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

Packages that use ObjectCollection

Package	Description
org.anchoranalysis.annotation.io.assignment	A pairing of objects from two collections (bipartite matching).
org.anchoranalysis.annotation.io.bean.comparer	What to compare an annotation (ground truth) against?
org.anchoranalysis.annotation.mark	Annotations that use one or more marks to describe entities in an image.
org.anchoranalysis.image.bean.nonbean.init	Classes that aren't AnchorBeans that pertain to the initialization of image-related beans.
org.anchoranalysis.image.bean.object	Beans pertaining to ObjectMask and their collections.
org.anchoranalysis.image.bean.provider	Base classes for providers of different core data entities related to images.
org.anchoranalysis.image.bean.segment.object	Base classes to segment a channel into objects.
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.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.feature.input	Image-related implementations of FeatureInput.
org.anchoranalysis.image.inference.segment	Non-beans pertaining to segmentation of images via model inference.
org.anchoranalysis.image.io.object.input	Non-bean classes for reading an ObjectCollection from the filesystem.
org.anchoranalysis.image.io.object.output.grayscale	Writing an ObjectCollection to the filesystem as a single-channeled stack.
org.anchoranalysis.image.io.object.output.hdf5	Writing an ObjectCollection to the filesystem in HDF5 format.
org.anchoranalysis.image.io.object.output.mask	Writing an ObjectCollection to the filesystem as multiple binary singled-channeled images.
org.anchoranalysis.image.voxel.binary.connected	Creating an ObjectCollection that is a connected component labelling of a BinaryVoxels.
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.mpp.io.input	Non-beans for reading data structures related to marked point processes from the file system.
org.anchoranalysis.mpp.mark	Non-bean classes related to Marks.
org.anchoranalysis.plugin.annotation.bean.comparer	Comparing the similarity of annotations from two images to each other.
org.anchoranalysis.plugin.annotation.comparison	Non-bean classes for comparing two sets of annotations.
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.intensity	Implementations of ChannelProvider that manipulate the intensity-values of the voxels of a Channel's voxels.
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	Implementations of ChannelProvider that assign a score to particular subregions of a channel.
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.combine	Implementations of ObjectFilter that combine two or more other ObjectFilters.
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	Implementations of ObjectMatcher.
org.anchoranalysis.plugin.image.bean.object.provider	Implementations of ObjectCollectionProvider.
org.anchoranalysis.plugin.image.bean.object.provider.connected	Implementations of ObjectCollectionProvider involving connected-components.
org.anchoranalysis.plugin.image.bean.object.provider.feature	Implementations of ObjectCollectionProvider involving feature calculation.
org.anchoranalysis.plugin.image.bean.object.provider.filter	Implementations of ObjectCollectionProvider that filter objects.
org.anchoranalysis.plugin.image.bean.object.provider.mask	Implementations of ObjectCollectionProvider involving a Mask.
org.anchoranalysis.plugin.image.bean.object.provider.merge	Implementations of ObjectCollectionProvider involving merging objects together.
org.anchoranalysis.plugin.image.bean.object.provider.morphological	Implementations of ObjectCollectionProvider involving morphological operations.
org.anchoranalysis.plugin.image.bean.object.provider.segment	Implementations of ObjectCollectionProvider involving segmentation.
org.anchoranalysis.plugin.image.bean.object.provider.slice	Implementations of ObjectCollectionProvider involving z-slice processing.
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	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.yeong	Implementation of a Watershed transformation based on Yeong et al. 2009.
org.anchoranalysis.plugin.image.bean.stack.provider.color	Implementations of StackProvider that color portions of an image.
org.anchoranalysis.plugin.image.bean.thumbnail.object	Implementations of ThumbnailFromObjects.
org.anchoranalysis.plugin.image.feature.bean.object.combine	Features from combinations of ObjectMasks.
org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting	Implementations of FeatureSingleObject that use SharedObjects for calculations, and measure the degree of intersection between objects.
org.anchoranalysis.plugin.image.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.task.feature.calculator	Non-beans for calculating Features.
org.anchoranalysis.plugin.imagej.bean.object.provider	Implementations of ObjectCollectionProvider that call ImageJ.
org.anchoranalysis.plugin.imagej.bean.object.segment	Implementations of ObjectCollectionProvider that call ImageJ to perform segmentation.
org.anchoranalysis.plugin.mpp.bean.object.provider	Implementations of ObjectCollectionProvider.
org.anchoranalysis.plugin.mpp.bean.stack.provider	Implementations of StackProvider involving Mark or related classes.
org.anchoranalysis.plugin.points.bean	Beans that fit or otherwise manipulate sets of points.
org.anchoranalysis.plugin.points.bean.fitter	Fitting geometric structures to points.
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.io	Utilities for testing-related reading and writing to the filesystem.
org.anchoranalysis.test.image.object	Fixtures for creating object-masks.

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

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

Modifier and Type	Method	Description
void	OverlappingObjects.addUnassignedLeft(ObjectCollection objects)	Add unassigned objects to the left set.
void	OverlappingObjects.addUnassignedRight(ObjectCollection objects)	Add unassigned objects to the right set.
OverlappingObjects	AssignOverlappingObjects.createAssignment(ObjectCollection left, ObjectCollection right, double maxAcceptedCost, Dimensions dimensions)	Creates an assignment from the objects in left to those in right.
static OverlappingObjects	OverlappingObjects.createWithLeftUnassigned(ObjectCollection objects)	Creates with only left unassigned objects.
static OverlappingObjects	OverlappingObjects.createWithRight(ObjectCollection objects)	Creates with only right unassigned objects.

Uses of ObjectCollection in org.anchoranalysis.annotation.io.bean.comparer

Methods in org.anchoranalysis.annotation.io.bean.comparer that return types with arguments of type ObjectCollection

Modifier and Type	Method	Description
abstract Findable<ObjectCollection>	ComparableSource.loadAsObjects(Path reference, Dimensions dimensions, boolean debugMode, OperationContext context)	Loads the source of elements from the file-system and converts to a ObjectCollection.

Uses of ObjectCollection in org.anchoranalysis.annotation.mark

Methods in org.anchoranalysis.annotation.mark that return ObjectCollection

Modifier and Type	Method	Description
default ObjectCollection	AnnotationWithMarks.convertToObjects(Dimensions dimensions)	Creates an object-collection that is a voxelized representation of the marks in the annotation.

Uses of ObjectCollection in org.anchoranalysis.image.bean.nonbean.init

Methods in org.anchoranalysis.image.bean.nonbean.init that return types with arguments of type ObjectCollection

Modifier and Type	Method	Description
NamedProviderStore<ObjectCollection>	ImageInitialization.objects()	A collection of ObjectCollections, indexed by name.

Method parameters in org.anchoranalysis.image.bean.nonbean.init with type arguments of type ObjectCollection

Modifier and Type	Method	Description
void	ImageInitialization.addObjectsFrom(NamedProvider<ObjectCollection> source)	Adds all the ObjectCollections available in a NamedProvider using the corresponding identifiers.

Uses of ObjectCollection in org.anchoranalysis.image.bean.object

Methods in org.anchoranalysis.image.bean.object that return ObjectCollection

Modifier and Type	Method	Description
abstract ObjectCollection	ObjectFilter.filter(ObjectCollection objectsToFilter, Optional<Dimensions> dimensions)	Filters an ObjectCollection to remove objects.

Methods in org.anchoranalysis.image.bean.object with parameters of type ObjectCollection

Modifier and Type	Method	Description
abstract ObjectCollection	ObjectFilter.filter(ObjectCollection objectsToFilter, Optional<Dimensions> dimensions)	Filters an ObjectCollection to remove objects.
abstract List<MatchedObject>	ObjectMatcher.findMatch(ObjectCollection sourceObjects)	Finds matches for objects.

Uses of ObjectCollection in org.anchoranalysis.image.bean.provider

Methods in org.anchoranalysis.image.bean.provider that return ObjectCollection

Modifier and Type	Method	Description
protected abstract ObjectCollection	ObjectCollectionProviderUnary.createFromObjects(ObjectCollection objects)	Creates a ObjectCollection given the entity provided by the delegate.
ObjectCollection	ObjectCollectionProviderUnary.get()

Methods in org.anchoranalysis.image.bean.provider that return types with arguments of type ObjectCollection

Modifier and Type	Method	Description
Provider<ObjectCollection>	ObjectCollectionProviderUnary.getObjects()	The delegate Provider<ObjectCollection> that is called.

Methods in org.anchoranalysis.image.bean.provider with parameters of type ObjectCollection

Modifier and Type	Method	Description
protected abstract ObjectCollection	ObjectCollectionProviderUnary.createFromObjects(ObjectCollection objects)	Creates a ObjectCollection given the entity provided by the delegate.

Method parameters in org.anchoranalysis.image.bean.provider with type arguments of type ObjectCollection

Modifier and Type	Method	Description
void	ObjectCollectionProviderUnary.setObjects(Provider<ObjectCollection> objects)	The delegate Provider<ObjectCollection> that is called.

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

Methods in org.anchoranalysis.image.bean.segment.object that return ObjectCollection

Modifier and Type	Method	Description
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.

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

Modifier and Type	Method	Description
protected static void	SegmentChannelIntoObjects.checkUnsupportedSeeds(Optional<ObjectCollection> seeds)	Throws an exception if seeds is present, as it is unsupported by the implementation.

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

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

Modifier and Type	Method	Description
static Mask	MaskFromObjects.createFromNotObjects(ObjectCollection objects, Dimensions dimensions, BinaryValuesInt outValues)	Create a Mask corresponding to all off voxels in an ObjectCollection.
static Mask	MaskFromObjects.createFromObjects(ObjectCollection objects, Dimensions dimensions, BinaryValuesInt outValues)	Create a Mask corresponding to all on voxels in an ObjectCollection.

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

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

Modifier and Type	Method	Description
static ObjectMask	ObjectMaskMerger.merge(ObjectCollection objects)	Merges all the objects together that are found in a collection.
static BoundingBox	ObjectMaskMerger.mergeBoundingBoxes(ObjectCollection objects)	Merges all the bounding boxes of a collection of objects.

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

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

Modifier and Type	Method	Description
ObjectCollection	MatchedObject.getMatches()	The matches associated with the source-object

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

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

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

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

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

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

Modifier and Type	Method	Description
ObjectCollection	ObjectCollectionWithProperties.withoutProperties()	Returns the contained-objects without the corresponding properties.

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

Modifier	Constructor	Description
	ObjectCollectionWithProperties(ObjectCollection objects)	Create with a stream of objects, assign empty properties to each.

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

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

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.

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

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

Modifier and Type	Method	Description
static List<Point2i>	PointsFromObject.listFromAllOutlines2i(ObjectCollection objects)	A list of points as three-dimensional integers from the outline of all objects in a collection.

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

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

Modifier and Type	Method	Description
ObjectCollection	FeatureInputObjectCollection.getObjects()	The collection of objects associated with this feature input.

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

Modifier	Constructor	Description
	FeatureInputObjectCollection(ObjectCollection objects)	Constructs a FeatureInputObjectCollection with a collection of objects.
	FeatureInputObjectCollection(ObjectCollection objects, Optional<EnergyStack> energyStack)	Constructs a FeatureInputObjectCollection with a collection of objects and an optional energy stack.

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

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

Modifier and Type	Method	Description
ObjectCollection	SegmentedObjectsAtScale.objects()	Create a ObjectCollection of all contained objects, excluding confidence.

Uses of ObjectCollection in org.anchoranalysis.image.io.object.input

Methods in org.anchoranalysis.image.io.object.input that return ObjectCollection

Modifier and Type	Method	Description
static ObjectCollection	ObjectCollectionReader.createFromPath(Path path, OperationContext context)	Reads an object-collection from a path (or path prefix) trying different methods to read the objects.

Uses of ObjectCollection in org.anchoranalysis.image.io.object.output.grayscale

Methods in org.anchoranalysis.image.io.object.output.grayscale with parameters of type ObjectCollection

Modifier and Type	Method	Description
Stack	ObjectsAsUniqueValueGenerator.transform(ObjectCollection element)
Stack	ObjectsMergedAsMaskGenerator.transform(ObjectCollection element)

Uses of ObjectCollection in org.anchoranalysis.image.io.object.output.hdf5

Methods in org.anchoranalysis.image.io.object.output.hdf5 that return types with arguments of type ObjectCollection

Modifier and Type	Method	Description
static Generator<ObjectCollection>	ObjectCollectionWriter.generator()	A Generator which writes an ObjectCollection to the file-system.

Methods in org.anchoranalysis.image.io.object.output.hdf5 with parameters of type ObjectCollection

Modifier and Type	Method	Description
void	HDF5ObjectsGenerator.writeToFile(ObjectCollection element, OutputWriteSettings settings, Path filePath)

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

Methods in org.anchoranalysis.image.io.object.output.mask that return types with arguments of type ObjectCollection

Modifier and Type	Method	Description
static Generator<ObjectCollection>	RasterDirectoryObjectsGenerator.create()	Creates the Generator to write each object as a binary Mask in a directory.

Uses of ObjectCollection in org.anchoranalysis.image.voxel.binary.connected

Methods in org.anchoranalysis.image.voxel.binary.connected that return ObjectCollection

Modifier and Type	Method	Description
ObjectCollection	ObjectsFromConnectedComponentsFactory.createUnsignedByte(BinaryVoxels<UnsignedByteBuffer> voxels)	Finds the connected-components in unsigned byte voxels.
ObjectCollection	ObjectsFromConnectedComponentsFactory.createUnsignedInt(BinaryVoxels<UnsignedIntBuffer> voxels)	Finds the connected-components in unsigned int voxels.

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

Methods in org.anchoranalysis.image.voxel.neighborhood with parameters of type ObjectCollection

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.

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

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

Modifier and Type	Method	Description
ObjectCollection	ObjectCollection.createSubset(Collection<Integer> indices)	A subset of the collection identified by particular indices.
ObjectCollection	ObjectCollection.duplicate()	Deep copy, including duplicating ObjectMasks.
ObjectCollection	ObjectCollection.duplicateShallow()	Shallow copy of objects.
static ObjectCollection	ObjectCollectionFactory.empty()	Creates a newly created object-collection that is empty.
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>).
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.
<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> ObjectCollection	ObjectCollectionFactory.flatMapFrom(Collection<T> collection, Function<T,ObjectCollection> mapFunction)	Creates a new collection by flat-mapping an incoming stream to ObjectCollection.
static <T, E extends Exception> ObjectCollection	ObjectCollectionFactory.flatMapFrom(Stream<T> stream, Class<? extends Exception> throwableClass, CheckedFunction<T,ObjectCollection,E> mapFunction)	Creates a new collection by flat-mapping an incoming stream to ObjectCollection and rethrowing any exception during mapping.
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 <E extends Exception> ObjectCollection	ObjectCollectionFactory.flatMapFromRange(int startInclusive, int endExclusive, Class<? extends Exception> throwableClass, CheckedIntFunction<ObjectCollection,E> mapFunction)	Creates a new collection by flat-mapping integers (from a range) each to a ObjectCollection.
static ObjectCollection	ObjectCollectionFactory.flatMapFromRange(int startInclusive, int endExclusive, IntFunction<ObjectCollection> mapFunction)	Creates a new collection by flat-mapping integers (from a range) each to a ObjectCollection.
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.
ObjectCollection	ObjectMaskStream.mapBoundingBoxChangeExtent(BoundingBox boxToAssign)	Creates a new ObjectCollection after mapping the bounding-box on each object (while maybe changing the extent).
ObjectCollection	ObjectMaskStream.mapBoundingBoxPreserveExtent(UnaryOperator<BoundingBox> mapFunction)	Creates a new ObjectCollection after mapping the bounding-box on each object (whose extent should remain unchanged).
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.
static ObjectCollection	ObjectCollectionFactory.of(Collection<ObjectMask>... collections)	Creates a new collection with elements copied from existing collections.
static ObjectCollection	ObjectCollectionFactory.of(Optional<ObjectCollection>... collections)	Creates a new collection with elements copied from existing collections, if they exist.
static ObjectCollection	ObjectCollectionFactory.of(BinaryVoxels<UnsignedByteBuffer>... masks)	Creates a new collection with elements from the parameter-list of BinaryVoxels converting the voxels in their entirety to an object-mask at the origin.
static ObjectCollection	ObjectCollectionFactory.of(ObjectCollection... collection)	Creates a new collection with elements copied from existing collections.
static ObjectCollection	ObjectCollectionFactory.of(ObjectMask... object)	Creates a new collection with elements from the parameter-list.
ObjectCollection	ObjectCollection.shiftBy(ReadableTuple3i shiftBy)	Shifts the bounding-box of each object by adding to it.

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

Modifier and Type	Method	Description
static IntersectingObjects<ObjectMask>	IntersectingObjects.create(ObjectCollection objects)	Creates from an ObjectCollection.
boolean	ObjectCollection.equalsDeep(ObjectCollection other)	Checks if two collections are equal in a deeper way.
static ObjectCollection	ObjectCollectionFactory.of(ObjectCollection... collection)	Creates a new collection with elements copied from existing collections.

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

Modifier and Type	Method	Description
<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> ObjectCollection	ObjectCollectionFactory.flatMapFrom(Collection<T> collection, Function<T,ObjectCollection> mapFunction)	Creates a new collection by flat-mapping an incoming stream to ObjectCollection.
static <T, E extends Exception> ObjectCollection	ObjectCollectionFactory.flatMapFrom(Stream<T> stream, Class<? extends Exception> throwableClass, CheckedFunction<T,ObjectCollection,E> mapFunction)	Creates a new collection by flat-mapping an incoming stream to ObjectCollection and rethrowing any exception during mapping.
static <E extends Exception> ObjectCollection	ObjectCollectionFactory.flatMapFromRange(int startInclusive, int endExclusive, Class<? extends Exception> throwableClass, CheckedIntFunction<ObjectCollection,E> mapFunction)	Creates a new collection by flat-mapping integers (from a range) each to a ObjectCollection.
static ObjectCollection	ObjectCollectionFactory.flatMapFromRange(int startInclusive, int endExclusive, IntFunction<ObjectCollection> mapFunction)	Creates a new collection by flat-mapping integers (from a range) each to a ObjectCollection.

Constructors in org.anchoranalysis.image.voxel.object with parameters of type ObjectCollection

Modifier	Constructor	Description
	ObjectMaskStream(ObjectCollection delegate)

Uses of ObjectCollection in org.anchoranalysis.mpp.io.input

Methods in org.anchoranalysis.mpp.io.input that return types with arguments of type ObjectCollection

Modifier and Type	Method	Description
MultiInputSubMap<ObjectCollection>	MultiInput.objects()	Gets the map of ObjectCollections.

Uses of ObjectCollection in org.anchoranalysis.mpp.mark

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

Modifier and Type	Method	Description
ObjectCollection	MarkCollection.deriveObjects(Dimensions dimensions, RegionMembershipWithFlags regionMembership)	Derives objects from the marks in the collection.

Uses of ObjectCollection in org.anchoranalysis.plugin.annotation.bean.comparer

Methods in org.anchoranalysis.plugin.annotation.bean.comparer that return types with arguments of type ObjectCollection

Modifier and Type	Method	Description
Findable<ObjectCollection>	MaskAsObject.loadAsObjects(Path reference, Dimensions dimensions, boolean debugMode, OperationContext context)
Findable<ObjectCollection>	Objects.loadAsObjects(Path filePathSource, Dimensions dimensions, boolean debugMode, OperationContext context)

Uses of ObjectCollection in org.anchoranalysis.plugin.annotation.comparison

Methods in org.anchoranalysis.plugin.annotation.comparison that return ObjectCollection

Modifier and Type	Method	Description
ObjectCollection	ObjectsToCompare.getLeft()	Objects on left-side of the comparison.
ObjectCollection	ObjectsToCompare.getRight()	Objects on right-side of the comparison.

Constructors in org.anchoranalysis.plugin.annotation.comparison with parameters of type ObjectCollection

Modifier	Constructor	Description
	ObjectsToCompare(ObjectCollection left, ObjectCollection right)	Creates a new ObjectsToCompare instance.

Uses of ObjectCollection in org.anchoranalysis.plugin.image.bean.channel.provider

Methods in org.anchoranalysis.plugin.image.bean.channel.provider with parameters of type ObjectCollection

Modifier and Type	Method	Description
protected abstract Channel	UnaryWithObjectsBase.createFromChannel(Channel channel, ObjectCollection objects)	Creates a new channel from an existing channel and a collection of objects.

Uses of ObjectCollection in org.anchoranalysis.plugin.image.bean.channel.provider.intensity

Methods in org.anchoranalysis.plugin.image.bean.channel.provider.intensity with parameters of type ObjectCollection

Modifier and Type	Method	Description
protected Channel	NormalizeDifferenceToMedian.createFromChannel(Channel channel, ObjectCollection objects)
protected Channel	NormalizeObjectIntensity.createFromChannel(Channel channel, ObjectCollection objects)

Uses of ObjectCollection in org.anchoranalysis.plugin.image.bean.channel.provider.object

Methods in org.anchoranalysis.plugin.image.bean.channel.provider.object with parameters of type ObjectCollection

Modifier and Type	Method	Description
protected abstract void	LevelPerObjectBase.writeLevelsForObjects(Channel input, ObjectCollection objects, Channel output)	Creates a channel with the levels for a set of objects.
protected void	LevelPerObjectIndependently.writeLevelsForObjects(Channel channelIntensity, ObjectCollection objects, Channel output)
protected void	LevelPerObjectNeighbors.writeLevelsForObjects(Channel channelIntensity, ObjectCollection objects, Channel output)

Uses of ObjectCollection in org.anchoranalysis.plugin.image.bean.channel.provider.score

Methods in org.anchoranalysis.plugin.image.bean.channel.provider.score with parameters of type ObjectCollection

Modifier and Type	Method	Description
protected Channel	IdentifyObjects.createFromChannel(Channel channel, ObjectCollection objects)
protected Channel	ScoreObjects.createFromChannel(Channel channel, ObjectCollection objects)

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

Methods in org.anchoranalysis.plugin.image.bean.object.filter that return ObjectCollection

Modifier and Type	Method	Description
ObjectCollection	ObjectFilterPredicate.filter(ObjectCollection objectsToFilter, Optional<Dimensions> dimensions)

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

Modifier and Type	Method	Description
ObjectCollection	ObjectFilterPredicate.filter(ObjectCollection objectsToFilter, Optional<Dimensions> dimensions)
protected abstract boolean	ObjectFilterPredicate.precondition(ObjectCollection objectsToFilter)	A precondition, which if evaluates to false, cancels the filter i.e. nothing is removed.
protected boolean	ObjectFilterRelation.precondition(ObjectCollection objectsToFilter)
protected void	ObjectFilterPredicate.start(Optional<Dimensions> dimensions, ObjectCollection objectsToFilter)	Performs any necessary initialization before filtering begins.
protected void	ObjectFilterRelation.start(Optional<Dimensions> dimensions, ObjectCollection objectsToFilter)

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

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

Modifier and Type	Method	Description
protected boolean	DiscardOutliers.precondition(ObjectCollection objectsToFilter)
protected void	DiscardOutliers.start(Optional<Dimensions> dimensions, ObjectCollection objectsToFilter)
protected void	RelationWithMatches.start(Optional<Dimensions> dimensions, ObjectCollection objectsToFilter)

Uses of ObjectCollection in org.anchoranalysis.plugin.image.bean.object.filter.combine

Methods in org.anchoranalysis.plugin.image.bean.object.filter.combine that return ObjectCollection

Modifier and Type	Method	Description
ObjectCollection	And.filter(ObjectCollection objects, Optional<Dimensions> dim)
ObjectCollection	Or.filter(ObjectCollection objectsToFilter, Optional<Dimensions> dim)

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

Modifier and Type	Method	Description
ObjectCollection	And.filter(ObjectCollection objects, Optional<Dimensions> dim)
ObjectCollection	Or.filter(ObjectCollection objectsToFilter, Optional<Dimensions> dim)

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

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

Modifier and Type	Method	Description
protected boolean	GreaterIntersectionWith.precondition(ObjectCollection objectsToFilter)
protected boolean	IntensityGreaterEqualThan.precondition(ObjectCollection objectsToFilter)
protected boolean	IntersectsWith.precondition(ObjectCollection objectsToFilter)
protected boolean	NotTouchingSceneBorder.precondition(ObjectCollection objectsToFilter)
protected void	GreaterIntersectionWith.start(Optional<Dimensions> dimensions, ObjectCollection objectsToFilter)
protected void	IntensityGreaterEqualThan.start(Optional<Dimensions> dimensions, ObjectCollection objectsToFilter)
protected void	IntersectsWith.start(Optional<Dimensions> dimensions, ObjectCollection objectsToFilter)
protected void	ThresholdedFeature.start(Optional<Dimensions> dimensions, ObjectCollection objectsToFilter)
protected void	ThresholdedVolume.start(Optional<Dimensions> dimensions, ObjectCollection objectsToFilter)

Uses of ObjectCollection in org.anchoranalysis.plugin.image.bean.object.match

Methods in org.anchoranalysis.plugin.image.bean.object.match with parameters of type ObjectCollection

Modifier and Type	Method	Description
List<MatchedObject>	Always.findMatch(ObjectCollection sourceObjects)
List<MatchedObject>	Bridge.findMatch(ObjectCollection sourceObjects)
List<MatchedObject>	Intersection.findMatch(ObjectCollection sourceObjects)
static List<MatchedObject>	MatcherIntersectionHelper.matchIntersectingObjects(ObjectCollection sourceObjects, ObjectCollection searchObjects)	Matches objects from the source collection with intersecting objects from the search collection.

Uses of ObjectCollection in org.anchoranalysis.plugin.image.bean.object.provider

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

Modifier and Type	Method	Description
protected ObjectCollection	WithContainerBase.containerRequired()	Retrieves the required container of objects.
protected abstract ObjectCollection	WithChannelBase.createFromChannel(Channel channelSrc)	Creates an ObjectCollection from a source Channel.
ObjectCollection	AtIndex.createFromObjects(ObjectCollection objects)
ObjectCollection	Duplicate.createFromObjects(ObjectCollection objects)
ObjectCollection	Scale.createFromObjects(ObjectCollection objects)
ObjectCollection	UnaryWithChannelBase.createFromObjects(ObjectCollection objectsSource)
protected abstract ObjectCollection	UnaryWithChannelBase.createFromObjects(ObjectCollection objectsSource, Channel channelSource)	Creates objects from a source collection and a channel.
ObjectCollection	Concatenate.get()
ObjectCollection	Empty.get()
ObjectCollection	IfParamEqual.get()
ObjectCollection	Permute.get()
ObjectCollection	Reference.get()
ObjectCollection	ReferenceOrElse.get()
ObjectCollection	WithChannelBase.get()

Methods in org.anchoranalysis.plugin.image.bean.object.provider that return types with arguments of type ObjectCollection

Modifier and Type	Method	Description
protected Optional<ObjectCollection>	WithContainerBase.containerOptional()	Retrieves the optional container of objects.

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

Modifier and Type	Method	Description
ObjectCollection	AtIndex.createFromObjects(ObjectCollection objects)
ObjectCollection	Duplicate.createFromObjects(ObjectCollection objects)
ObjectCollection	Scale.createFromObjects(ObjectCollection objects)
ObjectCollection	UnaryWithChannelBase.createFromObjects(ObjectCollection objectsSource)
protected abstract ObjectCollection	UnaryWithChannelBase.createFromObjects(ObjectCollection objectsSource, Channel channelSource)	Creates objects from a source collection and a channel.

Uses of ObjectCollection in org.anchoranalysis.plugin.image.bean.object.provider.connected

Methods in org.anchoranalysis.plugin.image.bean.object.provider.connected that return ObjectCollection

Modifier and Type	Method	Description
ObjectCollection	DecomposeIntoConnectedComponents.createFromObjects(ObjectCollection objects)
ObjectCollection	RejectIfNotConnected.createFromObjects(ObjectCollection objects)
ObjectCollection	ConnectedComponentsFromMask.get()

Methods in org.anchoranalysis.plugin.image.bean.object.provider.connected with parameters of type ObjectCollection

Modifier and Type	Method	Description
ObjectCollection	DecomposeIntoConnectedComponents.createFromObjects(ObjectCollection objects)
ObjectCollection	RejectIfNotConnected.createFromObjects(ObjectCollection objects)

Uses of ObjectCollection in org.anchoranalysis.plugin.image.bean.object.provider.feature

Methods in org.anchoranalysis.plugin.image.bean.object.provider.feature that return ObjectCollection

Modifier and Type	Method	Description
ObjectCollection	ObjectWithMaximumFeature.createFromObjects(ObjectCollection objects)
ObjectCollection	ObjectWithMaximumFeatureFromEachMatchedCollection.createFromObjects(ObjectCollection objects)
ObjectCollection	SortByFeature.createFromObjects(ObjectCollection objects)

Methods in org.anchoranalysis.plugin.image.bean.object.provider.feature with parameters of type ObjectCollection

Modifier and Type	Method	Description
ObjectCollection	ObjectWithMaximumFeature.createFromObjects(ObjectCollection objects)
ObjectCollection	ObjectWithMaximumFeatureFromEachMatchedCollection.createFromObjects(ObjectCollection objects)
ObjectCollection	SortByFeature.createFromObjects(ObjectCollection objects)

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

Methods in org.anchoranalysis.plugin.image.bean.object.provider.filter that return ObjectCollection

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)
ObjectCollection	IntersectsWithContainer.createFromObjects(ObjectCollection objects)
ObjectCollection	Match.createFromObjects(ObjectCollection objects)
ObjectCollection	NotInContainer.createFromObjects(ObjectCollection objects)
ObjectCollection	ObjectCollectionProviderFilterBase.createFromObjects(ObjectCollection objects)
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.
ObjectCollection	RemoveTouchingBorder.createFromObjects(ObjectCollection objects)
protected ObjectCollection	ObjectCollectionProviderFilterBase.filter(ObjectCollection objects, Optional<Dimensions> dimensions, Optional<List<ObjectMask>> objectsRejected)	Filters the given object collection using the specified filter.

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

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)
ObjectCollection	IntersectsWithContainer.createFromObjects(ObjectCollection objects)
ObjectCollection	Match.createFromObjects(ObjectCollection objects)
ObjectCollection	NotInContainer.createFromObjects(ObjectCollection objects)
ObjectCollection	ObjectCollectionProviderFilterBase.createFromObjects(ObjectCollection objects)
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.
ObjectCollection	RemoveTouchingBorder.createFromObjects(ObjectCollection objects)
protected ObjectCollection	ObjectCollectionProviderFilterBase.filter(ObjectCollection objects, Optional<Dimensions> dimensions, Optional<List<ObjectMask>> objectsRejected)	Filters the given object collection using the specified filter.

Uses of ObjectCollection in org.anchoranalysis.plugin.image.bean.object.provider.mask

Methods in org.anchoranalysis.plugin.image.bean.object.provider.mask that return ObjectCollection

Modifier and Type	Method	Description
ObjectCollection	AndObjectsWithMasks.createFromObjects(ObjectCollection objects)
ObjectCollection	FromMask.get()

Methods in org.anchoranalysis.plugin.image.bean.object.provider.mask with parameters of type ObjectCollection

Modifier and Type	Method	Description
ObjectCollection	AndObjectsWithMasks.createFromObjects(ObjectCollection objects)

Uses of ObjectCollection in org.anchoranalysis.plugin.image.bean.object.provider.merge

Methods in org.anchoranalysis.plugin.image.bean.object.provider.merge that return ObjectCollection

Modifier and Type	Method	Description
ObjectCollection	MergeGreedyToIncreaseObjectFeature.createFromObjects(ObjectCollection objectsSource)
ObjectCollection	MergeWithFeature.createFromObjects(ObjectCollection objectsSource)
ObjectCollection	MergeTwoCollectionsItemwise.get()
protected ObjectCollection	MergeBase.mergeMultiplex(ObjectCollection objects, MergeBase.MergeObjects mergeFunc)	Merges objects either in a container or altogether.
ObjectCollection	MergeBase.MergeObjects.mergeObjects(ObjectCollection objects)	Merges a collection of objects.

Methods in org.anchoranalysis.plugin.image.bean.object.provider.merge with parameters of type ObjectCollection

Modifier and Type	Method	Description
ObjectCollection	MergeGreedyToIncreaseObjectFeature.createFromObjects(ObjectCollection objectsSource)
ObjectCollection	MergeWithFeature.createFromObjects(ObjectCollection objectsSource)
protected ObjectCollection	MergeBase.mergeMultiplex(ObjectCollection objects, MergeBase.MergeObjects mergeFunc)	Merges objects either in a container or altogether.
ObjectCollection	MergeBase.MergeObjects.mergeObjects(ObjectCollection objects)	Merges a collection of objects.

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

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

Modifier and Type	Method	Description
ObjectCollection	ObjectCollectionProviderMorphological.createFromObjects(ObjectCollection objects)

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

Modifier and Type	Method	Description
ObjectCollection	ObjectCollectionProviderMorphological.createFromObjects(ObjectCollection objects)

Uses of ObjectCollection in org.anchoranalysis.plugin.image.bean.object.provider.segment

Methods in org.anchoranalysis.plugin.image.bean.object.provider.segment that return ObjectCollection

Modifier and Type	Method	Description
protected ObjectCollection	SegmentChannel.createFromChannel(Channel channelSource)
protected ObjectCollection	SegmentWithSeeds.createFromChannel(Channel channel)
protected ObjectCollection	BinarySegmentByObject.createFromObjects(ObjectCollection objectsSource, Channel channelSource)
ObjectCollection	SegmentChannelByObject.createFromObjects(ObjectCollection objectsSource, Channel channelToSegment)
ObjectCollection	SegmentStack.get()

Methods in org.anchoranalysis.plugin.image.bean.object.provider.segment with parameters of type ObjectCollection

Modifier and Type	Method	Description
protected ObjectCollection	BinarySegmentByObject.createFromObjects(ObjectCollection objectsSource, Channel channelSource)
ObjectCollection	SegmentChannelByObject.createFromObjects(ObjectCollection objectsSource, Channel channelToSegment)

Uses of ObjectCollection in org.anchoranalysis.plugin.image.bean.object.provider.slice

Methods in org.anchoranalysis.plugin.image.bean.object.provider.slice that return ObjectCollection

Modifier and Type	Method	Description
ObjectCollection	ExtendInZ.createFromObjects(ObjectCollection objects)
ObjectCollection	ExtendInZWithinContainer.createFromObjects(ObjectCollection objectsSource)
ObjectCollection	FlattenZ.createFromObjects(ObjectCollection objects)
ObjectCollection	SliceAt.createFromObjects(ObjectCollection objects)

Methods in org.anchoranalysis.plugin.image.bean.object.provider.slice with parameters of type ObjectCollection

Modifier and Type	Method	Description
ObjectCollection	ExtendInZ.createFromObjects(ObjectCollection objects)
ObjectCollection	ExtendInZWithinContainer.createFromObjects(ObjectCollection objectsSource)
ObjectCollection	FlattenZ.createFromObjects(ObjectCollection objects)
ObjectCollection	SliceAt.createFromObjects(ObjectCollection objects)

Uses of ObjectCollection in org.anchoranalysis.plugin.image.bean.object.provider.split

Methods in org.anchoranalysis.plugin.image.bean.object.provider.split that return ObjectCollection

Modifier and Type	Method	Description
ObjectCollection	RemoveIntersectingVoxels.createFromObjects(ObjectCollection objects)
ObjectCollection	SplitByObjects.createFromObjects(ObjectCollection objectCollection)
ObjectCollection	SplitIntoSquares.createFromObjects(ObjectCollection objectCollection)

Methods in org.anchoranalysis.plugin.image.bean.object.provider.split with parameters of type ObjectCollection

Modifier and Type	Method	Description
ObjectCollection	RemoveIntersectingVoxels.createFromObjects(ObjectCollection objects)
ObjectCollection	SplitByObjects.createFromObjects(ObjectCollection objectCollection)
ObjectCollection	SplitIntoSquares.createFromObjects(ObjectCollection objectCollection)

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

Methods in org.anchoranalysis.plugin.image.bean.object.segment.channel that return ObjectCollection

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 ObjectCollection in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima

Methods in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima with parameters of type ObjectCollection

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 ObjectCollection in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong

Methods in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong that return ObjectCollection

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

Uses of ObjectCollection in org.anchoranalysis.plugin.image.bean.stack.provider.color

Methods in org.anchoranalysis.plugin.image.bean.stack.provider.color that return ObjectCollection

Modifier and Type	Method	Description
protected abstract ObjectCollection	ColoredBaseWithGenerator.objectsToDraw(Dimensions backgroundDimensions)	The objects to draw (without any colors) on the background.
protected ObjectCollection	ColoredObjects.objectsToDraw(Dimensions backgroundDimensions)

Uses of ObjectCollection in org.anchoranalysis.plugin.image.bean.thumbnail.object

Methods in org.anchoranalysis.plugin.image.bean.thumbnail.object that return types with arguments of type ObjectCollection

Modifier and Type	Method	Description
ThumbnailBatch<ObjectCollection>	OutlinePreserveRelativeSize.start(ObjectCollection objects, StreamableCollection<BoundingBox> boundingBoxes, Optional<Stack> backgroundSource, ExecutionTimeRecorder executionTimeRecorder)
abstract ThumbnailBatch<ObjectCollection>	ThumbnailFromObjects.start(ObjectCollection objects, StreamableCollection<BoundingBox> boundingBoxes, Optional<Stack> background, ExecutionTimeRecorder executionTimeRecorder)	Initializes a batch to create thumbnails.

Methods in org.anchoranalysis.plugin.image.bean.thumbnail.object with parameters of type ObjectCollection

Modifier and Type	Method	Description
ThumbnailBatch<ObjectCollection>	OutlinePreserveRelativeSize.start(ObjectCollection objects, StreamableCollection<BoundingBox> boundingBoxes, Optional<Stack> backgroundSource, ExecutionTimeRecorder executionTimeRecorder)
abstract ThumbnailBatch<ObjectCollection>	ThumbnailFromObjects.start(ObjectCollection objects, StreamableCollection<BoundingBox> boundingBoxes, Optional<Stack> background, ExecutionTimeRecorder executionTimeRecorder)	Initializes a batch to create thumbnails.

Uses of ObjectCollection in org.anchoranalysis.plugin.image.feature.bean.object.combine

Methods in org.anchoranalysis.plugin.image.feature.bean.object.combine that return ObjectCollection

Modifier and Type	Method	Description
abstract ObjectCollection	CombineObjectsForFeatures.objectsForThumbnail(T input)	Selects objects from an input that will be used for thumbnail generation.
ObjectCollection	EachObjectIndependently.objectsForThumbnail(FeatureInputSingleObject input)
ObjectCollection	PairNeighbors.objectsForThumbnail(FeatureInputPairObjects input)

Methods in org.anchoranalysis.plugin.image.feature.bean.object.combine that return types with arguments of type ObjectCollection

Modifier and Type	Method	Description
ListWithThumbnails<T,ObjectCollection>	CombineObjectsForFeatures.deriveInputsStartBatch(ObjectCollection objects, EnergyStack energyStack, boolean thumbnailsEnabled, OperationContext context)	Derives a list of inputs (i.e. rows in a feature table) and starts a batch of related thumbnail generation.

Methods in org.anchoranalysis.plugin.image.feature.bean.object.combine with parameters of type ObjectCollection

Modifier and Type	Method	Description
ListWithThumbnails<T,ObjectCollection>	CombineObjectsForFeatures.deriveInputsStartBatch(ObjectCollection objects, EnergyStack energyStack, boolean thumbnailsEnabled, OperationContext context)	Derives a list of inputs (i.e. rows in a feature table) and starts a batch of related thumbnail generation.
protected abstract List<T>	CombineObjectsForFeatures.startBatchDeriveInputs(ObjectCollection objects, EnergyStack energyStack, Logger logger)	Derives a list of inputs from an object-collection.
List<FeatureInputSingleObject>	EachObjectIndependently.startBatchDeriveInputs(ObjectCollection objects, EnergyStack energyStack, Logger logger)
List<FeatureInputPairObjects>	PairNeighbors.startBatchDeriveInputs(ObjectCollection objects, EnergyStack energyStack, Logger logger)

Uses of ObjectCollection in org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting

Methods in org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting that return ObjectCollection

Modifier and Type	Method	Description
protected ObjectCollection	FeatureIntersectingObjects.getSearchObjects()	Gets the collection of objects to search for intersections.

Methods in org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting with parameters of type ObjectCollection

Modifier and Type	Method	Description
protected FeatureInputPairObjects	CalculateIntersecting.deriveFromDelegate(FeatureInputSingleObject input, ObjectCollection delegate)

Method parameters in org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting with type arguments of type ObjectCollection

Modifier and Type	Method	Description
protected abstract double	FeatureIntersectingObjects.valueFor(FeatureCalculationInput<FeatureInputSingleObject> input, ResolvedPart<ObjectCollection,FeatureInputSingleObject> intersecting)	Calculates a value based on the input and the intersecting objects.
protected double	FeatureIntersectingObjectsSingleElement.valueFor(FeatureCalculationInput<FeatureInputSingleObject> input, ResolvedPart<ObjectCollection,FeatureInputSingleObject> intersecting)
protected double	NumberIntersectingObjects.valueFor(FeatureCalculationInput<FeatureInputSingleObject> input, ResolvedPart<ObjectCollection,FeatureInputSingleObject> intersecting)

Constructor parameters in org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting with type arguments of type ObjectCollection

Modifier	Constructor	Description
	CalculateIntersecting(ResolvedPart<ObjectCollection,FeatureInputSingleObject> intersecting, int index)	Creates a new CalculateIntersecting instance.

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

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

Modifier and Type	Method	Description
static LevelResultCollection	LevelResultCollectionFactory.createCollection(Channel channel, ObjectCollection objects, CalculateLevel calculateLevel, int numberDilations, MessageLogger logger)	Creates a LevelResultCollection from a channel and object collection.

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

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

Modifier and Type	Method	Description
static ObjectCollection	ObjectIntersectionRemover.removeIntersectingVoxels(ObjectCollection objects, Dimensions dimensions, boolean errorDisconnectedObjects)	Removes intersecting voxels from a collection of objects.

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

Modifier and Type	Method	Description
static ObjectCollection	ObjectIntersectionRemover.removeIntersectingVoxels(ObjectCollection objects, Dimensions dimensions, boolean errorDisconnectedObjects)	Removes intersecting voxels from a collection of objects.

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

Modifier	Constructor	Description
	ColoredObjectCollection(ObjectCollection objects, ColorList colors)	Create with an existing object and color list.

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

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

Modifier and Type	Method	Description
ObjectCollection	MergeGraph.verticesAsObjects()	Retrieves all vertices in the graph as an ObjectCollection.

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

Modifier and Type	Method	Description
List<ObjectVertex>	MergeGraph.addObjectsToGraph(ObjectCollection objects)	Adds objects to the graph.

Uses of ObjectCollection in org.anchoranalysis.plugin.image.task.feature.calculator

Methods in org.anchoranalysis.plugin.image.task.feature.calculator with parameters of type ObjectCollection

Modifier and Type	Method	Description
void	CalculateFeaturesForObjects.calculateForObjects(ObjectCollection objects, EnergyStack energyStack, LabelsForInput labelsForInput)	Calculates the feature-results for objects, and stores the results.

Uses of ObjectCollection in org.anchoranalysis.plugin.imagej.bean.object.provider

Methods in org.anchoranalysis.plugin.imagej.bean.object.provider that return ObjectCollection

Modifier and Type	Method	Description
protected ObjectCollection	DrawLineAlongConvexHull.createFromObjects(ObjectCollection objects)
ObjectCollection	FillHoles.createFromObjects(ObjectCollection objects)

Methods in org.anchoranalysis.plugin.imagej.bean.object.provider with parameters of type ObjectCollection

Modifier and Type	Method	Description
protected ObjectCollection	DrawLineAlongConvexHull.createFromObjects(ObjectCollection objects)
ObjectCollection	FillHoles.createFromObjects(ObjectCollection objects)

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

Methods in org.anchoranalysis.plugin.imagej.bean.object.segment that return ObjectCollection

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

Uses of ObjectCollection in org.anchoranalysis.plugin.mpp.bean.object.provider

Methods in org.anchoranalysis.plugin.mpp.bean.object.provider that return ObjectCollection

Modifier and Type	Method	Description
ObjectCollection	FromMarks.get()

Uses of ObjectCollection in org.anchoranalysis.plugin.mpp.bean.stack.provider

Methods in org.anchoranalysis.plugin.mpp.bean.stack.provider that return ObjectCollection

Modifier and Type	Method	Description
protected ObjectCollection	ColoredMarks.objectsToDraw(Dimensions backgroundDimensions)

Uses of ObjectCollection in org.anchoranalysis.plugin.points.bean

Methods in org.anchoranalysis.plugin.points.bean that return ObjectCollection

Modifier and Type	Method	Description
ObjectCollection	SplitContourAtSaddlePoints.createFromObjects(ObjectCollection objects)

Methods in org.anchoranalysis.plugin.points.bean with parameters of type ObjectCollection

Modifier and Type	Method	Description
ObjectCollection	SplitContourAtSaddlePoints.createFromObjects(ObjectCollection objects)

Uses of ObjectCollection in org.anchoranalysis.plugin.points.bean.fitter

Methods in org.anchoranalysis.plugin.points.bean.fitter that return ObjectCollection

Modifier and Type	Method	Description
ObjectCollection	PointsFitterToMark.createObjects()	Creates and returns the ObjectCollection using the specified provider.

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

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

Modifier and Type	Method	Description
static List<Point2i>	ConvexHullUtilities.pointsOnAllOutlines(ObjectCollection objects)	Get points on all outlines of a collection of objects.

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

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

Modifier and Type	Method	Description
static ObjectCollection	IntersectingCircleObjectsFixture.generateIntersectingObjects(int numberIntersecting, int numberNotIntersecting, boolean sameSize)	Generates a collection of circular objects, some intersecting and some not intersecting.

Uses of ObjectCollection in org.anchoranalysis.test.image

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

Modifier and Type	Method	Description
void	WriteIntoDirectory.writeObjects(String outputName, ObjectCollection objects)	Writes the outline of objects on a blank RGB image, inferring dimensions of the image to center the object.
void	WriteIntoDirectory.writeObjects(String outputName, ObjectCollection objects, Stack background)	Writes the outline of objects on a background.

Uses of ObjectCollection in org.anchoranalysis.test.image.io

Methods in org.anchoranalysis.test.image.io that return ObjectCollection

Modifier and Type	Method	Description
ObjectCollection	TestLoaderImage.openObjectsFromFilePath(Path folderPath)	Opens an obj-mask-collection from a path to a file
ObjectCollection	TestLoaderImage.openObjectsFromTestPath(String testDirectoryPath)	Opens an object collection from a test path.

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

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

Modifier and Type	Method	Description
ObjectCollection	CutOffCornersObjectFixture.createAll()	Creates all three objects.
static ObjectCollection	CircleObjectFixture.successiveCircles(int numberCircles, Point2d startCenter, int radius, Point2d centerShift, double radiusShift)	Creates several successive circles whose center is incrementally shifted.