Uses of Class
org.anchoranalysis.image.io.ImageIOException

Packages that use ImageIOException

Package	Description
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.bean.stack.writer	Bean classes for writing raster-files to the filesystem.
org.anchoranalysis.image.io.channel.input	Non-bean classes for reading a Channel from the filesystem.
org.anchoranalysis.image.io.channel.map	Non-bean classes for a mapping of names to Channels.
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.generator	Base classes for generators that ultimately write a Stack to the filesystem.
org.anchoranalysis.io.bioformats.bean	Beans for filesystem I/O using Bioformats.
org.anchoranalysis.io.bioformats.bean.writer	Writing stacks to the file system using the Bioformats library.
org.anchoranalysis.io.bioformats.metadata	Reading metadata information from files using EXIF and/or other metadata headers.
org.anchoranalysis.io.imagej.bean.stack.writer	Raster-writers that use ImageJ to write images to the filesystem.
org.anchoranalysis.plugin.io.bean.input.stack	Implementations of InputManager that process Stacks.
org.anchoranalysis.plugin.io.bean.metadata.header	Different types of image-file-formats whose headers can provide ImageMetadata.
org.anchoranalysis.plugin.io.bean.metadata.reader	Implementations of ImageMetadataReader.
org.anchoranalysis.plugin.io.bean.stack.reader	Implementations of StackReader.
org.anchoranalysis.plugin.io.bean.stack.writer	Implementations of StackWriter.
org.anchoranalysis.plugin.io.bean.summarizer.image	Implementations of Summarizer that summarize images.
org.anchoranalysis.plugin.io.multifile	Non-bean classes to help use multiple files to represent a single Stack.
org.anchoranalysis.plugin.io.xml	Reading and writing metadata XML.
org.anchoranalysis.plugin.opencv.bean.stack	Implementations of StackWriter and StackReader that involve OpenCV.
org.anchoranalysis.test.image.stackwriter	Fixtures for testing StackWriter and related classes.

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

Methods in org.anchoranalysis.image.io.bean.stack.metadata.reader that throw ImageIOException

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.

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

Methods in org.anchoranalysis.image.io.bean.stack.reader that throw ImageIOException

Modifier and Type	Method	Description
abstract OpenedImageFile	StackReader.openFile(Path path, ExecutionTimeRecorder executionTimeRecorder)	Opens a file containing one or more images.
abstract OpenedImageFile	StackReaderOrientationCorrection.openFile(Path path, CalculateOrientationChange orientationCorrection, ExecutionTimeRecorder executionTimeRecorder)	Opens a file containing one or more images but does not read an image.
Stack	StackReader.readStack(Path path, OperationContext context)	Opens a file at path that should contain only a single-stack.

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

Methods in org.anchoranalysis.image.io.bean.stack.writer that return ImageIOException

Modifier and Type	Method	Description
static <T extends StackWriter> ImageIOException	WriterErrorMessageHelper.generalWriteException(Class<T> writerClass, Path path, Exception cause)	Creates a ImageIOException with an error message that image-writing failed.

Methods in org.anchoranalysis.image.io.bean.stack.writer that throw ImageIOException

Modifier and Type	Method	Description
ImageFileFormat	OneOrThreeChannelsWriter.fileFormat(StackWriteOptions writeOptions)
abstract ImageFileFormat	StackWriter.fileFormat(StackWriteOptions writeOptions)	The file format that will be written by the generator.
ImageFileFormat	StackWriter.fileFormatWarnUnexpected(StackWriteOptions writeOptions, Optional<Logger> logger)	The file format that will be written by the generator, warning with a log message if different to suggestion.
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 ImageIOException in org.anchoranalysis.image.io.channel.input

Methods in org.anchoranalysis.image.io.channel.input that throw ImageIOException

Modifier and Type	Method	Description
abstract int	NamedChannelsInput.bitDepth(Logger logger)	Bit-depth of image.
abstract NamedChannelsMap	NamedChannelsInput.createChannelsForSeries(int seriesIndex, Logger logger)	Creates a NamedChannelsMap representing the channels for a particular series in this input.
abstract Dimensions	NamedChannelsInput.dimensions(int seriesIndex, Logger logger)	Dimensions of a particular series.
abstract ImageMetadata	NamedChannelsInput.metadata(int seriesIndex, Logger logger)	The image-metadata associated with a particular series.
abstract int	NamedChannelsInput.numberChannels(Logger logger)	Number of channels.
abstract int	NamedChannelsInput.numberSeries()	Number of series that exist.

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

Methods in org.anchoranalysis.image.io.channel.map that throw ImageIOException

Modifier and Type	Method	Description
Dimensions	NamedChannelsConcatenate.dimensions(Logger logger)
Dimensions	NamedChannelsMap.dimensions(Logger logger)	The dimensions of each Channel.
Dimensions	OpenedNamedChannels.dimensions(Logger logger)
boolean	NamedChannelsConcatenate.isRGB(Logger logger)
boolean	NamedChannelsMap.isRGB(Logger logger)	Whether the channels describe an RGB image.
boolean	OpenedNamedChannels.isRGB(Logger logger)
int	NamedChannelsConcatenate.sizeT(Logger logger)
int	NamedChannelsMap.sizeT(Logger logger)	The number of frames along the time-axis.
int	OpenedNamedChannels.sizeT(Logger logger)

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

Methods in org.anchoranalysis.image.io.stack that throw ImageIOException

Modifier and Type	Method	Description
OrientationChange	CalculateOrientationChange.calculateOrientationChange(Logger logger)	Calculates any needed orientation change.

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

Methods in org.anchoranalysis.image.io.stack.input that throw ImageIOException

Modifier and Type	Method	Description
int	OpenedImageFile.bitDepth(Logger logger)	The bit-depth of the image voxels e.g. 8 for 8-bit, 16 for 16-bit etc.
Optional<List<String>>	OpenedImageFile.channelNames(Logger logger)	The names of each channel, if they are known.
void	OpenedImageFile.close()	Closes the opened image-file, removing any intermediate data-structures.
TimeSeries	StackSequenceInput.createStackSequenceForSeries(int seriesIndex, Logger logger)	Creates a supplier of a TimeSeries of stacks for a particular series number.
Dimensions	OpenedImageFile.dimensionsForSeries(int seriesIndex, Logger logger)	The Dimensions associated with a particular series.
boolean	OpenedImageFile.isRGB(Logger logger)	Whether the image-file has RGB encoded voxels.
ImageMetadata	ImageMetadataInput.metadata()	The associated image metadata.
default ImageMetadata	OpenedImageFile.metadata(int seriesIndex, Logger logger)	Extracts metadata about the image.
int	OpenedImageFile.numberChannels(Logger logger)	The number of channels in the image-file e.g. 1 for grayscale, 3 for RGB.
int	OpenedImageFile.numberFrames(Logger logger)	The number of frames in the image-file i.e. distinct images for a particular time-point.
TimeSeries	OpenedImageFile.open(int seriesIndex, Logger logger)	Open when we don't have a specific-type.
default TimeSeries	OpenedImageFile.open(Logger logger)	Open the first series when we don't have a specific-type.
default TimeSeries	OpenedImageFile.openCheckType(int seriesIndex, VoxelDataType channelDataType, Logger logger)	Opens a time-series, and checks that it is a particular type.
static Mask	MaskReader.openMask(StackReader stackReader, Path path, BinaryValuesInt binaryValues, OperationContext context)	Utility functions for opening a single-channeled stack as a Mask.
Optional<ImagePyramidMetadata>	OpenedImageFile.pyramid()	Metadata to describe an image-pyramid, if it exists for this opened-image.
ImageTimestampsAttributes	OpenedImageFile.timestamps()	The timestamps and file-attributes associated with the image.

Constructor parameters in org.anchoranalysis.image.io.stack.input with type arguments of type ImageIOException

Modifier	Constructor	Description
	ImageMetadataInput(NamedFile file, CheckedSupplier<ImageMetadata,ImageIOException> metadata)	Create for a particular file and metadata.

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

Methods in org.anchoranalysis.image.io.stack.output.generator that throw ImageIOException

Modifier and Type	Method	Description
static String	GeneratorOutputter.fileExtensionWriter(OutputWriteSettings settings, StackWriteOptions writeOptions, Optional<Logger> logger)	The file extension to use for the default StackWriter, as returned by GeneratorOutputter.writer(OutputWriteSettings).
static StackWriter	GeneratorOutputter.writer(OutputWriteSettings settings)	Gets the default StackWriter.

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

Methods in org.anchoranalysis.io.bioformats.bean that throw ImageIOException

Modifier and Type	Method	Description
OpenedImageFile	BioformatsReader.openFile(Path path, ExecutionTimeRecorder executionTimeRecorder)
OpenedImageFile	BioformatsReader.openFile(Path filePath, CalculateOrientationChange orientationCorrection, ExecutionTimeRecorder executionTimeRecorder)

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

Methods in org.anchoranalysis.io.bioformats.bean.writer that throw ImageIOException

Modifier and Type	Method	Description
byte[]	ByteRepresentationForChannel.bytesForSlice(int sliceIndex)	The byte-representation of the voxels for a particular slice.
protected abstract loci.formats.IFormatWriter	BioformatsWriter.createWriter()	Creates or gets an instance of IFormatWriter which dictates the file format to use for writing.
protected loci.formats.IFormatWriter	OMETiff.createWriter()
protected loci.formats.IFormatWriter	OMEXML.createWriter()
protected loci.formats.IFormatWriter	Tiff.createWriter()
void	BioformatsWriter.writeStack(Stack stack, Path filePath, StackWriteOptions options)
void	Tiff.writeStack(Stack stack, Path filePath, StackWriteOptions options)

Uses of ImageIOException in org.anchoranalysis.io.bioformats.metadata

Methods in org.anchoranalysis.io.bioformats.metadata that throw ImageIOException

Modifier and Type	Method	Description
static Optional<OrientationChange>	OrientationReader.determineOrientationCorrection(com.drew.metadata.Metadata metadata)	Determines the needed correction to orientation for the voxels if an EXIF orientation tag is present.
static Optional<OrientationChange>	OrientationReader.determineOrientationCorrection(Path path)	Determines the needed correction to orientation for the voxels if an EXIF orientation tag is present.
static ImageTimestampsAttributes	ImageTimestampsAttributesFactory.fromPath(Path path)	Reads ImageTimestampsAttributes from a path, trying to infer the acquisition-date from metadata headers.
static Optional<ZonedDateTime>	AcquisitionDateReader.readAcquisitionDate(Path path)	Reads an image acquisition-date from a file identified by path, based on the present of EXIF data.
static Optional<Extent>	ReadMetadataUtilities.readFromWidthHeightTags(com.drew.metadata.Directory directory, int tagWidth, int tagHeight)	Reads two metadata entries, representing width and height, and use them to form a Extent.
static <T extends com.drew.metadata.Directory> Optional<Extent>	ReadMetadataUtilities.readFromWidthHeightTags(com.drew.metadata.Metadata metadata, Class<T> directoryType, int tagWidth, int tagHeight)	Reads two metadata entries, representing width and height, and use them to form a Extent.
static Optional<com.drew.metadata.Metadata>	ReadMetadataUtilities.readMetadata(Path path)	Reads metadata, if it exists, from an image.

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

Methods in org.anchoranalysis.io.imagej.bean.stack.writer that throw ImageIOException

Modifier and Type	Method	Description
protected abstract boolean	ImageJRasterWriter.writeRaster(ij.io.FileSaver fileSaver, String path, boolean asStack)	Writes an annotation to the filesystem at outPath.
protected boolean	PNG.writeRaster(ij.io.FileSaver fileSaver, String path, boolean asStack)
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 ImageIOException in org.anchoranalysis.plugin.io.bean.input.stack

Methods in org.anchoranalysis.plugin.io.bean.input.stack that throw ImageIOException

Modifier and Type	Method	Description
TimeSeries	ConvertNamedChannelsInputToStack.createStackSequenceForSeries(int seriesIndex, Logger logger)

Uses of ImageIOException in org.anchoranalysis.plugin.io.bean.metadata.header

Methods in org.anchoranalysis.plugin.io.bean.metadata.header that throw ImageIOException

Modifier and Type	Method	Description
Optional<ImageMetadata>	HeaderFormat.populateFrom(Path path)	Creates a ImageMetadata, if possible, from the metadata at path.
protected Optional<ImageMetadata>	BMP.populateFromMetadata(com.drew.metadata.Metadata metadata, ImageFileAttributes attributes)
protected abstract Optional<ImageMetadata>	HeaderFormat.populateFromMetadata(com.drew.metadata.Metadata metadata, ImageFileAttributes attributes)	Creates a ImageMetadata, if possible, from metadata.
protected Optional<ImageMetadata>	JPEG.populateFromMetadata(com.drew.metadata.Metadata metadata, ImageFileAttributes attributes)
protected Optional<ImageMetadata>	PNG.populateFromMetadata(com.drew.metadata.Metadata metadata, ImageFileAttributes attributes)

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

Methods in org.anchoranalysis.plugin.io.bean.metadata.reader that throw ImageIOException

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 ImageIOException in org.anchoranalysis.plugin.io.bean.stack.reader

Methods in org.anchoranalysis.plugin.io.bean.stack.reader that throw ImageIOException

Modifier and Type	Method	Description
OpenedImageFile	BranchExtension.openFile(Path path, ExecutionTimeRecorder executionTimeRecorder)
OpenedImageFile	FlattenAsChannel.openFile(Path path, ExecutionTimeRecorder executionTimeRecorder)
OpenedImageFile	ImposeResolution.openFile(Path path, ExecutionTimeRecorder executionTimeRecorder)
OpenedImageFile	MultiFileReader.openFile(Path filePath, ExecutionTimeRecorder executionTimeRecorder)
OpenedImageFile	ReadVoxelExtentXml.openFile(Path path, ExecutionTimeRecorder executionTimeRecorder)
OpenedImageFile	RejectIfConditionXYResolution.openFile(Path path, ExecutionTimeRecorder executionTimeRecorder)
OpenedImageFile	RotateImageToMatchEXIFOrientation.openFile(Path path, ExecutionTimeRecorder executionTimeRecorder)
OpenedImageFile	RotateImageToMatchEXIFOrientation.openFile(Path path, CalculateOrientationChange orientationCorrection, ExecutionTimeRecorder executionTimeRecorder)
static Optional<Resolution>	ReadVoxelExtentXml.readMetadata(Path filePath, boolean acceptNoResolution)	Looks for a metadata file describing the resolution

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

Methods in org.anchoranalysis.plugin.io.bean.stack.writer that throw ImageIOException

Modifier and Type	Method	Description
ImageFileFormat	StackWriterDelegateBase.fileFormat(StackWriteOptions writeOptions)
ImageFileFormat	WriteResolutionXml.fileFormat(StackWriteOptions writeOptions)
protected StackWriter	BranchSuggestedFormat.selectDelegate(StackWriteOptions writeOptions)
protected abstract StackWriter	StackWriterDelegateBase.selectDelegate(StackWriteOptions writeOptions)	Selects a StackWriter to use as a delegate.
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 ImageIOException in org.anchoranalysis.plugin.io.bean.summarizer.image

Methods in org.anchoranalysis.plugin.io.bean.summarizer.image that throw ImageIOException

Modifier and Type	Method	Description
protected Integer	BitDepth.extractKey(ImageMetadataInput element)
protected Integer	NumberChannels.extractKey(ImageMetadataInput element)
protected abstract T	SummarizerImageMetadataSimple.extractKey(ImageMetadataInput element)

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

Methods in org.anchoranalysis.plugin.io.multifile that throw ImageIOException

Modifier and Type	Method	Description
int	OpenedMultiFile.bitDepth(Logger logger)
void	OpenedMultiFile.close()
Dimensions	OpenedMultiFile.dimensionsForSeries(int seriesIndex, Logger logger)
boolean	OpenedMultiFile.isRGB(Logger logger)
int	OpenedMultiFile.numberChannels(Logger logger)
int	OpenedMultiFile.numberFrames(Logger logger)
TimeSeries	OpenedMultiFile.open(int seriesIndex, Logger logger)
Optional<ImagePyramidMetadata>	OpenedMultiFile.pyramid()
ImageTimestampsAttributes	OpenedMultiFile.timestamps()

Uses of ImageIOException in org.anchoranalysis.plugin.io.xml

Methods in org.anchoranalysis.plugin.io.xml that throw ImageIOException

Modifier and Type	Method	Description
static Resolution	ResolutionAsXML.readResolutionXml(File file)	Retrieves resolution from a XML file previously written by ResolutionAsXML.writeResolutionXML(Resolution, Path).
static void	ResolutionAsXML.writeResolutionXML(Resolution resolution, Path path)	Writes a XML metadata file describing the image-resolution.

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

Methods in org.anchoranalysis.plugin.opencv.bean.stack that throw ImageIOException

Modifier and Type	Method	Description
OpenedImageFile	OpenCVReader.openFile(Path path, ExecutionTimeRecorder executionTimeRecorder)
protected void	OpenCVWriter.writeStackAfterCheck(Stack stack, Path filePath)

Uses of ImageIOException in org.anchoranalysis.test.image.stackwriter

Methods in org.anchoranalysis.test.image.stackwriter that throw ImageIOException

Modifier and Type	Method	Description
void	StackTester.performTest(VoxelDataType[] channelVoxelTypes, int numberChannels, boolean makeRGB, Optional<VoxelDataType> forceFirstChannel, Optional<ImageComparer> comparer)	Performs a test on stack writing for specified channel types, number of channels, RGB setting, and optional forced first channel type.
void	StackTester.performTest(VoxelDataType[] channelVoxelTypes, int numberChannels, boolean makeRGB, Optional<ImageComparer> comparer)	Performs a test on stack writing for specified channel types, number of channels, and RGB setting.
void	StackTester.performTest(ChannelSpecification channels, Optional<VoxelDataType> forceFirstChannel, Optional<ImageComparer> comparer)	Performs a test on stack writing for a specified channel specification and optional forced first channel type.
void	StackTester.performTest(ChannelSpecification channels, Optional<ImageComparer> comparer)	Performs a test on stack writing for a specified channel specification.
void	FourChannelStackTester.testFourChannels()	Tests a stack with four-channels of unsigned 8-bit data type.
void	FourChannelStackTester.testFourChannels(VoxelDataType[] channelVoxelTypes)	Tests a stack with four-channels of specified types
void	FourChannelStackTester.testSingleChannel()	Tests the creation of a single-channel stack of unsigned 8-bit data type with the RGB flag off.
void	FourChannelStackTester.testSingleChannel(VoxelDataType channelVoxelType)	Tests the creation of a single-channel stack of specified data type with the RGB flag off.
void	FourChannelStackTester.testSingleChannel(VoxelDataType[] channelVoxelTypes)	Tests the creation of a single-channel stack of specified data types with the RGB flag off.
void	FourChannelStackTester.testSingleChannelRGB()	Tests the creation of a single-channel stack of unsigned 8-bit data type with the RGB flag on, which should typically produce an exception.
void	FourChannelStackTester.testThreeChannelsHeterogeneous()	Tests the creation of a three-channel stack of heterogeneous channel types.
void	FourChannelStackTester.testThreeChannelsRGB()	Tests the creation of a three-channel stack of unsigned 8-bit data type with the rgb-flag set to true.
void	FourChannelStackTester.testThreeChannelsRGB(VoxelDataType channelVoxelType)	Tests the creation of a three-channel stack of specified data type with the rgb-flag set to true.
void	FourChannelStackTester.testThreeChannelsRGB(VoxelDataType[] channelVoxelTypes)	Tests the creation of a three-channel stack of specified data types with the rgb-flag set to true.
void	FourChannelStackTester.testThreeChannelsSeparate()	Tests the creation of a three-channel stack of unsigned 8-bit data type with the rgb-flag set to false.
void	FourChannelStackTester.testThreeChannelsSeparate(VoxelDataType[] channelVoxelTypes)	Tests the creation of a three-channel stack of specified data types with the rgb-flag set to false.
void	FourChannelStackTester.testTwoChannels()	Tests the creation of a two-channel stack of unsigned 8-bit data type.
void	FourChannelStackTester.testTwoChannels(VoxelDataType[] channelVoxelTypes)	Tests the creation of a two-channel stack of specified data types.