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.experiment.bean.convert |
Converting from
NamedChannelsInput to the
input-type expected by a Task . |
org.anchoranalysis.plugin.opencv.bean.stack | |
org.anchoranalysis.plugin.quick.bean.input |
Specifying inputs when quickly defining an experiment.
|
org.anchoranalysis.test.image.io |
Utilities for testing-related reading and writing to the filesystem.
|
Modifier and Type | Method and Description |
---|---|
StackReader |
AnnotatorStrategy.getStackReader()
How to read raster
Stack s from the file-system. |
Modifier and Type | Method and Description |
---|---|
void |
AnnotatorStrategy.setStackReader(StackReader stackReader)
How to read raster
Stack s from the file-system. |
Modifier and Type | Method and Description |
---|---|
StackReader |
FromStackReader.getStackReader()
The
StackReader to use to read the image metadata. |
Modifier and Type | Method and 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. |
Constructor and Description |
---|
FromStackReader(StackReader stackReader)
Create from a
StackReader . |
Modifier and Type | Class and Description |
---|---|
class |
StackReaderOrientationCorrection
A
StackReader that supports the correction of orientation as images are read from the
file-system. |
Modifier and Type | Method and Description |
---|---|
StackReader |
InputManagerWithStackReader.getStackReader()
How to read an image from the file-system.
|
Modifier and Type | Method and Description |
---|---|
void |
InputManagerWithStackReader.setStackReader(StackReader stackReader)
How to read an image from the file-system.
|
Modifier and Type | Method and Description |
---|---|
static Mask |
MaskReader.openMask(StackReader stackReader,
Path path,
BinaryValuesInt binaryValues,
OperationContext context)
Utility functions for opening a single-channeled stack as a
Mask . |
Modifier and Type | Class and Description |
---|---|
class |
BioformatsReader
Reads a stack using the Bioformats
library.
|
Modifier and Type | Method and Description |
---|---|
StackReader |
MaskAsObject.getStackReader()
How to read the
Mask from the file-system. |
Modifier and Type | Method and Description |
---|---|
void |
MaskAsObject.setStackReader(StackReader stackReader)
How to read the
Mask from the file-system. |
Modifier and Type | Method and Description |
---|---|
StackReader |
AnnotationComparisonInput.getStackReader() |
Constructor and Description |
---|
AnnotationComparisonInput(T input,
io.vavr.Tuple2<ComparableSource,ComparableSource> comparers,
io.vavr.Tuple2<String,String> names,
StackReader stackReader) |
Modifier and Type | Method and Description |
---|---|
StackReader |
Montage.getStackReader()
Fallback for
imageMetadataReader to read image files without a directy metadata
reader. |
Modifier and Type | Method and Description |
---|---|
void |
Montage.setStackReader(StackReader stackReader)
Fallback for
imageMetadataReader to read image files without a directy metadata
reader. |
Modifier and Type | Method and Description |
---|---|
StackReader |
ScaleImageCommonSize.getStackReader()
Fallback for
imageMetadataReader to read image files without a direct metadata
reader. |
Modifier and Type | Method and Description |
---|---|
void |
ScaleImageCommonSize.setStackReader(StackReader stackReader)
Fallback for
imageMetadataReader to read image files without a direct metadata
reader. |
Constructor and Description |
---|
ImageSizePrereader(ImageMetadataReader imageMetadataReader,
StackReader stackReader,
OperationContext context) |
Modifier and Type | Method and Description |
---|---|
ImageMetadata |
AlwaysReject.openFile(Path path,
StackReader defaultStackReader,
OperationContext context) |
ImageMetadata |
InferFromHeader.openFile(Path path,
StackReader defaultStackReader,
OperationContext context) |
Modifier and Type | Class and 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.
|
Modifier and Type | Method and 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 |
RejectIfConditionXYResolution.getStackReader()
Reads an image before a resolution is imposed.
|
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.
|
Modifier and Type | Method and 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 |
RejectIfConditionXYResolution.setStackReader(StackReader stackReader)
Reads an image before a resolution is imposed.
|
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.
|
Constructor and Description |
---|
OpenedMultiFile(StackReader stackReader,
ParsedFilePathBag fileBag,
ExecutionTimeRecorder executionTimeRecorder) |
Modifier and Type | Method and Description |
---|---|
StackReader |
ConvertNamedChannels.getDefaultStackReaderForMetadata()
Supplies to the
imageMetadataReader to use, if no other reader is specified. |
Modifier and Type | Method and Description |
---|---|
void |
ConvertNamedChannels.setDefaultStackReaderForMetadata(StackReader defaultStackReaderForMetadata)
Supplies to the
imageMetadataReader to use, if no other reader is specified. |
Modifier and Type | Class and Description |
---|---|
class |
OpenCVReader
Reads a stack from the file-system using OpenCV.
|
Modifier and Type | Method and Description |
---|---|
StackReader |
NamedChannelsQuick.getStackReaderAdjacent()
The raster-reader to use for opening any adjacent-channels
|
StackReader |
QuickBase.getStackReaderAppend()
The raster-reader for reading any appended files
|
Modifier and Type | Method and Description |
---|---|
void |
NamedChannelsQuick.setStackReaderAdjacent(StackReader stackReaderAdjacent)
The raster-reader to use for opening any adjacent-channels
|
void |
QuickBase.setStackReaderAppend(StackReader stackReaderAppend)
The raster-reader for reading any appended files
|
Modifier and Type | Method and Description |
---|---|
static StackReader |
BeanInstanceMapFixture.ensureStackReader()
Ensure a
StackReader instance exists in the underlying BeanInstanceMap . |
Constructor and Description |
---|
TestLoaderImage(TestLoader loader,
StackReader stackReader) |
Copyright © 2010–2023 Owen Feehan, ETH Zurich, University of Zurich, Hoffmann-La Roche. All rights reserved.