Uses of Class
org.anchoranalysis.image.core.stack.Stack

Packages that use Stack

Package	Description
org.anchoranalysis.annotation.io.assignment.generator	Generates output images to illustrate a Assignment between annotations.
org.anchoranalysis.annotation.io.bean.comparer	What to compare an annotation (ground truth) against?
org.anchoranalysis.feature.energy	A particular stack used in feature-calculations called a EnergyStack together with related classes.
org.anchoranalysis.image.bean.displayer
org.anchoranalysis.image.bean.nonbean.init	Classes that aren't AnchorBeans that pertain to the initialization of image-related beans.
org.anchoranalysis.image.bean.nonbean.spatial.arrange	Non-beans to specify how to form a single-image by spatially combining other images.
org.anchoranalysis.image.bean.provider	Base classes for providers of different core data entities related to images.
org.anchoranalysis.image.bean.provider.stack	A provider of Stacks.
org.anchoranalysis.image.core.bufferedimage	Conversions and operations involving Java AWT's BufferedImage.
org.anchoranalysis.image.core.channel.convert	Converts a channel to other data-types.
org.anchoranalysis.image.core.stack	Defines the key data object, Stack, and related classes.
org.anchoranalysis.image.core.stack.named	A collection of Stacks, each with a unique identifier as a name.
org.anchoranalysis.image.feature.bean.evaluator	Beans that define context (which feature, which energy-stack) for evaluating feature-inputs.
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.bean.stack.combine	Beans to combine multiple stacks into a single stack before outputting.
org.anchoranalysis.image.io.bean.stack.reader	Bean classes for reading raster-files from the filesystem.
org.anchoranalysis.image.io.bean.stack.writer	Bean classes for writing raster-files to the filesystem.
org.anchoranalysis.image.io.channel.map	Non-bean classes for a mapping of names to Channels.
org.anchoranalysis.image.io.channel.output	Non-bean classes for writing a Channel to 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.mask	Writing an ObjectCollection to the filesystem as multiple binary singled-channeled images.
org.anchoranalysis.image.io.object.output.rgb	Writing an ObjectCollection to the filesystem as RGB raster-images.
org.anchoranalysis.image.io.stack	Non-bean classes for reading / writing a Stack from and to the filesystem.
org.anchoranalysis.image.io.stack.input	Non-bean classes for reading a Stack from the filesystem.
org.anchoranalysis.image.io.stack.output	Non-bean classes for writing a Stack to the filesystem.
org.anchoranalysis.image.io.stack.output.box	Base classes for generators that ultimately write only a bounding-box portion of a Stack to the filesystem.
org.anchoranalysis.image.io.stack.output.generator	Base classes for generators that ultimately write a Stack to the filesystem.
org.anchoranalysis.image.io.stack.time	A time-sequence of Stacks.
org.anchoranalysis.io.bioformats.bean.writer	Writing stacks to the file system using the Bioformats library.
org.anchoranalysis.io.imagej.bean.stack.writer	Raster-writers that use ImageJ to write images to the filesystem.
org.anchoranalysis.io.imagej.convert	Converts to and from ImageJ data-structures for images.
org.anchoranalysis.mpp.io.output	Non-beans for writing data structures related to marked point processes from the file system.
org.anchoranalysis.plugin.image.bean.stack.provider	Implementations of StackProvider.
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.bean.thumbnail.stack	Implementations of ThumbnailFromStack.
org.anchoranalysis.plugin.image.task.bean.format	Tasks for converting image-formats.
org.anchoranalysis.plugin.image.task.bean.scale	Tasks to scale an image.
org.anchoranalysis.plugin.image.task.grouped	Non-bean classes about grouping channels or other inputs.
org.anchoranalysis.plugin.imagej.bean.stack.provider	Implementations of StackProvider that call ImageJ.
org.anchoranalysis.plugin.io.bean.stack.writer	Implementations of StackWriter.
org.anchoranalysis.plugin.io.multifile	Non-bean classes to help use multiple files to represent a single Stack.
org.anchoranalysis.plugin.io.multifile.buffer	Buffers used in org.anchoranalysis.plugin.io.multifile.
org.anchoranalysis.plugin.onnx.bean.object.segment.stack	Segmenting a Stack using the ONNX Runtime to produce an ObjectCollection.
org.anchoranalysis.plugin.opencv.bean.color	Operations involving color-spaces and OpenCV.
org.anchoranalysis.plugin.opencv.bean.object.segment.stack	Segmentation of a Stack using OpenCV.
org.anchoranalysis.plugin.opencv.bean.stack	Implementations of StackWriter and StackReader that involve OpenCV.
org.anchoranalysis.plugin.opencv.convert	Conversion to/from OpenCV data-structures.
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.load	Load test image data.
org.anchoranalysis.test.image.segment	Fixtures or other helper classes for testing image segmentation algorithms.

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

Methods in org.anchoranalysis.annotation.io.assignment.generator that return Stack

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 Stack in org.anchoranalysis.annotation.io.bean.comparer

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

Modifier and Type	Method	Description
List<NameValue<Stack>>	MultipleComparer.createComparisonStacks(AnnotationWithMarks annotation, DisplayStack background, Path annotationPath, ColorScheme colorScheme, Path modelDirectory, OperationContext context, boolean debugMode)	Creates a Stack illustrating the comparison between annotation and each source in sources.

Uses of Stack in org.anchoranalysis.feature.energy

Methods in org.anchoranalysis.feature.energy that return Stack

Modifier and Type	Method	Description
Stack	EnergyStack.asStack()	Derive a Stack representation containing the identical channels to the current instance.
Stack	EnergyStackWithoutParameters.asStack()	Derive a Stack representation containing the identical channels to the current instance.

Constructors in org.anchoranalysis.feature.energy with parameters of type Stack

Modifier	Constructor	Description
	EnergyStack(Stack stack)	Create from a EnergyStack without any additional parameters.
	EnergyStack(Stack stack, Dictionary dictionary)	Create from a Stack with associated parameters in a Dictionary.
	EnergyStackWithoutParameters(Stack stack)	Create a energy-stack comprised of all channels from a stack

Uses of Stack in org.anchoranalysis.image.bean.displayer

Methods in org.anchoranalysis.image.bean.displayer with parameters of type Stack

Modifier and Type	Method	Description
DisplayStack	StackDisplayer.deriveFrom(Stack stack)	Derives a DisplayStack from a RGBStack.

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

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

Modifier and Type	Method	Description
NamedProvider<Stack>	ImageInitialization.combinedStacks()	Exposes several entities that have natural Stack representations as a unified NamedProvider.
NamedProviderStore<Stack>	ImageInitialization.stacks()	A collection of Stacks, indexed by name.

Methods in org.anchoranalysis.image.bean.nonbean.init with parameters of type Stack

Modifier and Type	Method	Description
void	ImageInitialization.addStack(String identifier, Stack toAdd)	Adds a Stack to the corresponding named-collection of stacks.

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

Modifier and Type	Method	Description
void	ImageInitialization.addStacksFrom(NamedProvider<Stack> source)	Adds all the Stacks available in a NamedProvider using the corresponding identifiers.

Uses of Stack in org.anchoranalysis.image.bean.nonbean.spatial.arrange

Methods in org.anchoranalysis.image.bean.nonbean.spatial.arrange with parameters of type Stack

Modifier and Type	Method	Description
static void	StackCopierAtBox.copyImageInto(Stack source, Stack destination, BoundingBox box)	Copies a source stack into a destination stack at a particular BoundingBox.

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

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

Modifier and Type	Method	Description
Stack	ChannelProvider.getAsStack()
Stack	MaskProvider.getAsStack()

Uses of Stack in org.anchoranalysis.image.bean.provider.stack

Methods in org.anchoranalysis.image.bean.provider.stack that return Stack

Modifier and Type	Method	Description
protected abstract Stack	StackProviderUnary.createFromStack(Stack stack)	Creates a Stack given the entity provided by the delegate.
Stack	Arrange.get()
Stack	StackProviderUnary.get()
Stack	StackProvider.getAsStack()

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

Modifier and Type	Method	Description
List<Provider<Stack>>	Arrange.getList()	The stacks that are passed in respect order into arrange.
Provider<Stack>	StackProviderUnary.getStack()	The delegate Provider<Stack> that is called.

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

Modifier and Type	Method	Description
protected abstract Stack	StackProviderUnary.createFromStack(Stack stack)	Creates a Stack given the entity provided by the delegate.

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

Modifier and Type	Method	Description
void	Arrange.addStack(Provider<Stack> provider)	Adds a stack to the existing list of stack-providers.
void	Arrange.setList(List<Provider<Stack>> list)	The stacks that are passed in respect order into arrange.
void	StackProviderUnary.setStack(Provider<Stack> stack)	The delegate Provider<Stack> that is called.

Uses of Stack in org.anchoranalysis.image.core.bufferedimage

Methods in org.anchoranalysis.image.core.bufferedimage that return Stack

Modifier and Type	Method	Description
static Stack	CreateStackFromBufferedImage.createFrom(BufferedImage bufferedImage)	Create a Stack by converting a BufferedImage.

Methods in org.anchoranalysis.image.core.bufferedimage with parameters of type Stack

Modifier and Type	Method	Description
static BufferedImage	BufferedImageFromStack.create(Stack stack)	Creates a BufferedImage from a Stack.

Uses of Stack in org.anchoranalysis.image.core.channel.convert

Methods in org.anchoranalysis.image.core.channel.convert that return Stack

Modifier and Type	Method	Description
Stack	ChannelConverter.convert(Stack stack, ConversionPolicy changeExisting)	Like ChannelConverter.convert(Channel, ConversionPolicy) but converts every channel in a Stack.

Methods in org.anchoranalysis.image.core.channel.convert with parameters of type Stack

Modifier and Type	Method	Description
Stack	ChannelConverter.convert(Stack stack, ConversionPolicy changeExisting)	Like ChannelConverter.convert(Channel, ConversionPolicy) but converts every channel in a Stack.

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

Methods in org.anchoranalysis.image.core.stack that return Stack

Modifier and Type	Method	Description
Stack	RGBStack.asStack()	Exposes the underlying stack, storing the three RGB channels in respective order.
Stack	DisplayStack.deriveStack(boolean alwaysNew)	Derives a Stack from the display-stack that will be converted to 8-bit if necessary.
Stack	Stack.duplicateDeep()	Performs a deep copy of the stack, so that all channels are duplicated.
Stack	Stack.duplicateShallow()	Performs a shallow copy of the stack, so that all channels are reused.
Stack	Stack.extractSlice(int z)	Extract a particular z-slice from the Stack as a new stack.
Stack	Stack.extractUpToThreeChannels()	Extracts the first three Channels as a new Stack.
Stack	ProviderAsStack.getAsStack()	Retrieves or creates a Stack representation of an entity.
Stack	DisplayStack.getStack()	The underlying stack that will be displayed, possibly after conversion.
Stack	Stack.mapChannel(CheckedUnaryOperator<Channel,OperationFailedException> mapping)	Produces a new stack with a particular mapping applied to each channel.
Stack	Stack.mapChannelWithIndex(CheckedBiFunction<Channel,Integer,Channel,OperationFailedException> mapping)	Produces a new stack with a particular mapping applied to each channel (with an index of the channel also available).
Stack	Stack.projectMax()	Creates a Maximum Intensity Projection of each channel.

Methods in org.anchoranalysis.image.core.stack with parameters of type Stack

Modifier and Type	Method	Description
final void	Stack.addChannelsFrom(Stack stack)	Add the channels from another instance into this instance.
boolean	Stack.equalsDeep(Stack other, boolean compareResolution)	Are the two stack equal using a deep voxel by voxel comparison of each channel?

Constructors in org.anchoranalysis.image.core.stack with parameters of type Stack

Modifier	Constructor	Description
	DisplayStack(Stack stack)	Create for a particular Stack where all channels are already guaranteed to be unsigned-bit.
	DisplayStack(Stack stack, boolean eventuallyThree, Function<VoxelDataType,ChannelConverterAttached<Channel,UnsignedByteBuffer>> createConverter)	Create for a particular Stack that may needed to be converted.
	RGBStack(Stack stack)	Creates from an existing stack (which must have 1 or 3 channels).

Uses of Stack in org.anchoranalysis.image.core.stack.named

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

Modifier and Type	Method	Description
NamedProvider<Stack>	NamedStacksSupplier.get()	Gets the NamedProvider of Stacks.
Optional<Stack>	NamedStacks.getOptional(String identifier)

Methods in org.anchoranalysis.image.core.stack.named with parameters of type Stack

Modifier and Type	Method	Description
void	NamedStacks.add(String identifier, Stack stack)	Add a stack.
void	NamedStacksUniformSize.add(String identifier, Stack stack)	Adds an element to the store.

Method parameters in org.anchoranalysis.image.core.stack.named with type arguments of type Stack

Modifier and Type	Method	Description
void	NamedStacks.add(String identifier, StoreSupplier<Stack> supplier)
void	NamedStacks.addFrom(NamedProvider<Stack> source)	Adds a Stack from a NamedProvider.
void	NamedStacks.addFromWithPrefix(NamedProvider<Stack> source, String prefix)	Like NamedStacks.addFrom(NamedProvider) but additionally adds a prefix to the name when adding.
NamedStacks	NamedStacks.applyOperation(UnaryOperator<Stack> operation, Optional<Dimensions> dimensions)	Applies an operation on each Stack in the collection and returns a new derived collection.
<E extends Exception> void	NamedStacks.forEach(CheckedBiConsumer<String,StoreSupplier<Stack>,E> consumer)	Iterates over each entry in the map.

Uses of Stack in org.anchoranalysis.image.feature.bean.evaluator

Methods in org.anchoranalysis.image.feature.bean.evaluator that return types with arguments of type Stack

Modifier and Type	Method	Description
Provider<Stack>	FeatureEvaluator.getStackEnergy()	Optionally specifies an energy-stack to be associated with every calculation input.

Method parameters in org.anchoranalysis.image.feature.bean.evaluator with type arguments of type Stack

Modifier and Type	Method	Description
void	FeatureEvaluator.setStackEnergy(Provider<Stack> stackEnergy)	Optionally specifies an energy-stack to be associated with every calculation input.

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

Methods in org.anchoranalysis.image.inference.bean.segment.instance with parameters of type Stack

Modifier and Type	Method	Description
protected abstract T	SegmentStackIntoObjectsScaleDecode.deriveInput(Stack stack, Optional<double[]> subtractMeans)	Derives the input tensor from an image.
SegmentedObjects	SegmentStackIntoObjectsPooled.segment(Stack stack, ExecutionTimeRecorder executionTimeRecorder)	Segments individually using a pool of size 1 just for one stack.
abstract SegmentedObjects	SegmentStackIntoObjectsPooled.segment(Stack stack, ConcurrentModelPool<T> modelPool, ExecutionTimeRecorder executionTimeRecorder)	Segments a stack to produce an object-collection.
SegmentedObjects	SegmentStackIntoObjectsScaleDecode.segment(Stack stack, ConcurrentModelPool<S> modelPool, ExecutionTimeRecorder executionTimeRecorder)
SegmentedObjects	SuppressNonMaximum.segment(Stack stack, ConcurrentModelPool<T> modelPool, ExecutionTimeRecorder executionTimeRecorder)

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

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

Modifier and Type	Method	Description
Stack	SegmentedBackground.atInputScale()	The background scaled to match the size of the input-image.
Stack	SegmentedBackground.atModelScale()	The background scaled to match the size of the input for model inference.
Stack	SegmentedObjectsAtScale.background()	The background image associated with this particular scale.

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

Modifier and Type	Method	Description
DualScale<Stack>	SegmentedBackground.getBackground()	The background image to use for segmentation, when visualizing segmentations.

Constructors in org.anchoranalysis.image.inference.segment with parameters of type Stack

Modifier	Constructor	Description
	SegmentedObjectsAtScale(List<LabelledWithConfidence<MultiScaleObject>> source, Function<MultiScaleObject,ObjectMask> extractObject, Stack background, StackDisplayer displayer, ExecutionTimeRecorder executionTimeRecorder, String executionTimeSuffix)	Creates a new SegmentedObjectsAtScale instance.

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

Modifier	Constructor	Description
	SegmentedBackground(DualScale<Stack> background, StackDisplayer displayer)	Creates a new SegmentedBackground instance.

Uses of Stack in org.anchoranalysis.image.io.bean.stack.combine

Methods in org.anchoranalysis.image.io.bean.stack.combine that return Stack

Modifier and Type	Method	Description
Stack	TileWithLabels.get()
Stack	WriteText.get()

Methods in org.anchoranalysis.image.io.bean.stack.combine that return types with arguments of type Stack

Modifier and Type	Method	Description
Provider<Stack>	WriteText.getRepeatZProvider()	Repeats the generated (2D) string in z, so it's the same z-size as intensityProvider
Provider<Stack>	StackProviderWithLabel.getStack()	Provides the stack.

Method parameters in org.anchoranalysis.image.io.bean.stack.combine with type arguments of type Stack

Modifier and Type	Method	Description
void	WriteText.setRepeatZProvider(Provider<Stack> repeatZProvider)	Repeats the generated (2D) string in z, so it's the same z-size as intensityProvider
void	StackProviderWithLabel.setStack(Provider<Stack> stack)	Provides the stack.

Constructors in org.anchoranalysis.image.io.bean.stack.combine with parameters of type Stack

Modifier	Constructor	Description
	StackProviderWithLabel(Stack stack, String label)	Create for a particular Stack and label.

Uses of Stack in org.anchoranalysis.image.io.bean.stack.reader

Methods in org.anchoranalysis.image.io.bean.stack.reader that return Stack

Modifier and Type	Method	Description
Stack	StackReader.readStack(Path path, OperationContext context)	Opens a file at path that should contain only a single-stack.

Uses of Stack in org.anchoranalysis.image.io.bean.stack.writer

Methods in org.anchoranalysis.image.io.bean.stack.writer with parameters of type Stack

Modifier and Type	Method	Description
void	OneOrThreeChannelsWriter.writeStack(Stack stack, Path filePath, StackWriteOptions options)
abstract void	StackWriter.writeStack(Stack stack, Path filePath, StackWriteOptions options)	Writes a stack to the filesystem at a particular path.
protected abstract void	OneOrThreeChannelsWriter.writeStackAfterCheck(Stack stack, Path filePath)	Writes the Stack to the file-system, after a check has already occurred that the correct number of channels exist.
Path	StackWriter.writeStackWithExtension(Stack stack, Path filePath, StackWriteOptions options)	Writes a stack to the filesystem at a particular path with an extension appended to the path.

Uses of Stack in org.anchoranalysis.image.io.channel.map

Methods in org.anchoranalysis.image.io.channel.map that return types with arguments of type Stack

Modifier and Type	Method	Description
StoreSupplier<Stack>	NamedChannelsConcatenate.allChannelsAsStack(int t, Logger logger)
StoreSupplier<Stack>	NamedChannelsMap.allChannelsAsStack(int timeIndex, Logger logger)	Combines all channels as a single Stack at a particular time-frame.
StoreSupplier<Stack>	OpenedNamedChannels.allChannelsAsStack(int t, Logger logger)

Uses of Stack in org.anchoranalysis.image.io.channel.output

Methods in org.anchoranalysis.image.io.channel.output that return Stack

Modifier and Type	Method	Description
Stack	ChannelGenerator.transform(Channel element)

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

Methods in org.anchoranalysis.image.io.object.output.grayscale that return Stack

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

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

Methods in org.anchoranalysis.image.io.object.output.mask that return Stack

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

Uses of Stack in org.anchoranalysis.image.io.object.output.rgb

Methods in org.anchoranalysis.image.io.object.output.rgb that return Stack

Modifier and Type	Method	Description
Stack	ObjectsAsRGBGenerator.transform(ObjectCollectionWithProperties element)

Uses of Stack in org.anchoranalysis.image.io.stack

Methods in org.anchoranalysis.image.io.stack with parameters of type Stack

Modifier and Type	Method	Description
static RGBStack	ConvertStackToRGB.convert(Stack stack, StackDisplayer displayer, boolean alwaysNew)	Converts all of a DisplayStack to a RGBStack.

Uses of Stack in org.anchoranalysis.image.io.stack.input

Methods in org.anchoranalysis.image.io.stack.input that return Stack

Modifier and Type	Method	Description
default Stack	ProvidesStackInput.asStack(Logger logger)	Exposes the input as a single Stack throw an error if more than one exists.

Method parameters in org.anchoranalysis.image.io.stack.input with type arguments of type Stack

Modifier and Type	Method	Description
default void	ProvidesStackInput.addToStoreInferNames(NamedProviderStore<Stack> store, Logger logger)	Adds the current object to a named-store of stacks (using the default series).

Uses of Stack in org.anchoranalysis.image.io.stack.output

Methods in org.anchoranalysis.image.io.stack.output that return types with arguments of type Stack

Modifier and Type	Method	Description
OutputSequenceIncrementing<Stack>	OutputSequenceStackFactory.incrementingByOne(String subdirectoryName, OutputterChecked outputter)	Creates an sequence of stacks in a subdirectory with a number in the outputted file name that increments each time by one.
OutputSequenceIndexed<Stack,String>	OutputSequenceStackFactory.withoutOrderCurrentDirectory(String outputName, OutputterChecked outputter)	Creates a sequence of stacks in the current context's directory that has no pattern.

Methods in org.anchoranalysis.image.io.stack.output with parameters of type Stack

Modifier and Type	Method	Description
static StackWriteAttributes	StackWriteAttributesFactory.from(Stack stack)	The options that narrowly describe a stack as possible.
boolean	StackWriteAttributes.writeAsRGB(Stack stack)	Whether to write a stack in RGB mode?

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

Modifier and Type	Method	Description
static void	NamedStacksOutputter.output(NamedProvider<Stack> stacks, String outputName, boolean suppressSubdirectory, OutputterChecked outputter)	Writes all or a subset from a set of named-stacks to a directory as a raster.
void	OutputSequenceStackFactory.withoutOrderSubset(NamedProvider<Stack> stacks, String outputName, boolean suppressSubdirectory, OutputterChecked outputter)	Writes all or a subset from a set of named-stacks to a directory.

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

Methods in org.anchoranalysis.image.io.stack.output.box that return Stack

Modifier and Type	Method	Description
Stack	ScaleableBackground.extractRegionFromStack(BoundingBox box)	Extracts a portion of a stack (flattened and maybe scaled) corresponding to a bounding-box
Stack	DrawObjectOnStackGenerator.transform(BoundedList<ObjectMask> element)
Stack	ExtractBoundingBoxAreaFromStackGenerator.transform(BoundingBox element)

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

Modifier and Type	Method	Description
static DrawObjectOnStackGenerator	DrawObjectOnStackGenerator.createFromGenerator(TransformingGenerator<BoundingBox,Stack> backgroundGenerator, int outlineWidth, ColorIndex colors)	Creates an extracted-object generator that draws an outline - with default color green and flattened in Z.

Uses of Stack in org.anchoranalysis.image.io.stack.output.generator

Methods in org.anchoranalysis.image.io.stack.output.generator that return Stack

Modifier and Type	Method	Description
protected Stack	DisplayStackGenerator.convertBeforeAssign(DisplayStack element)
protected Stack	FlattenStackGenerator.convertBeforeAssign(Stack element)
protected Stack	DisplayStackGenerator.convertBeforeTransform(Stack stack)
protected Stack	FlattenStackGenerator.convertBeforeTransform(Stack stack)
protected Stack	RasterGeneratorBridge.convertBeforeTransform(Stack stack)
protected abstract Stack	RasterGeneratorDelegateToRaster.convertBeforeTransform(Stack stack)	Converts an element before calling RasterGeneratorDelegateToRaster.transform(T) on the delegate.
Stack	RasterGeneratorBridge.transform(T element)
Stack	RasterGeneratorDelegateToDisplayStack.transform(T element)
Stack	RasterGeneratorDelegateToRaster.transform(T element)
Stack	StackGenerator.transform(Stack element)

Methods in org.anchoranalysis.image.io.stack.output.generator with parameters of type Stack

Modifier and Type	Method	Description
protected Stack	FlattenStackGenerator.convertBeforeAssign(Stack element)
protected Stack	DisplayStackGenerator.convertBeforeTransform(Stack stack)
protected Stack	FlattenStackGenerator.convertBeforeTransform(Stack stack)
protected Stack	RasterGeneratorBridge.convertBeforeTransform(Stack stack)
protected abstract Stack	RasterGeneratorDelegateToRaster.convertBeforeTransform(Stack stack)	Converts an element before calling RasterGeneratorDelegateToRaster.transform(T) on the delegate.
protected abstract String	RasterGenerator.selectFileExtension(Stack stack, StackWriteOptions options, OutputWriteSettings settings, Optional<Logger> logger)	Selects the file-extension to use for a particular stack.
protected String	RasterGeneratorSelectFormat.selectFileExtension(Stack stack, StackWriteOptions options, OutputWriteSettings settings, Optional<Logger> logger)	Combines stack-write-options derived for a particular stack with the general write-options associated with the RasterGenerator.
Stack	StackGenerator.transform(Stack element)
protected abstract void	RasterGenerator.writeToFile(T untransformedElement, Stack transformedElement, StackWriteOptions options, OutputWriteSettings settings, Path filePath)	Writes a stack to the file-system.
protected void	RasterGeneratorSelectFormat.writeToFile(T element, Stack transformedElement, StackWriteOptions options, OutputWriteSettings settings, Path filePath)

Uses of Stack in org.anchoranalysis.image.io.stack.time

Methods in org.anchoranalysis.image.io.stack.time that return Stack

Modifier and Type	Method	Description
Stack	TimeSeries.getFrame(int index)	Gets a frame in the time-series.

Methods in org.anchoranalysis.image.io.stack.time that return types with arguments of type Stack

Modifier and Type	Method	Description
Iterator<Stack>	TimeSeries.iterator()

Constructors in org.anchoranalysis.image.io.stack.time with parameters of type Stack

Modifier	Constructor	Description
	TimeSeries(Stack frame)	Creates a TimeSeries containing a single frame only.

Constructor parameters in org.anchoranalysis.image.io.stack.time with type arguments of type Stack

Modifier	Constructor	Description
	ExtractFrameStore(NamedProviderStore<Stack> stacks)	Creates to extract at time-index 0.
	ExtractFrameStore(NamedProviderStore<Stack> stacks, int timeIndex)	Creates to extract at time-index timeIndex.
	TimeSeries(Stream<Stack> frames)	Creates a TimeSeries from a stream of frames.

Uses of Stack in org.anchoranalysis.io.bioformats.bean.writer

Methods in org.anchoranalysis.io.bioformats.bean.writer with parameters of type Stack

Modifier and Type	Method	Description
void	BioformatsWriter.writeStack(Stack stack, Path filePath, StackWriteOptions options)
void	Tiff.writeStack(Stack stack, Path filePath, StackWriteOptions options)

Uses of Stack in org.anchoranalysis.io.imagej.bean.stack.writer

Methods in org.anchoranalysis.io.imagej.bean.stack.writer with parameters of type Stack

Modifier and Type	Method	Description
void	ImageJRasterWriter.writeStack(Stack stack, Path filePath, StackWriteOptions options)
protected void	ImageJRasterWriter.writeStackTime(Stack stack, Path path, boolean makeRGB)	Writes a stack as a time-sequence (many images together in a single file.).

Uses of Stack in org.anchoranalysis.io.imagej.convert

Methods in org.anchoranalysis.io.imagej.convert with parameters of type Stack

Modifier and Type	Method	Description
static ij.ImagePlus	ConvertToImagePlus.from(Stack stack, boolean makeRGB)	Creates an ImagePlus from a Stack.

Uses of Stack in org.anchoranalysis.mpp.io.output

Method parameters in org.anchoranalysis.mpp.io.output with type arguments of type Stack

Modifier and Type	Method	Description
static DisplayStack	BackgroundCreator.createBackground(NamedProviderStore<Stack> stackCollection, String backgroundStackName, StackDisplayer displayer)	Creates a background DisplayStack from a named stack in a collection.

Uses of Stack in org.anchoranalysis.plugin.image.bean.stack.provider

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

Modifier and Type	Method	Description
Stack	Concatenate.get()
Stack	FromChannelOrMask.get()
Stack	FromInput.get()
Stack	Reference.get()

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

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

Modifier and Type	Method	Description
static Stack	ThreeChannels.createRGBStack(Channel channelRed, Channel channelGreen, Channel channelBlue, VoxelDataType outputType)	Creates an RGB stack from up to three channels.
Stack	ColoredBase.get()
Stack	ThreeChannels.get()

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

Method parameters in org.anchoranalysis.plugin.image.bean.thumbnail.object with type arguments of type Stack

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 Stack in org.anchoranalysis.plugin.image.bean.thumbnail.stack

Methods in org.anchoranalysis.plugin.image.bean.thumbnail.stack with parameters of type Stack

Modifier and Type	Method	Description
DisplayStack	ScaleToSize.thumbnailFor(Stack stack)
abstract DisplayStack	ThumbnailFromStack.thumbnailFor(Stack stack)	Creates a thumbnail for a stack.

Uses of Stack in org.anchoranalysis.plugin.image.task.bean.format

Methods in org.anchoranalysis.plugin.image.task.bean.format that return types with arguments of type Stack

Modifier and Type	Method	Description
protected OutputSequenceIndexed<Stack,String>	ConvertImageFormat.createSharedStateJob(InputOutputContext context)	Sets a new output-sequence for the series.

Method parameters in org.anchoranalysis.plugin.image.task.bean.format with type arguments of type Stack

Modifier and Type	Method	Description
void	ConvertImageFormat.doStack(InputBound<NamedChannelsInput,NoSharedState> input, OutputSequenceIndexed<Stack,String> sharedStateJob, int seriesIndex, int numberSeries, InputOutputContext context)
void	ConvertImageFormat.endSeries(NoSharedState sharedStateTask, OutputSequenceIndexed<Stack,String> sharedStateJob, InputOutputContext context)
void	ConvertImageFormat.startSeries(NoSharedState sharedStateTask, OutputSequenceIndexed<Stack,String> sharedStateJob, InputOutputContext context)

Uses of Stack in org.anchoranalysis.plugin.image.task.bean.scale

Methods in org.anchoranalysis.plugin.image.task.bean.scale that return Stack

Modifier and Type	Method	Description
protected abstract Stack	ScaleImage.scaleStack(Stack stack, Optional<ImageSizeSuggestion> suggestedSize, VoxelsResizer voxelsResizer, S sharedState)	Produce a scaled version of a Stack, mapping each channel to a scaled version of itself.
protected Stack	ScaleImageCommonSize.scaleStack(Stack stack, Optional<ImageSizeSuggestion> suggestedSize, VoxelsResizer voxelsResizer, CommonSize sharedState)
protected Stack	ScaleImageIndependently.scaleStack(Stack stack, Optional<ImageSizeSuggestion> suggestedSize, VoxelsResizer voxelsResizer, NoSharedState sharedState)

Methods in org.anchoranalysis.plugin.image.task.bean.scale with parameters of type Stack

Modifier and Type	Method	Description
protected abstract Stack	ScaleImage.scaleStack(Stack stack, Optional<ImageSizeSuggestion> suggestedSize, VoxelsResizer voxelsResizer, S sharedState)	Produce a scaled version of a Stack, mapping each channel to a scaled version of itself.
protected Stack	ScaleImageCommonSize.scaleStack(Stack stack, Optional<ImageSizeSuggestion> suggestedSize, VoxelsResizer voxelsResizer, CommonSize sharedState)
protected Stack	ScaleImageIndependently.scaleStack(Stack stack, Optional<ImageSizeSuggestion> suggestedSize, VoxelsResizer voxelsResizer, NoSharedState sharedState)

Uses of Stack in org.anchoranalysis.plugin.image.task.grouped

Methods in org.anchoranalysis.plugin.image.task.grouped with parameters of type Stack

Modifier and Type	Method	Description
Channel	ChannelSource.extractChannel(Stack stack, boolean checkType, int index)	Extracts a Channel from a given Stack.

Uses of Stack in org.anchoranalysis.plugin.imagej.bean.stack.provider

Methods in org.anchoranalysis.plugin.imagej.bean.stack.provider that return Stack

Modifier and Type	Method	Description
Stack	MontageSlices.createFromStack(Stack stack)

Methods in org.anchoranalysis.plugin.imagej.bean.stack.provider with parameters of type Stack

Modifier and Type	Method	Description
Stack	MontageSlices.createFromStack(Stack stack)

Uses of Stack in org.anchoranalysis.plugin.io.bean.stack.writer

Methods in org.anchoranalysis.plugin.io.bean.stack.writer with parameters of type Stack

Modifier and Type	Method	Description
void	StackWriterDelegateBase.writeStack(Stack stack, Path filePath, StackWriteOptions options)
void	WriteResolutionXml.writeStack(Stack stack, Path filePath, StackWriteOptions options)
protected void	ImageIOWriter.writeStackAfterCheck(Stack stack, Path filePath)

Uses of Stack in org.anchoranalysis.plugin.io.multifile

Methods in org.anchoranalysis.plugin.io.multifile with parameters of type Stack

Modifier and Type	Method	Description
void	SizeExtents.populateMissingFromArbitrarySlice(Stack stackArbitrarySlice)

Uses of Stack in org.anchoranalysis.plugin.io.multifile.buffer

Methods in org.anchoranalysis.plugin.io.multifile.buffer with parameters of type Stack

Modifier and Type	Method	Description
void	MultiBufferSized.populateFrom(Stack stackForFile, Optional<Integer> channelNum, Optional<Integer> sliceNum, Optional<Integer> timeIndex)

Constructors in org.anchoranalysis.plugin.io.multifile.buffer with parameters of type Stack

Modifier	Constructor	Description
	MultiBufferSized(Stack stack, SizeExtents size)

Uses of Stack in org.anchoranalysis.plugin.onnx.bean.object.segment.stack

Methods in org.anchoranalysis.plugin.onnx.bean.object.segment.stack with parameters of type Stack

Modifier and Type	Method	Description
protected ai.onnxruntime.OnnxTensor	SegmentObjectsFromONNXModel.deriveInput(Stack stack, Optional<double[]> subtractMeans)

Uses of Stack in org.anchoranalysis.plugin.opencv.bean.color

Methods in org.anchoranalysis.plugin.opencv.bean.color that return Stack

Modifier and Type	Method	Description
Stack	ColorConverterBase.createFromStack(Stack stackRGB)

Methods in org.anchoranalysis.plugin.opencv.bean.color with parameters of type Stack

Modifier and Type	Method	Description
Stack	ColorConverterBase.createFromStack(Stack stackRGB)

Uses of Stack in org.anchoranalysis.plugin.opencv.bean.object.segment.stack

Methods in org.anchoranalysis.plugin.opencv.bean.object.segment.stack with parameters of type Stack

Modifier and Type	Method	Description
protected org.opencv.core.Mat	SegmentObjectsFromTensorFlowModel.deriveInput(Stack stack, Optional<double[]> subtractMeans)

Uses of Stack in org.anchoranalysis.plugin.opencv.bean.stack

Methods in org.anchoranalysis.plugin.opencv.bean.stack with parameters of type Stack

Modifier and Type	Method	Description
protected void	OpenCVWriter.writeStackAfterCheck(Stack stack, Path filePath)

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

Methods in org.anchoranalysis.plugin.opencv.convert that return Stack

Modifier and Type	Method	Description
static Stack	ConvertFromMat.toStack(org.opencv.core.Mat mat)	Convert from an OpenCV Mat to a Stack.

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

Modifier and Type	Method	Description
static org.opencv.core.Mat	ConvertToMat.fromStack(Stack stack)	Converts a Stack to a Mat.
static org.opencv.core.Mat	ConvertToMat.makeRGBStack(Stack stack, boolean swapRedBlueChannels)	Derives a Mat representing an RGB stack.

Uses of Stack in org.anchoranalysis.test.image

Methods in org.anchoranalysis.test.image that return Stack

Modifier and Type	Method	Description
Stack	StackFixture.create(ChannelSpecification channelSpecification, Extent extent)	Creates a stack with a particular number of the channels of particular size.

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

Modifier and Type	Method	Description
void	WriteIntoDirectory.writeObjects(String outputName, ObjectCollection objects, Stack background)	Writes the outline of objects on a background.

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

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

Modifier and Type	Method	Description
Stack	TestLoaderImage.openStackFromFilePath(Path filePath)	Opens a stack from a file path.
Stack	TestLoaderImage.openStackFromTestPath(String testPath)	Opens a stack from a test path.

Uses of Stack in org.anchoranalysis.test.image.load

Methods in org.anchoranalysis.test.image.load that return Stack

Modifier and Type	Method	Description
Stack	CarImageLoader.carGrayscale16Bit()	Loads and returns the 16-bit grayscale image of a car.
Stack	CarImageLoader.carGrayscale8Bit()	Loads and returns the 8-bit grayscale image of a car.
Stack	CarImageLoader.carRGB()	Loads and returns the RGB image of a car.

Uses of Stack in org.anchoranalysis.test.image.segment

Methods in org.anchoranalysis.test.image.segment that return Stack

Modifier and Type	Method	Description
protected Stack	InstanceSegmentationTestBase.stackGrayscale()	Provides the grayscale stack to be tested.
protected Stack	InstanceSegmentationTestBase.stackRGB()	Provides the RGB stack to be tested.