Uses of Class
io.scif.FormatException

Packages that use FormatException

Package	Description
io.scif	Provides the interfaces and default implementations for the components of SCIFIO, and the context for instantiating these components.
io.scif.codec	Codecs for encoding and decoding streams of bytes.
io.scif.filters	Provides wrapping classes for modifying the performance of one or more of a {link io.scif.Format}'s components.
io.scif.formats	Provides Format implementations for all file formats that are supported by default in SCIFIO.
io.scif.formats.qt
io.scif.formats.tiff	This package contains utility classes for working with a variety of Tiff-based formats.
io.scif.gui	Provides classes for working with BufferedImage in SCIFIO.
io.scif.img.cell	Provides a Reader backed CachedCellImg implementation and supporting classes.
io.scif.img.cell.loaders	Provides implementations of SCIFIOArrayLoader for each basic ArrayDataAccess type.
io.scif.services	Provides a set of Services (singletons within a given context) for working with SCIFIO objects.
io.scif.util	Provides utility classes for common operations on or by SCIFIO components.

Uses of FormatException in io.scif

Subclasses of FormatException in io.scif

Modifier and Type	Class and Description
class	MissingLibraryException MissingLibraryException is the exception thrown when a particular data stream or filename requires a library that is not present on the system.
class	UnsupportedCompressionException UnsupportedCompressionException is the exception thrown when the compression scheme used in a particular file or stream is unsupported.

Methods in io.scif that throw FormatException

Modifier and Type	Method and Description
protected org.scijava.io.location.BrowsableLocation	AbstractHasFormat.asBrowsableLocation(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> handle) Convenience overload of AbstractHasFormat.asBrowsableLocation(Location) that operates on a handle.
protected org.scijava.io.location.BrowsableLocation	AbstractHasFormat.asBrowsableLocation(org.scijava.io.location.Location loc) Safely casts a Location to a BrowsableLocation, throwing a FormatException if the cast is not possible.
protected void	AbstractWriter.checkLocation(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> out, SCIFIOConfig config) Validate that the given output is consistent with the given configuration.
protected void	AbstractWriter.checkParams(int imageIndex, long planeIndex, byte[] buf, net.imglib2.Interval bounds) Ensure that the arguments that are being passed to saveBytes(...) are valid.
Checker	Format.createChecker() Create an instance of the Checker associated with this format.
Checker	AbstractFormat.createChecker()
Metadata	Format.createMetadata() Create an instance of the Metadata associated with this format.
Metadata	AbstractFormat.createMetadata()
Parser	Format.createParser() Create an instance of the Parser associated with this format.
Parser	AbstractFormat.createParser()
Reader	Format.createReader() Creates an instance of the Reader associated with this format.
Reader	AbstractFormat.createReader()
Writer	Format.createWriter() Creates an instance of the Writer associated with this format.
Writer	AbstractFormat.createWriter()
int	Groupable.fileGroupOption(org.scijava.io.location.Location id) Returns an int indicating that we cannot, must, or might group the files in a given dataset.
int	AbstractGroupable.fileGroupOption(org.scijava.io.location.Location id)
protected void	AbstractWriter.initialize(int imageIndex, long planeIndex, net.imglib2.Interval bounds) Ensures this writer is prepared to write the given plane of the given image.
boolean	Groupable.isSingleFile(org.scijava.io.location.Location id) Returns true if this is a single-file format.
boolean	AbstractGroupable.isSingleFile(org.scijava.io.location.Location id)
void	AbstractWriter.isSupportedCompression(String compression)
void	Writer.isSupportedCompression(String compress) Checks if the given compression type is supported.
P	TypedReader.openPlane(int imageIndex, long planeIndex)
Plane	Reader.openPlane(int imageIndex, long planeIndex) Creates a Plane representation of the pixels at the specified indices.
P	AbstractReader.openPlane(int imageIndex, long planeIndex)
ByteArrayPlane	DefaultReader.openPlane(int imageIndex, long planeIndex, ByteArrayPlane plane, net.imglib2.Interval bounds, SCIFIOConfig config) Non-functional openPlane implementation.
P	TypedReader.openPlane(int imageIndex, long planeIndex, net.imglib2.Interval bounds)
Plane	Reader.openPlane(int imageIndex, long planeIndex, net.imglib2.Interval bounds) Creates a Plane representation of a desired sub-region from the pixels at the specified indices.
P	AbstractReader.openPlane(int imageIndex, long planeIndex, net.imglib2.Interval bounds)
P	TypedReader.openPlane(int imageIndex, long planeIndex, net.imglib2.Interval bounds, SCIFIOConfig config)
Plane	Reader.openPlane(int imageIndex, long planeIndex, net.imglib2.Interval bounds, SCIFIOConfig config) As Reader.openPlane(int, long, Interval) with configuration options.
P	AbstractReader.openPlane(int imageIndex, long planeIndex, net.imglib2.Interval bounds, SCIFIOConfig config)
P	TypedReader.openPlane(int imageIndex, long planeIndex, P plane) Generic-parameterized openPlane method, using TypedMetadata to avoid type erasure conflicts with Reader.openPlane(int, long, Plane).
P	AbstractReader.openPlane(int imageIndex, long planeIndex, P plane)
P	TypedReader.openPlane(int imageIndex, long planeIndex, P plane, net.imglib2.Interval bounds) Generic-parameterized openPlane method, using TypedMetadata to avoid type erasure conflicts with Reader.openPlane(int, long, Plane, Interval).
P	AbstractReader.openPlane(int imageIndex, long planeIndex, P plane, net.imglib2.Interval bounds)
P	TypedReader.openPlane(int imageIndex, long planeIndex, P plane, net.imglib2.Interval bounds, SCIFIOConfig config)
Plane	Reader.openPlane(int imageIndex, long planeIndex, Plane plane) Allows a single Plane object to be reused by reference when opening complete planes.
P	AbstractReader.openPlane(int imageIndex, long planeIndex, Plane plane)
Plane	Reader.openPlane(int imageIndex, long planeIndex, Plane plane, net.imglib2.Interval bounds) Allows a single Plane object to be reused by reference when opening sub-regions of planes.
P	AbstractReader.openPlane(int imageIndex, long planeIndex, Plane plane, net.imglib2.Interval bounds)
Plane	Reader.openPlane(int imageIndex, long planeIndex, Plane plane, net.imglib2.Interval bounds, SCIFIOConfig config) Allows a single Plane object to be reused by reference when opening sub-regions of planes.
Plane	AbstractReader.openPlane(int imageIndex, long planeIndex, Plane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
Plane	Reader.openPlane(int imageIndex, long planeIndex, Plane plane, SCIFIOConfig config) Allows a single Plane object to be reused by reference when opening complete planes.
Plane	AbstractReader.openPlane(int imageIndex, long planeIndex, Plane plane, SCIFIOConfig config)
P	TypedReader.openPlane(int imageIndex, long planeIndex, P plane, SCIFIOConfig config)
P	AbstractReader.openPlane(int imageIndex, long planeIndex, P plane, SCIFIOConfig config)
P	TypedReader.openPlane(int imageIndex, long planeIndex, SCIFIOConfig config)
Plane	Reader.openPlane(int imageIndex, long planeIndex, SCIFIOConfig config) As Reader.openPlane(int, long) with configuration options.
P	AbstractReader.openPlane(int imageIndex, long planeIndex, SCIFIOConfig config)
Metadata	Parser.parse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream) Creates a Metadata object from the provided image source.
M	TypedParser.parse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> handle)
M	AbstractParser.parse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream)
M	TypedParser.parse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, M meta) Generic-parameterized parse method, using TypedMetadata to avoid type erasure conflicts with Parser.parse(DataHandle, Metadata).
M	AbstractParser.parse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> handle, M meta)
Metadata	Parser.parse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, Metadata meta) Parses metadata from the provided image source to an existing Metadata object (overwriting may occur).
M	AbstractParser.parse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> handle, Metadata meta)
Metadata	Parser.parse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, Metadata meta, SCIFIOConfig config) /** As Parser.parse(DataHandle, Metadata) with configuration options.
M	AbstractParser.parse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> handle, Metadata meta, SCIFIOConfig config)
M	TypedParser.parse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, M meta, SCIFIOConfig config) Generic-parameterized parse method, using TypedMetadata to avoid type erasure conflicts with Parser.parse(DataHandle, Metadata).
M	AbstractParser.parse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> handle, M meta, SCIFIOConfig config)
Metadata	Parser.parse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> handle, SCIFIOConfig config) As Parser.parse(DataHandle) with configuration options.
M	TypedParser.parse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> handle, SCIFIOConfig config)
M	AbstractParser.parse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, SCIFIOConfig config)
Metadata	Parser.parse(org.scijava.io.location.Location location) Creates a Metadata object using the provided location of an image source.
M	TypedParser.parse(org.scijava.io.location.Location loc)
M	AbstractParser.parse(org.scijava.io.location.Location fileName)
Metadata	Parser.parse(org.scijava.io.location.Location location, Metadata meta) Parses metadata using the provided name of an image source, and writes to an existing Metadata object (overwriting may occur).
M	AbstractParser.parse(org.scijava.io.location.Location loc, Metadata meta)
Metadata	Parser.parse(org.scijava.io.location.Location fileName, Metadata meta, SCIFIOConfig config) As Parser.parse(Location, Metadata) with configuration options.
M	AbstractParser.parse(org.scijava.io.location.Location loc, Metadata meta, SCIFIOConfig config)
M	TypedParser.parse(org.scijava.io.location.Location fileName, M meta, SCIFIOConfig config) Generic-parameterized parse method, using TypedMetadata to avoid type erasure conflicts with Parser.parse(Location, Metadata).
M	AbstractParser.parse(org.scijava.io.location.Location loc, M meta, SCIFIOConfig config)
Metadata	Parser.parse(org.scijava.io.location.Location fileName, SCIFIOConfig config) As Parser.parse(Location) with configuration options.
M	TypedParser.parse(org.scijava.io.location.Location loc, SCIFIOConfig config)
M	AbstractParser.parse(org.scijava.io.location.Location loc, SCIFIOConfig config)
void	AbstractWriter.savePlane(int imageIndex, long planeIndex, Plane plane)
void	Writer.savePlane(int imageIndex, long planeIndex, Plane plane) Saves the provided plane to the specified image and plane index of this Writer's destination image.
void	AbstractWriter.savePlane(int imageIndex, long planeIndex, Plane plane, net.imglib2.Interval bounds)
void	Writer.savePlane(int imageIndex, long planeIndex, Plane plane, net.imglib2.Interval bounds) Saves the specified tile (sub-region) of the provided plane to the specified image and plane index of this Writer's destination image.
void	AbstractWriter.setDest(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> out)
void	Writer.setDest(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> handle) Sets the source that will be written to during Writer.savePlane(int, long, io.scif.Plane) calls.
void	AbstractWriter.setDest(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> out, int imageIndex)
void	Writer.setDest(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> handle, int imageIndex) As Writer.setDest(DataHandle), with specification for source image index.
void	AbstractWriter.setDest(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> out, int imageIndex, SCIFIOConfig config)
void	Writer.setDest(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> handle, int imageIndex, SCIFIOConfig config) As Writer.setDest(DataHandle, int), with specification for new configuration options.
void	AbstractWriter.setDest(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> out, SCIFIOConfig config)
void	Writer.setDest(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> handle, SCIFIOConfig config) As Writer.setDest(DataHandle), with specification for new configuration options.
void	AbstractWriter.setDest(org.scijava.io.location.Location fileName)
void	Writer.setDest(org.scijava.io.location.Location location) Sets the source that will be written to during Writer.savePlane(int, long, io.scif.Plane) calls.
void	AbstractWriter.setDest(org.scijava.io.location.Location loc, int imageIndex)
void	Writer.setDest(org.scijava.io.location.Location location, int imageIndex) As Writer.setDest(Location) with specification for source image index.
void	AbstractWriter.setDest(org.scijava.io.location.Location loc, int imageIndex, SCIFIOConfig config)
void	Writer.setDest(org.scijava.io.location.Location location, int imageIndex, SCIFIOConfig config) As Writer.setDest(Location, int) with specification for new configuration options.
void	AbstractWriter.setDest(org.scijava.io.location.Location loc, SCIFIOConfig config)
void	Writer.setDest(org.scijava.io.location.Location location, SCIFIOConfig config) As Writer.setDest(Location) with specification for new configuration options.
void	TypedWriter.setMetadata(M meta) Generic-parameterized setMetadata method, using TypedMetadata to avoid type erasure conflicts with Writer.setMetadata(Metadata).
void	AbstractWriter.setMetadata(M meta)
void	AbstractWriter.setMetadata(Metadata meta)
void	Writer.setMetadata(Metadata meta) Provides this Writer with a Metadata object to use when interpreting Planes during calls to Writer.savePlane(int, long, io.scif.Plane).
protected void	DefaultParser.typedParse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, DefaultMetadata meta, SCIFIOConfig config)
protected abstract void	AbstractParser.typedParse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> handle, M meta, SCIFIOConfig config) A helper method, called by AbstractParser.parse(DataHandle, TypedMetadata).
protected abstract void	AbstractWriter.writePlane(int imageIndex, long planeIndex, Plane plane, net.imglib2.Interval bounds) Helper method invoked by AbstractWriter.savePlane(int, long, io.scif.Plane) to perform actual format- specific output.
protected void	DefaultWriter.writePlane(int imageIndex, long planeIndex, Plane plane, net.imglib2.Interval bounds) Non-functional savePlane implementation.

Uses of FormatException in io.scif.codec

Methods in io.scif.codec that throw FormatException

Modifier and Type	Method and Description
byte[]	Codec.compress(byte[][] data, CodecOptions options) Compresses a block of data.
byte[]	AbstractCodec.compress(byte[][] data, CodecOptions options) 2D data block encoding default implementation.
byte[]	JPEG2000Codec.compress(byte[] data, CodecOptions options) The CodecOptions parameter should have the following fields set: width height bitsPerSample channels interleaved littleEndian lossless
byte[]	LuraWaveCodec.compress(byte[] data, CodecOptions options)
byte[]	MJPBCodec.compress(byte[] data, CodecOptions options)
byte[]	Codec.compress(byte[] data, CodecOptions options) Compresses a block of data.
byte[]	JPEGCodec.compress(byte[] data, CodecOptions options) The CodecOptions parameter should have the following fields set: width height channels bitsPerSample interleaved littleEndian signed
byte[]	PassthroughCodec.compress(byte[] data, CodecOptions options)
byte[]	LZWCodec.compress(byte[] input, CodecOptions options)
byte[]	QTRLECodec.compress(byte[] data, CodecOptions options)
byte[]	NikonCodec.compress(byte[] data, CodecOptions options)
byte[]	PackbitsCodec.compress(byte[] data, CodecOptions options)
byte[]	LosslessJPEGCodec.compress(byte[] data, CodecOptions options)
byte[]	MSVideoCodec.compress(byte[] data, CodecOptions options)
byte[]	RPZACodec.compress(byte[] input, CodecOptions options)
byte[]	HuffmanCodec.compress(byte[] data, CodecOptions options)
byte[]	MSRLECodec.compress(byte[] data, CodecOptions options)
byte[]	ZlibCodec.compress(byte[] data, CodecOptions options)
byte[]	Base64Codec.compress(byte[] input, CodecOptions options)
byte[]	Codec.decompress(byte[] data) Decompresses a block of data.
byte[]	AbstractCodec.decompress(byte[] data)
byte[]	Codec.decompress(byte[][] data) Decompresses a block of data.
byte[]	AbstractCodec.decompress(byte[][] data)
byte[]	Codec.decompress(byte[][] data, CodecOptions options) Decompresses a block of data.
byte[]	AbstractCodec.decompress(byte[][] data, CodecOptions options) 2D data block decoding default implementation.
byte[]	JPEG2000Codec.decompress(byte[] buf, CodecOptions options) The CodecOptions parameter should have the following fields set: interleaved littleEndian
byte[]	LuraWaveCodec.decompress(byte[] buf, CodecOptions options) The CodecOptions parameter should have the following fields set: maxBytes
byte[]	Codec.decompress(byte[] data, CodecOptions options) Decompresses a block of data.
byte[]	PassthroughCodec.decompress(byte[] data, CodecOptions options)
byte[]	QTRLECodec.decompress(byte[] data, CodecOptions options) The CodecOptions parameter should have the following fields set: width height bitsPerSample previousImage
byte[]	AbstractCodec.decompress(byte[] data, CodecOptions options)
byte[]	JPEG2000Codec.decompress(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> in, CodecOptions options) The CodecOptions parameter should have the following fields set: interleaved littleEndian
byte[]	LuraWaveCodec.decompress(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> in, CodecOptions options)
byte[]	MJPBCodec.decompress(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> in, CodecOptions options) The CodecOptions parameter must be an instance of MJPBCodecOptions, and should have the following fields set: interlaced width height bitsPerSample littleEndian interleaved
byte[]	Codec.decompress(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> in, CodecOptions options) Decompresses data from the given DataHandle.
byte[]	JPEGCodec.decompress(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> in, CodecOptions options) The CodecOptions parameter should have the following fields set: interleaved littleEndian
byte[]	PassthroughCodec.decompress(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> in, CodecOptions options)
byte[]	LZWCodec.decompress(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> in, CodecOptions options) The CodecOptions parameter should have the following fields set: maxBytes
byte[]	QTRLECodec.decompress(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> in, CodecOptions options)
byte[]	NikonCodec.decompress(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> in, CodecOptions options) The CodecOptions parameter must be an instance of NikonCodecOptions , and should have the following fields set: vPredictor curve split bitsPerSample maxBytes width height
byte[]	PackbitsCodec.decompress(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> in, CodecOptions options) The CodecOptions parameter should have the following fields set: maxBytes
byte[]	LosslessJPEGCodec.decompress(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> in, CodecOptions options) The CodecOptions parameter should have the following fields set: interleaved littleEndian
byte[]	MSVideoCodec.decompress(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> in, CodecOptions options) The CodecOptions parameter should have the following fields set: width height bitsPerSample previousImage
byte[]	RPZACodec.decompress(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> in, CodecOptions options) The CodecOptions parameter should have the following fields set: width height
byte[]	HuffmanCodec.decompress(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> in, CodecOptions options) The CodecOptions parameter must be an instance of HuffmanCodecOptions, and should have the following fields set: table bitsPerSample maxBytes
byte[]	MSRLECodec.decompress(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> in, CodecOptions options) The CodecOptions parameter should have the following fields set: width height previousImage
byte[]	ZlibCodec.decompress(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> in, CodecOptions options)
byte[]	Base64Codec.decompress(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> in, CodecOptions options)
int	HuffmanCodec.getSample(BitBuffer bb, CodecOptions options)
void	AbstractCodec.test() Main testing method default implementation.

Uses of FormatException in io.scif.filters

Methods in io.scif.filters that throw FormatException

Modifier and Type	Method and Description
int	AbstractReaderFilter.fileGroupOption(org.scijava.io.location.Location id)
Double	MinMaxFilter.getAxisGlobalMaximum(int imageIndex, net.imagej.axis.AxisType type, int index) Retrieves a specified planar axis's global maximum.
Double	MinMaxFilter.getAxisGlobalMinimum(int imageIndex, net.imagej.axis.AxisType type, int index) Retrieves a specified planar axis's global minimum.
boolean	AbstractReaderFilter.isSingleFile(org.scijava.io.location.Location id)
Plane	ChannelFiller.openPlane(int imageIndex, long planeIndex)
Plane	PlaneSeparator.openPlane(int imageIndex, long planeIndex)
Plane	MinMaxFilter.openPlane(int imageIndex, long planeIndex)
Plane	DimensionSwapper.openPlane(int imageIndex, long planeIndex)
Plane	AbstractReaderFilter.openPlane(int imageIndex, long planeIndex)
Plane	ChannelFiller.openPlane(int imageIndex, long planeIndex, net.imglib2.Interval bounds)
Plane	PlaneSeparator.openPlane(int imageIndex, long planeIndex, net.imglib2.Interval bounds)
Plane	MinMaxFilter.openPlane(int imageIndex, long planeIndex, net.imglib2.Interval bounds)
Plane	DimensionSwapper.openPlane(int imageIndex, long planeIndex, net.imglib2.Interval bounds)
Plane	AbstractReaderFilter.openPlane(int imageIndex, long planeIndex, net.imglib2.Interval bounds)
Plane	FileStitcher.openPlane(int imageIndex, long planeIndex, net.imglib2.Interval bounds, SCIFIOConfig config)
Plane	ChannelFiller.openPlane(int imageIndex, long planeIndex, net.imglib2.Interval bounds, SCIFIOConfig config)
Plane	PlaneSeparator.openPlane(int imageIndex, long planeIndex, net.imglib2.Interval bounds, SCIFIOConfig config)
Plane	MinMaxFilter.openPlane(int imageIndex, long planeIndex, net.imglib2.Interval bounds, SCIFIOConfig config)
Plane	DimensionSwapper.openPlane(int imageIndex, long planeIndex, net.imglib2.Interval bounds, SCIFIOConfig config)
Plane	AbstractReaderFilter.openPlane(int imageIndex, long planeIndex, net.imglib2.Interval bounds, SCIFIOConfig config)
Plane	ChannelFiller.openPlane(int imageIndex, long planeIndex, Plane plane)
Plane	PlaneSeparator.openPlane(int imageIndex, long planeIndex, Plane plane)
Plane	MinMaxFilter.openPlane(int imageIndex, long planeIndex, Plane plane)
Plane	DimensionSwapper.openPlane(int imageIndex, long planeIndex, Plane plane)
Plane	AbstractReaderFilter.openPlane(int imageIndex, long planeIndex, Plane plane)
Plane	ChannelFiller.openPlane(int imageIndex, long planeIndex, Plane plane, net.imglib2.Interval bounds)
Plane	PlaneSeparator.openPlane(int imageIndex, long planeIndex, Plane plane, net.imglib2.Interval bounds)
Plane	MinMaxFilter.openPlane(int imageIndex, long planeIndex, Plane plane, net.imglib2.Interval bounds)
Plane	DimensionSwapper.openPlane(int imageIndex, long planeIndex, Plane plane, net.imglib2.Interval bounds)
Plane	AbstractReaderFilter.openPlane(int imageIndex, long planeIndex, Plane plane, net.imglib2.Interval bounds)
Plane	FileStitcher.openPlane(int imageIndex, long planeIndex, Plane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
Plane	ChannelFiller.openPlane(int imageIndex, long planeIndex, Plane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
Plane	PlaneSeparator.openPlane(int imageIndex, long planeIndex, Plane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
Plane	MinMaxFilter.openPlane(int imageIndex, long planeIndex, Plane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
Plane	DimensionSwapper.openPlane(int imageIndex, long planeIndex, Plane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
Plane	AbstractReaderFilter.openPlane(int imageIndex, long planeIndex, Plane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
Plane	ChannelFiller.openPlane(int imageIndex, long planeIndex, Plane plane, SCIFIOConfig config)
Plane	PlaneSeparator.openPlane(int imageIndex, long planeIndex, Plane plane, SCIFIOConfig config)
Plane	MinMaxFilter.openPlane(int imageIndex, long planeIndex, Plane plane, SCIFIOConfig config)
Plane	DimensionSwapper.openPlane(int imageIndex, long planeIndex, Plane plane, SCIFIOConfig config)
Plane	AbstractReaderFilter.openPlane(int imageIndex, long planeIndex, Plane plane, SCIFIOConfig config)
Plane	ChannelFiller.openPlane(int imageIndex, long planeIndex, SCIFIOConfig config)
Plane	PlaneSeparator.openPlane(int imageIndex, long planeIndex, SCIFIOConfig config)
Plane	MinMaxFilter.openPlane(int imageIndex, long planeIndex, SCIFIOConfig config)
Plane	DimensionSwapper.openPlane(int imageIndex, long planeIndex, SCIFIOConfig config)
Plane	AbstractReaderFilter.openPlane(int imageIndex, long planeIndex, SCIFIOConfig config)

Uses of FormatException in io.scif.formats

Methods in io.scif.formats that throw FormatException

Modifier and Type	Method and Description
byte[]	JPEG2000Format.Writer.compressBuffer(int imageIndex, long planeIndex, Plane plane, net.imglib2.Interval bounds) Compresses the buffer.
int	NRRDFormat.Parser.fileGroupOption(org.scijava.io.location.Location id)
int	NRRDFormat.Reader.fileGroupOption(org.scijava.io.location.Location id)
int	DICOMFormat.Parser.fileGroupOption(org.scijava.io.location.Location id)
protected void	APNGFormat.Writer.initialize(int imageIndex, long planeIndex, net.imglib2.Interval bounds)
protected void	TIFFFormat.Writer.initialize(int imageIndex, long planeIndex, net.imglib2.Interval bounds)
protected void	EPSFormat.Writer.initialize(int imageIndex, long planeIndex, net.imglib2.Interval bounds)
protected void	ICSFormat.Writer.initialize(int imageIndex, long planeIndex, net.imglib2.Interval bounds)
protected void	TIFFFormat.Parser.initMetadata(TIFFFormat.Metadata meta, SCIFIOConfig config)
protected void	TIFFFormat.BaseTIFFParser.initMetadata(TIFFFormat.Metadata meta, SCIFIOConfig config) Populates the metadata hashtable and metadata store.
boolean	NRRDFormat.Parser.isSingleFile(org.scijava.io.location.Location id)
boolean	NRRDFormat.Reader.isSingleFile(org.scijava.io.location.Location id)
protected static BufferedImage	TIFFJAIFormat.openBufferedImage(TIFFJAIFormat.Metadata meta, long planeIndex) Obtains a BufferedImage from the given data source using JAI.
BufferedImagePlane	ImageIOFormat.Reader.openPlane(int imageIndex, long planeIndex, BufferedImagePlane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
BufferedImagePlane	MNGFormat.Reader.openPlane(int imageIndex, long planeIndex, BufferedImagePlane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
BufferedImagePlane	TIFFJAIFormat.Reader.openPlane(int imageIndex, long planeIndex, BufferedImagePlane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
BufferedImagePlane	APNGFormat.Reader.openPlane(int imageIndex, long planeIndex, BufferedImagePlane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
ByteArrayPlane	NRRDFormat.Reader.openPlane(int imageIndex, long planeIndex, ByteArrayPlane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
ByteArrayPlane	FITSFormat.Reader.openPlane(int imageIndex, long planeIndex, ByteArrayPlane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
ByteArrayPlane	MinimalTIFFFormat.Reader.openPlane(int imageIndex, long planeIndex, ByteArrayPlane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
ByteArrayPlane	PGMFormat.Reader.openPlane(int imageIndex, long planeIndex, ByteArrayPlane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
ByteArrayPlane	JPEGTileFormat.Reader.openPlane(int imageIndex, long planeIndex, ByteArrayPlane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
ByteArrayPlane	JPEG2000Format.Reader.openPlane(int imageIndex, long planeIndex, ByteArrayPlane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
ByteArrayPlane	BMPFormat.Reader.openPlane(int imageIndex, long planeIndex, ByteArrayPlane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
ByteArrayPlane	KontronFormat.Reader.openPlane(int imageIndex, long planeIndex, ByteArrayPlane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
ByteArrayPlane	PCXFormat.Reader.openPlane(int imageIndex, long planeIndex, ByteArrayPlane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
ByteArrayPlane	EPSFormat.Reader.openPlane(int imageIndex, long planeIndex, ByteArrayPlane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
ByteArrayPlane	MicromanagerFormat.Reader.openPlane(int imageIndex, long planeIndex, ByteArrayPlane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
ByteArrayPlane	GIFFormat.Reader.openPlane(int imageIndex, long planeIndex, ByteArrayPlane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
ByteArrayPlane	ScancoISQFormat.Reader.openPlane(int imageIndex, long planeIndex, ByteArrayPlane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
ByteArrayPlane	StratecPQCTFormat.Reader.openPlane(int imageIndex, long planeIndex, ByteArrayPlane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
ByteArrayPlane	DICOMFormat.Reader.openPlane(int imageIndex, long planeIndex, ByteArrayPlane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
ByteArrayPlane	AVIFormat.Reader.openPlane(int imageIndex, long planeIndex, ByteArrayPlane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
ByteArrayPlane	ICSFormat.Reader.openPlane(int imageIndex, long planeIndex, ByteArrayPlane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
ByteArrayPlane	TestImgFormat.Reader.openPlane(int imageIndex, long planeIndex, ByteArrayPlane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
NRRDFormat.Metadata	NRRDFormat.Parser.parse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, NRRDFormat.Metadata meta, SCIFIOConfig config)
void	MicromanagerFormat.Parser.populateMetadata(String[] jsonData, MicromanagerFormat.Metadata source, Metadata dest)
void	TIFFFormat.Writer.savePlane(int imageIndex, long planeIndex, Plane plane, IFD ifd, net.imglib2.Interval bounds) Saves the given image to the specified series in the current file.
void	APNGFormat.Writer.setDest(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> out, int imageIndex, SCIFIOConfig config)
void	TIFFFormat.Writer.setDest(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> dest, int imageIndex, SCIFIOConfig config)
void	AVIFormat.Writer.setDest(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> out, int imageIndex, SCIFIOConfig config)
void	ICSFormat.Writer.setDest(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> out, int imageIndex, SCIFIOConfig config)
protected void	APNGFormat.Parser.typedParse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> handle, APNGFormat.Metadata meta, SCIFIOConfig config)
protected void	AVIFormat.Parser.typedParse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> handle, AVIFormat.Metadata meta, SCIFIOConfig config)
protected void	BMPFormat.Parser.typedParse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, BMPFormat.Metadata meta, SCIFIOConfig config)
protected void	DICOMFormat.Parser.typedParse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, DICOMFormat.Metadata meta, SCIFIOConfig config)
protected void	EPSFormat.Parser.typedParse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, EPSFormat.Metadata meta, SCIFIOConfig config)
protected void	FITSFormat.Parser.typedParse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, FITSFormat.Metadata meta, SCIFIOConfig config)
protected void	GIFFormat.Parser.typedParse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, GIFFormat.Metadata meta, SCIFIOConfig config)
protected void	ICSFormat.Parser.typedParse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, ICSFormat.Metadata meta, SCIFIOConfig config)
protected void	JPEG2000Format.Parser.typedParse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, JPEG2000Format.Metadata meta, SCIFIOConfig config)
void	JPEGFormat.Parser.typedParse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> handle, JPEGFormat.Metadata meta, SCIFIOConfig config)
protected void	JPEGTileFormat.Parser.typedParse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> handle, JPEGTileFormat.Metadata meta, SCIFIOConfig config)
void	KontronFormat.Parser.typedParse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, KontronFormat.Metadata meta, SCIFIOConfig config)
protected void	MicromanagerFormat.Parser.typedParse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, MicromanagerFormat.Metadata meta, SCIFIOConfig config)
protected void	MNGFormat.Parser.typedParse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, MNGFormat.Metadata meta, SCIFIOConfig config)
protected void	MinimalTIFFFormat.Parser.typedParse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, M meta, SCIFIOConfig config)
protected void	ImageIOFormat.Parser.typedParse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> handle, M meta, SCIFIOConfig config)
protected void	NRRDFormat.Parser.typedParse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, NRRDFormat.Metadata meta, SCIFIOConfig config)
protected void	PCXFormat.Parser.typedParse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, PCXFormat.Metadata meta, SCIFIOConfig config)
protected void	PGMFormat.Parser.typedParse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, PGMFormat.Metadata meta, SCIFIOConfig config)
protected void	ScancoISQFormat.Parser.typedParse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, ScancoISQFormat.Metadata meta, SCIFIOConfig config)
void	StratecPQCTFormat.Parser.typedParse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, StratecPQCTFormat.Metadata meta, SCIFIOConfig config)
protected void	TestImgFormat.Parser.typedParse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, TestImgFormat.Metadata meta, SCIFIOConfig config)
protected void	TIFFFormat.BaseTIFFParser.typedParse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, TIFFFormat.Metadata meta, SCIFIOConfig config)
protected void	TIFFJAIFormat.Parser.typedParse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, TIFFJAIFormat.Metadata meta, SCIFIOConfig config)
void	ImageIOFormat.Writer.writePlane(int imageIndex, long planeIndex, Plane plane, net.imglib2.Interval bounds)
void	JPEG2000Format.Writer.writePlane(int imageIndex, long planeIndex, Plane plane, net.imglib2.Interval bounds)
void	APNGFormat.Writer.writePlane(int imageIndex, long planeIndex, Plane plane, net.imglib2.Interval bounds)
void	TIFFFormat.Writer.writePlane(int imageIndex, long planeIndex, Plane plane, net.imglib2.Interval bounds)
void	EPSFormat.Writer.writePlane(int imageIndex, long planeIndex, Plane plane, net.imglib2.Interval bounds)
void	AVIFormat.Writer.writePlane(int imageIndex, long planeIndex, Plane plane, net.imglib2.Interval bounds)
void	ICSFormat.Writer.writePlane(int imageIndex, long planeIndex, Plane plane, net.imglib2.Interval bounds)

Uses of FormatException in io.scif.formats.qt

Methods in io.scif.formats.qt that throw FormatException

Modifier and Type	Method and Description
Dimension	QTJavaService.getPictDimensions(byte[] bytes) Gets width and height for the given PICT bytes.
Dimension	DefaultQTJavaService.getPictDimensions(byte[] bytes)
protected void	NativeQTFormat.Writer.initialize(int imageIndex, long planeIndex, net.imglib2.Interval bounds)
protected void	LegacyQTFormat.Writer.initialize(int imageIndex, long planeIndex, net.imglib2.Interval bounds)
BufferedImagePlane	LegacyQTFormat.Reader.openPlane(int imageIndex, long planeIndex, BufferedImagePlane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
ByteArrayPlane	PICTFormat.Reader.openPlane(int imageIndex, long planeIndex, ByteArrayPlane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
ByteArrayPlane	NativeQTFormat.Reader.openPlane(int imageIndex, long planeIndex, ByteArrayPlane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
Image	QTJavaService.pictToImage(byte[] bytes) Converts the given byte array in PICT format to a Java image.
Image	DefaultQTJavaService.pictToImage(byte[] bytes)
void	NativeQTFormat.Writer.setDest(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, int imageIndex, SCIFIOConfig config)
protected void	LegacyQTFormat.Parser.typedParse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, LegacyQTFormat.Metadata meta, SCIFIOConfig config)
protected void	NativeQTFormat.Parser.typedParse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, NativeQTFormat.Metadata meta, SCIFIOConfig config)
protected void	PICTFormat.Parser.typedParse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, PICTFormat.Metadata meta, SCIFIOConfig config)
void	NativeQTFormat.Writer.writePlane(int imageIndex, long planeIndex, Plane plane, net.imglib2.Interval bounds)
void	LegacyQTFormat.Writer.writePlane(int imageIndex, long planeIndex, Plane plane, net.imglib2.Interval bounds)

Uses of FormatException in io.scif.formats.tiff

Methods in io.scif.formats.tiff that throw FormatException

Modifier and Type	Method and Description
byte[]	TiffCompression.compress(CodecService codecService, byte[] input, CodecOptions options) Encodes a strip of data.
byte[]	TiffCompression.decompress(CodecService codecService, byte[] input, CodecOptions options) Decodes a strip of data.
void	TiffService.difference(byte[] input, IFD ifd) Performs in-place differencing according to the given predictor value.
void	DefaultTiffService.difference(byte[] input, IFD ifd)
int[]	IFD.getBitsPerSample() Retrieves the image's bits per sample (TIFF tag BitsPerSample) from a given TIFF IFD.
int[]	IFD.getBytesPerSample() Retrieves the image's bytes per sample (derived from tag BitsPerSample) from this IFD.
TiffCompression	IFD.getCompression() Retrieves the image's compression type (TIFF tag Compression) from this IFD.
CodecOptions	TiffCompression.getCompressionCodecOptions(IFD ifd) Creates a set of codec options for compression.
CodecOptions	TiffCompression.getCompressionCodecOptions(IFD ifd, CodecOptions opt) Creates a set of codec options for compression.
IFDList	TiffParser.getExifIFDs() Returns EXIF IFDs.
FillOrder	IFD.getFillOrder() Retrieves the image's fill order (TIFF tag FillOrder) from this IFD.
int[]	IFD.getIFDIntArray(int tag) Gets the given directory entry values in int format from this IFD, performing some error checking.
int	IFD.getIFDIntValue(int tag, int defaultValue) Gets the given directory entry value in int format from this IFD, performing some error checking.
long[]	IFD.getIFDLongArray(int tag) Gets the given directory entry values in long format from this IFD, performing some error checking.
long	IFD.getIFDLongValue(int tag, long defaultValue) Gets the given directory entry value in long format from this IFD, performing some error checking.
TiffRational	IFD.getIFDRationalValue(int tag) Gets the given directory entry value in rational format from this IFD, performing some error checking.
short[]	IFD.getIFDShortArray(int tag) Gets the given directory entry values in short format from this IFD, performing some error checking.
String	IFD.getIFDStringValue(int tag) Gets the given directory entry value as a string from this IFD, performing some error checking.
Object	IFD.getIFDValue(int tag, Class<?> checkClass) Gets the given directory entry value from this IFD, performing some error checking.
long	IFD.getImageLength() Retrieves the image's length (TIFF tag ImageLength) from a given TIFF IFD.
long	IFD.getImageWidth() Retrieves the image's width (TIFF tag ImageWidth) from a given TIFF IFD.
PhotoInterp	IFD.getPhotometricInterpretation() Retrieves the image's photometric interpretation (TIFF tag PhotometricInterpretation) from this IFD.
int	IFD.getPixelType() Retrieves the image's pixel type based on the BitsPerSample tag.
int	IFD.getPlanarConfiguration() Retrieves the image's planar configuration (TIFF tag PlanarConfiguration) from this IFD.
int	IFD.getResolutionMultiplier() Retrieve the value by which to multiply the X and Y resolution so that the resolutions are in microns per pixel.
ResolutionUnit	IFD.getResolutionUnit() Retrieves the image's resolution unit (TIFF tag ResolutionUnit) from this IFD.
long[]	IFD.getRowsPerStrip() Retrieves the number of rows per strip for image (TIFF tag RowsPerStrip) from this IFD.
byte[]	TiffParser.getSamples(IFD ifd, byte[] buf)
byte[]	TiffParser.getSamples(IFD ifd, byte[] buf, int x, int y, long width, long height)
byte[]	TiffParser.getSamples(IFD ifd, byte[] buf, int x, int y, long width, long height, int overlapX, int overlapY)
int	IFD.getSamplesPerPixel() Retrieves the number of samples per pixel for the image (TIFF tag SamplesPerPixel) from this IFD.
long[]	IFD.getStripByteCounts() Retrieves strip byte counts for the image (TIFF tag StripByteCounts) from this IFD.
long[]	IFD.getStripOffsets() Retrieves the strip offsets for the image (TIFF tag StripOffsets) from this IFD.
byte[]	TiffParser.getTile(IFD ifd, byte[] buf, int row, int col)
long	IFD.getTileLength() Returns the length of an image tile.
long	IFD.getTilesPerColumn() Returns the number of image tiles per column.
long	IFD.getTilesPerRow() Returns the number of image tiles per row.
long	IFD.getTileWidth() Returns the width of an image tile.
Double	IFD.getXResolution() Retrieve the X resolution (TIFF tag XResolution) from this IFD.
Double	IFD.getYResolution() Retrieve the Y resolution (TIFF tag YResolution) from this IFD.
boolean	IFD.isBigTiff() Gets whether this is a BigTIFF IFD.
boolean	IFD.isLittleEndian() Gets whether the TIFF information in this IFD is little-endian.
void	TiffSaver.overwriteComment(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> in, Object value) Convenience method for overwriting a file's first ImageDescription.
void	TiffSaver.overwriteIFDValue(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> raf, int ifd, int tag, Object value) Surgically overwrites an existing IFD value with the given one.
void	TiffSaver.overwriteLastIFDOffset(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> handle)
void	TiffService.undifference(byte[] input, IFD ifd) Undoes in-place differencing according to the given predictor value.
void	DefaultTiffService.undifference(byte[] input, IFD ifd)
void	TiffSaver.writeIFD(IFD ifd, long nextOffset)
void	TiffSaver.writeIFDValue(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> extraOut, long offset, int tag, Object value) Writes the given IFD value to the given output object.
void	TiffSaver.writeImage(byte[][] buf, IFDList ifds, int pixelType)
void	TiffSaver.writeImage(byte[] buf, IFD ifd, int no, int pixelType, boolean last)
void	TiffSaver.writeImage(byte[] buf, IFD ifd, long planeIndex, int pixelType, int x, int y, int w, int h, boolean last) Writes to any rectangle from the passed block.
void	TiffSaver.writeImage(byte[] buf, IFD ifd, long planeIndex, int pixelType, int x, int y, int w, int h, boolean last, Integer nChannels, boolean copyDirectly)

Uses of FormatException in io.scif.gui

Methods in io.scif.gui that throw FormatException

Modifier and Type	Method and Description
static BufferedImage	AWTImageTools.openImage(Plane plane, byte[] bytes, Reader r, long[] axes, int imageIndex) Creates an image from the given Plane.
static BufferedImage	AWTImageTools.openImage(Plane plane, Reader r, int imageIndex) Creates an image from the given Plane.
static BufferedImage	AWTImageTools.openImage(Plane plane, Reader r, long[] axes, int imageIndex) Creates an image from the given Plane.
static BufferedImage	AWTImageTools.openThumbImage(Plane plane, Reader r, int imageIndex, long[] axes, int thumbSizeX, int thumbSizeY, boolean pad) Creates a thumbnail image from the provided plane, scaling it to the specified thumbnail dimensions.

Uses of FormatException in io.scif.img.cell

Methods in io.scif.img.cell that throw FormatException

Modifier and Type	Method and Description
net.imglib2.display.ColorTable	SCIFIOCellImg.getColorTable(int imageIndex, int planeIndex) Returns the ColorTable of the specified image and plane index.

Uses of FormatException in io.scif.img.cell.loaders

Methods in io.scif.img.cell.loaders that throw FormatException

Modifier and Type	Method and Description
net.imglib2.display.ColorTable	AbstractArrayLoader.loadTable(int imageIndex, int planeIndex)
net.imglib2.display.ColorTable	SCIFIOArrayLoader.loadTable(int imageIndex, int planeIndex) Returns the ColorTable for a given set of indices.

Uses of FormatException in io.scif.services

Methods in io.scif.services that throw FormatException

Modifier and Type	Method and Description
Format	DefaultFormatService.getFormat(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> source)
Format	FormatService.getFormat(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> source) As FormatService.getFormat(Location) but takes an initialized DataHandle.
Format	DefaultFormatService.getFormat(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> source, SCIFIOConfig config)
Format	FormatService.getFormat(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> source, SCIFIOConfig config) As FormatService.getFormat(Location, SCIFIOConfig) but takes an initialized DataHandle.
Format	DefaultFormatService.getFormat(org.scijava.io.location.Location id)
Format	FormatService.getFormat(org.scijava.io.location.Location id) Returns the first Format known to be compatible with the source provided.
Format	DefaultFormatService.getFormat(org.scijava.io.location.Location id, SCIFIOConfig config)
Format	FormatService.getFormat(org.scijava.io.location.Location id, SCIFIOConfig config) Returns the first Format known to be compatible with the source provided.
List<Format>	DefaultFormatService.getFormatList(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> source)
List<Format>	FormatService.getFormatList(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> source) As FormatService.getFormatList(Location) but takes an initialized DataHandle.
List<Format>	DefaultFormatService.getFormatList(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> source, SCIFIOConfig config, boolean greedy)
List<Format>	FormatService.getFormatList(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> source, SCIFIOConfig config, boolean greedy) As FormatService.getFormatList(Location, SCIFIOConfig, boolean) but takes an initialized DataHandle.
List<Format>	DefaultFormatService.getFormatList(org.scijava.io.location.Location id)
List<Format>	FormatService.getFormatList(org.scijava.io.location.Location id) Returns a list of all formats that are compatible with the source provided, ordered by their priority.
List<Format>	DefaultFormatService.getFormatList(org.scijava.io.location.Location id, SCIFIOConfig config, boolean greedy)
List<Format>	FormatService.getFormatList(org.scijava.io.location.Location id, SCIFIOConfig config, boolean greedy) Returns a list of all formats that are compatible with the source provided, ordered by their priority.
Writer	DefaultFormatService.getWriterForLocation(org.scijava.io.location.Location fileId)
Writer	FormatService.getWriterForLocation(org.scijava.io.location.Location fileId) Writer lookup method using the suffix or other methods to locate a fitting writer.
ReaderFilter	InitializeService.initializeReader(org.scijava.io.location.Location id) See InitializeService.initializeReader(Location, SCIFIOConfig).
ReaderFilter	DefaultInitializeService.initializeReader(org.scijava.io.location.Location id)
ReaderFilter	InitializeService.initializeReader(org.scijava.io.location.Location id, SCIFIOConfig config) Convenience method for creating a Reader component that is ready to open planes of the provided image source.
ReaderFilter	DefaultInitializeService.initializeReader(org.scijava.io.location.Location id, SCIFIOConfig config)
Writer	InitializeService.initializeWriter(org.scijava.io.location.Location source, org.scijava.io.location.Location destination) See InitializeService.initializeWriter(Location, Location, SCIFIOConfig).
Writer	DefaultInitializeService.initializeWriter(org.scijava.io.location.Location source, org.scijava.io.location.Location destination)
Writer	InitializeService.initializeWriter(org.scijava.io.location.Location source, org.scijava.io.location.Location destination, SCIFIOConfig config) As InitializeService.initializeWriter(Location, Location) with configuration options.
Writer	DefaultInitializeService.initializeWriter(org.scijava.io.location.Location source, org.scijava.io.location.Location destination, SCIFIOConfig config)
Writer	InitializeService.initializeWriter(Metadata sourceMeta, org.scijava.io.location.Location destination) See InitializeService.initializeWriter(Location, Location, SCIFIOConfig).
Writer	DefaultInitializeService.initializeWriter(Metadata sourceMeta, org.scijava.io.location.Location destination)
Writer	InitializeService.initializeWriter(Metadata sourceMeta, org.scijava.io.location.Location destination, SCIFIOConfig config) As InitializeService.initializeWriter(Metadata, Location) with configuration options.
Writer	DefaultInitializeService.initializeWriter(Metadata sourceMeta, org.scijava.io.location.Location destination, SCIFIOConfig config)
Metadata	InitializeService.parseMetadata(org.scijava.io.location.Location id) Convenience method to parse Metadata without reading the underlying pixels.
Metadata	DefaultInitializeService.parseMetadata(org.scijava.io.location.Location id)
Metadata	InitializeService.parseMetadata(org.scijava.io.location.Location id, SCIFIOConfig config) As InitializeService.parseMetadata(Location) with a flag to open the underlying dataset when parsing, if desired.
Metadata	DefaultInitializeService.parseMetadata(org.scijava.io.location.Location id, SCIFIOConfig config)

Uses of FormatException in io.scif.util

Methods in io.scif.util that throw FormatException

Modifier and Type	Method and Description
static void	FormatTools.checkBufferSize(int imageIndex, Metadata m, int len) Checks that the given buffer length is long enough to hold planes of the specified image index, using the provided Reader.
static void	FormatTools.checkBufferSize(Metadata m, int len, net.imglib2.Interval bounds, int imageIndex) Checks that the given buffer size is large enough to hold an image with the given planar lengths.
static void	FormatTools.checkPlaneForReading(Metadata m, int imageIndex, long planeIndex, int bufLength, net.imglib2.Interval bounds) As FormatTools.checkPlaneForWriting(io.scif.Metadata, int, long, int, net.imglib2.Interval) but also asserts that the Metadata has a non-null source attached.
static void	FormatTools.checkPlaneForWriting(Metadata m, int imageIndex, long planeIndex, int bufLength, net.imglib2.Interval bounds) Convenience method for checking that the plane number, tile size and buffer sizes are all valid for the given Metadata.
static void	FormatTools.checkPlaneNumber(Metadata m, int imageIndex, long planeIndex) Checks that the given plane number is valid for the given reader.
static void	FormatTools.checkTileSize(Metadata m, net.imglib2.Interval bounds, int imageIndex) Checks that the given tile size is valid for the given reader.
static void	FormatTools.convert(Reader input, Writer output, String outputFile) Convenience method for writing all of the images and metadata obtained from the specified Reader into the specified Writer.
static void	FormatTools.convert(Reader input, Writer output, String outputFile, SCIFIOConfig config) As FormatTools.convert(Reader, Writer, String), with configuration options.
static String	FormatTools.getFilename(int imageIndex, int image, Reader r, String pattern)
static String[]	FormatTools.getFilenames(String pattern, Reader r)
static int	FormatTools.getImagesPerFile(String pattern, Reader r)
static int	FormatTools.pixelTypeFromBytes(int bytes, boolean signed, boolean fp) Returns an appropriate pixel type given the number of bytes per pixel.
static void	SCIFIOMetadataTools.verifyMinimumPopulated(Metadata src, org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> out) Checks whether the given metadata object has the minimum metadata populated to successfully describe an Image.
static void	SCIFIOMetadataTools.verifyMinimumPopulated(Metadata src, org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> out, int imageIndex) Checks whether the given metadata object has the minimum metadata populated to successfully describe the nth Image.
static void	SCIFIOMetadataTools.verifyMinimumPopulated(Metadata src, org.scijava.io.location.Location loc)
static void	SCIFIOMetadataTools.verifyMinimumPopulated(Metadata src, org.scijava.io.location.Location loc, int imageIndex)