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.

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.
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.
Optional<ImageLocation>	OpenedImageFile.location()	The location associated with the image, if it is known.
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.
int	OpenedImageFile.numberFrames(Logger logger)	The number of frames in the image-file i.e.
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.