Uses of Class
loci.formats.FormatException

Packages that use FormatException

Package	Description
loci.formats	Bio-Formats: a library for reading and writing popular microscopy file formats.
loci.formats.cache	Package containing Bio-Formats caching logic, for managing subsets of large collections of image planes in memory.
loci.formats.codec
loci.formats.dicom
loci.formats.gui	Package containing Bio-Formats graphical user interface code.
loci.formats.in	Package containing Bio-Formats file format readers.
loci.formats.in.LeicaMicrosystemsMetadata
loci.formats.out	Package containing Bio-Formats file format writers.
loci.formats.services
loci.formats.tiff	Package containing Bio-Formats TIFF code of general utility.
loci.formats.tools	Package containing utility methods corresponding to the Bio-Formats command line tools.
loci.plugins	Bio-Formats Plugins: a collection of plugins for ImageJ, including the Bio-Formats Importer, Bio-Formats Exporter, Bio-Formats Macro Extensions, Data Browser and Stack Slicer.
loci.plugins.in	Bio-Formats Importer plugin for ImageJ.
loci.plugins.macro	Bio-Formats Macro Extensions plugin for ImageJ.
loci.plugins.util	Utility classes and methods for the Bio-Formats plugins for ImageJ.

Uses of FormatException in loci.formats

Subclasses of FormatException in loci.formats

Modifier and Type	Class	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	UnknownFormatException	UnknownFormatException is the exception thrown when the format of a particular data stream or filename cannot be recognized or is unsupported.
class	UnsupportedCompressionException	UnsupportedCompressionException is the exception thrown when the compression scheme used in a particular file or stream is unsupported.

Methods in loci.formats that throw FormatException

Modifier and Type	Method	Description
static boolean	FormatTools.canUsePrecompressedTiles(IFormatReader reader, IFormatWriter writer, int series, int resolution)	Compare the given reader and writer at the specified series and resolution to see if pre-compressed tiles can be transferred directly from the reader to the writer.
void	FormatWriter.changeOutputFile(String id)
void	IFormatWriter.changeOutputFile(String id)	Switch the output file for the current dataset.
void	ImageWriter.changeOutputFile(String id)
void	WriterWrapper.changeOutputFile(String id)
static void	FormatTools.checkBufferSize(IFormatReader r, int len)
static void	FormatTools.checkBufferSize(IFormatReader r, int len, int w, int h)	Checks that the given buffer size is large enough to hold a w * h image as returned by the given reader.
protected void	FormatWriter.checkParams(int no, byte[] buf, int x, int y, int w, int h)	Ensure that the arguments that are being passed to saveBytes(...) are valid.
static void	FormatTools.checkPlaneNumber(IFormatReader r, int no)	Checks that the given plane number is valid for the given reader.
static void	FormatTools.checkPlaneParameters(IFormatReader r, int no, int bufLength, int x, int y, int w, int h)	Convenience method for checking that the plane number, tile size and buffer sizes are all valid for the given reader.
static void	FormatTools.checkTileSize(IFormatReader r, int x, int y, int w, int h)	Checks that the given tile size is valid for the given reader.
protected void	FileStitcher.computeAxisLengths()	Computes axis length arrays, and total axis lengths.
protected int[]	FileStitcher.computeIndices(int no)	Gets the file index, and image index into that file, corresponding to the given global image index.
static void	FormatTools.convert(String input, String output)	Convenience method for converting the specified input file to the specified output file.
static void	FormatTools.convert(IFormatReader input, IFormatWriter output, String outputFile)	Convenience method for writing all of the images and metadata obtained from the specified IFormatReader into the specified IFormatWriter.
ReaderWrapper	ReaderWrapper.duplicate(Class<? extends IFormatReader> imageReaderClass)	Performs a deep copy of the reader, including nested wrapped readers.
WriterWrapper	WriterWrapper.duplicate(Class<? extends IFormatWriter> imageWriterClass)	Performs a deep copy of the writer, including nested wrapped writers.
private ReaderWrapper	ReaderWrapper.duplicateRecurse(Class<? extends IFormatReader> imageReaderClass)
private WriterWrapper	WriterWrapper.duplicateRecurse(Class<? extends IFormatWriter> imageWriterClass)
int	FormatReader.fileGroupOption(String id)
int	IFormatReader.fileGroupOption(String id)	Returns an indication of whether the files in a multi-file dataset can be handled individually.
int	ImageReader.fileGroupOption(String id)
int	ReaderWrapper.fileGroupOption(String id)
short[][]	ChannelFiller.get16BitLookupTable()
short[][]	DelegateReader.get16BitLookupTable()
short[][]	FileStitcher.get16BitLookupTable()
short[][]	FormatReader.get16BitLookupTable()
short[][]	IFormatReader.get16BitLookupTable()	Gets the 16-bit color lookup table associated with the most recently opened image.
short[][]	ImageReader.get16BitLookupTable()
short[][]	ReaderWrapper.get16BitLookupTable()
short[][]	WrappedReader.get16BitLookupTable()
byte[][]	ChannelFiller.get8BitLookupTable()
byte[][]	DelegateReader.get8BitLookupTable()
byte[][]	FileStitcher.get8BitLookupTable()
byte[][]	FormatReader.get8BitLookupTable()
byte[][]	IFormatReader.get8BitLookupTable()	Gets the 8-bit color lookup table associated with the most recently opened image.
byte[][]	ImageReader.get8BitLookupTable()
byte[][]	ReaderWrapper.get8BitLookupTable()
byte[][]	WrappedReader.get8BitLookupTable()
protected ome.xml.model.enums.AcquisitionMode	FormatReader.getAcquisitionMode(String value)	Deprecated. Use MetadataTools.getAcquisitionMode(String).
static ome.xml.model.enums.AcquisitionMode	MetadataTools.getAcquisitionMode(String value)	Retrieves an AcquisitionMode enumeration value for the given String.
int	FileStitcher.getAdjustedIndex(int no)	Gets the local reader index for use with the given image plane.
protected ome.xml.model.enums.ArcType	FormatReader.getArcType(String value)	Deprecated. Use MetadataTools.getArcType(String).
static ome.xml.model.enums.ArcType	MetadataTools.getArcType(String value)	Retrieves an ArcType enumeration value for the given String.
protected ome.xml.model.enums.Binning	FormatReader.getBinning(String value)	Deprecated. Use MetadataTools.getBinning(String).
static ome.xml.model.enums.Binning	MetadataTools.getBinning(String value)	Retrieves an Binning enumeration value for the given String.
Double	MinMaxCalculator.getChannelGlobalMaximum(int theC)	Retrieves a specified channel's global maximum.
Double	MinMaxCalculator.getChannelGlobalMinimum(int theC)	Retrieves a specified channel's global minimum.
Double	MinMaxCalculator.getChannelKnownMaximum(int theC)	Retrieves the specified channel's maximum based on the images that have been read.
Double	MinMaxCalculator.getChannelKnownMinimum(int theC)	Retrieves the specified channel's minimum based on the images that have been read.
protected ome.xml.model.enums.Compression	FormatReader.getCompression(String value)	Deprecated. Use MetadataTools.getCompression(String).
static ome.xml.model.enums.Compression	MetadataTools.getCompression(String value)	Retrieves an Compression enumeration value for the given String.
protected ome.xml.model.enums.ContrastMethod	FormatReader.getContrastMethod(String value)	Deprecated. Use MetadataTools.getContrastMethod(String).
static ome.xml.model.enums.ContrastMethod	MetadataTools.getContrastMethod(String value)	Retrieves an ContrastMethod enumeration value for the given String.
protected ome.xml.model.enums.Correction	FormatReader.getCorrection(String value)	Deprecated. Use MetadataTools.getCorrection(String).
static ome.xml.model.enums.Correction	MetadataTools.getCorrection(String value)	Retrieves an Correction enumeration value for the given String.
protected ome.xml.model.enums.DetectorType	FormatReader.getDetectorType(String value)	Deprecated. Use MetadataTools.getDetectorType(String).
static ome.xml.model.enums.DetectorType	MetadataTools.getDetectorType(String value)	Retrieves an DetectorType enumeration value for the given String.
protected ome.xml.model.enums.DimensionOrder	FormatReader.getDimensionOrder(String value)	Deprecated. Use MetadataTools.getDimensionOrder(String).
static ome.xml.model.enums.DimensionOrder	MetadataTools.getDimensionOrder(String value)	Retrieves an DimensionOrder enumeration value for the given String.
protected ome.xml.model.enums.ExperimentType	FormatReader.getExperimentType(String value)	Deprecated. Use MetadataTools.getExperimentType(String).
static ome.xml.model.enums.ExperimentType	MetadataTools.getExperimentType(String value)	Retrieves an ExperimentType enumeration value for the given String.
protected ome.xml.model.enums.FilamentType	FormatReader.getFilamentType(String value)	Deprecated. Use MetadataTools.getFilamentType(String).
static ome.xml.model.enums.FilamentType	MetadataTools.getFilamentType(String value)	Retrieves an FilamentType enumeration value for the given String.
static String	FormatTools.getFilename(int series, int image, IFormatReader r, String pattern)
static String	FormatTools.getFilename(int series, int image, IFormatReader r, String pattern, boolean padded)
static String	FormatTools.getFilename(int series, int image, MetadataRetrieve retrieve, String pattern, boolean padded)
static String[]	FormatTools.getFilenames(String pattern, IFormatReader r)
protected ome.xml.model.enums.FillRule	FormatReader.getFillRule(String value)	Deprecated. Use MetadataTools.getFillRule(String).
static ome.xml.model.enums.FillRule	MetadataTools.getFillRule(String value)	Retrieves an FillRule enumeration value for the given String.
protected ome.xml.model.enums.FilterType	FormatReader.getFilterType(String value)	Deprecated. Use MetadataTools.getFilterType(String).
static ome.xml.model.enums.FilterType	MetadataTools.getFilterType(String value)	Retrieves an FilterType enumeration value for the given String.
protected ome.xml.model.enums.FontFamily	FormatReader.getFontFamily(String value)	Deprecated. Use MetadataTools.getFontFamily(String).
static ome.xml.model.enums.FontFamily	MetadataTools.getFontFamily(String value)	Retrieves an FontFamily enumeration value for the given String.
protected ome.xml.model.enums.FontStyle	FormatReader.getFontStyle(String value)	Deprecated. Use MetadataTools.getFontStyle(String).
static ome.xml.model.enums.FontStyle	MetadataTools.getFontStyle(String value)	Retrieves an FontStyle enumeration value for the given String.
String	ImageReader.getFormat(String id)	Gets a string describing the file format for the given file.
String	ImageWriter.getFormat(String id)	Gets a string describing the file format for the given file.
protected ome.xml.model.enums.IlluminationType	FormatReader.getIlluminationType(String value)	Deprecated. Use MetadataTools.getIlluminationType(String).
static ome.xml.model.enums.IlluminationType	MetadataTools.getIlluminationType(String value)	Retrieves an IlluminationType enumeration value for the given String.
static int	FormatTools.getImagesPerFile(String pattern, IFormatReader r)
protected ome.xml.model.enums.Immersion	FormatReader.getImmersion(String value)	Deprecated. Use MetadataTools.getImmersion(String).
static ome.xml.model.enums.Immersion	MetadataTools.getImmersion(String value)	Retrieves an Immersion enumeration value for the given String.
protected ome.xml.model.enums.LaserMedium	FormatReader.getLaserMedium(String value)	Deprecated. Use MetadataTools.getLaserMedium(String).
static ome.xml.model.enums.LaserMedium	MetadataTools.getLaserMedium(String value)	Retrieves an LaserMedium enumeration value for the given String.
protected ome.xml.model.enums.LaserType	FormatReader.getLaserType(String value)	Deprecated. Use MetadataTools.getLaserType(String).
static ome.xml.model.enums.LaserType	MetadataTools.getLaserType(String value)	Retrieves an LaserType enumeration value for the given String.
private int	ChannelFiller.getLookupTableComponentCount()	Gets the number of color components in the lookup table.
protected ome.xml.model.enums.Marker	FormatReader.getMarker(String value)	Deprecated. Use MetadataTools.getMarker(String).
static ome.xml.model.enums.Marker	MetadataTools.getMarker(String value)	Retrieves an Marker enumeration value for the given String.
protected ome.xml.model.enums.Medium	FormatReader.getMedium(String value)	Deprecated. Use MetadataTools.getMedium(String).
static ome.xml.model.enums.Medium	MetadataTools.getMedium(String value)	Retrieves an Medium enumeration value for the given String.
protected ome.xml.model.enums.MicrobeamManipulationType	FormatReader.getMicrobeamManipulationType(String value)	Deprecated. Use MetadataTools.getMicrobeamManipulationType(String).
static ome.xml.model.enums.MicrobeamManipulationType	MetadataTools.getMicrobeamManipulationType(String value)	Retrieves an MicrobeamManipulationType enumeration value for the given String.
protected ome.xml.model.enums.MicroscopeType	FormatReader.getMicroscopeType(String value)	Deprecated. Use MetadataTools.getMicroscopeType(String).
static ome.xml.model.enums.MicroscopeType	MetadataTools.getMicroscopeType(String value)	Retrieves an MicroscopeType enumeration value for the given String.
protected ome.xml.model.enums.NamingConvention	FormatReader.getNamingConvention(String value)	Deprecated. Use MetadataTools.getNamingConvention(String).
static ome.xml.model.enums.NamingConvention	MetadataTools.getNamingConvention(String value)	Retrieves an NamingConvention enumeration value for the given String.
int	ChannelMerger.getOriginalIndex(int no)	Returns the image number in the original dataset that corresponds to the given image number.
protected ome.xml.model.enums.PixelType	FormatReader.getPixelType(String value)	Deprecated. Use MetadataTools.getPixelType(String).
static ome.xml.model.enums.PixelType	MetadataTools.getPixelType(String value)	Retrieves an PixelType enumeration value for the given String.
Double[]	MinMaxCalculator.getPlaneMaximum(int no)	Retrieves the maximum pixel value for the specified plane.
Double[]	MinMaxCalculator.getPlaneMinimum(int no)	Retrieves the minimum pixel value for the specified plane.
String[]	FormatReader.getPossibleDomains(String id)
String[]	IFormatReader.getPossibleDomains(String id)	Returns a list of scientific domains in which this format is used.
String[]	ImageReader.getPossibleDomains(String id)
String[]	ReaderWrapper.getPossibleDomains(String id)
String[]	WrappedReader.getPossibleDomains(String id)
protected ome.xml.model.enums.Pulse	FormatReader.getPulse(String value)	Deprecated. Use MetadataTools.getPulse(String).
static ome.xml.model.enums.Pulse	MetadataTools.getPulse(String value)	Retrieves an Pulse enumeration value for the given String.
IFormatReader	FileStitcher.getReader(int no)	Gets the reader appropriate for use with the given image plane.
IFormatReader	ImageReader.getReader(String id)	Gets the reader used to open the given file.
static int	FormatTools.getReorderedIndex(IFormatReader reader, String newOrder, int newIndex)	Converts index from the given dimension order to the reader's native one.
int	FileStitcher.getRequiredDirectories(String[] files)
int	FormatReader.getRequiredDirectories(String[] files)
int	IFormatReader.getRequiredDirectories(String[] files)	Returns the number of parent directories that are important when processing the given list of files.
int	ImageReader.getRequiredDirectories(String[] files)
int	ReaderWrapper.getRequiredDirectories(String[] files)
protected int	FormatWriter.getSizeX()
protected int	FormatWriter.getSizeY()
Codec	ChannelFiller.getTileCodec(int no)
Codec	ChannelMerger.getTileCodec(int no)
Codec	ChannelSeparator.getTileCodec(int no)
Codec	DimensionSwapper.getTileCodec(int no)
Codec	FileStitcher.getTileCodec(int no)
default Codec	ICompressedTileReader.getTileCodec(int no)	Retrieve a codec that can be used to decompress compressed tiles.
Codec	ImageReader.getTileCodec(int no)
Codec	ReaderWrapper.getTileCodec(int no)
Codec	TileStitcher.getTileCodec(int no)
CodecOptions	ChannelFiller.getTileCodecOptions(int no, int x, int y)
CodecOptions	ChannelMerger.getTileCodecOptions(int no, int x, int y)
CodecOptions	ChannelSeparator.getTileCodecOptions(int no, int x, int y)
CodecOptions	DimensionSwapper.getTileCodecOptions(int no, int x, int y)
CodecOptions	FileStitcher.getTileCodecOptions(int no, int x, int y)
default CodecOptions	ICompressedTileReader.getTileCodecOptions(int no, int x, int y)	Retrieve codec options that can be used to decompressed the specified tile.
CodecOptions	ImageReader.getTileCodecOptions(int no, int x, int y)
CodecOptions	ReaderWrapper.getTileCodecOptions(int no, int x, int y)
CodecOptions	TileStitcher.getTileCodecOptions(int no, int x, int y)
int	FormatWriter.getTileSizeX()
int	IFormatWriter.getTileSizeX()	Retrieves the current tile width Defaults to 0 if not supported
int	ImageWriter.getTileSizeX()
int	WriterWrapper.getTileSizeX()
int	FormatWriter.getTileSizeY()
int	IFormatWriter.getTileSizeY()	Retrieves the current tile height Defaults to 0 if not supported
int	ImageWriter.getTileSizeY()
int	WriterWrapper.getTileSizeY()
IFormatWriter	ImageWriter.getWriter(String id)	Gets the writer used to save the given file.
protected void	FileStitcher.initFile(String id)	Initializes the given file or file pattern.
protected void	FormatReader.initFile(String id)	Initializes the given file (parsing header information, etc.).
protected void	SubResolutionFormatReader.initFile(String id)	Initializes the given file (parsing header information, etc.).
protected void	MinMaxCalculator.initMinMax()	Ensures internal min/max variables are initialized properly.
protected boolean	FormatWriter.isFullPlane(int x, int y, int w, int h)	Returns true if the given rectangle coordinates correspond to a full image in the given series.
boolean	MinMaxCalculator.isMinMaxPopulated()	Returns true if the values returned by getChannelGlobalMinimum/Maximum can be trusted.
boolean	FormatReader.isSingleFile(String id)
boolean	IFormatReader.isSingleFile(String id)	Returns true if the named file is expected to be the only file in the dataset.
boolean	ImageReader.isSingleFile(String id)
boolean	ReaderWrapper.isSingleFile(String id)
boolean	WrappedReader.isSingleFile(String id)
IFormatReader	Memoizer.loadMemo()	Load a memo file if possible, returning a null if not.
byte[]	ChannelFiller.openBytes(int no)
byte[]	ChannelFiller.openBytes(int no, byte[] buf)
byte[]	ChannelFiller.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	ChannelFiller.openBytes(int no, int x, int y, int w, int h)
byte[]	ChannelMerger.openBytes(int no)
byte[]	ChannelMerger.openBytes(int no, byte[] buf)
byte[]	ChannelMerger.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	ChannelMerger.openBytes(int no, int x, int y, int w, int h)
byte[]	ChannelSeparator.openBytes(int no)
byte[]	ChannelSeparator.openBytes(int no, byte[] buf)
byte[]	ChannelSeparator.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	ChannelSeparator.openBytes(int no, int x, int y, int w, int h)
byte[]	DelegateReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	DimensionSwapper.openBytes(int no)
byte[]	DimensionSwapper.openBytes(int no, byte[] buf)
byte[]	DimensionSwapper.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	DimensionSwapper.openBytes(int no, int x, int y, int w, int h)
byte[]	FileStitcher.openBytes(int no)
byte[]	FileStitcher.openBytes(int no, byte[] buf)
byte[]	FileStitcher.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	FileStitcher.openBytes(int no, int x, int y, int w, int h)
byte[]	FormatReader.openBytes(int no)
byte[]	FormatReader.openBytes(int no, byte[] buf)
abstract byte[]	FormatReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	FormatReader.openBytes(int no, int x, int y, int w, int h)
byte[]	IFormatReader.openBytes(int no)	Obtains the specified image plane from the current file as a byte array.
byte[]	IFormatReader.openBytes(int no, byte[] buf)	Obtains the specified image plane from the current file into a pre-allocated byte array of (sizeX * sizeY * bytesPerPixel * RGB channel count).
byte[]	IFormatReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)	Obtains a sub-image of the specified image plane into a pre-allocated byte array.
byte[]	IFormatReader.openBytes(int no, int x, int y, int w, int h)	Obtains a sub-image of the specified image plane, whose upper-left corner is given by (x, y).
byte[]	ImageReader.openBytes(int no)
byte[]	ImageReader.openBytes(int no, byte[] buf)
byte[]	ImageReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	ImageReader.openBytes(int no, int x, int y, int w, int h)
byte[]	MinMaxCalculator.openBytes(int no)
byte[]	MinMaxCalculator.openBytes(int no, byte[] buf)
byte[]	MinMaxCalculator.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	MinMaxCalculator.openBytes(int no, int x, int y, int w, int h)
byte[]	ReaderWrapper.openBytes(int no)
byte[]	ReaderWrapper.openBytes(int no, byte[] buf)
byte[]	ReaderWrapper.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	ReaderWrapper.openBytes(int no, int x, int y, int w, int h)
byte[]	TileStitcher.openBytes(int no)
byte[]	TileStitcher.openBytes(int no, byte[] buf)
byte[]	TileStitcher.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	TileStitcher.openBytes(int no, int x, int y, int w, int h)
byte[]	WrappedReader.openBytes(int no)
byte[]	WrappedReader.openBytes(int no, byte[] buf)
byte[]	WrappedReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	WrappedReader.openBytes(int no, int x, int y, int w, int h)
byte[]	ChannelFiller.openCompressedBytes(int no, byte[] buf, int x, int y)
byte[]	ChannelFiller.openCompressedBytes(int no, int x, int y)
byte[]	ChannelMerger.openCompressedBytes(int no, byte[] buf, int x, int y)
byte[]	ChannelMerger.openCompressedBytes(int no, int x, int y)
byte[]	ChannelSeparator.openCompressedBytes(int no, byte[] buf, int x, int y)
byte[]	ChannelSeparator.openCompressedBytes(int no, int x, int y)
byte[]	DimensionSwapper.openCompressedBytes(int no, byte[] buf, int x, int y)
byte[]	DimensionSwapper.openCompressedBytes(int no, int x, int y)
byte[]	FileStitcher.openCompressedBytes(int no, byte[] buf, int x, int y)
byte[]	FileStitcher.openCompressedBytes(int no, int x, int y)
default byte[]	ICompressedTileReader.openCompressedBytes(int no, byte[] buf, int x, int y)	Retrieve the specified tile without performing any decompression.
default byte[]	ICompressedTileReader.openCompressedBytes(int no, int x, int y)	Retrieve the specified tile without performing any decompression.
byte[]	ImageReader.openCompressedBytes(int no, byte[] buf, int x, int y)
byte[]	ImageReader.openCompressedBytes(int no, int x, int y)
byte[]	ReaderWrapper.openCompressedBytes(int no, byte[] buf, int x, int y)
byte[]	ReaderWrapper.openCompressedBytes(int no, int x, int y)
byte[]	TileStitcher.openCompressedBytes(int no, byte[] buf, int x, int y)
byte[]	TileStitcher.openCompressedBytes(int no, int x, int y)
Object	FileStitcher.openPlane(int no, int x, int y, int w, int h)
Object	FormatReader.openPlane(int no, int x, int y, int w, int h)
Object	IFormatReader.openPlane(int no, int x, int y, int w, int h)	Obtains the specified image plane (or sub-image thereof) in the reader's native data structure.
Object	ImageReader.openPlane(int no, int x, int y, int w, int h)
Object	ReaderWrapper.openPlane(int no, int x, int y, int w, int h)
Object	WrappedReader.openPlane(int no, int x, int y, int w, int h)
byte[]	ChannelSeparator.openThumbBytes(int no)
byte[]	DimensionSwapper.openThumbBytes(int no)
byte[]	FileStitcher.openThumbBytes(int no)
byte[]	FormatReader.openThumbBytes(int no)
static byte[]	FormatTools.openThumbBytes(IFormatReader reader, int no)	Default implementation for IFormatReader.openThumbBytes(int).
byte[]	IFormatReader.openThumbBytes(int no)	Obtains a thumbnail for the specified image plane from the current file, as a byte array.
byte[]	ImageReader.openThumbBytes(int no)
byte[]	ReaderWrapper.openThumbBytes(int no)
byte[]	WrappedReader.openThumbBytes(int no)
static int	FormatTools.pixelTypeFromBytes(int bytes, boolean signed, boolean fp)	Returns an appropriate pixel type given the number of bytes per pixel.
void	FormatWriter.saveBytes(int no, byte[] buf)
void	FormatWriter.saveBytes(int no, byte[] buf, loci.common.Region tile)
void	IFormatWriter.saveBytes(int no, byte[] buf)	Saves the given image to the current series in the current file.
void	IFormatWriter.saveBytes(int no, byte[] buf, int x, int y, int w, int h)	Saves the given image tile to the current series in the current file.
void	IFormatWriter.saveBytes(int no, byte[] buf, loci.common.Region tile)	Saves the given image tile to the current series in the current file.
void	ImageWriter.saveBytes(int no, byte[] buf)
void	ImageWriter.saveBytes(int no, byte[] buf, int x, int y, int w, int h)
void	ImageWriter.saveBytes(int no, byte[] buf, loci.common.Region tile)
void	WriterWrapper.saveBytes(int no, byte[] buf)
void	WriterWrapper.saveBytes(int no, byte[] buf, int x, int y, int w, int h)
void	WriterWrapper.saveBytes(int no, byte[] buf, loci.common.Region tile)
default void	ICompressedTileWriter.saveCompressedBytes(int no, byte[] buf, int x, int y, int w, int h)	Save a compressed tile to the current output file.
void	ImageWriter.saveCompressedBytes(int no, byte[] buf, int x, int y, int w, int h)
void	WriterWrapper.saveCompressedBytes(int no, byte[] buf, int x, int y, int w, int h)
void	FormatWriter.savePlane(int no, Object plane)
void	FormatWriter.savePlane(int no, Object plane, int x, int y, int w, int h)
void	FormatWriter.savePlane(int no, Object plane, loci.common.Region tile)
void	IFormatWriter.savePlane(int no, Object plane)	Saves the given image plane to the current series in the current file.
void	IFormatWriter.savePlane(int no, Object plane, int x, int y, int w, int h)	Saves the given image plane to the current series in the current file.
void	IFormatWriter.savePlane(int no, Object plane, loci.common.Region tile)	Saves the given image plane to the current series in the current file.
void	ImageWriter.savePlane(int no, Object plane)
void	ImageWriter.savePlane(int no, Object plane, int x, int y, int w, int h)
void	ImageWriter.savePlane(int no, Object plane, loci.common.Region tile)
void	WriterWrapper.savePlane(int no, Object plane)
void	WriterWrapper.savePlane(int no, Object plane, int x, int y, int w, int h)
void	WriterWrapper.savePlane(int no, Object plane, loci.common.Region tile)
void	FileStitcher.setAxisTypes(int[] axes)	Sets the axis type for each dimensional block.
void	FormatWriter.setCompression(String compress)
void	IFormatWriter.setCompression(String compress)	Sets the current compression type.
void	ImageWriter.setCompression(String compress)
void	WriterWrapper.setCompression(String compress)
void	ChannelFiller.setId(String id)
void	ChannelMerger.setId(String id)
void	ChannelSeparator.setId(String id)
void	DelegateReader.setId(String id)
void	DimensionSwapper.setId(String id)
void	FileStitcher.setId(String id)
void	FormatReader.setId(String id)	Initialize a reader from the input file name.
void	FormatWriter.setId(String id)	Initializes a writer from the input file name.
void	IFormatHandler.setId(String id)	Sets the current file name.
void	ImageReader.setId(String id)
void	ImageWriter.setId(String id)
void	Memoizer.setId(String id)
void	ReaderWrapper.setId(String id)
void	TileStitcher.setId(String id)
void	WriterWrapper.setId(String id)
void	FormatWriter.setSeries(int series)
void	IFormatWriter.setSeries(int series)	Sets the current series.
void	ImageWriter.setSeries(int series)
void	WriterWrapper.setSeries(int series)
int	FormatWriter.setTileSizeX(int tileSize)
int	IFormatWriter.setTileSizeX(int tileSize)	Will attempt to set the tile width to the desired value and return the actual value which will be used
int	ImageWriter.setTileSizeX(int tileSize)
int	WriterWrapper.setTileSizeX(int tileSize)
int	FormatWriter.setTileSizeY(int tileSize)
int	IFormatWriter.setTileSizeY(int tileSize)	Will attempt to set the tile height to the desired value and return the actual value which will be used
int	ImageWriter.setTileSizeY(int tileSize)
int	WriterWrapper.setTileSizeY(int tileSize)
IFormatReader	ReaderWrapper.unwrap()	Unwraps nested wrapped readers until the core reader (i.e., not a ReaderWrapper or ImageReader) is found.
IFormatReader	ReaderWrapper.unwrap(Class<? extends IFormatReader> readerClass, String id)	Unwraps nested wrapped readers until the given reader class is found.
IFormatReader	ReaderWrapper.unwrap(String id)	Unwraps nested wrapped readers until the core reader (i.e., not a ReaderWrapper or ImageReader) is found.
IFormatWriter	WriterWrapper.unwrap()	Unwraps nested wrapped writers until the core writer (i.e., not a WriterWrapper or ImageWriter) is found.
IFormatWriter	WriterWrapper.unwrap(Class<? extends IFormatWriter> writerClass, String id)	Unwraps nested wrapped writers until the given writer class is found.
IFormatWriter	WriterWrapper.unwrap(String id)	Unwraps nested wrapped writers until the core writer (i.e., not a WriterWrapper or ImageWriter) is found.
protected void	MinMaxCalculator.updateMinMax(int no, byte[] buf, int len)	Updates min/max values based on the given byte array.
static void	MetadataTools.verifyMinimumPopulated(MetadataRetrieve src)	Checks whether the given metadata object has the minimum metadata populated to successfully describe an Image.
static void	MetadataTools.verifyMinimumPopulated(MetadataRetrieve src, int n)	Checks whether the given metadata object has the minimum metadata populated to successfully describe the nth Image.

Constructors in loci.formats that throw FormatException

Modifier	Constructor	Description
	ExternalSeries(FilePattern pattern)

Uses of FormatException in loci.formats.cache

Subclasses of FormatException in loci.formats.cache

Modifier and Type	Class	Description
class	CacheException	CacheException is the exception thrown when something goes wrong performing a cache operation.

Uses of FormatException in loci.formats.codec

Methods in loci.formats.codec that return FormatException

Modifier and Type	Method	Description
(package private) static FormatException	WrappedCodec.unwrapCodecException(ome.codecs.CodecException e)

Methods in loci.formats.codec that throw FormatException

Modifier and Type	Method	Description
byte[]	BaseCodec.compress(byte[][] data, CodecOptions options)	2D data block encoding default implementation.
byte[]	Codec.compress(byte[][] data, CodecOptions options)	Compresses a block of data.
byte[]	Codec.compress(byte[] data, CodecOptions options)	Compresses a block of data.
byte[]	JPEGXRCodec.compress(byte[] data, CodecOptions options)
byte[]	NikonCodec.compress(byte[] data, CodecOptions options)
byte[]	TargaRLECodec.compress(byte[] data, CodecOptions options)
byte[]	WrappedCodec.compress(byte[][] data, CodecOptions options)
byte[]	WrappedCodec.compress(byte[] data, CodecOptions options)
private static void	WrappedCodec.copyOptions(CodecOptions src, ome.codecs.CodecOptions dest)
byte[]	BaseCodec.decompress(byte[] data)
byte[]	BaseCodec.decompress(byte[][] data)
byte[]	BaseCodec.decompress(byte[][] data, CodecOptions options)	2D data block decoding default implementation.
byte[]	BaseCodec.decompress(byte[] data, CodecOptions options)
abstract byte[]	BaseCodec.decompress(loci.common.RandomAccessInputStream in, CodecOptions options)
byte[]	Codec.decompress(byte[] data)	Decompresses a block of data.
byte[]	Codec.decompress(byte[][] data)	Decompresses a block of data.
byte[]	Codec.decompress(byte[][] data, CodecOptions options)	Decompresses a block of data.
byte[]	Codec.decompress(byte[] data, CodecOptions options)	Decompresses a block of data.
byte[]	Codec.decompress(loci.common.RandomAccessInputStream in, CodecOptions options)	Decompresses data from the given RandomAccessInputStream.
byte[]	JPEGXRCodec.decompress(byte[] buf, CodecOptions options)	The CodecOptions parameter should have the following fields set: maxBytes interleaved bitsPerSample littleEndian width height
byte[]	JPEGXRCodec.decompress(loci.common.RandomAccessInputStream in, CodecOptions options)
byte[]	NikonCodec.decompress(loci.common.RandomAccessInputStream in, CodecOptions options)	The CodecOptions parameter must be an instance of NikonCodecOptions, and should have the following fields set: lossless vPredictor curve split bitsPerSample maxBytes width height
byte[]	TargaRLECodec.decompress(loci.common.RandomAccessInputStream in, CodecOptions options)	The CodecOptions parameter should have the following fields set: maxBytes CodecOptions.bitsPerSample
byte[]	WrappedCodec.decompress(byte[] data)
byte[]	WrappedCodec.decompress(byte[][] data)
byte[]	WrappedCodec.decompress(byte[][] data, CodecOptions options)
byte[]	WrappedCodec.decompress(byte[] data, CodecOptions options)
byte[]	WrappedCodec.decompress(loci.common.RandomAccessInputStream in, CodecOptions options)
byte[]	ZstdCodec.decompress(byte[] data, int pointer, int length)
protected static ome.codecs.CodecOptions	WrappedCodec.getOptions(CodecOptions options)
int	HuffmanCodec.getSample(loci.common.RandomAccessInputStream bb, CodecOptions options)
int	HuffmanCodec.getSample(BitBuffer bb, CodecOptions options)	Deprecated.
private void	JPEGXRCodec.initialize()	Initializes the JPEG-XR dependency service.
void	BaseCodec.test()	Main testing method default implementation.

Uses of FormatException in loci.formats.dicom

Methods in loci.formats.dicom that throw FormatException

Modifier and Type	Method	Description
private int	DicomTag.getNextTag(loci.common.RandomAccessInputStream in)	Get the next 4 byte DICOM tag from the given input stream.

Constructors in loci.formats.dicom that throw FormatException

Modifier	Constructor	Description
	DicomFileInfo(String filePath)	Construct an object from the given file.
	DicomTag(loci.common.RandomAccessInputStream in, boolean bigEndian, long location, boolean oddLocations)	Read a complete tag and value from the given input stream.
	DicomTag(loci.common.RandomAccessInputStream in, boolean bigEndian, long location, boolean oddLocations, boolean readValue)	Read a complete tag and optionally a value from the given input stream.

Uses of FormatException in loci.formats.gui

Methods in loci.formats.gui that throw FormatException

Modifier and Type	Method	Description
static BufferedImage	AWTImageTools.makeImage(byte[] data, boolean interleaved, MetadataRetrieve meta, int series)	Creates an image from the given raw byte array, obtaining the dimensional parameters from the specified metadata object.
static BufferedImage	AWTImageTools.openImage(byte[] buf, IFormatReader r, int w, int h)	Creates an image from the given byte array, using the given IFormatReader to retrieve additional information.
static BufferedImage	AWTImageTools.openImage(byte[] buf, IFormatReader r, int w, int h, boolean normal)	Creates an image from the given byte array, using the given IFormatReader to retrieve additional information.
BufferedImage	BufferedImageReader.openImage(int no)	Obtains the specified image from the current file.
BufferedImage	BufferedImageReader.openImage(int no, int x, int y, int w, int h)	Obtains a sub-image of the specified image, whose upper-left corner is given by (x, y).
BufferedImage	BufferedImageReader.openThumbImage(int no)	Obtains a thumbnail for the specified image from the current file.
void	BufferedImageWriter.saveImage(int no, BufferedImage image)	Saves the given BufferedImage to the current file.
void	BufferedImageWriter.saveImage(int no, BufferedImage image, int x, int y, int w, int h)	Saves the given BufferedImage to the current file.

Uses of FormatException in loci.formats.in

Methods in loci.formats.in that throw FormatException

Modifier and Type	Method	Description
private void	DCIMGReader.addFileToList(String file)
private void	DicomReader.addFileToList(String file, boolean checkSeries)	Determine if the given file belongs in the same dataset as this file.
private void	FV1000Reader.addPtyFiles()
private void	OMETiffReader.addSubResolutions()
private void	LIFReader.addUserCommentMeta(Element imageNode, int image)
static void	FlexReader.appendServerMap(String alias, String realName)	Add the path 'realName' to the mapping for the server named 'alias'.
private void	MicromanagerReader.buildTIFFList(int posIndex)
private void	DicomReader.calculatePixelsOffsets(long baseOffset)	Calculate offsets to all pixel data (tiles or planes) in the file, starting from the given offset.
private void	LOFReader.checkForLofLayout(loci.common.RandomAccessInputStream in, String filename)	Checks if file layout meets lof file specifications
private boolean	ZeissCZIReader.checkPALM(String xml)
private int	CellSensReader.convertPixelType(int pixelType)
private void	KLBReader.convertPixelType(CoreMetadata ms0, int pixelType)
private int	TillVisionReader.convertPixelType(int type)
private void	ZeissCZIReader.convertPixelType(int pixelType)
private void	ZeissCZIReader.convertPixelType(CoreMetadata ms0, int pixelType)
private void	TissueFAXSReader.copyCorrectionImageToBuffer(TissueFAXSReader.ScanRegion region, loci.common.Region dest, int[] zct, byte[] buf)
private void	TissueFAXSReader.copyRegionToBuffer(TissueFAXSReader.ScanRegion region, int level, loci.common.Region dest, int[] zct, byte[] buf)
protected byte[]	MinimalTiffReader.copyTile(IFD ifd, byte[] buf, int x, int y)
private DicomFileInfo	DicomReader.createFileInfo(String file)	Construct a DicomFileInfo for the given file.
private byte[]	APNGReader.decode(APNGReader.PNGInputStream bytes)
private byte[]	APNGReader.decode(APNGReader.PNGInputStream bytes, int width, int height)
private byte[]	CellSensReader.decodeTile(int no, int row, int col)
byte[]	SlideBook7Reader.CCompressionBase.DecompressBuffer(byte[] inBuffer)
private boolean	PictReader.drivePictDecoder(int opcode)	Handles the opcodes in the PICT file.
protected ZeissTIFFReader.TIFFInfo	ZeissTIFFReader.evalFile(String id)	Evaluate the metadata of a TIFF/XML file collection, and return this to the user.
private void	PictReader.expandPixels(int bitSize, byte[] ib, byte[] ob, int outLen)	Expand an array of bytes.
private String	BDVReader.fetchXMLId()
int	AFIReader.fileGroupOption(String id)
int	AnalyzeReader.fileGroupOption(String id)
int	APLReader.fileGroupOption(String id)
int	BDReader.fileGroupOption(String id)
int	BioRadReader.fileGroupOption(String id)
int	BrukerReader.fileGroupOption(String id)
int	CellomicsReader.fileGroupOption(String id)
int	CellSensReader.fileGroupOption(String id)
int	CellVoyagerReader.fileGroupOption(String id)
int	CellWorxReader.fileGroupOption(String id)
int	ColumbusReader.fileGroupOption(String id)
int	CV7000Reader.fileGroupOption(String id)
int	DCIMGReader.fileGroupOption(String id)
int	DicomReader.fileGroupOption(String id)
int	FlexReader.fileGroupOption(String id)
int	FujiReader.fileGroupOption(String id)
int	FV1000Reader.fileGroupOption(String id)
int	HitachiReader.fileGroupOption(String id)
int	ICSReader.fileGroupOption(String id)
int	ImagicReader.fileGroupOption(String id)
int	InCellReader.fileGroupOption(String id)
int	JDCEReader.fileGroupOption(String id)
int	KLBReader.fileGroupOption(String id)
int	L2DReader.fileGroupOption(String id)
int	LeicaReader.fileGroupOption(String id)
int	MetamorphReader.fileGroupOption(String id)
int	MIASReader.fileGroupOption(String id)
int	MicroCTReader.fileGroupOption(String id)
int	MicromanagerReader.fileGroupOption(String id)
int	NDPIReader.fileGroupOption(String id)
int	NDPISReader.fileGroupOption(String id)
int	NiftiReader.fileGroupOption(String id)
int	NRRDReader.fileGroupOption(String id)
int	OIRReader.fileGroupOption(String id)
int	OlympusTileReader.fileGroupOption(String id)
int	OperettaReader.fileGroupOption(String id)
int	PerkinElmerReader.fileGroupOption(String id)
int	PrairieReader.fileGroupOption(String id)
int	ScanrReader.fileGroupOption(String id)
int	SPCReader.fileGroupOption(String id)
int	SVSReader.fileGroupOption(String id)
int	TCSReader.fileGroupOption(String id)
int	TecanReader.fileGroupOption(String id)
int	TillVisionReader.fileGroupOption(String id)
int	TrestleReader.fileGroupOption(String id)
int	VentanaReader.fileGroupOption(String id)
int	VisitechReader.fileGroupOption(String id)
int	XLEFReader.fileGroupOption(String id)
int	ZeissLSMReader.fileGroupOption(String id)
int	ZeissTIFFReader.fileGroupOption(String id)
protected void	BaseZeissReader.fillMetadataPass1(MetadataStore store)	Read and store basic dimensions in model
protected void	ZeissTIFFReader.fillMetadataPass1(MetadataStore store)
protected void	ZeissZVIReader.fillMetadataPass1(MetadataStore store)
protected void	BaseZeissReader.fillMetadataPass2(MetadataStore store)	Read and store basic dimensions in model
protected void	ZeissTIFFReader.fillMetadataPass2(MetadataStore store)
protected void	BaseZeissReader.fillMetadataPass3(MetadataStore store)	Read and store basic dimensions in model
protected void	ZeissZVIReader.fillMetadataPass3(MetadataStore store)
protected void	BaseZeissReader.fillMetadataPass4(MetadataStore store)	Read and store basic dimensions in model
protected void	BaseZeissReader.fillMetadataPass5(MetadataStore store)	Read and store basic dimensions in model
protected void	ZeissTIFFReader.fillMetadataPass5(MetadataStore store)
protected void	ZeissZVIReader.fillMetadataPass5(MetadataStore store)
protected void	BaseZeissReader.fillMetadataPass6(MetadataStore store)	Read and store basic dimensions in model
protected void	BaseZeissReader.fillMetadataPass7(MetadataStore store)	Store basic dimensions in model
private String	LeicaReader.findLEIFile(String baseFile)	Find the .lei file that belongs to the same dataset as the given file.
private String	FV1000Reader.findOIFFile(String baseFile)
protected void	CellWorxReader.findPixelsFiles()
protected void	MetaxpressTiffReader.findPixelsFiles()
short[][]	BaseZeissReader.get16BitLookupTable()
short[][]	FakeReader.get16BitLookupTable()
short[][]	FilePatternReader.get16BitLookupTable()
short[][]	ImprovisionTiffReader.get16BitLookupTable()
short[][]	InCellReader.get16BitLookupTable()
short[][]	LeicaReader.get16BitLookupTable()
short[][]	MIASReader.get16BitLookupTable()
short[][]	MinimalTiffReader.get16BitLookupTable()
short[][]	OIRReader.get16BitLookupTable()
short[][]	OMETiffReader.get16BitLookupTable()
short[][]	PDSReader.get16BitLookupTable()
short[][]	PerkinElmerReader.get16BitLookupTable()
short[][]	SlidebookTiffReader.get16BitLookupTable()
short[][]	TCSReader.get16BitLookupTable()
short[][]	VentanaReader.get16BitLookupTable()
short[][]	ZeissCZIReader.get16BitLookupTable()
short[][]	ZeissLSMReader.get16BitLookupTable()
short[][]	ZipReader.get16BitLookupTable()
byte[][]	BaseZeissReader.get8BitLookupTable()
byte[][]	BMPReader.get8BitLookupTable()
byte[][]	FakeReader.get8BitLookupTable()
byte[][]	FilePatternReader.get8BitLookupTable()
byte[][]	GIFReader.get8BitLookupTable()
byte[][]	ImprovisionTiffReader.get8BitLookupTable()
byte[][]	InCellReader.get8BitLookupTable()
byte[][]	IPWReader.get8BitLookupTable()
byte[][]	KhorosReader.get8BitLookupTable()
byte[][]	LeicaReader.get8BitLookupTable()
byte[][]	MIASReader.get8BitLookupTable()
byte[][]	MinimalTiffReader.get8BitLookupTable()
byte[][]	OIRReader.get8BitLookupTable()
byte[][]	OMETiffReader.get8BitLookupTable()
byte[][]	PerkinElmerReader.get8BitLookupTable()
byte[][]	PictReader.get8BitLookupTable()
byte[][]	SlidebookTiffReader.get8BitLookupTable()
byte[][]	TargaReader.get8BitLookupTable()
byte[][]	TCSReader.get8BitLookupTable()
byte[][]	VentanaReader.get8BitLookupTable()
byte[][]	ZeissCZIReader.get8BitLookupTable()
byte[][]	ZeissLSMReader.get8BitLookupTable()
byte[][]	ZipReader.get8BitLookupTable()
protected ome.xml.model.enums.AcquisitionMode	OperettaReader.getAcquisitionMode(String mode)	Deprecated.
private List<TissueFAXSReader.ScanRegion>	TissueFAXSReader.getAllRegions(int t)
private int	OBFReader.getBitsPerPixel(int type)
int	SPEReader.SpeHeader.getByte(SPEReader.SpeHeaderEntry entry)	Method used to retrieve data values for Byte entries into the SPE header table
private ome.xml.model.primitives.Color	MIASReader.getChannelColorFromFile(String file)	Get the color associated with the given file's channel.
protected long	MinimalTiffReader.getCompressedByteCount(IFD ifd, int x, int y)
private boolean	OBFReader.getCompression(int compression)
private loci.common.RandomAccessInputStream	ZeissLSMReader.getCZTag(IFD ifd)
private loci.common.RandomAccessInputStream	CellomicsReader.getDecompressedStream(String filename)
private int	ZeissLSMReader.getExtraSeries(String file)
private loci.common.RandomAccessInputStream	FV1000Reader.getFile(String name)
private String	SlidebookTiffReader.getFirstChannel(String path)
private Object	BDVReader.getImageData(int no, int x, int y, int width, int height)
private Object	CellH5Reader.getImageData(int no, int y, int height)
private Object	ImarisHDFReader.getImageData(int no, int x, int y, int width, int height)	Retrieve an array corresponding to the specified image tile.
private loci.common.IniList	FV1000Reader.getIniFile(String filename)
int	SPEReader.SpeHeader.getInt(SPEReader.SpeHeaderEntry entry)	Method used to retrieve data values for Integer entries into the SPE header table
int[]	SPEReader.SpeHeader.getIntArray(SPEReader.SpeHeaderEntry entry)	Method used to retrieve data values for Integer Array entries into the SPE header table
private long	OBFReader.getLength(long length)
private int	TissueFAXSReader.getLevel()
long	SPEReader.SpeHeader.getLong(SPEReader.SpeHeaderEntry entry)	Method used to retrieve data values for Long enteries into the SPE header table
long[]	SPEReader.SpeHeader.getLongArray(SPEReader.SpeHeaderEntry entry)	Method used to retrieve data values for Long Array entries into the SPE header table
(package private) byte[][]	AmiraReader.getLookupTable(Map materials)
private long[]	NDPIReader.getMarkers(IFD ifd)	Get the array of restart markers (offsets) for the given IFD.
private String	ZeissLSMReader.getMDBFile(String id)
private String	ZeissXRMReader.getMetadataPixelType(int dataType)
private Element	LIFReader.getMetadataRoot(String xml)
private Element	OlympusTileReader.getMetadataRoot(String xml)
int	ZeissCZIReader.SubBlock.getPhysicalHeight()
int	ZeissCZIReader.SubBlock.getPhysicalWidth()
private int	OBFReader.getPixelType(int type)
private int	ZeissXRMReader.getPixelType(int dataType)	Convert an XRM data type to a Bio-Formats pixel type.
private int	LiFlimReader.getPixelTypeFromString(String type)
protected IFormatReader	CellWorxReader.getReader(String file, boolean omexml)
protected IFormatReader	MetaxpressTiffReader.getReader(String file, boolean omexml)
private TissueFAXSReader.ScanRegion	TissueFAXSReader.getRegion()
private TissueFAXSReader.ScanRegion	TissueFAXSReader.getRegion(int t)
int	BrukerReader.getRequiredDirectories(String[] files)
int	CellVoyagerReader.getRequiredDirectories(String[] files)
int	ColumbusReader.getRequiredDirectories(String[] files)
int	CV7000Reader.getRequiredDirectories(String[] files)
int	DicomReader.getRequiredDirectories(String[] files)
int	MIASReader.getRequiredDirectories(String[] files)
int	MicroCTReader.getRequiredDirectories(String[] files)
int	OMETiffReader.getRequiredDirectories(String[] files)
int	OperettaReader.getRequiredDirectories(String[] files)
int	TecanReader.getRequiredDirectories(String[] files)
SPEReader.SpeROI[]	SPEReader.SpeHeader.getROIs()	Method used to read and return meta data for upto 10 rectangular ROI's stored in the SPE header table
private Object	ImarisHDFReader.getSampleData()
int	SPEReader.SpeHeader.getShort(SPEReader.SpeHeaderEntry entry)	Method used to retrieve data values for Short entries into the SPE header table
int[]	SPEReader.SpeHeader.getShortArray(SPEReader.SpeHeaderEntry entry)	Method used to retrieve data values for Short Array entries into the SPE header table
int	SPEReader.SpeHeader.getStackSize()	Method used to determined the stack size of the SPE file.
String	SPEReader.SpeHeader.getString(SPEReader.SpeHeaderEntry entry)	Method used to retrieve data values for String entries into the SPE header table
private String[]	MetaxpressTiffReader.getTiffFiles(String plateName, char rowLetter, int col, int channels, int nTimepoints, int zSteps)
private void	DicomReader.getTile(DicomTile tile, byte[] buf, int x, int y, int w, int h)	Decompress pixel data associated with the given DicomTile.
private byte[]	MIASReader.getTile(int well, int no, int row, int col, loci.common.Region intersection)
Codec	DicomReader.getTileCodec(int no)
Codec	NDPIReader.getTileCodec(int no)
Codec	SVSReader.getTileCodec(int no)
CodecOptions	DicomReader.getTileCodecOptions(int no, int x, int y)
CodecOptions	NDPIReader.getTileCodecOptions(int no, int x, int y)
CodecOptions	SVSReader.getTileCodecOptions(int no, int x, int y)
protected int	MinimalTiffReader.getTileIndex(IFD ifd, int x, int y)	Get the index of the tile corresponding to given IFD (plane) and tile XY indexes.
private long	BDReader.getTimestamp(String file)
private String	SlidebookTiffReader.getTimestamp(String path)
private String	ImprovisionTiffReader.getUUID(String path)
private void	FlexReader.groupFiles(String[] fileList, MetadataStore store)
private void	TCSReader.groupFiles()
private void	PictReader.handleBitmap(int opcode)	Extract the image data in a PICT bitmap structure.
private void	PictReader.handlePixmap(int opcode)	Extracts the image data in a PICT pixmap structure.
private void	PictReader.handlePixmap(int pixelSize, int compCount)	Handles the unpacking of the image data.
private void	FluoviewReader.initAlternateMetadata()
private void	FluoviewReader.initAlternateMetadataStore()
protected void	LeicaSCNReader.initCoreMetadata(int series, int resolution)
private void	LiFlimReader.initCoreMetadata()
protected void	DeltavisionReader.initExtraMetadata()
protected void	AFIReader.initFile(String id)
protected void	AIMReader.initFile(String id)
protected void	AliconaReader.initFile(String id)
protected void	AmiraReader.initFile(String id)
protected void	AnalyzeReader.initFile(String id)
protected void	APLReader.initFile(String id)
protected void	APNGReader.initFile(String id)
protected void	ARFReader.initFile(String id)
protected void	AVIReader.initFile(String id)
protected void	BaseTiffReader.initFile(String id)
protected void	BDReader.initFile(String id)
protected void	BDVReader.initFile(String id)
protected void	BioRadGelReader.initFile(String id)
protected void	BioRadReader.initFile(String id)
protected void	BioRadSCNReader.initFile(String id)
protected void	BMPReader.initFile(String id)
protected void	BrukerReader.initFile(String id)
protected void	BurleighReader.initFile(String id)
protected void	CanonRawReader.initFile(String id)
protected void	CellH5Reader.initFile(String id)
protected void	CellomicsReader.initFile(String id)
protected void	CellSensReader.initFile(String id)
protected void	CellVoyagerReader.initFile(String id)
protected void	CellWorxReader.initFile(String id)
protected void	ColumbusReader.initFile(String id)
protected void	CV7000Reader.initFile(String id)
protected void	DCIMGReader.initFile(String id)
protected void	DeltavisionReader.initFile(String id)
protected void	DicomReader.initFile(String id)
protected void	DNGReader.initFile(String id)
protected void	Ecat7Reader.initFile(String id)
protected void	EPSReader.initFile(String id)
protected void	FakeReader.initFile(String id)
protected void	FEIReader.initFile(String id)
protected void	FilePatternReader.initFile(String id)
protected void	FitsReader.initFile(String id)
protected void	FlexReader.initFile(String id)
protected void	FlowSightReader.initFile(String id)
protected void	FujiReader.initFile(String id)
protected void	FV1000Reader.initFile(String id)
protected void	GatanDM2Reader.initFile(String id)
protected void	GatanReader.initFile(String id)
protected void	GIFReader.initFile(String id)
protected void	HamamatsuVMSReader.initFile(String id)
protected void	HISReader.initFile(String id)
protected void	HitachiReader.initFile(String id)
protected void	HRDGDFReader.initFile(String id)
void	I2IReader.initFile(String id)
protected void	ICSReader.initFile(String id)
protected void	IM3Reader.initFile(String id)
protected void	ImageIOReader.initFile(String id)
protected void	ImagicReader.initFile(String id)
protected void	ImarisHDFReader.initFile(String id)
protected void	ImarisReader.initFile(String id)
protected void	ImarisTiffReader.initFile(String id)
protected void	IMODReader.initFile(String id)
protected void	ImspectorReader.initFile(String id)
protected void	InCell3000Reader.initFile(String id)
protected void	InCellReader.initFile(String id)
protected void	INRReader.initFile(String id)
protected void	InveonReader.initFile(String id)
protected void	IPLabReader.initFile(String id)
protected void	IPWReader.initFile(String id)
protected void	IvisionReader.initFile(String id)
protected void	JDCEReader.initFile(String id)
protected void	JEOLReader.initFile(String id)
protected void	JPEG2000Reader.initFile(String id)
protected void	JPEGReader.DefaultJPEGReader.initFile(String id)
protected void	JPXReader.initFile(String id)
protected void	KhorosReader.initFile(String id)
protected void	KLBReader.initFile(String id)
protected void	KodakReader.initFile(String id)
protected void	L2DReader.initFile(String id)
protected void	LeicaReader.initFile(String id)
protected void	LiFlimReader.initFile(String id)
protected void	LIFReader.initFile(String id)
protected void	LIMReader.initFile(String id)
protected void	LOFReader.initFile(String id)
protected void	MetamorphReader.initFile(String id)
protected void	MetamorphTiffReader.initFile(String id)
protected void	MIASReader.initFile(String id)
protected void	MicroCTReader.initFile(String id)
void	MicromanagerReader.initFile(String id)
protected void	MINCReader.initFile(String id)
protected void	MinimalTiffReader.initFile(String id)
protected void	MNGReader.initFile(String id)
protected void	MolecularImagingReader.initFile(String id)
void	MRCReader.initFile(String id)
protected void	MRWReader.initFile(String id)
protected void	NAFReader.initFile(String id)
protected void	ND2Reader.initFile(String id)
protected void	NDPIReader.initFile(String id)
protected void	NDPISReader.initFile(String id)
protected void	NiftiReader.initFile(String id)
protected void	NikonReader.initFile(String id)
protected void	NRRDReader.initFile(String id)
protected void	OBFReader.initFile(String id)
protected void	OIRReader.initFile(String id)
protected void	OlympusTileReader.initFile(String id)
protected void	OMETiffReader.initFile(String id)
protected void	OMEXMLReader.initFile(String id)
protected void	OpenlabRawReader.initFile(String id)
protected void	OpenlabReader.initFile(String id)
protected void	OperettaReader.initFile(String id)
protected void	OxfordInstrumentsReader.initFile(String id)
protected void	PCIReader.initFile(String id)
protected void	PCORAWReader.initFile(String id)
protected void	PCXReader.initFile(String id)
protected void	PDSReader.initFile(String id)
protected void	PerkinElmerReader.initFile(String id)
protected void	PGMReader.initFile(String id)
protected void	PhotoshopTiffReader.initFile(String id)
protected void	PictReader.initFile(String id)
protected void	PovrayReader.initFile(String id)
protected void	PQBinReader.initFile(String id)
protected void	PrairieReader.initFile(String id)
protected void	PSDReader.initFile(String id)
protected void	QTReader.initFile(String id)
protected void	QuesantReader.initFile(String id)
protected void	RHKReader.initFile(String id)
protected void	SBIGReader.initFile(String id)
protected void	ScanrReader.initFile(String id)
protected void	SDTReader.initFile(String id)
protected void	SeikoReader.initFile(String id)
protected void	SEQReader.initFile(String id)
protected void	SIFReader.initFile(String id)
protected void	SlideBook7Reader.initFile(String id)
protected void	SlidebookReader.initFile(String id)
protected void	SMCameraReader.initFile(String id)
protected void	SPCReader.initFile(String id)
protected void	SPEReader.initFile(String id)
protected void	SpiderReader.initFile(String id)
protected void	TargaReader.initFile(String id)
protected void	TCSReader.initFile(String id)
protected void	TecanReader.initFile(String id)
protected void	TextReader.initFile(String id)
protected void	TiffJAIReader.initFile(String id)
void	TileJPEGReader.initFile(String id)
protected void	TillVisionReader.initFile(String id)
protected void	TissueFAXSReader.initFile(String id)
protected void	TopometrixReader.initFile(String id)
protected void	TrestleReader.initFile(String id)
protected void	UBMReader.initFile(String id)
protected void	UnisokuReader.initFile(String id)
protected void	VarianFDFReader.initFile(String id)
protected void	VeecoReader.initFile(String id)
protected void	VGSAMReader.initFile(String id)
protected void	VisitechReader.initFile(String id)
protected void	VolocityClippingReader.initFile(String id)
protected void	VolocityReader.initFile(String id)
protected void	WATOPReader.initFile(String id)
protected void	XLEFReader.initFile(String id)
protected void	ZeissCZIReader.initFile(String id)
void	ZeissLMSReader.initFile(String id)
protected void	ZeissLSMReader.initFile(String id)
protected void	ZeissTIFFReader.initFile(String id)
protected void	ZeissXRMReader.initFile(String id)
protected void	ZeissZVIReader.initFile(String id)
protected void	ZipReader.initFile(String id)
protected void	BaseZeissReader.initFileMain(String id)
private void	FlexReader.initFlexFile(String id)
private void	OMETiffReader.initializeReader(IFormatReader r, String file)
protected void	ImageIOReader.initImage()
private void	FlexReader.initMeaFile(String id)	Initialize the dataset from a .mea file.
protected void	BaseTiffReader.initMetadata()	Populates the metadata hashtable and metadata store.
protected void	GelReader.initMetadata()
private void	LIFReader.initMetadata(String xml)	Parses a string of XML and puts the values in a Hashtable.
protected void	ZeissLSMReader.initMetadata(int series)
protected void	BaseTiffReader.initMetadataStore()	Populates the metadata store using the data parsed in BaseTiffReader.initStandardMetadata() along with some further parsing done in the method itself.
protected void	FEITiffReader.initMetadataStore()
protected void	FluoviewReader.initMetadataStore()
protected void	ImaconReader.initMetadataStore()
protected void	ImprovisionTiffReader.initMetadataStore()
protected void	IonpathMIBITiffReader.initMetadataStore()
protected void	JPKReader.initMetadataStore()
protected void	LeicaSCNReader.initMetadataStore()
protected void	LEOReader.initMetadataStore()
protected void	NDPIReader.initMetadataStore()
protected void	NikonElementsTiffReader.initMetadataStore()
protected void	NikonTiffReader.initMetadataStore()
protected void	PyramidTiffReader.initMetadataStore()
protected void	SimplePCITiffReader.initMetadataStore()
protected void	SISReader.initMetadataStore()
protected void	SlidebookTiffReader.initMetadataStore()
protected void	SVSReader.initMetadataStore()
protected void	TiffReader.initMetadataStore()
protected void	TrestleReader.initMetadataStore()
protected void	VectraReader.initMetadataStore()
protected void	VentanaReader.initMetadataStore()
protected void	DeltavisionReader.initPixels()
private void	FV1000Reader.initPOIService()
private void	IPWReader.initPOIService()
private void	PCIReader.initPOIService()
private void	ZeissXRMReader.initPOIService()
private void	ZeissZVIReader.initPOIService()
protected void	CellWorxReader.initReader(IFormatReader reader, String file, boolean omexml)
private void	FlexReader.initResFile(String id)	Initialize the dataset from a .res file.
private long	OBFReader.initStack(long current)
protected void	BaseTiffReader.initStandardMetadata()	Parses standard metadata.
protected void	DNGReader.initStandardMetadata()
protected void	FEITiffReader.initStandardMetadata()
protected void	FluoviewReader.initStandardMetadata()
protected void	ImaconReader.initStandardMetadata()
protected void	ImprovisionTiffReader.initStandardMetadata()
protected void	IonpathMIBITiffReader.initStandardMetadata()
protected void	JPKReader.initStandardMetadata()
protected void	LeicaSCNReader.initStandardMetadata()
protected void	LEOReader.initStandardMetadata()
protected void	MetamorphReader.initStandardMetadata()
protected void	NDPIReader.initStandardMetadata()
protected void	NikonElementsTiffReader.initStandardMetadata()
protected void	NikonReader.initStandardMetadata()
protected void	NikonTiffReader.initStandardMetadata()
protected void	PyramidTiffReader.initStandardMetadata()
protected void	SEQReader.initStandardMetadata()
protected void	SimplePCITiffReader.initStandardMetadata()
protected void	SISReader.initStandardMetadata()
protected void	SlidebookTiffReader.initStandardMetadata()
protected void	SVSReader.initStandardMetadata()
protected void	TiffReader.initStandardMetadata()
protected void	TrestleReader.initStandardMetadata()
protected void	VectraReader.initStandardMetadata()
protected void	VentanaReader.initStandardMetadata()
protected void	BaseZeissReader.initVars(String id)
protected void	ZeissTIFFReader.initVars(String id)
protected void	ZeissZVIReader.initVars(String id)
boolean	AFIReader.isSingleFile(String id)
boolean	AnalyzeReader.isSingleFile(String id)
boolean	APLReader.isSingleFile(String id)
boolean	BDReader.isSingleFile(String id)
boolean	BioRadReader.isSingleFile(String id)
boolean	BrukerReader.isSingleFile(String id)
boolean	CellSensReader.isSingleFile(String id)
boolean	CellVoyagerReader.isSingleFile(String id)
boolean	ColumbusReader.isSingleFile(String id)
boolean	CV7000Reader.isSingleFile(String id)
boolean	DCIMGReader.isSingleFile(String id)
boolean	DeltavisionReader.isSingleFile(String id)
boolean	FakeReader.isSingleFile(String id)
boolean	FilePatternReader.isSingleFile(String id)
boolean	FlexReader.isSingleFile(String id)
boolean	FujiReader.isSingleFile(String id)
boolean	FV1000Reader.isSingleFile(String id)
boolean	HitachiReader.isSingleFile(String id)
boolean	ICSReader.isSingleFile(String id)
boolean	ImagicReader.isSingleFile(String id)
boolean	InCellReader.isSingleFile(String id)
boolean	JDCEReader.isSingleFile(String id)
boolean	L2DReader.isSingleFile(String id)
boolean	LeicaReader.isSingleFile(String id)
boolean	MetamorphReader.isSingleFile(String id)
boolean	MIASReader.isSingleFile(String id)
boolean	MicroCTReader.isSingleFile(String id)
boolean	MicromanagerReader.isSingleFile(String id)
boolean	NDPISReader.isSingleFile(String id)
boolean	NiftiReader.isSingleFile(String id)
boolean	NRRDReader.isSingleFile(String id)
boolean	OIRReader.isSingleFile(String id)
boolean	OlympusTileReader.isSingleFile(String id)
boolean	OMETiffReader.isSingleFile(String id)
boolean	OperettaReader.isSingleFile(String id)
boolean	PerkinElmerReader.isSingleFile(String id)
boolean	PrairieReader.isSingleFile(String id)
boolean	ScanrReader.isSingleFile(String id)
boolean	SlideBook7Reader.isSingleFile(String id)
boolean	SPCReader.isSingleFile(String id)
boolean	TCSReader.isSingleFile(String id)
boolean	TecanReader.isSingleFile(String id)
boolean	TillVisionReader.isSingleFile(String id)
boolean	VisitechReader.isSingleFile(String id)
boolean	XLEFReader.isSingleFile(String id)
boolean	ZeissLSMReader.isSingleFile(String id)
boolean	ZeissTIFFReader.isSingleFile(String id)
void	DynamicMetadataOptions.loadOptions(String optionsFile, ArrayList<String> availableOptionKeys)
private String	BDReader.locateExperimentFile(String id)
private void	DicomReader.makeFileList()	Build a list of files that belong with the current file.
private String	FV1000Reader.mapOIBFiles()
static void	FlexReader.mapServersFromConfigurationFile(String configFile)	Read a configuration file with lines of the form: <server alias>=<real server name> and call mapServer(String, String) accordingly.
private byte[]	FlowSightReader.openBitmaskBytes(IFD ifd, int imageWidth, int imageHeight)	Decode the whole IFD plane using bitmask compression
protected BufferedImage	TiffJAIReader.openBufferedImage(int no)	Obtains a BufferedImage from the given data source using JAI.
byte[]	AFIReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	AIMReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	AliconaReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	AmiraReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	AnalyzeReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	APLReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	APNGReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	ARFReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	AVIReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	BDReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	BDVReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	BIFormatReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	BioRadGelReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	BioRadReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	BioRadSCNReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	BMPReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	BrukerReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	BurleighReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	CanonRawReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	CellH5Reader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	CellomicsReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	CellSensReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	CellVoyagerReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	CellWorxReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	ColumbusReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	CV7000Reader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	DCIMGReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	DeltavisionReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	DicomReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	DNGReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	Ecat7Reader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	EPSReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	FakeReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	FEIReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	FitsReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	FlexReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	FlowSightReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	FluoviewReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	FujiReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	FV1000Reader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	GatanDM2Reader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	GatanReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	GelReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	GIFReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	HamamatsuVMSReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	HISReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	HitachiReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	HRDGDFReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	I2IReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	ICSReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	IM3Reader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	ImaconReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	ImagicReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	ImarisHDFReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	ImarisReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	IMODReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	ImprovisionTiffReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	ImspectorReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	InCell3000Reader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	InCellReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	INRReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	InveonReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	IonpathMIBITiffReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	IPLabReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	IPWReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	IvisionReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	JDCEReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	JEOLReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	JPEG2000Reader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	JPKReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	JPXReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	KhorosReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	KLBReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	KodakReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	L2DReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	LeicaReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	LeicaSCNReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	LiFlimReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	LIFReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	LIMReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	LOFReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	MetamorphReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	MetamorphTiffReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	MIASReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	MicroCTReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	MicromanagerReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	MINCReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	MinimalTiffReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	MolecularImagingReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	MRCReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	MRWReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	NAFReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	ND2Reader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	NDPIReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	NDPISReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	NiftiReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	NikonReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	NRRDReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	OBFReader.openBytes(int no, byte[] buffer, int x, int y, int w, int h)
byte[]	OIRReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	OlympusTileReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	OMETiffReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	OMEXMLReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	OpenlabRawReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	OpenlabReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	OperettaReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	OxfordInstrumentsReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	PCIReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	PCORAWReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	PCXReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	PDSReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	PerkinElmerReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	PGMReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	PhotoshopTiffReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	PictReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	PovrayReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	PQBinReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	PrairieReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	PSDReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	PyramidTiffReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	QTReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	QuesantReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	RHKReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	SBIGReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	ScanrReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	SDTReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	SeikoReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	SEQReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	SIFReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	SimplePCITiffReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	SlideBook7Reader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	SlidebookReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	SlidebookTiffReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	SMCameraReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	SPCReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	SPEReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	SpiderReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	SVSReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	TargaReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	TCSReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	TecanReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	TextReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	TiffDelegateReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	TileJPEGReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	TillVisionReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	TissueFAXSReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	TopometrixReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	TrestleReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	UBMReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	UnisokuReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	VarianFDFReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	VectraReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	VeecoReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	VentanaReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	VGSAMReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	VisitechReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	VolocityClippingReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	VolocityReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	WATOPReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	XLEFReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	XLEFReader.openBytes(int no, int x, int y, int w, int h)
byte[]	ZeissCZIReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	ZeissLMSReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	ZeissLSMReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	ZeissTIFFReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	ZeissXRMReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	ZeissZVIReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	ZipReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
private byte[]	XLEFReader.openBytesJpeg(int no, byte[] buf, int x, int y, int w, int h)	Gets bytes of jpeg images.
byte[]	DicomReader.openCompressedBytes(int no, byte[] buf, int x, int y)
byte[]	DicomReader.openCompressedBytes(int no, int x, int y)
byte[]	NDPIReader.openCompressedBytes(int no, byte[] buf, int x, int y)
byte[]	NDPIReader.openCompressedBytes(int no, int x, int y)
byte[]	SVSReader.openCompressedBytes(int no, byte[] buf, int x, int y)
byte[]	SVSReader.openCompressedBytes(int no, int x, int y)
private byte[]	FlowSightReader.openGreyscaleBytes(IFD ifd, int imageWidth, int imageHeight)	Decode the whole IFD plane using greyscale compression
Object	ImageIOReader.openPlane(int no, int x, int y, int w, int h)
Object	MNGReader.openPlane(int no, int x, int y, int w, int h)
Object	TextReader.openPlane(int no, int x, int y, int w, int h)
Object	TiffJAIReader.openPlane(int no, int x, int y, int w, int h)
byte[]	AFIReader.openThumbBytes(int no)
byte[]	CellSensReader.openThumbBytes(int no)
byte[]	LeicaSCNReader.openThumbBytes(int no)
byte[]	MinimalTiffReader.openThumbBytes(int no)
byte[]	NDPIReader.openThumbBytes(int no)
byte[]	SVSReader.openThumbBytes(int no)
byte[]	VectraReader.openThumbBytes(int no)
byte[]	VentanaReader.openThumbBytes(int no)
private void	QTReader.parse(int depth, long offset, long length)	Parse all of the atoms in the file.
private void	TiffReader.parseCommentImageJ(String comment)
private void	DCIMGReader.parseDCAMVersion0Footer(loci.common.RandomAccessInputStream stream)
private void	LeicaReader.parseDimensionTag(int seriesIndex)
private boolean	CellSensReader.parseETSFile(loci.common.RandomAccessInputStream etsFile, String file, int s, boolean hasOrphanEtsFiles)
private void	VarianFDFReader.parseFDF(String file)
private void	MetamorphTiffReader.parseFile(String tiff, MetamorphHandler handler)
private int	TextReader.parseFileHeader(List<String> lines)	Parses the file looking for the file header.
private void	FlexReader.parseFlexFile(int currentWell, int wellRow, int wellCol, int field, boolean firstFile, MetadataStore store)	Parses XML metadata from the Flex file corresponding to the given well.
private void	OIRReader.parseFrameProperties(Element root)
protected void	CellWorxReader.parseHTD()
private void	OIRReader.parseImageProperties(Element root)
private void	ColumbusReader.parseImageXML(String filename, int externalTime)
private void	LeicaReader.parseInstrumentData(MetadataStore store, int blockNum)
private boolean	DeltavisionReader.parseLogFile(MetadataStore store)	Extract metadata from associated log file, if it exists.
private void	OIRReader.parseLUT(Element root, String uid)
(package private) void	BaseZeissReader.parseMainTags(int image, MetadataStore store, ArrayList<BaseZeissReader.Tag> tags)
void	MIASReader.parseMasks(MetadataStore overlayStore)	Parse masks into a separate overlay-specific MetadataStore.
private int	MIASReader.parseMasks(MetadataStore store, int series, int roi, String overlayTiff)	Parse Mask ROIs from the given TIFF and place them in the given MetadataStore.
private String[]	ZeissLSMReader.parseMDB(String mdbFile)	Parse a .mdb file and return a list of referenced .lsm files.
private boolean	BioRadReader.parseNotes(MetadataStore store)
private void	ZeissCZIReader.parseObjectives(NodeList objectives)
private void	MicromanagerReader.parsePosition(int posIndex)
private void	MicromanagerReader.parsePosition(String jsonData, int posIndex)
private void	PrairieReader.parsePrairieMetadata()	This step parses the Prairie metadata files into the Prairie-specific metadata structure, PrairieReader.meta.
private int	FV1000Reader.parseROIFile(String filename, MetadataStore store, int nextROI, int plane)
private void	TrestleReader.parseROIs(MetadataStore store)
private void	BDVReader.parseStructure()
private void	CellH5Reader.parseStructure()
private void	GatanReader.parseTags(int numTags, String parent, String indent)	Parses Gatan DM3 tags.
private void	IPLabReader.parseTags(MetadataStore store)
private void	ZeissZVIReader.parseTags(int image, String file, MetadataStore store)	Parse all of the tags in a stream.
private void	OIRReader.parseXML(loci.common.RandomAccessInputStream s, String xml, long startFilePointer)
private void	FlexReader.populateCoreMetadata(int wellRow, int wellCol, int field, List<String> imageNames)	Populate core metadata using the given list of image names.
private void	PrairieReader.populateCoreMetadata()	This step populates the CoreMetadata by extracting relevant values from the parsed PrairieReader.meta structure.
private void	SPEReader.populateGlobalMetaData()	This function is used to populate values not contained in Core Meta Data to the Global Meta Data
boolean	MIASReader.populateMaskPixels(int imageIndex, int roiIndex, int shapeIndex, MetadataStore store)	Populate the MaskPixels.BinData attribute for the Mask identified by the given Image index, ROI index, and Shape index.
protected void	CellWorxReader.populateMetadata()
private void	MicromanagerReader.populateMetadata()
private void	FlexReader.populateMetadataStore(MetadataStore store)
private void	FV1000Reader.populateMetadataStore(MetadataStore store, String path)
void	MicromanagerReader.populateMetadataStore(String[] jsonData)
private void	ND2Reader.populateMetadataStore(ND2Handler handler)
private void	TillVisionReader.populateMetadataStore()
protected void	ZeissLSMReader.populateMetadataStore(ZeissLSMReader.SubBlock block, MetadataStore store, int series)
protected void	DeltavisionReader.populateObjective(MetadataStore store, int lensID)	Populate an Objective based upon the lens ID.
protected void	RCPNLReader.populateObjective(MetadataStore store, int lensID)
private void	PrairieReader.populateOMEMetadata()	This step populates the OME MetadataStore by extracting relevant values from the parsed PrairieReader.meta structure.
private void	NiftiReader.populatePixelType(int dataType)
private void	SPEReader.populateRoiMetaData(MetadataStore store)	Reads and populates ROI Meta Data values.
byte[]	AmiraReader.ASCII.read(int no, byte[] buf)
(package private) void	AmiraReader.HxRLE.read(byte[] buf, int len)
byte[]	AmiraReader.HxRLE.read(int no, byte[] buf)
byte[]	AmiraReader.HxZip.read(int no, byte[] buf)
byte[]	AmiraReader.PlaneReader.read(int no, byte[] buf)
private void	ZeissCZIReader.readAttachments()
private void	AVIReader.readChunk()
byte[]	SlideBook7Reader.CCompressionBase.ReadData(loci.common.RandomAccessInputStream inStream, int inBlock)
private void	OBFReader.readFlimFrame(OBFReader.Stack stack, int no, byte[] buffer, int x, int y, int w, int h)
private void	OBFReader.readFromStack(OBFReader.Stack stack, byte[] buffer, int bufferOffset, int bytes)
private void	OBFReader.readFromStackRaw(OBFReader.Stack stack, byte[] buffer, int bufferOffset, int bytes)
private void	KLBReader.readHeader(CoreMetadata coreMeta)
private void	GIFReader.readImageBlock()
private void	CellVoyagerReader.readInfo(Document msDocument, Document omeDocument)
private int[]	GIFReader.readLut(int size)	Read a color lookup table of the specified size.
private void	OlympusTileReader.readMetadata(String xml)
byte[]	ZeissCZIReader.SubBlock.readPixelData()
byte[]	ZeissCZIReader.SubBlock.readPixelData(loci.common.RandomAccessInputStream s)
byte[]	ZeissCZIReader.SubBlock.readPixelData(loci.common.RandomAccessInputStream s, loci.common.Region tile, byte[] buf)
private void	OIRReader.readPixelsFile(String file, loci.common.RandomAccessInputStream s)
private void	OBFReader.readStackFrame(OBFReader.Stack stack, long sampleOffset, byte[] buffer, int bufferOffset, int w, int h)
private void	FluoviewReader.readStamps()
private void	OpenlabReader.readVariable()
private void	DeltavisionReader.readWavelength(int channel, MetadataStore store)
private void	OIRReader.readXMLBlock(String file, loci.common.RandomAccessInputStream s)
private void	KLBReader.reCalculateBlockOffsets(int no)
private long	OBFReader.remainingBytesInChunk(OBFReader.Stack stack)
private void	NDPIReader.resetStream(IFD ifd)
private void	DCIMGReader.scanDirectory(loci.common.Location dir)
private void	DicomReader.scanDirectory(loci.common.Location dir, boolean checkSeries)	Scan the given directory for files that belong to this dataset.
private static int[]	FV1000Reader.scanFormat(String pattern, String string)
private void	OBFReader.seekToFrameStart(OBFReader.Stack stack, long sampleOffset)
void	MIASReader.setAutomaticallyParseMasks(boolean parse)	Toggle whether or not Mask pixel data should be parsed in setId.
void	JPEGReader.setId(String id)
void	TiffDelegateReader.setId(String id)
void	LOFReader.setIdWithMetadata(String id, XlifDocument xml)	Inits the LOFReader using passed xml (from XLIF) for metadata initiation, instead of reading the LOF's included xml
private void	OMETiffReader.setupService()
private void	OBFReader.skipBytes(OBFReader.Stack stack, long byteCount)
private void	XLEFReader.sortMultipleImagesReaders()	Sorts frames of all MultipleImagesReaders as per core dimension sizes and order
private IFD	VentanaReader.splitIFD(IFD ifd, int no)	Take the real IFD on disk and reshape it into something that represents only the given plane.
protected void	BaseZeissReader.storeROIs(MetadataStore store)	Store basic dimensions in model
private void	OBFReader.switchChunk(OBFReader.Stack stack, int chunkIndex)
private void	LIFReader.translateAttachmentNodes(Element imageNode, int image)
private void	LIFReader.translateDetectors(Element imageNode, int image)
private void	ZeissCZIReader.translateDisplaySettings(Element root)
private void	ZeissCZIReader.translateExperiment(Element root)
private void	LIFReader.translateFilterSettings(Element imageNode, int image)
private void	ZeissCZIReader.translateHardwareSettings(Element root)
private void	LIFReader.translateImageNodes(Element imageNode, int i)
private void	ZeissCZIReader.translateInformation(Element root)
private void	LIFReader.translateLaserLines(Element imageNode, int image)
private void	LIFReader.translateMetadata(Element root)
private void	ZeissCZIReader.translateMetadata(String xml)
private void	LIFReader.translateROIs(Element imageNode, int image)
private void	LIFReader.translateScannerSettings(Element imageNode, int image)
private void	LIFReader.translateSingleROIs(Element imageNode, int image)
private void	LIFReader.translateTimestamps(Element imageNode, int image)
private byte[]	AVIReader.uncompress(int no, byte[] buf)
private byte[]	QTReader.uncompress(byte[] pixs, String code)	Uncompresses an image plane according to the the codec identifier.
private void	APNGReader.unfilter(byte[] filters, byte[] image, int width, int height)	See http://www.w3.org/TR/PNG/#9Filters.
private boolean	NDPIReader.useTiffParser(IFD ifd)

Uses of FormatException in loci.formats.in.LeicaMicrosystemsMetadata

Methods in loci.formats.in.LeicaMicrosystemsMetadata that throw FormatException

Modifier and Type	Method	Description
private void	LMSMetadataExtractor.addUserCommentMeta(Element imageNode, int image)	Extracts user comments and adds them to the reader's CoreMetadata
void	MetadataStoreInitializer.initMetadataStore()	Translates metadata information from the reader's MetadataTempBuffer and adds it to its MetadataStore
private void	MultipleImagesReader.initReaders(List<String> ids)	Creates an internal reader for each image file
void	MetadataStoreInitializer.initStandDetails(int series)	Adds microscope and objective details from the reader's MetadataTempBuffer to its MetadataStore
byte[]	MultipleImagesReader.openBytes(int no, byte[] buf, int x, int y, int w, int h)
private void	LMSMetadataExtractor.setPixelType(int coreIndex)	Sets CoreMetadata.pixelType depending on extracted x bytesInc
void	MultipleImagesReader.swapDimensions()	Rearranges frame order from ZSTC order (used in XLIFs) to desired CoreMetadata.dimensionOrder
void	LMSMetadataExtractor.translateAttachmentNodes(Element imageNode, int image)	Extracts information from dimension descriptions and writes it to reader's MetadataTempBuffer
void	LMSMetadataExtractor.translateChannelDescriptions(Element imageNode, int coreIndex)	Extracts i.a.
void	LMSMetadataExtractor.translateDetectors(Element imageNode, int image)	Extracts detector information and writes it to reader's MetadataTempBuffer
private void	LMSMetadataExtractor.translateDimensionDescriptions(Element imageNode, int coreIndex)	Extracts information from dimension descriptions and writes it to reader's CoreMetadata and MetadataTempBuffer
void	LMSMetadataExtractor.translateFilterSettings(Element imageNode, int image)	Extracts filter information and writes it to reader's MetadataTempBuffer
void	LMSMetadataExtractor.translateImage(Element image, int i)	Extracts information from element node and writes it to reader's CoreMetadata and MetadataTempBuffer
void	LMSMetadataExtractor.translateLaserLines(Element imageNode, int image)	Extracts laser information and writes it to reader's MetadataTempBuffer
void	LMSFileReader.translateMetadata(List<LMSImageXmlDocument> docs)	Extracts metadata from a list of Leica image XML Documents and writes them to the reader's CoreMetadata, MetadataTempBuffer and MetadataStore
void	LMSFileReader.translateMetadata(LMSImageXmlDocument doc)
void	LMSMetadataExtractor.translateMetadata(List<LMSImageXmlDocument> docs)	Extracts all information from Leica image xml Documents and writes it to reader's CoreMetadata and MetadataTempBuffer
void	LMSMetadataExtractor.translateROIs(Element imageNode, int image)	Extracts ROIs and writes them to reader's MetadataTempBuffer
void	LMSMetadataExtractor.translateScannerSettings(Element imageNode, int image)	Extracts scanner information and writes it to reader's CoreMetadata and MetadataTempBuffer
void	LMSMetadataExtractor.translateSingleROIs(Element imageNode, int image)	Extracts single ROIs and writes them to reader's MetadataTempBuffer
void	LMSMetadataExtractor.translateTimestamps(Element imageNode, int image)	Extracts timestamps and writes them to reader's MetadataTempBuffer

Constructors in loci.formats.in.LeicaMicrosystemsMetadata that throw FormatException

Modifier	Constructor	Description
	MultipleImagesReader(XlifDocument xlif, int imageIndex)

Uses of FormatException in loci.formats.out

Methods in loci.formats.out that throw FormatException

Modifier and Type	Method	Description
private void	DicomWriter.checkPixelCount(boolean warn)
private byte[]	OMEXMLWriter.compress(byte[] b)	Compress the given byte array using the current codec.
byte[]	JPEG2000Writer.compressBuffer(int no, byte[] buf, int x, int y, int w, int h)	Compresses the buffer.
private void	TiffWriter.formatCompression(IFD ifd)	Sets the compression code for the specified IFD.
private String	OMETiffWriter.getBinaryOnlyOMEXML(String file, String companion, String companionUUID)
private String	OMETiffWriter.getOMEXML(String file)
int	TiffWriter.getTileSizeX()
int	TiffWriter.getTileSizeY()
protected IFD	PyramidOMETiffWriter.makeIFD()
protected IFD	TiffWriter.makeIFD()
protected int	TiffWriter.prepareToWriteImage(int no, byte[] buf, IFD ifd, int x, int y, int w, int h)	Performs the preparation for work prior to the usage of the TIFF saver.
void	APNGWriter.saveBytes(int no, byte[] buf, int x, int y, int w, int h)
void	AVIWriter.saveBytes(int no, byte[] buf, int x, int y, int w, int h)
void	CellH5Writer.saveBytes(int no, byte[] buf)	Saves the given image to the specified (possibly already open) file.
void	CellH5Writer.saveBytes(int no, byte[] buf, int x, int y, int w, int h)
void	DicomWriter.saveBytes(int no, byte[] buf, int x, int y, int w, int h)
void	EPSWriter.saveBytes(int no, byte[] buf, int x, int y, int w, int h)
void	ICSWriter.saveBytes(int no, byte[] buf, int x, int y, int w, int h)
void	ImageIOWriter.saveBytes(int no, byte[] buf, int x, int y, int w, int h)
void	JavaWriter.saveBytes(int no, byte[] buf, int x, int y, int w, int h)
void	JPEG2000Writer.saveBytes(int no, byte[] buf, int x, int y, int w, int h)
void	OMETiffWriter.saveBytes(int no, byte[] buf, int x, int y, int w, int h)
void	OMETiffWriter.saveBytes(int no, byte[] buf, IFD ifd, int x, int y, int w, int h)
void	OMEXMLWriter.saveBytes(int no, byte[] buf, int x, int y, int w, int h)
void	PyramidOMETiffWriter.saveBytes(int no, byte[] buf, IFD ifd, int x, int y, int w, int h)
void	QTWriter.saveBytes(int no, byte[] buf, int x, int y, int w, int h)
void	TiffWriter.saveBytes(int no, byte[] buf, int x, int y, int w, int h)
void	TiffWriter.saveBytes(int no, byte[] buf, IFD ifd)	Saves the given image to the specified (possibly already open) file.
void	TiffWriter.saveBytes(int no, byte[] buf, IFD ifd, int x, int y, int w, int h)	Saves the given image to the specified series in the current file.
void	V3DrawWriter.saveBytes(int no, byte[] buf, int x, int y, int w, int h)
void	DicomWriter.saveCompressedBytes(int no, byte[] buf, int x, int y, int w, int h)
void	OMETiffWriter.saveCompressedBytes(int no, byte[] buf, int x, int y, int w, int h)
void	TiffWriter.saveCompressedBytes(int no, byte[] buf, int x, int y, int w, int h)
void	ImageIOWriter.savePlane(int no, Object plane, int x, int y, int w, int h)
void	APNGWriter.setId(String id)
void	AVIWriter.setId(String id)
void	CellH5Writer.setId(String id)
void	DicomWriter.setId(String id)
void	ICSWriter.setId(String id)
void	JavaWriter.setId(String id)
void	OMETiffWriter.setId(String id)
void	OMEXMLWriter.setId(String id)
void	QTWriter.setId(String id)
void	TiffWriter.setId(String id)
void	V3DrawWriter.setId(String id)
void	DicomWriter.setSeries(int s)
int	DicomWriter.setTileSizeX(int tileSize)
int	TiffWriter.setTileSizeX(int tileSize)
int	DicomWriter.setTileSizeY(int tileSize)
int	TiffWriter.setTileSizeY(int tileSize)
private void	APNGWriter.writePixels(String chunk, byte[] stream, int x, int y, int width, int height)

Uses of FormatException in loci.formats.services

Methods in loci.formats.services that throw FormatException

Modifier and Type	Method	Description
byte[]	JPEGXRService.decompress(byte[] compressed)	Decompress the given JPEG-XR compressed byte array and return as a byte array.
byte[]	JPEGXRServiceImpl.decompress(byte[] compressed)
private short[]	JPEGXRServiceImpl.getPixelFormat(byte[] stream)

Uses of FormatException in loci.formats.tiff

Methods in loci.formats.tiff that throw FormatException

Modifier and Type	Method	Description
byte[]	TiffCompression.compress(byte[] input, CodecOptions options)	Encodes a strip of data.
byte[]	TiffCompression.decompress(byte[] input, CodecOptions options)	Decodes a strip of data.
static void	TiffCompression.difference(byte[] input, IFD ifd)	Performs in-place differencing according to the given predictor value.
int[]	IFD.getBitsPerSample()	Retrieves the image's bits per sample (TIFF tag BitsPerSample) from a given TIFF IFD.
long	IFD.getByteCount(boolean bigTiff)	Get the maximum number of bytes needed to represent this 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.
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.
OnDemandLongArray	IFD.getOnDemandStripOffsets()
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.
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.
static IFDType	IFDType.getType(Object value, boolean bigTiff)	Get the type corresponding to the given value.
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.
boolean	IFD.isTiled()
void	TiffSaver.overwriteComment(loci.common.RandomAccessInputStream in, Object value)	Convenience method for overwriting a file's first ImageDescription.
void	TiffSaver.overwriteIFDOffset(loci.common.RandomAccessInputStream raf, long offset, long nextPointer)
void	TiffSaver.overwriteIFDValue(loci.common.RandomAccessInputStream raf, int ifd, int tag, Object value)	Surgically overwrites an existing IFD value with the given one.
void	TiffSaver.overwriteIFDValue(loci.common.RandomAccessInputStream raf, long ifdOffset, int tag, Object value)	Surgically overwrites an existing IFD value with the given one.
void	TiffSaver.overwriteIFDValue(loci.common.RandomAccessInputStream raf, long ifdOffset, int tag, Object value, boolean skipHeaderCheck)	Surgically overwrites an existing IFD value with the given one.
void	TiffSaver.overwriteLastIFDOffset(loci.common.RandomAccessInputStream raf)
static void	TiffCompression.undifference(byte[] input, IFD ifd)	Undoes in-place differencing according to the given predictor value.
static void	TiffParser.unpackBytes(byte[] samples, int startIndex, byte[] bytes, IFD ifd)	Extracts pixel information from the given byte array according to the bits per sample, photometric interpretation and color map IFD directory entry values, and the specified byte ordering.
void	TiffSaver.writeIFD(IFD ifd, long nextOffset)	Write the given IFD to the open stream.
void	TiffSaver.writeIFD(IFD ifd, long nextOffset, boolean calculateOffset)	Write the given IFD to the open stream.
private void	TiffSaver.writeIFDStrips(IFD ifd, int no, byte[][] strips, int nChannels, boolean last, int x, int y, long defaultByteCount)
void	TiffSaver.writeIFDValue(loci.common.RandomAccessOutputStream 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, int no, 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, int no, int pixelType, int x, int y, int w, int h, boolean last, Integer nChannels, boolean copyDirectly)
void	TiffSaver.writeImageIFD(IFD ifd, int no, byte[][] strips, int nChannels, boolean last, int x, int y)	Performs the actual work of dealing with IFD data and writing it to the TIFF for a given image or sub-image.

Uses of FormatException in loci.formats.tools

Methods in loci.formats.tools that throw FormatException

Modifier and Type	Method	Description
private OMETiffWriter	MakeTestOmeTiff.createWriter(String name, CoreMetadata info, String id)
static String	AmiraParameters.entryToString(Object object, String indent)
protected void	AmiraParameters.extractCoreMetaData()
static void	CacheConsole.main(String[] args)	Interactive interpreter for testing Bio-Formats caching implementation.
static void	MakeTestOmeTiff.main(String[] args)
int	MakeTestOmeTiff.makeOmeTiff(String... args)
void	MakeTestOmeTiff.makeOmeTiff(String name, CoreMetadata info)
void	MakeTestOmeTiff.makeOmeTiffExtensions(String... args)
void	MakeTestOmeTiff.makeSamples()
protected Double[]	AmiraParameters.readDoubleArray(int count)
protected void	AmiraParameters.readFile(String path)
protected void	AmiraParameters.readFile(loci.common.RandomAccessInputStream inputStream)
protected Integer[]	AmiraParameters.readIntArray()
protected Integer[]	AmiraParameters.readIntArray(int count)
protected Map	AmiraParameters.readMap()
protected Number	AmiraParameters.readNumber()
protected Number[]	AmiraParameters.readNumberArray()
protected String	AmiraParameters.readQuotedString()
protected void	AmiraParameters.readTopLevel()
protected void	AmiraParameters.syntaxError(String message)
static String	AmiraParameters.toString(Map map, String indent)
private void	MakeTestOmeTiff.writeData(String name, CoreMetadata info, String id, OMETiffWriter out)

Constructors in loci.formats.tools that throw FormatException

Modifier	Constructor	Description
	AmiraParameters(String path)
	AmiraParameters(loci.common.RandomAccessInputStream inputStream)

Uses of FormatException in loci.plugins

Methods in loci.plugins that throw FormatException

Modifier and Type	Method	Description
static ij.ImagePlus[]	BF.openImagePlus(String path)
static ij.ImagePlus[]	BF.openImagePlus(ImporterOptions options)
static ij.ImagePlus[]	BF.openThumbImagePlus(String path)
static ij.ImagePlus[]	BF.openThumbImagePlus(ImporterOptions options)

Uses of FormatException in loci.plugins.in

Methods in loci.plugins.in that throw FormatException

Modifier and Type	Method	Description
private void	ImportProcess.createBaseReader()	Initializes an IFormatReader according to the current configuration.
private ij.ImageStack	ImagePlusReader.createVirtualStack(ImportProcess process, int s, List<ij.process.LUT> luts)
XMLWindow	DisplayHandler.displayOMEXML()	Displays OME-XML metadata in a tree in its own window.
boolean	ImportProcess.execute()	Performs the import preparation process, notifying status listeners at each step.
private void	ImportProcess.initializeFile()	Performed following ImportStep.FILE notification.
private void	ImportProcess.initializeReader()	Performed following ImportStep.READER notification.
private void	ImportProcess.initializeStack()	Performed following ImportStep.STACK notification.
ij.ImagePlus[]	ImagePlusReader.openImagePlus()	Opens one or more ImagePlus objects corresponding to the reader's associated options.
ij.ImagePlus[]	ImagePlusReader.openThumbImagePlus()
private ij.ImagePlus	ImagePlusReader.readImage(int s, boolean thumbnail)
private List<ij.ImagePlus>	ImagePlusReader.readImages()
private List<ij.ImagePlus>	ImagePlusReader.readImages(boolean thumbnail)
ij.ImagePlus[]	Importer.readPixels(ImagePlusReader reader, ImporterOptions options, DisplayHandler displayHandler)
private ij.ImageStack	ImagePlusReader.readPlanes(ImportProcess process, int s, List<ij.process.LUT> luts, boolean thumbnail)
private List<ij.ImagePlus>	ImagePlusReader.readThumbImages()
void	Importer.showDialogs(ImportProcess process)

Uses of FormatException in loci.plugins.macro

Methods in loci.plugins.macro that throw FormatException

Modifier and Type	Method	Description
void	LociFunctions.fileGroupOption(String id, String[] fileGroupOption)
void	LociFunctions.getFormat(String id, String[] format)
void	LociFunctions.openImage(String title, Double no)
void	LociFunctions.openSubImage(String title, Double no, Double x, Double y, Double w, Double h)
void	LociFunctions.openThumbImage(String title, Double no)
void	LociFunctions.setId(String id)

Uses of FormatException in loci.plugins.util

Methods in loci.plugins.util that throw FormatException

Modifier and Type	Method	Description
private ij.process.LUT	ImageProcessorReader.createColorModel()
protected static int	BFVirtualStack.getHeight(IFormatReader r, String path, int series)
protected static int	BFVirtualStack.getWidth(IFormatReader r, String path, int series)
Object	ImageProcessorReader.openPlane(int no, int x, int y, int w, int h)
ij.process.ImageProcessor[]	ImageProcessorReader.openProcessors(int no)	Creates an ImageJ image processor object for the image plane at the given position.
ij.process.ImageProcessor[]	ImageProcessorReader.openProcessors(int no, int x, int y, int w, int h)	Returns an array of ImageProcessors that represent the given slice.
ij.process.ImageProcessor[]	ImageProcessorReader.openThumbProcessors(int no)

Constructors in loci.plugins.util that throw FormatException

Modifier	Constructor	Description
	BFVirtualStack(String path, IFormatReader r, boolean colorize, boolean merge, boolean record)