Uses of Class
org.anchoranalysis.image.io.bean.stack.reader.StackReader

Packages that use StackReader

Package	Description
org.anchoranalysis.annotation.io.bean	Beans related to reading / writing / specifying annotations.
org.anchoranalysis.image.io.bean.stack.metadata.reader	Bean classes for reading ImageMetadata from the file-system.
org.anchoranalysis.image.io.bean.stack.reader	Bean classes for reading raster-files from the filesystem.
org.anchoranalysis.image.io.stack.input	Non-bean classes for reading a Stack from the filesystem.
org.anchoranalysis.io.bioformats.bean	Beans for filesystem I/O using Bioformats.
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.task.bean.combine	Combining multiple images together into a single image.
org.anchoranalysis.plugin.image.task.bean.scale	Tasks to scale an image.
org.anchoranalysis.plugin.image.task.stack	Non-bean classes pertaining to stacks and channels as used in tasks.
org.anchoranalysis.plugin.io.bean.metadata.reader	Implementations of ImageMetadataReader.
org.anchoranalysis.plugin.io.bean.stack.reader	Implementations of StackReader.
org.anchoranalysis.plugin.io.multifile	Non-bean classes to help use multiple files to represent a single Stack.
org.anchoranalysis.plugin.mpp.bean.convert	Converting from NamedChannelsInput to the input-type expected by a Task.
org.anchoranalysis.plugin.opencv.bean.stack	Implementations of StackWriter and StackReader that involve OpenCV.
org.anchoranalysis.test.image.io	Utilities for testing-related reading and writing to the filesystem.

Uses of StackReader in org.anchoranalysis.annotation.io.bean

Methods in org.anchoranalysis.annotation.io.bean that return StackReader

Modifier and Type	Method	Description
StackReader	AnnotatorStrategy.getStackReader()	How to read raster Stacks from the file-system.

Methods in org.anchoranalysis.annotation.io.bean with parameters of type StackReader

Modifier and Type	Method	Description
void	AnnotatorStrategy.setStackReader(StackReader stackReader)	How to read raster Stacks from the file-system.

Uses of StackReader in org.anchoranalysis.image.io.bean.stack.metadata.reader

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

Modifier and Type	Method	Description
StackReader	FromStackReader.getStackReader()	The StackReader to use to read the image metadata.

Methods in org.anchoranalysis.image.io.bean.stack.metadata.reader with parameters of type StackReader

Modifier and Type	Method	Description
ImageMetadata	FromStackReader.openFile(Path path, StackReader defaultStackReader, OperationContext context)
abstract ImageMetadata	ImageMetadataReader.openFile(Path path, StackReader defaultStackReader, OperationContext context)	Opens a file containing one or more images but does not read an image.
void	FromStackReader.setStackReader(StackReader stackReader)	The StackReader to use to read the image metadata.

Constructors in org.anchoranalysis.image.io.bean.stack.metadata.reader with parameters of type StackReader

Modifier	Constructor	Description
	FromStackReader(StackReader stackReader)	Create from a StackReader.

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

Subclasses of StackReader in org.anchoranalysis.image.io.bean.stack.reader

Modifier and Type	Class	Description
class	StackReaderOrientationCorrection	A StackReader that supports the correction of orientation as images are read from the file-system.

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

Modifier and Type	Method	Description
StackReader	InputManagerWithStackReader.getStackReader()	How to read an image from the file-system.

Methods in org.anchoranalysis.image.io.bean.stack.reader with parameters of type StackReader

Modifier and Type	Method	Description
void	InputManagerWithStackReader.setStackReader(StackReader stackReader)	How to read an image from the file-system.

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

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

Modifier and Type	Method	Description
static Mask	MaskReader.openMask(StackReader stackReader, Path path, BinaryValuesInt binaryValues, OperationContext context)	Utility functions for opening a single-channeled stack as a Mask.

Uses of StackReader in org.anchoranalysis.io.bioformats.bean

Subclasses of StackReader in org.anchoranalysis.io.bioformats.bean

Modifier and Type	Class	Description
class	BioformatsReader	Reads a stack using the Bioformats library.

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

Methods in org.anchoranalysis.plugin.annotation.bean.comparer that return StackReader

Modifier and Type	Method	Description
StackReader	MaskAsObject.getStackReader()	How to read the Mask from the file-system.

Methods in org.anchoranalysis.plugin.annotation.bean.comparer with parameters of type StackReader

Modifier and Type	Method	Description
void	MaskAsObject.setStackReader(StackReader stackReader)	How to read the Mask from the file-system.

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

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

Modifier and Type	Method	Description
StackReader	AnnotationComparisonInput.getStackReader()	The StackReader to use for reading image stacks.

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

Modifier	Constructor	Description
	AnnotationComparisonInput(T input, io.vavr.Tuple2<ComparableSource,ComparableSource> comparers, io.vavr.Tuple2<String,String> names, StackReader stackReader)	Creates an annotation comparison input.

Uses of StackReader in org.anchoranalysis.plugin.image.task.bean.combine

Methods in org.anchoranalysis.plugin.image.task.bean.combine that return StackReader

Modifier and Type	Method	Description
StackReader	Montage.getStackReader()	Fallback for imageMetadataReader to read image files without a directy metadata reader.

Methods in org.anchoranalysis.plugin.image.task.bean.combine with parameters of type StackReader

Modifier and Type	Method	Description
void	Montage.setStackReader(StackReader stackReader)	Fallback for imageMetadataReader to read image files without a directy metadata reader.

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

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

Modifier and Type	Method	Description
StackReader	ScaleImageCommonSize.getStackReader()	Fallback for imageMetadataReader to read image files without a direct metadata reader.

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

Modifier and Type	Method	Description
void	ScaleImageCommonSize.setStackReader(StackReader stackReader)	Fallback for imageMetadataReader to read image files without a direct metadata reader.

Uses of StackReader in org.anchoranalysis.plugin.image.task.stack

Constructors in org.anchoranalysis.plugin.image.task.stack with parameters of type StackReader

Modifier	Constructor	Description
	ImageSizePrereader(ImageMetadataReader imageMetadataReader, StackReader stackReader, OperationContext context)	Creates a new ImageSizePrereader instance.

Uses of StackReader in org.anchoranalysis.plugin.io.bean.metadata.reader

Methods in org.anchoranalysis.plugin.io.bean.metadata.reader with parameters of type StackReader

Modifier and Type	Method	Description
ImageMetadata	AlwaysReject.openFile(Path path, StackReader defaultStackReader, OperationContext context)
ImageMetadata	InferFromHeader.openFile(Path path, StackReader defaultStackReader, OperationContext context)

Uses of StackReader in org.anchoranalysis.plugin.io.bean.stack.reader

Subclasses of StackReader in org.anchoranalysis.plugin.io.bean.stack.reader

Modifier and Type	Class	Description
class	BranchExtension	If the extension(s) of a path matches a particular value, then use a particular reader, otherwise a fallback.
class	FlattenAsChannel	Combines all series and frames returned by a reader by converting them into multiple channels in the same image.
class	ImposeResolution	Adds an explicit Resolution to an image after it has been read.
class	MultiFileReader
class	ReadVoxelExtentXml	Reads Resolution from an XML file associated an image.
class	RejectIfConditionXYResolution	If the XY resolution of an opened-image meets a certain condition then the resolution is scaled by a factor.
class	RotateImageToMatchEXIFOrientation	Rotates an image to match any EXIF orientation information, if it exists.

Methods in org.anchoranalysis.plugin.io.bean.stack.reader that return StackReader

Modifier and Type	Method	Description
StackReader	BranchExtension.getReaderMatching()	The reader to use if the extension matches.
StackReader	BranchExtension.getReaderNotMatching()	The reader to use if the extension does not match.
StackReader	FlattenAsChannel.getStackReader()	Reads the image that is subsequently flattened.
StackReader	ImposeResolution.getStackReader()	Reads an image before a resolution is imposed.
StackReader	MultiFileReader.getStackReader()
StackReader	ReadVoxelExtentXml.getStackReader()	Reads an image before a resolution is imposed.
StackReader	RejectIfConditionXYResolution.getStackReader()	Reads an image before a resolution is imposed.

Methods in org.anchoranalysis.plugin.io.bean.stack.reader with parameters of type StackReader

Modifier and Type	Method	Description
void	BranchExtension.setReaderMatching(StackReader readerMatching)	The reader to use if the extension matches.
void	BranchExtension.setReaderNotMatching(StackReader readerNotMatching)	The reader to use if the extension does not match.
void	FlattenAsChannel.setStackReader(StackReader stackReader)	Reads the image that is subsequently flattened.
void	ImposeResolution.setStackReader(StackReader stackReader)	Reads an image before a resolution is imposed.
void	MultiFileReader.setStackReader(StackReader stackReader)
void	ReadVoxelExtentXml.setStackReader(StackReader stackReader)	Reads an image before a resolution is imposed.
void	RejectIfConditionXYResolution.setStackReader(StackReader stackReader)	Reads an image before a resolution is imposed.

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

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

Modifier	Constructor	Description
	OpenedMultiFile(StackReader stackReader, ParsedFilePathBag fileBag, ExecutionTimeRecorder executionTimeRecorder)

Uses of StackReader in org.anchoranalysis.plugin.mpp.bean.convert

Methods in org.anchoranalysis.plugin.mpp.bean.convert that return StackReader

Modifier and Type	Method	Description
StackReader	ConvertNamedChannels.getDefaultStackReaderForMetadata()	Supplies to the imageMetadataReader to use, if no other reader is specified.

Methods in org.anchoranalysis.plugin.mpp.bean.convert with parameters of type StackReader

Modifier and Type	Method	Description
void	ConvertNamedChannels.setDefaultStackReaderForMetadata(StackReader defaultStackReaderForMetadata)	Supplies to the imageMetadataReader to use, if no other reader is specified.

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

Subclasses of StackReader in org.anchoranalysis.plugin.opencv.bean.stack

Modifier and Type	Class	Description
class	OpenCVReader	Reads a stack from the file-system using OpenCV.

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

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

Modifier and Type	Method	Description
static StackReader	BeanInstanceMapFixture.ensureStackReader()	Ensure a StackReader instance exists in the underlying BeanInstanceMap.

Constructors in org.anchoranalysis.test.image.io with parameters of type StackReader

Modifier	Constructor	Description
	TestLoaderImage(TestLoader loader, StackReader stackReader)	Creates a new TestLoaderImage instance.