter.invertObjectDuplicate(ObjectMask object)	Creates a new object-mask where off voxels become on voxels and vice versa.
ObjectMask	Mask.region(BoundingBox box, boolean reuseIfPossible)	Creates an ObjectMask corresponding to the on/off state in a bounding-box.

Methods in org.anchoranalysis.image.core.mask with parameters of type ObjectMask

Modifier and Type	Method	Description
static ObjectMask	MaskInverter.invertObjectDuplicate(ObjectMask object)	Creates a new object-mask where off voxels become on voxels and vice versa.

Uses of ObjectMask in org.anchoranalysis.image.core.merge

Methods in org.anchoranalysis.image.core.merge that return ObjectMask

Modifier and Type	Method	Description
static ObjectMask	ObjectMaskMerger.merge(ObjectCollection objects)	Merges all the objects together that are found in a collection.
static ObjectMask	ObjectMaskMerger.merge(ObjectMask first, ObjectMask second)	Merges two objects together.

Methods in org.anchoranalysis.image.core.merge with parameters of type ObjectMask

Modifier and Type	Method	Description
static ObjectMask	ObjectMaskMerger.merge(ObjectMask first, ObjectMask second)	Merges two objects together.

Method parameters in org.anchoranalysis.image.core.merge with type arguments of type ObjectMask

Modifier and Type	Method	Description
static BoundingBox	ObjectMaskMerger.mergeBoundingBoxes(Stream<ObjectMask> objects)	Merges all the bounding boxes of a stream of objects.

Uses of ObjectMask in org.anchoranalysis.image.core.object

Methods in org.anchoranalysis.image.core.object that return ObjectMask

Modifier and Type	Method	Description
static ObjectMask	ObjectFromPointsFactory.create(Collection<Point3i> points)	Create an ObjectMask from a collection of points.
ObjectMask	MatchedObject.getSource()	The source object (which is matched against others)

Methods in org.anchoranalysis.image.core.object with parameters of type ObjectMask

Modifier and Type	Method	Description
static Histogram	HistogramFromObjectsFactory.createFrom(Channel channel, ObjectMask object)	Creates a Histogram of voxel intensity values in channel corresponding to object.

Method parameters in org.anchoranalysis.image.core.object with type arguments of type ObjectMask

Modifier and Type	Method	Description
static Histogram	HistogramFromObjectsFactory.createFrom(VoxelsUntyped voxels, Optional<ObjectMask> object)	Creates a Histogram of voxel intensity values in voxels, all or only those in object.

Constructors in org.anchoranalysis.image.core.object with parameters of type ObjectMask

Modifier	Constructor	Description
	MatchedObject(ObjectMask source, ObjectCollection matches)	Creates a new MatchedObject instance.

Uses of ObjectMask in org.anchoranalysis.image.core.object.label

Methods in org.anchoranalysis.image.core.object.label that return ObjectMask

Modifier and Type	Method	Description
ObjectMask	OverlappingObject.getAfterPreoperation()	After pre-operation but before scaling

Methods in org.anchoranalysis.image.core.object.label with parameters of type ObjectMask

Modifier and Type	Method	Description
T	DecodeLabels.CreateElementFromScaledObject.createFrom(int index, ObjectMask scaledObject)	Create from an index and it's scaled-object.

Constructors in org.anchoranalysis.image.core.object.label with parameters of type ObjectMask

Modifier	Constructor	Description
	OverlappingObject(T original, ObjectMask afterPreoperation)	Creates a new OverlappingObject instance.

Constructor parameters in org.anchoranalysis.image.core.object.label with type arguments of type ObjectMask

Modifier	Constructor	Description
	LabelObjects(Function<T,ObjectMask> extractObject, BiFunction<T,ReadableTuple3i,T> shiftElement)	Creates a new LabelObjects instance.
	LabelObjects(Optional<UnaryOperator<T>> operationBeforeLabelling, Optional<Consumer<OverlappingObject<T>>> overlappingObjectConsumer, Function<T,ObjectMask> extractObject, BiFunction<T,ReadableTuple3i,T> shiftElement)	Creates a new LabelObjects instance.

Uses of ObjectMask in org.anchoranalysis.image.core.object.properties

Methods in org.anchoranalysis.image.core.object.properties that return ObjectMask

Modifier and Type	Method	Description
ObjectMask	ObjectWithProperties.asObjectMask()	Exposes the underlying ObjectMask ignoring any properties.

Methods in org.anchoranalysis.image.core.object.properties with parameters of type ObjectMask

Modifier and Type	Method	Description
void	ObjectCollectionWithProperties.add(ObjectMask object)	Add an ObjectMask to the collection, assigning empty properties to it.

Method parameters in org.anchoranalysis.image.core.object.properties with type arguments of type ObjectMask

Modifier and Type	Method	Description
ObjectWithProperties	ObjectWithProperties.map(UnaryOperator<ObjectMask> operator)	Maps the underlying object-mask to another object-mask, reusing the same properties object.

Constructors in org.anchoranalysis.image.core.object.properties with parameters of type ObjectMask

Modifier	Constructor	Description
	ObjectCollectionWithProperties(ObjectMask object)	Create with a single object.
	ObjectWithProperties(ObjectMask object)	Creates with an existing ObjectMask and empty properties.
	ObjectWithProperties(ObjectMask object, Map<String,Object> properties)	Creates a new ObjectWithProperties instance.

Uses of ObjectMask in org.anchoranalysis.image.core.object.scale

Methods in org.anchoranalysis.image.core.object.scale that return ObjectMask

Modifier and Type	Method	Description
ObjectMask	AccessObjectMaskSimple.clipTo(ObjectMask element, Extent extent)
ObjectMask	AccessObjectMaskSimple.createFrom(int index, ObjectMask object)
ObjectMask	AccessObjectMask.objectFor(T element)	An object-mask for a given element.
ObjectMask	AccessObjectMaskSimple.objectFor(ObjectMask element)
ObjectMask	AccessObjectMaskSimple.shiftBy(ObjectMask element, ReadableTuple3i quantity)

Methods in org.anchoranalysis.image.core.object.scale that return types with arguments of type ObjectMask

Modifier and Type	Method	Description
static ScaledElements<ObjectMask>	Scaler.scaleObjects(ObjectCollection objects, ScaleFactor factor)	Scales every object-mask in a collection collectively.
static ScaledElements<ObjectMask>	Scaler.scaleObjects(ObjectCollection objects, ScaleFactor factor, boolean overlappingObjects, Optional<UnaryOperator<ObjectMask>> preOperation, Optional<UnaryOperator<ObjectMask>> postOperation)	Scales every object-mask in a collection collectively (if not overlappjng), allowing for additional manipulation before and after scaling.
static ScaledElements<ObjectMask>	Scaler.scaleObjects(ObjectCollection objects, ScaleFactor factor, boolean overlappingObjects, Extent clipTo)	Scales every object-mask in a collection collectively, ensuring the results remain inside a particular region.

Methods in org.anchoranalysis.image.core.object.scale with parameters of type ObjectMask

Modifier and Type	Method	Description
ObjectMask	AccessObjectMaskSimple.clipTo(ObjectMask element, Extent extent)
T	AccessObjectMask.createFrom(int index, ObjectMask object)	Creates an element of type T from an object-representation and index.
ObjectMask	AccessObjectMaskSimple.createFrom(int index, ObjectMask object)
ObjectMask	AccessObjectMaskSimple.objectFor(ObjectMask element)
ObjectMask	AccessObjectMaskSimple.shiftBy(ObjectMask element, ReadableTuple3i quantity)

Method parameters in org.anchoranalysis.image.core.object.scale with type arguments of type ObjectMask

Modifier and Type	Method	Description
static ScaledElements<ObjectMask>	Scaler.scaleObjects(ObjectCollection objects, ScaleFactor factor, boolean overlappingObjects, Optional<UnaryOperator<ObjectMask>> preOperation, Optional<UnaryOperator<ObjectMask>> postOperation)	Scales every object-mask in a collection collectively (if not overlappjng), allowing for additional manipulation before and after scaling.

Uses of ObjectMask in org.anchoranalysis.image.core.points

Methods in org.anchoranalysis.image.core.points with parameters of type ObjectMask

Modifier and Type	Method	Description
static List<Point2i>	PointsFromObject.listFrom2i(ObjectMask object)	A list of two-dimensional integer points from the entire object-mask.
static List<Point3d>	PointsFromObject.listFrom3d(ObjectMask object)	A list of points from the entire object-mask as Point3d.
static List<Point3i>	PointsFromObject.listFrom3i(ObjectMask object)	A list of three-dimensional integer points from the entire object-mask.
static List<Point2i>	PointsFromObject.listFromOutline2i(ObjectMask object)	A list of points as three-dimensional integers from the outline of an object-mask
static List<Point3i>	PointsFromObject.listFromOutline3i(ObjectMask object)	A list of points as Point3i from the outline of an object-mask.
static SortedSet<Point3i>	PointsFromObject.setFrom3i(ObjectMask object)	A sorted-set of three-dimensional integer points from the entire object-mask
static Set<Point3i>	PointsFromObject.setFromContour(ObjectMask object)	A set of points from the contour of object in three dimensions.

Uses of ObjectMask in org.anchoranalysis.image.core.stack

Methods in org.anchoranalysis.image.core.stack that return types with arguments of type ObjectMask

Modifier and Type	Method	Description
Optional<ObjectMask>	RGBStack.objectWithColor(RGBColor color)	Extracts an ObjectMask from a Channel of all voxels that have a particular color.

Uses of ObjectMask in org.anchoranalysis.image.feature.input

Methods in org.anchoranalysis.image.feature.input that return ObjectMask

Modifier and Type	Method	Description
ObjectMask	FeatureInputPairObjects.getFirst()	Gets the first ObjectMask.
ObjectMask	FeatureInputPairObjects.getMerged()	Returns a merged version of the two objects.
ObjectMask	FeatureInputSingleObject.getObject()	The object mask associated with this input.
ObjectMask	FeatureInputPairObjects.getSecond()	Gets the second ObjectMask.

Methods in org.anchoranalysis.image.feature.input that return types with arguments of type ObjectMask

Modifier and Type	Method	Description
Optional<ObjectMask>	FeatureInputPairObjects.getMergedOptional()	Gets the optional merged ObjectMask.

Constructors in org.anchoranalysis.image.feature.input with parameters of type ObjectMask

Modifier	Constructor	Description
	FeatureInputPairObjects(ObjectMask first, ObjectMask second)	Constructs a FeatureInputPairObjects with two ObjectMasks.
	FeatureInputPairObjects(ObjectMask first, ObjectMask second, Optional<EnergyStack> energyStack)	Constructs a FeatureInputPairObjects with two ObjectMasks and an optional EnergyStack.
	FeatureInputPairObjects(ObjectMask first, ObjectMask second, Optional<EnergyStack> energyStack, Optional<ObjectMask> merged)	Constructs a FeatureInputPairObjects with two ObjectMasks, an optional EnergyStack, and an optional merged ObjectMask.
	FeatureInputPairObjects(ObjectMask first, ObjectMask second, EnergyStack energyStack)	Constructs a FeatureInputPairObjects with two ObjectMasks and an EnergyStack.
	FeatureInputSingleObject(ObjectMask object)	Constructs a FeatureInputSingleObject with an ObjectMask.
	FeatureInputSingleObject(ObjectMask object, Optional<EnergyStack> energyStack)	Constructs a FeatureInputSingleObject with an ObjectMask and an optional EnergyStack.
	FeatureInputSingleObject(ObjectMask object, EnergyStack energyStack)	Constructs a FeatureInputSingleObject with an ObjectMask and an EnergyStack.

Uses of ObjectMask in org.anchoranalysis.image.inference.bean.reduce

Methods in org.anchoranalysis.image.inference.bean.reduce that return ObjectMask

Modifier and Type	Method	Description
ObjectMask	ObjectForReduction.getElement()	The underlying ObjectMask with whom a confidence and label is associated.

Methods in org.anchoranalysis.image.inference.bean.reduce that return types with arguments of type ObjectMask

Modifier and Type	Method	Description
LabelledWithConfidence<ObjectMask>	ObjectForReduction.getLabelled()	The underlying labelled ObjectMask for input to a reduction algorithm.
ReductionOutcome<LabelledWithConfidence<ObjectMask>>	ReduceElementsGreedy.reduce(List<LabelledWithConfidence<ObjectMask>> elements, Extent extent, ExecutionTimeRecorder executionTimeRecorder)

Methods in org.anchoranalysis.image.inference.bean.reduce with parameters of type ObjectMask

Modifier and Type	Method	Description
protected abstract boolean	ReduceElementsGreedy.shouldObjectsBeProcessed(ObjectMask source, ObjectMask other)	Whether to include another (possibly-overlapping with source) element in processing?
protected boolean	RemoveOverlappingObjects.shouldObjectsBeProcessed(ObjectMask source, ObjectMask other)

Method parameters in org.anchoranalysis.image.inference.bean.reduce with type arguments of type ObjectMask

Modifier and Type	Method	Description
static List<ObjectForReduction>	ObjectForReductionFactory.populateFromList(List<LabelledWithConfidence<ObjectMask>> list)	Creates a list of ObjectForReductions from a corresponding list of labelled ObjectMasks.
ReductionOutcome<LabelledWithConfidence<ObjectMask>>	ReduceElementsGreedy.reduce(List<LabelledWithConfidence<ObjectMask>> elements, Extent extent, ExecutionTimeRecorder executionTimeRecorder)

Constructor parameters in org.anchoranalysis.image.inference.bean.reduce with type arguments of type ObjectMask

Modifier	Constructor	Description
	ObjectForReduction(LabelledWithConfidence<ObjectMask> labelled)	Creates with a ObjectMask that is considered newly-added.
	ObjectForReduction(LabelledWithConfidence<ObjectMask> labelled, int index)	Creates a new ObjectForReduction instance.
	ReduceObjectsGraph(List<LabelledWithConfidence<ObjectMask>> elements)	Create with a list of elements.

Uses of ObjectMask in org.anchoranalysis.image.inference.bean.segment.instance

Methods in org.anchoranalysis.image.inference.bean.segment.instance that return types with arguments of type ObjectMask

Modifier and Type	Method	Description
ReduceElements<ObjectMask>	SuppressNonMaximum.getReduce()	The algorithm for reducing the number of object-masks.

Method parameters in org.anchoranalysis.image.inference.bean.segment.instance with type arguments of type ObjectMask

Modifier and Type	Method	Description
void	SuppressNonMaximum.setReduce(ReduceElements<ObjectMask> reduce)	The algorithm for reducing the number of object-masks.

Constructor parameters in org.anchoranalysis.image.inference.bean.segment.instance with type arguments of type ObjectMask

Modifier	Constructor	Description
	SuppressNonMaximum(SegmentStackIntoObjectsPooled<T> segment, ReduceElements<ObjectMask> reduce, boolean separateEachLabel)	Creates a new SuppressNonMaximum instance.

Uses of ObjectMask in org.anchoranalysis.image.inference.segment

Methods in org.anchoranalysis.image.inference.segment that return ObjectMask

Modifier and Type	Method	Description
ObjectMask	MultiScaleObject.getInputScale()	Gets the ObjectMask at the scale associated with the input-image.
ObjectMask	MultiScaleObject.getModelScale()	Gets the ObjectMask at the scale associated with the segmentation.

Methods in org.anchoranalysis.image.inference.segment that return types with arguments of type ObjectMask

Modifier and Type	Method	Description
List<LabelledWithConfidence<ObjectMask>>	SegmentedObjectsAtScale.listWithLabels()	Create a List of all contained objects, including confidence.
List<WithConfidence<ObjectMask>>	SegmentedObjectsAtScale.listWithoutLabels()	Create a List of all contained objects, including confidence.

Method parameters in org.anchoranalysis.image.inference.segment with type arguments of type ObjectMask

Modifier and Type	Method	Description
static <T> MultiScaleObject	MultiScaleObject.extractFrom(DualScale<T> dual, Function<T,ObjectMask> extractObject)	Creates a new MultiScaleObject by extracting a ObjectMask from a DualScale.
static <T, S> MultiScaleObject	MultiScaleObject.extractFrom(DualScale<T> dual1, DualScale<S> dual2, BiFunction<T,S,ObjectMask> extractObject)	Creates a new MultiScaleObject by extracting a ObjectMask from two DualScales.
SegmentedObjects	SegmentedObjects.reduce(ReduceElements<ObjectMask> reduce, boolean separateEachLabel, ExecutionTimeRecorder executionTimeRecorder)	Reduces the segmented-objects, applying a reduction algorithm separately to each object-class.

Constructor parameters in org.anchoranalysis.image.inference.segment with type arguments of type ObjectMask

Modifier	Constructor	Description
	MultiScaleObject(Supplier<ObjectMask> inputScale, Supplier<ObjectMask> modelScale)	Creates with a separate supplier of an ObjectMask for each respective scale.
	SegmentedObjectsAtScale(List<LabelledWithConfidence<MultiScaleObject>> source, Function<MultiScaleObject,ObjectMask> extractObject, Stack background, StackDisplayer displayer, ExecutionTimeRecorder executionTimeRecorder, String executionTimeSuffix)	Creates a new SegmentedObjectsAtScale instance.

Uses of ObjectMask in org.anchoranalysis.image.io.object.output.mask

Methods in org.anchoranalysis.image.io.object.output.mask with parameters of type ObjectMask

Modifier and Type	Method	Description
Stack	ObjectAsMaskGenerator.transform(ObjectMask element)

Uses of ObjectMask in org.anchoranalysis.image.io.stack.output.box

Method parameters in org.anchoranalysis.image.io.stack.output.box with type arguments of type ObjectMask

Modifier and Type	Method	Description
Stack	DrawObjectOnStackGenerator.transform(BoundedList<ObjectMask> element)

Uses of ObjectMask in org.anchoranalysis.image.voxel

Methods in org.anchoranalysis.image.voxel with parameters of type ObjectMask

Modifier and Type	Method	Description
void	VoxelsUntyped.copyVoxelsTo(ObjectMask objectSource, VoxelsUntyped destination, BoundingBox boxDestination)	Copies the voxels into a destination, but only those voxels inside an ObjectMask.

Uses of ObjectMask in org.anchoranalysis.image.voxel.arithmetic

Methods in org.anchoranalysis.image.voxel.arithmetic with parameters of type ObjectMask

Modifier and Type	Method	Description
void	VoxelsArithmetic.addTo(ObjectMask object, int valueToBeAdded)	Adds a constant-value to each voxel but only for voxels inside an object-mask.
void	VoxelsArithmetic.multiplyBy(ObjectMask object, double factor)	Multiplies each voxel by constant factor but only for voxels inside an ObjectMask.

Uses of ObjectMask in org.anchoranalysis.image.voxel.assigner

Methods in org.anchoranalysis.image.voxel.assigner with parameters of type ObjectMask

Modifier and Type	Method	Description
void	VoxelsAssigner.toEitherTwoObjects(ObjectMask object1, ObjectMask object2, BoundingBox restrictTo)	Sets voxels to a value if the position is on in either of two masks
void	VoxelsAssigner.toObject(ObjectMask object)	Sets voxels in a box to a particular value if they match an object-mask
void	VoxelsAssigner.toObject(ObjectMask object, BoundingBox restrictTo)	Sets voxels in a box to a particular value if they match a object-mask (but only a part of the object-mask)
void	VoxelsAssigner.toObjectIf(ObjectMask object, IntPredicate voxelPredicate)	Sets voxels in a box to a particular value if they match an object-mask and a voxel matches a predicate
boolean	VoxelsAssigner.toObjectWhile(ObjectMask object, IntPredicate voxelPredicate)	Sets voxels in a box to a particular value if they match an object-mask and each voxel matches a predicate

Uses of ObjectMask in org.anchoranalysis.image.voxel.extracter

Methods in org.anchoranalysis.image.voxel.extracter with parameters of type ObjectMask

Modifier and Type	Method	Description
void	VoxelsExtracter.objectCopyTo(ObjectMask from, Voxels<T> voxelsDestination, BoundingBox destinationBox)	Copies an area corresponding to an object-mask to another Voxels.

Uses of ObjectMask in org.anchoranalysis.image.voxel.extracter.predicate

Methods in org.anchoranalysis.image.voxel.extracter.predicate that return ObjectMask

Modifier and Type	Method	Description
ObjectMask	PredicateAtCorner.deriveObject(BoundingBox box)
ObjectMask	PredicateImplementation.deriveObject(BoundingBox box)
ObjectMask	VoxelsPredicate.deriveObject(BoundingBox box)	Creates an ObjectMask for all the voxels inside the bounding-box satisfying the predicate.

Methods in org.anchoranalysis.image.voxel.extracter.predicate that return types with arguments of type ObjectMask

Modifier and Type	Method	Description
Optional<ObjectMask>	PredicateAtCorner.deriveObjectTight()
Optional<ObjectMask>	PredicateImplementation.deriveObjectTight()
Optional<ObjectMask>	VoxelsPredicate.deriveObjectTight()	Creates an ObjectMask for all the voxels satisfying the predicate, minimally fitting the bounding-box to the on voxels only.

Methods in org.anchoranalysis.image.voxel.extracter.predicate with parameters of type ObjectMask

Modifier and Type	Method	Description
int	PredicateAtCorner.countForObject(ObjectMask object)
int	PredicateImplementation.countForObject(ObjectMask object)
int	VoxelsPredicate.countForObject(ObjectMask object)	Counts the number of values satisfying the predicate - but restricted to voxels corresponding to on in an object-mask.

Uses of ObjectMask in org.anchoranalysis.image.voxel.iterator

Methods in org.anchoranalysis.image.voxel.iterator with parameters of type ObjectMask

Modifier and Type	Method	Description
static <T> boolean	IterateVoxelsObjectMask.allMatchIntensity(ObjectMask object, Voxels<T> voxels, IntPredicate predicate)	Do all points on an object-mask match a predicate on the point's voxel-intensity?
static <T> void	IterateVoxelsObjectMask.withBuffer(ObjectMask object, Voxels<T> voxels, ProcessBufferUnary<T> process)	Iterate over each voxel in an object-mask - with one associated buffer for each slice from Voxels.
static void	IterateVoxelsObjectMask.withPoint(ObjectMask firstMask, Optional<ObjectMask> secondMask, ProcessPoint process)	Iterate over each point that is located on an object-mask AND optionally a second-mask
static void	IterateVoxelsObjectMask.withPoint(ObjectMask object, ProcessPoint process)	Iterate over each voxel that is located on an object-mask
static <S, T> void	IterateVoxelsObjectMask.withTwoBuffers(ObjectMask object, Voxels<S> voxels1, Voxels<T> voxels2, ProcessBufferBinary<S,T> process)	Iterate over each voxel with a corresponding on value in an object-mask - and with two associated buffers for each slice covering the all the global space i.e. the entire image.
static <S, T> void	IterateVoxelsObjectMask.withTwoMixedBuffers(ObjectMask object, Voxels<S> voxels1, Voxels<T> voxels2, ProcessVoxelBufferBinaryMixed<S,T> process)	Iterate over each voxel in an object-mask - with one associated voxel-buffer and one associated buffer for each slice.
static <S, T> void	IterateVoxelsObjectMask.withTwoVoxelBuffers(ObjectMask object, Voxels<S> voxels1, Voxels<T> voxels2, ProcessVoxelBufferBinary<S,T> process)	Iterate over each voxel in an object-mask - with two associated voxel-buffers and for each slice.
static <T> void	IterateVoxelsObjectMask.withVoxelBuffer(ObjectMask object, Voxels<T> voxels, Optional<BoundingBox> restrictTo, ProcessVoxelBufferUnary<T> process)	Iterate over each voxel on an object-mask with one associated VoxelBuffer.
static <T> void	IterateVoxelsObjectMask.withVoxelBuffer(ObjectMask object, Voxels<T> voxels, ProcessVoxelBufferUnary<T> process)	Iterate over each voxel on an object-mask with one associated VoxelBuffer.

Method parameters in org.anchoranalysis.image.voxel.iterator with type arguments of type ObjectMask

Modifier and Type	Method	Description
static <T> void	IterateVoxelsObjectMaskOptional.withBuffer(Optional<ObjectMask> objectMask, Voxels<T> voxels, ProcessBufferUnary<T> process)	Iterate over each voxel (or optionally only on object-mask) with one associated buffer.
static void	IterateVoxelsObjectMask.withPoint(ObjectMask firstMask, Optional<ObjectMask> secondMask, ProcessPoint process)	Iterate over each point that is located on an object-mask AND optionally a second-mask
static void	IterateVoxelsObjectMaskOptional.withPoint(Optional<ObjectMask> objectMask, Extent extent, ProcessPoint process)	Iterate over all points that are located on a object-mask or else all points in an extent.
static void	IterateVoxelsObjectMaskOptional.withSlidingBuffer(Optional<ObjectMask> objectMask, SlidingBuffer<?> buffer, ProcessPoint process)	Iterate over each voxel in a sliding-buffer, optionally restricting it to be only voxels in a certain object
static <S, T> void	IterateVoxelsObjectMaskOptional.withTwoBuffers(Optional<ObjectMask> objectMask, Voxels<S> voxels1, Voxels<T> voxels2, ProcessBufferBinary<S,T> process)	Iterate over each voxel (or optionally only on object-mask) with two associated buffers.

Uses of ObjectMask in org.anchoranalysis.image.voxel.iterator.intersecting

Methods in org.anchoranalysis.image.voxel.iterator.intersecting with parameters of type ObjectMask

Modifier and Type	Method	Description
static int	CountVoxelsIntersectingObjects.countIntersectingVoxels(ObjectMask object1, ObjectMask object2)	Counts the number of intersecting-voxels between two object-masks.
static boolean	CountVoxelsIntersectingObjects.hasIntersectingVoxels(ObjectMask object1, ObjectMask object2)	Determines whether there are any intersecting voxels on two object-masks.

Uses of ObjectMask in org.anchoranalysis.image.voxel.iterator.neighbor

Methods in org.anchoranalysis.image.voxel.iterator.neighbor with parameters of type ObjectMask

Modifier and Type	Method	Description
static <T> ProcessVoxelNeighbor<T>	ProcessVoxelNeighborFactory.withinMask(ObjectMask object, ProcessChangedPointAbsoluteMasked<T> process)	Creates to process neighbors that must lie within an ObjectMask.
static <T> ProcessVoxelNeighbor<T>	ProcessVoxelNeighborFactory.withinMask(ObjectMask object, ProcessVoxelNeighborAbsolute<T> process)	Creates to process neighbors that must lie within an ObjectMask.

Method parameters in org.anchoranalysis.image.voxel.iterator.neighbor with type arguments of type ObjectMask

Modifier and Type	Method	Description
static <T> ProcessVoxelNeighbor<T>	ProcessVoxelNeighborFactory.within(Optional<ObjectMask> containingMask, Extent extentFallback, ProcessVoxelNeighborAbsolute<T> process)	Creates to process neighbors that must lie within either an object-mask or an extent (as a fallback).

Uses of ObjectMask in org.anchoranalysis.image.voxel.kernel.count

Constructors in org.anchoranalysis.image.voxel.kernel.count with parameters of type ObjectMask

Modifier	Constructor	Description
	CountKernelNeighborhoodMask(ObjectMask objectRequireHigh)	Create with object-mask.

Uses of ObjectMask in org.anchoranalysis.image.voxel.neighborhood

Methods in org.anchoranalysis.image.voxel.neighborhood that return types with arguments of type ObjectMask

Modifier and Type	Method	Description
static GraphWithPayload<ObjectMask,Integer>	NeighborGraph.create(ObjectCollection objects, Extent sceneExtent, boolean preventObjectIntersection, boolean do3D)	Create the graph with object-masks as vertices, where edges represent the number of neighboring voxels between objects.

Method parameters in org.anchoranalysis.image.voxel.neighborhood with type arguments of type ObjectMask

Modifier and Type	Method	Description
static <V> GraphWithPayload<V,Integer>	NeighborGraph.create(List<V> vertices, Function<V,ObjectMask> vertexToObject, Extent sceneExtent, boolean preventObjectIntersection, boolean do3D)	Like NeighborGraph.create(ObjectCollection, Extent, boolean, boolean) but extracts objects from a list of elements which form the vertices.

Uses of ObjectMask in org.anchoranalysis.image.voxel.object

Methods in org.anchoranalysis.image.voxel.object that return ObjectMask

Modifier and Type	Method	Description
ObjectMask	ObjectMask.clampTo(Extent extent)	Makes sure an object fits inside an extent, removing any parts which do not.
ObjectMask	ObjectMask.duplicate()	Creates a deep-copy of the current object-mask.
ObjectMask	ObjectMask.extractSlice(int sliceIndex, boolean keepIndex)	Extracts one particular slice as an object-mask
ObjectMask	ObjectMask.flattenZ()	A maximum-intensity projection.
ObjectMask	ObjectCollection.get(int index)	Get an ObjectMask at a particular position in the collection.
ObjectMask	ObjectMask.growBuffer(Point3i growthNegative, Point3i growthPositive, Optional<Extent> clipRegion)	Grows the object-mask's voxel buffers in the positive and negative directions by a certain amount.
ObjectMask	ObjectMask.growToZ(int sizeZ)	Grows a single z-sliced ObjectMask by duplicating the slice across the z-dimension sizeZ number of times.
ObjectMask	ObjectMask.invert()	Produces a new object-mask that uses the same voxel-buffer but switches the off and on mapping.
ObjectMask	ObjectMask.mapBoundingBoxChangeExtent(BoundingBox boxToAssign)	Applies a function to map the bounding-box to a new-value (whose extent is expected to change in value).
ObjectMask	ObjectMask.mapBoundingBoxPreserveExtent(UnaryOperator<BoundingBox> mapOperation)	Applies a function to map the bounding-box to a new-value (whose extent should be unchanged in value).
ObjectMask	ObjectMask.region(BoundingBox box, boolean reuseIfPossible)	A (sub-)region of the object-mask.
ObjectMask	ObjectMask.regionIntersecting(BoundingBox box)	Creates an object-mask covering the a bounding-box (that is required to intersect at least partially)
ObjectMask	ObjectMask.regionZ(int zMin, int zMax)	Creates an object-mask with a subrange of the slices.
ObjectMask	ObjectMask.relativeMaskTo(BoundingBox box)	Creates a new object-mask with coordinates changed to be relative to another box.
ObjectMask	ObjectMask.replaceVoxels(Voxels<UnsignedByteBuffer> voxelsToAssign)	Replaces the voxels in the object-mask.
ObjectMask	ObjectMask.scale(ScaleFactor factor)	Produces a scaled-version of an object-mask.
ObjectMask	ObjectMask.scale(ScaleFactor factor, Optional<Extent> clipTo)	Produces a scaled-version of an object-mask.
ObjectMask	ObjectMask.shiftBackBy(ReadableTuple3i shift)	Shifts the object-mask by moving its bounding-box backwards.
ObjectMask	ObjectMask.shiftBy(ReadableTuple3i shift)	Shifts the object-mask by moving its bounding-box forwards.
ObjectMask	ObjectMask.shiftToOrigin()	Creates a new object-mask with identical voxels but with the bounding-box beginning at the origin (0,0,0).

Methods in org.anchoranalysis.image.voxel.object that return types with arguments of type ObjectMask

Modifier and Type	Method	Description
List<ObjectMask>	ObjectCollection.asList()	Exposes the underlying objects as a ArrayList.
static IntersectingObjects<ObjectMask>	IntersectingObjects.create(ObjectCollection objects)	Creates from an ObjectCollection.
Optional<ObjectMask>	DeriveObjectFromPoints.deriveObject()	Derives an ObjectMask that includes all points that were previously added.
Stream<ObjectMask>	ObjectMaskStream.filterSubsetStream(Predicate<ObjectMask> predicate, Collection<Integer> indices)	Like ObjectMaskStream.filterSubset(java.util.function.Predicate<org.anchoranalysis.image.voxel.object.ObjectMask>, java.util.Collection<java.lang.Integer>) but returns a stream rather than a ObjectCollection.
Optional<ObjectMask>	ObjectMask.intersect(ObjectMask other, Extent extent)	Intersects this object-mask with another
Iterator<ObjectMask>	ObjectCollection.iterator()
Stream<ObjectMask>	ObjectCollection.streamIndices(Collection<Integer> indices)	Streams only objects at specific indices.
Stream<ObjectMask>	ObjectCollection.streamStandardJava()	A stream of object-masks as per Java's standard collections interface.
Set<ObjectMask>	ObjectMaskStream.toSet()	Converts to a HashSet.

Methods in org.anchoranalysis.image.voxel.object with parameters of type ObjectMask

Modifier and Type	Method	Description
int	ObjectMask.countIntersectingVoxels(ObjectMask other)	Counts the number of intersecting-voxels between two object-masks.
boolean	ObjectMask.equalsDeep(ObjectMask other)	A deep equality check with another ObjectMask.
boolean	ObjectMask.hasIntersectingVoxels(ObjectMask other)	Determines whether there are any intersecting voxels on two object-masks.
Optional<ObjectMask>	ObjectMask.intersect(ObjectMask other, Extent extent)	Intersects this object-mask with another
Set<T>	IntersectingObjects.intersectsWith(ObjectMask object)	All elements that intersect with a particular object.
Stream<T>	IntersectingObjects.intersectsWithStream(ObjectMask object)	Like IntersectingObjects.intersectsWith(ObjectMask) but returns the objects as a Stream rather than a Set.
static ObjectCollection	ObjectCollectionFactory.of(ObjectMask... object)	Creates a new collection with elements from the parameter-list.

Method parameters in org.anchoranalysis.image.voxel.object with type arguments of type ObjectMask

Modifier and Type	Method	Description
boolean	ObjectMaskStream.anyMatch(Predicate<ObjectMask> predicate)	Does the predicate evaluate to true on any object in the collection?
ObjectCollection	ObjectMaskStream.filter(Predicate<ObjectMask> predicate)	Filters a ObjectCollection to include certain items based on a predicate
<E extends Exception> ObjectCollection	ObjectMaskStream.filter(CheckedPredicate<ObjectMask,E> predicate, Class<? extends Exception> throwableClass)	Filters a ObjectCollection to include certain items based on a predicate
ObjectCollection	ObjectMaskStream.filterAndMap(Predicate<ObjectMask> predicate, UnaryOperator<ObjectMask> mapFunction)	Performs a ObjectMaskStream.filter(java.util.function.Predicate<org.anchoranalysis.image.voxel.object.ObjectMask>) and then a ObjectMaskStream.map(org.anchoranalysis.core.functional.checked.CheckedFunction<org.anchoranalysis.image.voxel.object.ObjectMask, org.anchoranalysis.image.voxel.object.ObjectMask, E>).
ObjectCollection	ObjectMaskStream.filterAndMap(Predicate<ObjectMask> predicate, UnaryOperator<ObjectMask> mapFunction)	Performs a ObjectMaskStream.filter(java.util.function.Predicate<org.anchoranalysis.image.voxel.object.ObjectMask>) and then a ObjectMaskStream.map(org.anchoranalysis.core.functional.checked.CheckedFunction<org.anchoranalysis.image.voxel.object.ObjectMask, org.anchoranalysis.image.voxel.object.ObjectMask, E>).
static <T, E extends Exception> ObjectCollection	ObjectCollectionFactory.filterAndMapFrom(Collection<T> collection, Predicate<T> predicate, Class<? extends E> throwableClass, CheckedFunction<T,ObjectMask,E> mapFunction)	Creates a new collection by filtering an iterable and then mapping it to ObjectMask.
static <T> ObjectCollection	ObjectCollectionFactory.filterAndMapFrom(Collection<T> collection, Predicate<T> predicate, Function<T,ObjectMask> mapFunction)	Creates a new collection by filtering an iterable and then mapping it to ObjectMask.
static <T, E extends Exception> ObjectCollection	ObjectCollectionFactory.filterAndMapWithIndexFrom(List<T> list, Predicate<T> predicate, Class<? extends E> throwableClass, CheckedBiFunction<T,Integer,ObjectMask,E> mapFunctionWithIndex)	Creates a new collection by filtering a list and then mapping from it to ObjectMask.
ObjectCollection	ObjectMaskStream.filterExclude(Predicate<ObjectMask> predicate)	Filters a ObjectCollection to exclude certain items based on a predicate
ObjectCollection	ObjectMaskStream.filterSubset(Predicate<ObjectMask> predicate, Collection<Integer> indices)	Like ObjectMaskStream.filter(java.util.function.Predicate<org.anchoranalysis.image.voxel.object.ObjectMask>) but only operates on certain indices of the collection.
Stream<ObjectMask>	ObjectMaskStream.filterSubsetStream(Predicate<ObjectMask> predicate, Collection<Integer> indices)	Like ObjectMaskStream.filterSubset(java.util.function.Predicate<org.anchoranalysis.image.voxel.object.ObjectMask>, java.util.Collection<java.lang.Integer>) but returns a stream rather than a ObjectCollection.
<E extends Exception> ObjectCollection	ObjectMaskStream.flatMap(Class<? extends Exception> throwableClass, CheckedFunction<ObjectMask,ObjectCollection,E> mapFunction)	Like a typical flatMap() operation but accepts a mapping function that throws a checked exception.
ObjectCollection	ObjectMaskStream.flatMap(Function<ObjectMask,ObjectCollection> mapFunction)	Creates a new ObjectCollection after mapping each item to several others.
static <T, E extends Exception> ObjectCollection	ObjectCollectionFactory.flatMapFromCollection(Stream<T> stream, Class<? extends Exception> throwableClass, CheckedFunction<T,Stream<? extends ObjectMask>,E> mapFunction)	Creates a new ObjectCollection by flatMapping an incoming stream to Collection<ObjectMask> and rethrowing any exception during mapping.
static <T, E extends Exception> ObjectCollection	ObjectCollectionFactory.flatMapFromStream(Stream<T> stream, Class<? extends Exception> throwableClass, CheckedFunction<T,Stream<ObjectMask>,E> mapFunction)	Creates a new collection by flat-mapping an incoming stream to ObjectCollection and rethrowing any exception during mapping.
static ObjectCollection	ObjectCollectionFactory.fromRepeated(int repeats, Supplier<ObjectMask> createObjectMask)	Creates a new collection by repeatedly calling a function to create a single ObjectMask.
static ObjectCollection	ObjectCollectionFactory.fromSet(Set<ObjectMask> set)	Creates a new collection from a set of ObjectMask.
<E extends Exception> ObjectCollection	ObjectMaskStream.map(CheckedFunction<ObjectMask,ObjectMask,E> mapFunction)	Creates a new ObjectCollection after mapping each item to another.
<E extends Exception> ObjectCollection	ObjectMaskStream.map(CheckedFunction<ObjectMask,ObjectMask,E> mapFunction)	Creates a new ObjectCollection after mapping each item to another.
static <T, E extends Exception> ObjectCollection	ObjectCollectionFactory.mapFrom(Iterable<T> iterable, Class<? extends E> throwableClass, CheckedFunction<T,ObjectMask,E> mapFunction)	Creates a new collection by mapping an Iterable to ObjectMask.
static <T> ObjectCollection	ObjectCollectionFactory.mapFrom(Iterable<T> iterable, Function<T,ObjectMask> mapFunction)	Creates a new collection by mapping an Iterable to ObjectMask.
static <T, E extends Exception> ObjectCollection	ObjectCollectionFactory.mapFromOptional(Iterable<T> iterable, Class<? extends Exception> throwableClass, CheckedFunction<T,Optional<ObjectMask>,E> mapFunction)	Creates a new collection by mapping an Iterable to Optional.
static <T> ObjectCollection	ObjectCollectionFactory.mapFromOptional(Iterable<T> iterable, Function<T,Optional<ObjectMask>> mapFunction)	Creates a new collection by mapping an Iterable to Optional.
static <T, E extends Exception> ObjectCollection	ObjectCollectionFactory.mapFromOptional(Iterator<T> iterator, Class<? extends Exception> throwableClass, CheckedFunction<T,Optional<ObjectMask>,E> mapFunction)	Creates a new collection by mapping an Iterator to Optional.
static <T> ObjectCollection	ObjectCollectionFactory.mapFromOptional(Iterator<T> iterator, Function<T,Optional<ObjectMask>> mapFunction)	Creates a new collection by mapping an Iterator to Optional.
static <E extends Exception> ObjectCollection	ObjectCollectionFactory.mapFromRange(int startInclusive, int endExclusive, Class<? extends Exception> throwableClass, CheckedIntFunction<ObjectMask,E> mapFunction)	Creates a new collection by mapping integers (from a range) each to a ObjectMask.
static ObjectCollection	ObjectCollectionFactory.mapFromRange(int startInclusive, int endExclusive, IntFunction<ObjectMask> mapFunction)	Creates a new collection by mapping integers (from a range) each to a ObjectMask.
<T, E extends Exception> List<T>	ObjectMaskStream.mapToList(CheckedFunction<ObjectMask,T,E> mapFunction)	Creates a new List after mapping each item to another type.
<T, E extends Exception> List<T>	ObjectMaskStream.mapToListOptional(CheckedFunction<ObjectMask,Optional<T>,E> mapFunction)	Creates a new List after mapping each item to another (optional) type
<T, E extends Exception> SortedSet<T>	ObjectMaskStream.mapToSortedSet(CheckedFunction<ObjectMask,T,E> mapFunction)	Creates a new SortedSet after mapping each item to another type.
OptionalInt	ObjectMaskStream.maxAsInt(ToIntFunction<ObjectMask> function)	Finds the maximum value of a function applied to each object in the collection.
OptionalInt	ObjectMaskStream.minAsInt(ToIntFunction<ObjectMask> function)	Finds the minimum value of a function applied to each object in the collection.

Constructor parameters in org.anchoranalysis.image.voxel.object with type arguments of type ObjectMask

Modifier	Constructor	Description
	IntersectingObjects(Collection<T> elements, Function<T,ObjectMask> extractObject)	Creates an r-tree for particular objects, as extracted from elements.
	ObjectCollection(ArrayList<ObjectMask> objects)	Creates with the underlying list.
	ObjectCollection(Stream<ObjectMask> stream)	Creates with elements from a stream.

Uses of ObjectMask in org.anchoranalysis.image.voxel.object.morphological

Methods in org.anchoranalysis.image.voxel.object.morphological that return ObjectMask

Modifier and Type	Method	Description
static ObjectMask	MorphologicalDilation.dilate(ObjectMask object, Optional<Extent> extent, boolean useZ, int iterations, boolean bigNeighborhood)	Dilates an ObjectMask, growing the bounding-box as necessary.
static ObjectMask	MorphologicalErosion.erode(ObjectMask object, int iterations, boolean useZ)	Performs a morphological erosion on an ObjectMask.
static ObjectMask	MorphologicalErosion.erode(ObjectMask object, int iterations, boolean useZ, Optional<AcceptIterationPredicate> postcondition)	Performs a morphological erosion on an ObjectMask - with a postcondition.

Methods in org.anchoranalysis.image.voxel.object.morphological with parameters of type ObjectMask

Modifier and Type	Method	Description
static ObjectMask	MorphologicalDilation.dilate(ObjectMask object, Optional<Extent> extent, boolean useZ, int iterations, boolean bigNeighborhood)	Dilates an ObjectMask, growing the bounding-box as necessary.
static ObjectMask	MorphologicalErosion.erode(ObjectMask object, int iterations, boolean useZ)	Performs a morphological erosion on an ObjectMask.
static ObjectMask	MorphologicalErosion.erode(ObjectMask object, int iterations, boolean useZ, Optional<AcceptIterationPredicate> postcondition)	Performs a morphological erosion on an ObjectMask - with a postcondition.

Uses of ObjectMask in org.anchoranalysis.image.voxel.thresholder

Method parameters in org.anchoranalysis.image.voxel.thresholder with type arguments of type ObjectMask

Modifier and Type	Method	Description
static BinaryVoxels<UnsignedByteBuffer>	VoxelsThresholder.threshold(VoxelsUntyped voxels, float level, BinaryValuesByte binaryValues, Optional<ObjectMask> objectMask, boolean alwaysDuplicate)	Applies thresholding to VoxelsUntyped.

Uses of ObjectMask in org.anchoranalysis.mpp.mark

Methods in org.anchoranalysis.mpp.mark that return ObjectMask

Modifier and Type	Method	Description
ObjectMask	MarkToObjectConverter.convert(Mark mark)	Converts a Mark to an equivalent ObjectMask.
ObjectMask	Mark.deriveObject(Dimensions dimensions, RegionMembershipWithFlags region, BinaryValuesByte binaryValues)	Creates an ObjectMask representation of the mark.

Uses of ObjectMask in org.anchoranalysis.overlay.object

Constructors in org.anchoranalysis.overlay.object with parameters of type ObjectMask

Modifier	Constructor	Description
	OverlayObjectMask(ObjectMask object, int id)	Creates with a particular ObjectMask and identifier.

Uses of ObjectMask in org.anchoranalysis.plugin.annotation.bean.comparison

Classes in org.anchoranalysis.plugin.annotation.bean.comparison with type parameters of type ObjectMask

Modifier and Type	Class	Description
class	CompareAnnotations<T extends Assignment<ObjectMask>>	Task to compare a set of annotations to a segmentation or another set of annotations.
class	ComparisonSharedState<T extends Assignment<ObjectMask>>	Shared state for comparison operations, including grouping and statistics.

Uses of ObjectMask in org.anchoranalysis.plugin.annotation.bean.comparison.assigner

Classes in org.anchoranalysis.plugin.annotation.bean.comparison.assigner with type parameters of type ObjectMask

Modifier and Type	Class	Description
class	AnnotationComparisonAssigner<T extends Assignment<ObjectMask>>	Compares similar object-sets produced from two different sources.

Uses of ObjectMask in org.anchoranalysis.plugin.annotation.counter

Classes in org.anchoranalysis.plugin.annotation.counter with type parameters of type ObjectMask

Modifier and Type	Class	Description
class	ImageCounterList<T extends Assignment<ObjectMask>>	Allows operations to be applied to several ImageCounters collectively.

Uses of ObjectMask in org.anchoranalysis.plugin.fiji.bean.channel.grayscalereconstruction

Method parameters in org.anchoranalysis.plugin.fiji.bean.channel.grayscalereconstruction with type arguments of type ObjectMask

Modifier and Type	Method	Description
VoxelsUntyped	GrayscaleReconstruction2DIJ.reconstruction(VoxelsUntyped mask, VoxelsUntyped marker, Optional<ObjectMask> containingMask)

Uses of ObjectMask in org.anchoranalysis.plugin.image.bean.object.filter

Methods in org.anchoranalysis.plugin.image.bean.object.filter with parameters of type ObjectMask

Modifier and Type	Method	Description
protected abstract boolean	ObjectFilterPredicate.match(ObjectMask object, Optional<Dimensions> dimensions)	A predicate condition for an object to be kept in the collection.
protected boolean	ObjectFilterRelation.match(ObjectMask object, Optional<Dimensions> dimensions)
protected abstract boolean	ObjectFilterRelation.match(ObjectMask object, Optional<Dimensions> dim, DoubleBiPredicate relation)	Performs the matching operation using the resolved relation.

Uses of ObjectMask in org.anchoranalysis.plugin.image.bean.object.filter.collective

Methods in org.anchoranalysis.plugin.image.bean.object.filter.collective with parameters of type ObjectMask

Modifier and Type	Method	Description
protected boolean	DiscardOutliers.match(ObjectMask object, Optional<Dimensions> dimensions)
protected boolean	RelationWithMatches.match(ObjectMask object, Optional<Dimensions> dim, DoubleBiPredicate relation)

Uses of ObjectMask in org.anchoranalysis.plugin.image.bean.object.filter.independent

Methods in org.anchoranalysis.plugin.image.bean.object.filter.independent with parameters of type ObjectMask

Modifier and Type	Method	Description
protected boolean	GreaterIntersectionWith.match(ObjectMask object, Optional<Dimensions> dimensions)
protected boolean	IntensityGreaterEqualThan.match(ObjectMask object, Optional<Dimensions> dimensions)
protected boolean	IntersectsWith.match(ObjectMask objectToIntersectWith, Optional<Dimensions> dimensions)
protected boolean	NotTouchingSceneBorder.match(ObjectMask object, Optional<Dimensions> dimensions)
protected boolean	ThresholdedFeature.match(ObjectMask object, Optional<Dimensions> dim, DoubleBiPredicate relation)
protected boolean	ThresholdedVolume.match(ObjectMask object, Optional<Dimensions> dim, DoubleBiPredicate relation)

Uses of ObjectMask in org.anchoranalysis.plugin.image.bean.object.provider.filter

Method parameters in org.anchoranalysis.plugin.image.bean.object.provider.filter with type arguments of type ObjectMask

Modifier and Type	Method	Description
protected ObjectCollection	Filter.createFromObjects(ObjectCollection objects, Optional<List<ObjectMask>> objectsRejected, Optional<Dimensions> dim)
protected ObjectCollection	FilterByGroup.createFromObjects(ObjectCollection objects, Optional<List<ObjectMask>> objectsRejected, Optional<Dimensions> dim)
protected abstract ObjectCollection	ObjectCollectionProviderFilterBase.createFromObjects(ObjectCollection objects, Optional<List<ObjectMask>> objectsRejected, Optional<Dimensions> dimensions)	Creates an ObjectCollection from the given objects, potentially applying a filter and considering dimensions.

Uses of ObjectMask in org.anchoranalysis.plugin.image.bean.object.provider.morphological

Methods in org.anchoranalysis.plugin.image.bean.object.provider.morphological that return ObjectMask

Modifier and Type	Method	Description
protected ObjectMask	Dilate.applyMorphologicalOperation(ObjectMask object, Optional<Extent> extent)
protected ObjectMask	Erode.applyMorphologicalOperation(ObjectMask object, Optional<Extent> extent)
protected abstract ObjectMask	ObjectCollectionProviderMorphological.applyMorphologicalOperation(ObjectMask object, Optional<Extent> extent)	Applies the morphological operation to a single ObjectMask.

Methods in org.anchoranalysis.plugin.image.bean.object.provider.morphological with parameters of type ObjectMask

Modifier and Type	Method	Description
protected ObjectMask	Dilate.applyMorphologicalOperation(ObjectMask object, Optional<Extent> extent)
protected ObjectMask	Erode.applyMorphologicalOperation(ObjectMask object, Optional<Extent> extent)
protected abstract ObjectMask	ObjectCollectionProviderMorphological.applyMorphologicalOperation(ObjectMask object, Optional<Extent> extent)	Applies the morphological operation to a single ObjectMask.

Uses of ObjectMask in org.anchoranalysis.plugin.image.bean.object.segment.channel

Method parameters in org.anchoranalysis.plugin.image.bean.object.segment.channel with type arguments of type ObjectMask

Modifier and Type	Method	Description
ObjectCollection	AtScale.segment(Channel channel, Optional<ObjectMask> objectMask, Optional<ObjectCollection> seeds, SegmentChannelIntoObjects upstreamSegmenter)
ObjectCollection	ConnectedComponentsFromBinarySegmentation.segment(Channel channel, Optional<ObjectMask> objectMask, Optional<ObjectCollection> seeds)
ObjectCollection	Filter.segment(Channel channel, Optional<ObjectMask> object, Optional<ObjectCollection> seeds, SegmentChannelIntoObjects upstreamSegmenter)
ObjectCollection	ImposeMinima.segment(Channel channel, Optional<ObjectMask> objectMask, Optional<ObjectCollection> seeds, SegmentChannelIntoObjects upstreamSegmenter)
ObjectCollection	Mser.segment(Channel channel, Optional<ObjectMask> objectMask, Optional<ObjectCollection> seeds)
ObjectCollection	SegmentOnMaximumIntensityAndExpandInZ.segment(Channel channel, Optional<ObjectMask> objectMask, Optional<ObjectCollection> seeds, SegmentChannelIntoObjects upstreamSegmenter)

Uses of ObjectMask in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima

Method parameters in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima with type arguments of type ObjectMask

Modifier and Type	Method	Description
abstract Channel	MinimaImposition.imposeMinima(Channel channel, ObjectCollection seeds, Optional<ObjectMask> containingMask)	Imposes minima on a channel based on seed objects and an optional containing mask.
Channel	MinimaImpositionGrayscaleReconstruction.imposeMinima(Channel channel, ObjectCollection seeds, Optional<ObjectMask> containingMask)

Uses of ObjectMask in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction

Method parameters in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction with type arguments of type ObjectMask

Modifier and Type	Method	Description
abstract VoxelsUntyped	GrayscaleReconstructionByErosion.reconstruction(VoxelsUntyped mask, VoxelsUntyped marker, Optional<ObjectMask> containingMask)	Performs grayscale reconstruction of a mask image from a marker image.
VoxelsUntyped	GrayscaleReconstructionRobinson.reconstruction(VoxelsUntyped mask, VoxelsUntyped marker, Optional<ObjectMask> containingMask)

Uses of ObjectMask in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong

Method parameters in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong with type arguments of type ObjectMask

Modifier and Type	Method	Description
ObjectCollection	WatershedYeong.segment(Channel channel, Optional<ObjectMask> objectMask, Optional<ObjectCollection> seeds)

Uses of ObjectMask in org.anchoranalysis.plugin.image.bean.object.segment.reduce

Methods in org.anchoranalysis.plugin.image.bean.object.segment.reduce that return types with arguments of type ObjectMask

Modifier and Type	Method	Description
ReductionOutcome<LabelledWithConfidence<ObjectMask>>	ThresholdConfidence.reduce(List<LabelledWithConfidence<ObjectMask>> elements, Extent extent, ExecutionTimeRecorder executionTimeRecorder)

Method parameters in org.anchoranalysis.plugin.image.bean.object.segment.reduce with type arguments of type ObjectMask

Modifier and Type	Method	Description
ReductionOutcome<LabelledWithConfidence<ObjectMask>>	ThresholdConfidence.reduce(List<LabelledWithConfidence<ObjectMask>> elements, Extent extent, ExecutionTimeRecorder executionTimeRecorder)

Uses of ObjectMask in org.anchoranalysis.plugin.image.bean.segment.binary

Method parameters in org.anchoranalysis.plugin.image.bean.segment.binary with type arguments of type ObjectMask

Modifier and Type	Method	Description
BinaryVoxels<UnsignedByteBuffer>	Sequence.segment(VoxelsUntyped voxels, BinarySegmentationParameters parameters, Optional<ObjectMask> objectMask)
BinaryVoxels<UnsignedByteBuffer>	ThresholdAgainstChannel.segment(VoxelsUntyped voxels, BinarySegmentationParameters parameters, Optional<ObjectMask> object)
BinaryVoxels<UnsignedByteBuffer>	Invert.segmentFromExistingSegmentation(VoxelsUntyped voxels, BinarySegmentationParameters parameters, Optional<ObjectMask> objectMask, BinarySegmentation segment)
BinaryVoxels<UnsignedByteBuffer>	Repeat.segmentFromExistingSegmentation(VoxelsUntyped voxels, BinarySegmentationParameters parameters, Optional<ObjectMask> objectMask, BinarySegmentation segment)

Uses of ObjectMask in org.anchoranalysis.plugin.image.feature.bean.object.pair.touching

Methods in org.anchoranalysis.plugin.image.feature.bean.object.pair.touching with parameters of type ObjectMask

Modifier and Type	Method	Description
protected double	HasTouchingVoxels.calculateWithIntersection(ObjectMask first, ObjectMask second, BoundingBox boxIntersect)
protected double	NumberTouchingVoxelFaces.calculateWithIntersection(ObjectMask object1, ObjectMask object2, BoundingBox boxIntersect)
protected double	NumberTouchingVoxels.calculateWithIntersection(ObjectMask object1, ObjectMask object2, BoundingBox boxIntersect)
protected abstract double	TouchingVoxels.calculateWithIntersection(ObjectMask object1, ObjectMask object2, BoundingBox boxIntersect)	Calculates the feature value for the intersection of two objects.
protected CountKernel	TouchingVoxels.createCountKernelMask(ObjectMask object2Relative)	Creates a CountKernel for the given object mask.

Uses of ObjectMask in org.anchoranalysis.plugin.image.feature.bean.object.single

Methods in org.anchoranalysis.plugin.image.feature.bean.object.single with parameters of type ObjectMask

Modifier and Type	Method	Description
protected abstract double	OutlineKernelBase.calculateWithParameters(ObjectMask object, KernelApplicationParameters parameters, CheckedSupplier<EnergyStack,FeatureCalculationException> energyStack)	Calculates the feature value using the specified parameters.

Uses of ObjectMask in org.anchoranalysis.plugin.image.feature.bean.object.single.border

Methods in org.anchoranalysis.plugin.image.feature.bean.object.single.border with parameters of type ObjectMask

Modifier and Type	Method	Description
protected double	NumberVoxelsAtBorder.calculateWithParameters(ObjectMask object, KernelApplicationParameters parameters, CheckedSupplier<EnergyStack,FeatureCalculationException> energyStack)
static int	NumberVoxelsAtBorder.numberBorderPixels(ObjectMask object, KernelApplicationParameters parameters)	Calculates the number of border voxels for a given object.

Uses of ObjectMask in org.anchoranalysis.plugin.image.feature.bean.object.single.energy

Methods in org.anchoranalysis.plugin.image.feature.bean.object.single.energy with parameters of type ObjectMask

Modifier and Type	Method	Description
protected double	CountEqual.calculateWithChannel(ObjectMask object, Channel channel)	Calculates the number of voxels in the object that have the specified intensity value in the channel.
protected abstract double	SpecificEnergyChannelBase.calculateWithChannel(ObjectMask object, Channel channel)	Calculates the feature value for a specific object and channel.
protected double	NumberNeighboringVoxels.calculateWithParameters(ObjectMask object, KernelApplicationParameters parameters, CheckedSupplier<EnergyStack,FeatureCalculationException> energyStack)

Uses of ObjectMask in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity

Methods in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity with parameters of type ObjectMask

Modifier and Type	Method	Description
protected double	IntensityMeanShell.calculateForShell(ObjectMask object, Channel channel)
protected abstract double	IntensityMeanShellBase.calculateForShell(ObjectMask shell, Channel channel)	Calculates the feature value for the given shell and channel.
protected double	IntensityMeanShellMaxSlice.calculateForShell(ObjectMask object, Channel channel)

Uses of ObjectMask in org.anchoranalysis.plugin.image.feature.bean.object.single.morphological

Methods in org.anchoranalysis.plugin.image.feature.bean.object.single.morphological that return types with arguments of type ObjectMask

Modifier and Type	Method	Description
protected abstract CalculationPart<ObjectMask,FeatureInputSingleObject>	DerivedObject.createCachedCalculationForDerived(CalculationPartResolver<FeatureInputSingleObject> session)	Creates a CalculationPart for deriving the object mask.
protected CalculationPart<ObjectMask,FeatureInputSingleObject>	Erode.createCachedCalculationForDerived(CalculationPartResolver<FeatureInputSingleObject> session)	Creates a CalculationPart for eroding the object mask.
protected CalculationPart<ObjectMask,FeatureInputSingleObject>	Shell.createCachedCalculationForDerived(CalculationPartResolver<FeatureInputSingleObject> session)

Uses of ObjectMask in org.anchoranalysis.plugin.image.feature.object.calculation.single

Methods in org.anchoranalysis.plugin.image.feature.object.calculation.single that return ObjectMask

Modifier and Type	Method	Description
protected abstract ObjectMask	CalculateIncrementalOperationMap.applyOperation(ObjectMask object, Extent extent, boolean do3D)	Applies the incremental operation to the input object.
protected ObjectMask	CalculateIncrementalOperationMap.execute(FeatureInputSingleObject input, Integer key)
protected ObjectMask	CalculateObjectMask.execute(FeatureInputSingleObject input)
protected ObjectMask	CalculateShellObjectMask.execute(FeatureInputSingleObject input)

Methods in org.anchoranalysis.plugin.image.feature.object.calculation.single that return types with arguments of type ObjectMask

Modifier and Type	Method	Description
static CalculationPart<ObjectMask,FeatureInputSingleObject>	CalculateShellObjectMask.of(CalculationPartResolver<FeatureInputSingleObject> resolver, MorphologicalIterations iterations, int iterationsErosionSecond, boolean inverse)	Creates a new CalculateShellObjectMask instance.

Methods in org.anchoranalysis.plugin.image.feature.object.calculation.single with parameters of type ObjectMask

Modifier and Type	Method	Description
protected abstract ObjectMask	CalculateIncrementalOperationMap.applyOperation(ObjectMask object, Extent extent, boolean do3D)	Applies the incremental operation to the input object.

Constructor parameters in org.anchoranalysis.plugin.image.feature.object.calculation.single with type arguments of type ObjectMask

Modifier	Constructor	Description
protected	CalculateObjectMask(int iterations, ResolvedPartMap<ObjectMask,FeatureInputSingleObject,Integer> map)	Creates a new CalculateObjectMask instance.
	CalculateShellObjectMask(ResolvedPart<ObjectMask,FeatureInputSingleObject> calculateDilation, ResolvedPart<ObjectMask,FeatureInputSingleObject> calculateErosion, int iterationsErosionSecond, boolean do3D, boolean inverse)	Creates a new CalculateShellObjectMask instance.

Uses of ObjectMask in org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological

Methods in org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological that return ObjectMask

Modifier and Type	Method	Description
protected ObjectMask	CalculateDilationMap.applyOperation(ObjectMask object, Extent extent, boolean do3D)
protected ObjectMask	CalculateErosionMap.applyOperation(ObjectMask object, Extent extent, boolean do3D)

Methods in org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological that return types with arguments of type ObjectMask

Modifier and Type	Method	Description
static ResolvedPart<ObjectMask,FeatureInputSingleObject>	CalculateDilation.of(CalculationPartResolver<FeatureInputSingleObject> cache, int iterations, boolean do3D)	Creates a new ResolvedPart for calculating dilation.
static CalculationPart<ObjectMask,FeatureInputSingleObject>	CalculateErosion.of(CalculationPartResolver<FeatureInputSingleObject> cache, int iterations, boolean do3D)	Creates a new CalculationPart for calculating erosion.
static ResolvedPart<ObjectMask,FeatureInputSingleObject>	CalculateErosion.ofResolved(CalculationPartResolver<FeatureInputSingleObject> cache, int iterations, boolean do3D)	Creates a new ResolvedPart for calculating erosion.

Methods in org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological with parameters of type ObjectMask

Modifier and Type	Method	Description
protected ObjectMask	CalculateDilationMap.applyOperation(ObjectMask object, Extent extent, boolean do3D)
protected ObjectMask	CalculateErosionMap.applyOperation(ObjectMask object, Extent extent, boolean do3D)

Uses of ObjectMask in org.anchoranalysis.plugin.image.intensity

Methods in org.anchoranalysis.plugin.image.intensity with parameters of type ObjectMask

Modifier and Type	Method	Description
static double	IntensityMeanCalculator.calculateMeanIntensityObject(Channel channel, ObjectMask object)	Calculates the mean intensity of an object in a channel.
static double	IntensityMeanCalculator.calculateMeanIntensityObject(Channel channel, ObjectMask object, boolean excludeZero)	Calculates the mean intensity of an object in a channel, with an option to exclude zero values.

Uses of ObjectMask in org.anchoranalysis.plugin.image.intensity.level

Methods in org.anchoranalysis.plugin.image.intensity.level that return ObjectMask

Modifier and Type	Method	Description
ObjectMask	LevelResult.getObject()	The ObjectMask associated with this level.

Constructors in org.anchoranalysis.plugin.image.intensity.level with parameters of type ObjectMask

Modifier	Constructor	Description
	LevelResult(int level, ObjectMask object, Histogram histogram)	Creates a new LevelResult instance.

Uses of ObjectMask in org.anchoranalysis.plugin.image.object

Methods in org.anchoranalysis.plugin.image.object that return ObjectMask

Modifier and Type	Method	Description
ObjectMask	ColoredObject.getObject()	The object-mask.

Constructors in org.anchoranalysis.plugin.image.object with parameters of type ObjectMask

Modifier	Constructor	Description
	ColoredObject(ObjectMask object, RGBColor color)	Creates a new ColoredObject instance.
	ColoredObjectCollection(ObjectMask object, RGBColor color)	Create with a single object and color.

Uses of ObjectMask in org.anchoranalysis.plugin.image.object.merge

Methods in org.anchoranalysis.plugin.image.object.merge that return ObjectMask

Modifier and Type	Method	Description
ObjectMask	ObjectVertex.getObject()	The ObjectMask represented by this vertex.

Methods in org.anchoranalysis.plugin.image.object.merge with parameters of type ObjectMask

Modifier and Type	Method	Description
double	PayloadCalculator.calculate(ObjectMask object)	Calculates the payload value for a given object mask.

Constructors in org.anchoranalysis.plugin.image.object.merge with parameters of type ObjectMask

Modifier	Constructor	Description
	ObjectVertex(ObjectMask object, double payload)	Creates a new ObjectVertex instance.

Uses of ObjectMask in org.anchoranalysis.plugin.image.object.merge.condition

Methods in org.anchoranalysis.plugin.image.object.merge.condition with parameters of type ObjectMask

Modifier and Type	Method	Description
boolean	AfterCondition.accept(ObjectMask source, ObjectMask destination, ObjectMask merged)	Checks if the merged object satisfies the condition.
boolean	AndCondition.accept(ObjectMask destination)
boolean	BeforeCondition.accept(ObjectMask source, ObjectMask destination, Optional<UnitConverter> unitConverter)	Checks if the source and destination objects satisfy the condition for merging.
boolean	DistanceCondition.accept(ObjectMask source, ObjectMask destination, Optional<UnitConverter> unitConverter)
boolean	IncreaseFeatureCondition.accept(ObjectMask source, ObjectMask destination, ObjectMask merged)
boolean	NeighborhoodCondition.accept(ObjectMask destination)
boolean	UpdatableBeforeCondition.accept(ObjectMask destination)	Checks if the destination object should be merged with the previously set source object.
boolean	WrapAsUpdatable.accept(ObjectMask destination)
void	AndCondition.updateSourceObject(ObjectMask source, Optional<UnitConverter> unitConverter)
void	NeighborhoodCondition.updateSourceObject(ObjectMask source, Optional<UnitConverter> unitConverter)
void	UpdatableBeforeCondition.updateSourceObject(ObjectMask source, Optional<UnitConverter> unitConverter)	Updates the source object and performs any necessary pre-computations.
void	WrapAsUpdatable.updateSourceObject(ObjectMask source, Optional<UnitConverter> unitConverter)

Uses of ObjectMask in org.anchoranalysis.plugin.image.object.merge.priority

Methods in org.anchoranalysis.plugin.image.object.merge.priority with parameters of type ObjectMask

Modifier and Type	Method	Description
protected abstract PrioritisedVertex	AssignPriority.assignPriorityToEdge(ObjectVertex source, ObjectVertex destination, ObjectMask merge, ErrorReporter errorReporter)	Assigns a priority to an edge between two objects.
PrioritisedVertex	AssignPriorityFromImprovement.assignPriorityToEdge(ObjectVertex source, ObjectVertex destination, ObjectMask merged, ErrorReporter errorReporter)
PrioritisedVertex	AssignPriorityFromPair.assignPriorityToEdge(ObjectVertex source, ObjectVertex destination, ObjectMask merged, ErrorReporter errorReporter)

Constructors in org.anchoranalysis.plugin.image.object.merge.priority with parameters of type ObjectMask

Modifier	Constructor	Description
	PrioritisedVertex(ObjectMask object, double payload, double priority, boolean considerForMerge)	Constructor

Uses of ObjectMask in org.anchoranalysis.plugin.image.segment.thresholder.slice

Constructors in org.anchoranalysis.plugin.image.segment.thresholder.slice with parameters of type ObjectMask

Modifier	Constructor	Description
	SliceThresholderMask(boolean clearOutsideMask, ObjectMask object, BinaryValuesByte binaryValues)	Creates a new SliceThresholderMask.

Uses of ObjectMask in org.anchoranalysis.plugin.image.segment.watershed.encoding

Constructor parameters in org.anchoranalysis.plugin.image.segment.watershed.encoding with type arguments of type ObjectMask

Modifier	Constructor	Description
	Steepest(SlidingBuffer<?> buffer, WatershedEncoding encoder, boolean do3D, boolean bigNeighborhood, Optional<ObjectMask> objectMask)	Creates a Steepest instance for a specific buffer.

Uses of ObjectMask in org.anchoranalysis.plugin.imagej.bean.object.segment

Method parameters in org.anchoranalysis.plugin.imagej.bean.object.segment with type arguments of type ObjectMask

Modifier and Type	Method	Description
ObjectCollection	FloodFillEachIntensityLevel.segment(Channel channel, Optional<ObjectMask> objectMask, Optional<ObjectCollection> seeds)

Uses of ObjectMask in org.anchoranalysis.plugin.opencv

Methods in org.anchoranalysis.plugin.opencv with parameters of type ObjectMask

Modifier and Type	Method	Description
static List<Contour>	CVFindContours.contoursForObject(ObjectMask object)	Calculates the extreme outer contours from an ObjectMask as OpenCV defines contours.

Uses of ObjectMask in org.anchoranalysis.plugin.opencv.convert

Methods in org.anchoranalysis.plugin.opencv.convert with parameters of type ObjectMask

Modifier and Type	Method	Description
static org.opencv.core.Mat	ConvertToMat.fromObject(ObjectMask object)	Convert a ObjectMask to a Mat.

Uses of ObjectMask in org.anchoranalysis.plugin.points.calculate.ellipse

Methods in org.anchoranalysis.plugin.points.calculate.ellipse that return ObjectMask

Modifier and Type	Method	Description
ObjectMask	ObjectWithEllipse.getObject()	The object mask.

Constructors in org.anchoranalysis.plugin.points.calculate.ellipse with parameters of type ObjectMask

Modifier	Constructor	Description
	ObjectWithEllipse(ObjectMask object, Ellipse mark)	Creates a new ObjectWithEllipse instance.

Uses of ObjectMask in org.anchoranalysis.plugin.points.calculate.ellipsoid

Methods in org.anchoranalysis.plugin.points.calculate.ellipsoid with parameters of type ObjectMask

Modifier and Type	Method	Description
static Ellipsoid	EllipsoidFactory.createMarkEllipsoidLeastSquares(ObjectMask object, Dimensions dimensions, boolean suppressZCovariance, double shell)	Creates a Ellipsoid using least-squares fitting to the points on the outline of an ObjectMask.

Uses of ObjectMask in org.anchoranalysis.plugin.points.convexhull

Methods in org.anchoranalysis.plugin.points.convexhull with parameters of type ObjectMask

Modifier and Type	Method	Description
static List<Point2i>	ConvexHullUtilities.pointsOnOutline(ObjectMask object)	Get points on the outline of a single object.

Uses of ObjectMask in org.anchoranalysis.test.feature.plugins.objects

Methods in org.anchoranalysis.test.feature.plugins.objects that return ObjectMask

Modifier and Type	Method	Description
static ObjectMask	CircleObjectFixture.circleAt(Point2i center, double radius)	Creates a circular object mask at a specified center point with a given radius.

Uses of ObjectMask in org.anchoranalysis.test.image

Methods in org.anchoranalysis.test.image with parameters of type ObjectMask

Modifier and Type	Method	Description
void	WriteIntoDirectory.writeObject(String outputName, ObjectMask object)	Writes an ObjectMask to the output directory.

Uses of ObjectMask in org.anchoranalysis.test.image.object

Methods in org.anchoranalysis.test.image.object that return ObjectMask

Modifier and Type	Method	Description
static ObjectMask	CircleObjectFixture.circleAt(Point2d center, int radius)	Creates a single circular mask at a particular center point and radius.
ObjectMask	CutOffCornersObjectFixture.create1()	Create the first object.
ObjectMask	CutOffCornersObjectFixture.create2()	Create the second object.
ObjectMask	CutOffCornersObjectFixture.create3()	Create the third object.
ObjectMask	TestLoaderObjects.openLargestObjectFrom(String suffix)	Opens the largest object from an image stack identified by a suffix.