Uses of Interface
loci.formats.IFormatReader

Packages that use IFormatReader

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.gui	Package containing Bio-Formats graphical user interface code.
loci.formats.in	Package containing Bio-Formats file format readers.
loci.formats.tools	Package containing utility methods corresponding to the Bio-Formats command line tools.
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 IFormatReader in loci.formats

Classes in loci.formats that implement IFormatReader

Modifier and Type	Class and Description
class	ChannelFiller For indexed color data representing true color, factors out the indices, replacing them with the color table values directly.
class	ChannelMerger Logic to automatically merge channels in a file.
class	ChannelSeparator Logic to automatically separate the channels in a file.
class	DelegateReader DelegateReader is a file format reader that selects which reader to use for a format if there are two readers which handle the same format.
class	DimensionSwapper Handles swapping the dimension order of an image series.
class	FileStitcher Logic to stitch together files with similar names.
class	FormatReader Abstract superclass of all biological file format readers.
class	ImageReader ImageReader is the master file format reader for all supported formats.
class	Memoizer ReaderWrapper implementation which caches the state of the delegate (including and other ReaderWrapper instances) after Memoizer.setId(String) has been called.
class	MinMaxCalculator Logic to compute minimum and maximum values for each channel.
class	ReaderWrapper Abstract superclass of reader logic that wraps other readers.
class	SubResolutionFormatReader Abstract superclass of all biological file format readers that can handle image pyramids.
class	TileStitcher
class	WrappedReader Helper class for readers which wrap other readers.

Fields in loci.formats declared as IFormatReader

Modifier and Type	Field and Description
protected IFormatReader	DelegateReader.legacyReader Legacy reader.
protected IFormatReader	DelegateReader.nativeReader Native reader.
protected IFormatReader	ReaderWrapper.reader FormatReader used to read the file.
private IFormatReader[]	ImageReader.readers List of supported file format readers.

Fields in loci.formats with type parameters of type IFormatReader

Modifier and Type	Field and Description
private ClassList<IFormatReader>	FileStitcher.classList
private static ClassList<IFormatReader>	ImageReader.defaultClasses Default list of reader classes, for use with noargs constructor.

Methods in loci.formats that return IFormatReader

Modifier and Type	Method and Description
IFormatReader	FileStitcher.getReader() Gets the wrapped reader prototype.
IFormatReader	ReaderWrapper.getReader() Gets the wrapped reader.
IFormatReader	ImageReader.getReader() Gets the reader used to open the current file.
IFormatReader	ImageReader.getReader(java.lang.Class<? extends IFormatReader> c) Gets the file format reader instance matching the given class.
static IFormatReader	FormatTools.getReader(IFormatReader r, java.lang.Class<? extends IFormatReader> c) Recursively look for the first underlying reader that is an instance of the given class.
IFormatReader	FileStitcher.getReader(int no) Gets the reader appropriate for use with the given image plane.
IFormatReader	ImageReader.getReader(java.lang.String id) Gets the reader used to open the given file.
IFormatReader[]	ImageReader.getReaders() Gets all constituent file format readers.
IFormatReader[]	FileStitcher.getUnderlyingReaders()
IFormatReader[]	WrappedReader.getUnderlyingReaders()
IFormatReader[]	ReaderWrapper.getUnderlyingReaders()
IFormatReader[]	ImageReader.getUnderlyingReaders()
IFormatReader[]	IFormatReader.getUnderlyingReaders() Retrieves all underlying readers.
IFormatReader[]	FormatReader.getUnderlyingReaders()
protected IFormatReader	Memoizer.handleMetadataStore(IFormatReader memo) Return the IFormatReader instance that is passed in or null if it has been invalidated, which will include the instance being closed.
IFormatReader	Memoizer.loadMemo() Load a memo file if possible, returning a null if not.
IFormatReader	Memoizer.Deser.loadReader()
IFormatReader	Memoizer.KryoDeser.loadReader()
IFormatReader	Memoizer.RandomAccessDeser.loadReader()
protected abstract IFormatReader	Memoizer.RandomAccessDeser.readerFromBytes(java.lang.Class<IFormatReader> c, byte[] rArr)
IFormatReader	ReaderWrapper.unwrap() Unwraps nested wrapped readers until the core reader (i.e., not a ReaderWrapper or ImageReader) is found.
IFormatReader	ReaderWrapper.unwrap(java.lang.Class<? extends IFormatReader> readerClass, java.lang.String id) Unwraps nested wrapped readers until the given reader class is found.
IFormatReader	ReaderWrapper.unwrap(java.lang.String id) Unwraps nested wrapped readers until the core reader (i.e., not a ReaderWrapper or ImageReader) is found.

Methods in loci.formats that return types with arguments of type IFormatReader

Modifier and Type	Method and Description
static ClassList<IFormatReader>	ImageReader.getDefaultReaderClasses()

Methods in loci.formats with parameters of type IFormatReader

Modifier and Type	Method and Description
protected abstract byte[]	Memoizer.RandomAccessDeser.bytesFromReader(IFormatReader reader)
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.
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.
CoreMetadata	SwappableMetadata.clone(IFormatReader r, int coreIndex)
CoreMetadata	CoreMetadata.clone(IFormatReader r, int coreIndex)
static void	FormatTools.convert(IFormatReader input, IFormatWriter output, java.lang.String outputFile) Convenience method for writing all of the images and metadata obtained from the specified IFormatReader into the specified IFormatWriter.
static boolean	FormatTools.equalReaders(IFormatReader a, IFormatReader b) Check if the two given readers are equal.
static java.lang.String	FormatTools.getFilename(int series, int image, IFormatReader r, java.lang.String pattern)
static java.lang.String	FormatTools.getFilename(int series, int image, IFormatReader r, java.lang.String pattern, boolean padded)
static java.lang.String[]	FormatTools.getFilenames(java.lang.String pattern, IFormatReader r)
static int	FormatTools.getImagesPerFile(java.lang.String pattern, IFormatReader r)
static int	FormatTools.getIndex(IFormatReader reader, int z, int c, int t) Gets the rasterized index corresponding to the given Z, C and T coordinates (real sizes).
static int	FormatTools.getIndex(IFormatReader reader, int z, int c, int t, int moduloZ, int moduloC, int moduloT) Gets the rasterized index corresponding to the given Z, C, T, ModuloZ, ModuloC and ModuloT coordinates (effective sizes).
static int	FormatTools.getPlaneSize(IFormatReader r) Returns the size in bytes of a single plane.
static int	FormatTools.getPlaneSize(IFormatReader r, int w, int h) Returns the size in bytes of a w * h tile.
static IFormatReader	FormatTools.getReader(IFormatReader r, java.lang.Class<? extends IFormatReader> c) Recursively look for the first underlying reader that is an instance of the given class.
static int	FormatTools.getReorderedIndex(IFormatReader reader, java.lang.String newOrder, int newIndex) Converts index from the given dimension order to the reader's native one.
static int[]	FormatTools.getZCTCoords(IFormatReader reader, int index) Gets the Z, C and T coordinates corresponding to the given rasterized index value (real sizes).
static int[]	FormatTools.getZCTModuloCoords(IFormatReader reader, int index) Gets the Z, C, T, ModuloZ, ModuloC and ModuloZ coordinates corresponding to the given rasterized index value (effective sizes).
protected IFormatReader	Memoizer.handleMetadataStore(IFormatReader memo) Return the IFormatReader instance that is passed in or null if it has been invalidated, which will include the instance being closed.
static boolean	FormatTools.isFloatingPoint(IFormatReader reader) Determines whether the given reader represents any floating point data.
private boolean	ImageReader.isThisType(IFormatReader reader, byte[] block)
private boolean	ImageReader.isThisType(IFormatReader reader, loci.common.RandomAccessInputStream rais)
private boolean	ImageReader.isThisType(IFormatReader reader, java.lang.String name, boolean allowOpen)
private void	ImageReader.logIsThisTypeError(IFormatReader reader, java.lang.Exception e)
static ChannelFiller	ChannelFiller.makeChannelFiller(IFormatReader r) Converts the given reader into a ChannelFiller, wrapping if needed.
static ChannelMerger	ChannelMerger.makeChannelMerger(IFormatReader r) Converts the given reader into a ChannelMerger, wrapping if needed.
static ChannelSeparator	ChannelSeparator.makeChannelSeparator(IFormatReader r) Converts the given reader into a ChannelSeparator, wrapping if needed.
static DimensionSwapper	DimensionSwapper.makeDimensionSwapper(IFormatReader r) Converts the given reader into a DimensionSwapper, wrapping if needed.
static MinMaxCalculator	MinMaxCalculator.makeMinMaxCalculator(IFormatReader r) Converts the given reader into a MinMaxCalculator, wrapping if needed.
static TileStitcher	TileStitcher.makeTileStitcher(IFormatReader r) Converts the given reader into a TileStitcher, wrapping if needed.
static byte[]	FormatTools.openThumbBytes(IFormatReader reader, int no) Default implementation for openThumbBytes(int).
static void	MetadataTools.populatePixels(MetadataStore store, IFormatReader r) Populates the Pixels element of the given metadata store, using core metadata from the given reader.
static void	MetadataTools.populatePixels(MetadataStore store, IFormatReader r, boolean doPlane) Populates the Pixels element of the given metadata store, using core metadata from the given reader.
static void	MetadataTools.populatePixels(MetadataStore store, IFormatReader r, boolean doPlane, boolean doImageName) Populates the Pixels element of the given metadata store, using core metadata from the given reader.
static void	MetadataTools.populatePixelsOnly(MetadataStore store, IFormatReader r)
void	Memoizer.Deser.saveReader(IFormatReader reader)
void	Memoizer.KryoDeser.saveReader(IFormatReader reader)
void	Memoizer.RandomAccessDeser.saveReader(IFormatReader reader)

Method parameters in loci.formats with type arguments of type IFormatReader

Modifier and Type	Method and Description
ReaderWrapper	ReaderWrapper.duplicate(java.lang.Class<? extends IFormatReader> imageReaderClass) Performs a deep copy of the reader, including nested wrapped readers.
private ReaderWrapper	ReaderWrapper.duplicateRecurse(java.lang.Class<? extends IFormatReader> imageReaderClass)
IFormatReader	ImageReader.getReader(java.lang.Class<? extends IFormatReader> c) Gets the file format reader instance matching the given class.
static IFormatReader	FormatTools.getReader(IFormatReader r, java.lang.Class<? extends IFormatReader> c) Recursively look for the first underlying reader that is an instance of the given class.
protected abstract IFormatReader	Memoizer.RandomAccessDeser.readerFromBytes(java.lang.Class<IFormatReader> c, byte[] rArr)
void	FileStitcher.setReaderClassList(ClassList<IFormatReader> classList) Set the ClassList object to use when constructing any helper readers.
IFormatReader	ReaderWrapper.unwrap(java.lang.Class<? extends IFormatReader> readerClass, java.lang.String id) Unwraps nested wrapped readers until the given reader class is found.

Constructors in loci.formats with parameters of type IFormatReader

Constructor and Description
ChannelFiller(IFormatReader r) Constructs a ChannelFiller with a given reader.
ChannelMerger(IFormatReader r) Constructs a ChannelMerger with the given reader.
ChannelSeparator(IFormatReader r) Constructs a ChannelSeparator with the given reader.
CoreMetadata(IFormatReader r, int coreIndex)
DimensionSwapper(IFormatReader r) Constructs a DimensionSwapper with the given reader.
FileStitcher(IFormatReader r) Constructs a FileStitcher with the given reader.
FileStitcher(IFormatReader r, boolean patternIds) Constructs a FileStitcher with the given reader.
Memoizer(IFormatReader r) Constructs a memoizer around the given IFormatReader creating memo files under the same directory as the original file only if the call to Memoizer.setId(java.lang.String) takes longer than 100L in milliseconds.
Memoizer(IFormatReader r, long minimumElapsed) Constructs a memoizer around the given IFormatReader creating memo files under the same directory as the original file only if the call to Memoizer.setId(java.lang.String) takes longer than minimumElapsed in milliseconds.
Memoizer(IFormatReader r, long minimumElapsed, java.io.File directory) Constructs a memoizer around the given IFormatReader creating memo files under the directory argument including the full path of the original file only if the call to Memoizer.setId(java.lang.String) takes longer than minimumElapsed in milliseconds.
MinMaxCalculator(IFormatReader r) Constructs a MinMaxCalculator with the given reader.
ReaderWrapper(IFormatReader r) Constructs a reader wrapper around the given reader.
SwappableMetadata(IFormatReader r, int seriesNo)
TileStitcher(IFormatReader r) Constructs a TileStitcher with the given reader.

Constructor parameters in loci.formats with type arguments of type IFormatReader

Constructor and Description
ImageReader(ClassList<IFormatReader> classList) Constructs a new ImageReader from the given list of reader classes.

Uses of IFormatReader in loci.formats.cache

Fields in loci.formats.cache declared as IFormatReader

Modifier and Type	Field and Description
protected IFormatReader	CacheSource.reader Reader from which to draw image planes.

Constructors in loci.formats.cache with parameters of type IFormatReader

Constructor and Description
ByteArraySource(IFormatReader r) Constructs a byte array source from the given Bio-Formats reader.
CacheSource(IFormatReader r) Constructs a cache source from the given Bio-Formats reader.

Uses of IFormatReader in loci.formats.gui

Classes in loci.formats.gui that implement IFormatReader

Modifier and Type	Class and Description
class	BufferedImageReader A reader wrapper for reading image planes as BufferedImage objects.

Fields in loci.formats.gui declared as IFormatReader

Modifier and Type	Field and Description
protected IFormatReader	ImageViewer.fileReader Reader for files on disk.
protected IFormatReader	ImageViewer.in
private IFormatReader	FormatFileFilter.reader Associated file format reader.

Methods in loci.formats.gui that return IFormatReader

Modifier and Type	Method and Description
IFormatReader	FormatFileFilter.getReader() Returns the filter's reader.

Methods in loci.formats.gui with parameters of type IFormatReader

Modifier and Type	Method and Description
static BufferedImageReader	BufferedImageReader.makeBufferedImageReader(IFormatReader r) Converts the given reader into a BufferedImageReader, wrapping if needed.
protected void	ImageViewer.open(java.lang.String id, IFormatReader r) Opens from the given data source using the specified reader in a separate thread.
static java.awt.image.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 java.awt.image.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.
void	ImageViewer.setImages(IFormatReader reader, java.awt.image.BufferedImage[] img) Sets the viewer to display the given images, obtaining corresponding core metadata from the specified format reader.

Constructors in loci.formats.gui with parameters of type IFormatReader

Constructor and Description
BufferedImageReader(IFormatReader r) Constructs a BufferedImageReader with the given reader.
BufferedImageSource(IFormatReader reader)
FormatFileFilter(IFormatReader reader) Constructs a new filter that accepts files of the given reader's type.
FormatFileFilter(IFormatReader reader, boolean allowOpen) Constructs a new filter that accepts files of the given reader's type, allowing the reader to open files only if the allowOpen flag is set.

Uses of IFormatReader in loci.formats.in

Classes in loci.formats.in that implement IFormatReader

Modifier and Type	Class and Description
class	AFIReader AFIReader is the file format reader for Aperio AFI files.
class	AIMReader AIMReader is the file format reader for .aim files.
class	AliconaReader AliconaReader is the file format reader for Alicona AL3D files.
class	AmiraReader This is a file format reader for AmiraMesh data.
class	AnalyzeReader AnalyzeReader is the file format reader for Analyze 7.5 files.
class	APLReader APLReader is the file format reader for Olympus APL files.
class	APNGReader APNGReader is the file format reader for Animated Portable Network Graphics (APNG) images.
class	ARFReader ARFReader is the file format reader for Axon Raw Format (ARF) files, produced by INDEC BioSystems's Imaging Workbench software.
class	AVIReader AVIReader is the file format reader for AVI files.
class	BaseTiffReader BaseTiffReader is the superclass for file format readers compatible with or derived from the TIFF 6.0 file format.
class	BaseZeissReader BaseZeissReader contains common functionality required by readers for Zeiss AxioVision formats.
class	BDReader BDReader is the file format reader for BD Pathway datasets.
class	BDVReader Reader for BDV files.
class	BIFormatReader BIFormatReader is the superclass for file format readers that use java.awt.image.BufferedImage as the native data type.
class	BioRadGelReader BioRadGelReader is the file format reader for Bio-Rad gel files.
class	BioRadReader BioRadReader is the file format reader for Bio-Rad PIC files.
class	BioRadSCNReader BioRadSCNReader is the reader for Bio-Rad .scn files
class	BMPReader BMPReader is the file format reader for Microsoft Bitmap (BMP) files.
class	BrukerReader BrukerReader is the file format reader for Bruker MRI files.
class	BurleighReader BurleighReader is the file format reader for Burleigh .img files.
class	CanonRawReader CanonRawReader is the file format reader for Canon RAW files.
class	CellH5Reader Reader for CellH5 (HDF) files.
class	CellomicsReader Reader for Cellomics C01 files.
class	CellSensReader CellSensReader is the file format reader for cellSens .vsi files.
class	CellVoyagerReader A bioformat reader for the Yokagawa Cellvoyager CV1000 automated microscope ( http://www.yokogawa.com/scanner/products/cv1000e.htm).
class	CellWorxReader CellWorxReader is the file format reader for CellWorx .pnl files.
class	ColumbusReader ColumbusReader is the file format reader for screens exported from PerkinElmer Columbus.
class	CV7000Reader
class	DeltavisionReader DeltavisionReader is the file format reader for Deltavision files.
class	DicomReader DicomReader is the file format reader for DICOM files.
class	DNGReader DNGReader is the file format reader for Canon DNG (TIFF) files.
class	Ecat7Reader Ecat7Reader is the file format reader for ECAT 7 files.
class	EPSReader Reader is the file format reader for Encapsulated PostScript (EPS) files.
class	FakeReader FakeReader is the file format reader for faking input data.
class	FEIReader FEIReader is the file format reader for FEI and Philips .img files.
class	FEITiffReader FEITiffReader is the file format reader for TIFF files produced by various FEI software.
class	FilePatternReader
class	FitsReader FitsReader is the file format reader for Flexible Image Transport System (FITS) images.
class	FlexReader FlexReader is a file format reader for Evotec Flex files.
class	FlowSightReader
class	FluoviewReader FluoviewReader is the file format reader for Olympus Fluoview TIFF files AND Andor Bio-imaging Division (ABD) TIFF files.
class	FujiReader FujiReader is the file format reader for Fuji LAS 3000 datasets.
class	FV1000Reader FV1000Reader is the file format reader for Fluoview FV 1000 OIB and Fluoview FV 1000 OIF files.
class	GatanDM2Reader GatanDM2Reader is the file format reader for Gatan .dm2 files.
class	GatanReader GatanReader is the file format reader for Gatan files.
class	GelReader GelReader is the file format reader for Molecular Dynamics GEL TIFF files.
class	GIFReader GIFReader is the file format reader for Graphics Interchange Format (GIF) files.
class	HamamatsuVMSReader HamamatsuVMSReader is the file format reader for Hamamatsu VMS datasets.
class	HISReader HISReader is the file format reader for Hamamatsu .his files.
class	HitachiReader HitachiReader is the file format reader for S-4800 files.
class	HRDGDFReader HRDGDFReader is the file format reader for the Gridded Data Format used by NOAA's Hurricane Research Division.
class	I2IReader I2IReader is the file format reader for I2I files.
class	ICSReader ICSReader is the file format reader for ICS (Image Cytometry Standard) files.
class	IM3Reader
class	ImaconReader ImaconReader is the file format reader for Imacon .fff (TIFF) files.
class	ImageIOReader ImageIOReader is the superclass for file format readers that use the javax.imageio package.
class	ImagicReader ImagicReader is the file format reader for IMAGIC files.
class	ImarisHDFReader Reader for Bitplane Imaris 5.5 (HDF) files.
class	ImarisReader ImarisReader is the file format reader for Bitplane Imaris files.
class	ImarisTiffReader ImarisTiffReader is the file format reader for Bitplane Imaris 3 files (TIFF variant).
class	IMODReader Reader for IMOD binary files.
class	ImprovisionTiffReader ImprovisionTiffReader is the file format reader for Improvision TIFF files.
class	ImspectorReader ImspectorReader is the file format reader for Imspector .msr files.
class	InCell3000Reader InCell3000Reader is the file format reader for InCell 3000.
class	InCellReader InCellReader is the file format reader for InCell 1000/2000 datasets.
class	INRReader INRReader is the file format reader for INR files.
class	InveonReader InveonReader is the file format reader for Inveon files.
class	IonpathMIBITiffReader IonpathMIBITiffReader is the file format reader for Ionpath MIBI TIFF files.
class	IPLabReader IPLabReader is the file format reader for IPLab (.IPL) files.
class	IPWReader IPWReader is the file format reader for Image-Pro Workspace (IPW) files.
class	IvisionReader IvisionReader is the file format reader for IVision (.IPM) files.
class	JEOLReader JEOLReader is the file format reader for JEOL files.
class	JPEG2000Reader JPEG2000Reader is the file format reader for JPEG-2000 images.
class	JPEGReader JPEGReader is the file format reader for JPEG images.
(package private) static class	JPEGReader.DefaultJPEGReader
class	JPKReader JPKReader is the file format reader for JPK Instruments files.
class	JPXReader JPXReader is the file format reader for JPX (3D JPEG-2000) images.
class	KhorosReader Reader for Khoros XV files.
class	KLBReader Reader for Keller Lab Block (KLB) files.
class	KodakReader KodakReader is the file format reader for Kodak Molecular Imaging .bip files.
class	L2DReader L2DReader is the file format reader for Li-Cor L2D datasets.
class	LegacyND2Reader LegacyND2Reader is a file format reader for Nikon ND2 files that uses the Nikon ND2 SDK - it is only usable on Windows machines.
class	LegacyQTReader LegacyQTReader is a file format reader for QuickTime movie files.
class	LeicaReader LeicaReader is the file format reader for Leica files.
class	LeicaSCNReader LeicaSCNReader is the file format reader for Leica SCN TIFF files.
class	LEOReader LEOReader is the file format reader for LEO EM files.
class	LiFlimReader LiFlimReader is the file format reader for LI-FLIM files.
class	LIFReader LIFReader is the file format reader for Leica LIF files.
class	LIMReader LIMReader is the file format reader for Laboratory Imaging/Nikon LIM files.
class	MetamorphReader Reader is the file format reader for Metamorph STK files.
class	MetamorphTiffReader MetamorphTiffReader is the file format reader for TIFF files produced by Metamorph software version 7.5 and above.
class	MetaxpressTiffReader MetaxpressTiffReader is the file format reader for MetaXpress .htd + TIFF files.
class	MIASReader MIASReader is the file format reader for Maia Scientific MIAS-2 datasets.
class	MicroCTReader MicroCTReader is the file format reader for VFF files from a GE MicroCT scanner.
class	MicromanagerReader MicromanagerReader is the file format reader for Micro-Manager files.
class	MikroscanTiffReader MikroscanTiffReader is the file format reader for Mikroscan TIFF files.
class	MINCReader MINCReader is the file format reader for MINC MRI files.
class	MinimalTiffReader MinimalTiffReader is the superclass for file format readers compatible with or derived from the TIFF 6.0 file format.
class	MNGReader MNGReader is the file format reader for Multiple-image Network Graphics (MNG) files.
class	MolecularImagingReader MolecularImagingReader is the file format reader for Molecular Imaging files.
class	MRCReader MRCReader is the file format reader for MRC files.
class	MRWReader MRWReader is the file format reader for Minolta MRW files.
class	NAFReader NAFReader is the file format reader for Hamamatsu Aquacosmos NAF files.
class	NativeND2Reader NativeND2Reader is the file format reader for Nikon ND2 files.
class	NativeQTReader NativeQTReader is the file format reader for QuickTime movie files.
class	ND2Reader ND2Reader is the file format reader for Nikon ND2 files.
class	NDPIReader NDPIReader is the file format reader for Hamamatsu .ndpi files.
class	NDPISReader NDPISReader is the file format reader for Hamamatsu .ndpis files.
class	NiftiReader NiftiReader is the file format reader for NIfTI files.
class	NikonElementsTiffReader NikonElementsTiffReader is the file format reader for TIFF files produced by Nikon Elements.
class	NikonReader NikonReader is the file format reader for Nikon NEF (TIFF) files.
class	NikonTiffReader NikonTiffReader is the file format reader for Nikon TIFF files.
class	NRRDReader File format reader for NRRD files; see http://teem.sourceforge.net/nrrd.
class	OBFReader OBFReader is the file format reader for Imspector OBF files.
class	OIRReader OIRReader is the file format reader for Olympus .oir files.
class	OMETiffReader OMETiffReader is the file format reader for OME-TIFF files.
class	OMEXMLReader OMEXMLReader is the file format reader for OME-XML files.
class	OpenlabRawReader OpenlabRawReader is the file format reader for Openlab RAW files.
class	OpenlabReader OpenlabReader is the file format reader for Openlab LIFF files.
class	OperettaReader OperettaReader is the file format reader for PerkinElmer Operetta data.
class	OxfordInstrumentsReader OxfordInstrumentsReader is the file format reader for Oxford Instruments .top files.
class	PCIReader PCIReader is the file format reader for SimplePCI (Compix) .cxd files.
class	PCORAWReader PCORAWReader is the file format reader for PCORAW files.
class	PCXReader PCXReader is the file format reader for PCX files (originally used by PC Paintbrush; now used in Zeiss' LSM Image Browser).
class	PDSReader PDSReader is the file format reader for Perkin Elmer densitometer files.
class	PerkinElmerReader PerkinElmerReader is the file format reader for PerkinElmer files.
class	PGMReader PGMReader is the file format reader for Portable Gray Map (PGM) images.
class	PhotoshopTiffReader PhotoshopTiffReader is the file format reader for Adobe Photoshop TIFF files.
class	PictReader PictReader is the file format reader for Apple PICT files.
class	PovrayReader PovrayReader is the file format reader for POV-Ray .df3 files.
class	PQBinReader PQBinReader is the file format reader for PicoQuant .bin files.
class	PrairieReader PrairieReader is the file format reader for Prairie Technologies' TIFF variant.
class	PSDReader PSDReader is the file format reader for Photoshop PSD files.
class	PyramidTiffReader PyramidTiffReader is the file format reader for pyramid TIFFs.
class	QTReader QTReader is the file format reader for QuickTime movie files.
class	QuesantReader QuesantReader is the file format reader for Quesant .afm files.
class	RCPNLReader
class	RHKReader RHKReader is the file format reader for RHK Technologies files.
class	SBIGReader SBIGReader is the file format reader for SBIG files.
class	ScanrReader ScanrReader is the file format reader for Olympus ScanR datasets.
class	SDTReader SDTReader is the file format reader for Becker & Hickl SPC-Image SDT files.
class	SeikoReader SeikoReader is the file format reader for Seiko .xqd/.xqf files.
class	SEQReader SEQReader is the file format reader for Image-Pro Sequence files.
class	SIFReader SIFReader is the file format reader for Andor SIF files.
class	SimplePCITiffReader SimplePCITiffReader is the file format reader for TIFF files produced by SimplePCI software.
class	SISReader SISReader is the file format reader for Olympus Soft Imaging Solutions TIFF files.
class	SlidebookReader SlidebookReader is the file format reader for 3I Slidebook files.
class	SlidebookTiffReader
class	SMCameraReader SMCameraReader is the file format reader for SM camera files.
class	SPCReader SPCReader is the file format reader for Becker & Hickl SPC-Image SPC FIFO files.
class	SPEReader SPEReader is the file format reader for Princeton Instruments SPE .spe files.
class	SpiderReader SpiderReader is the file format reader for SPIDER files.
class	SVSReader SVSReader is the file format reader for Aperio SVS TIFF files.
class	TargaReader File format reader for Truevision Targa files.
class	TCSReader TCSReader is the file format reader for Leica TCS TIFF files and their companion XML file.
class	TecanReader
class	TextReader Reader for text files containing tables of data.
class	TiffDelegateReader TiffDelegateReader is a file format reader for TIFF files.
class	TiffJAIReader TiffJAIReader is a file format reader for TIFF images.
class	TiffReader TiffReader is the file format reader for regular TIFF files, not of any specific TIFF variant.
class	TileJPEGReader Reader for decoding JPEG images using java.awt.Toolkit and TurboJPEG.
class	TillVisionReader TillVisionReader is the file format reader for TillVision files.
class	TopometrixReader TopometrixReader is the file format reader for TopoMetrix .tfr, .ffr, .zfr, .zfp, and .2fl files.
class	TrestleReader TrestleReader is the file format reader for Trestle slide datasets.
class	UBMReader UBMReader is the file format reader for UBM .pr3 files.
class	UnisokuReader UnisokuReader is the file format reader for Unisoku STM files.
class	VarianFDFReader VarianFDFReader is the file format reader for Varian FDF files.
class	VectraReader VectraReader is the reader for PerkinElmer Vectra QPTIFF data
class	VeecoReader VeecoReader is the file format reader for Veeco HDF files.
class	VentanaReader VentanaReader is the file format reader for Ventana .bif files.
class	VGSAMReader VGSAMReader is the file format reader for VG SAM .dti files.
class	VisitechReader VisitechReader is the file format reader for Visitech XYS files.
class	VolocityClippingReader VolocityClippingReader is the file format reader for Volocity library clipping files.
class	VolocityReader VolocityReader is the file format reader for Volocity library files.
class	WATOPReader WATOPReader is the file format reader for WA Technology .wat files.
class	WlzReader WlzReader is a file format reader for Woolz files.
class	ZeissCZIReader ZeissCZIReader is the file format reader for Zeiss .czi files.
class	ZeissLMSReader Zeiss LMS reader for data from Zeiss CSM 700 systems.
class	ZeissLSMReader ZeissLSMReader is the file format reader for Zeiss LSM files.
class	ZeissTIFFReader ZeissTIFFReader is the file format reader for Zeiss AxioVision TIFF files and their companion XML file.
class	ZeissZVIReader ZeissZVIReader is the file format reader for Zeiss ZVI files.
class	ZipReader Reader for Zip files.

Fields in loci.formats.in declared as IFormatReader

Modifier and Type	Field and Description
private IFormatReader	CellWorxReader.lastReader
IFormatReader	OMETiffReader.OMETiffPlane.reader Reader to use for accessing this plane.

Methods in loci.formats.in that return IFormatReader

Modifier and Type	Method and Description
protected IFormatReader	MetaxpressTiffReader.getReader(java.lang.String file, boolean omexml)
protected IFormatReader	CellWorxReader.getReader(java.lang.String file, boolean omexml)

Methods in loci.formats.in with parameters of type IFormatReader

Modifier and Type	Method and Description
private void	OMETiffReader.initializeReader(IFormatReader r, java.lang.String file)
protected void	CellWorxReader.initReader(IFormatReader reader, java.lang.String file, boolean omexml)
private void	OMETiffReader.removeIFDComments(IFormatReader r)

Uses of IFormatReader in loci.formats.tools

Methods in loci.formats.tools with parameters of type IFormatReader

Modifier and Type	Method and Description
private static int[]	CacheConsole.getLengths(IFormatReader r) Helper utility for constructing lengths array, used by main.

Uses of IFormatReader in loci.plugins.in

Fields in loci.plugins.in declared as IFormatReader

Modifier and Type	Field and Description
private IFormatReader	ImportProcess.baseReader

Methods in loci.plugins.in that return IFormatReader

Modifier and Type	Method and Description
IFormatReader	ImportProcess.getBaseReader() Valid only after ImportStep.READER.

Methods in loci.plugins.in with parameters of type IFormatReader

Modifier and Type	Method and Description
private void	ImportProcess.computeSeriesLabels(IFormatReader r)
private java.lang.String	ImagePlusReader.constructImageTitle(IFormatReader r, java.lang.String file, java.lang.String seriesName, boolean groupFiles)
private java.lang.String	ImagePlusReader.constructSliceLabel(int ndx, IFormatReader r, IMetadata meta, int series, int zCount, int cCount, int tCount)

Constructors in loci.plugins.in with parameters of type IFormatReader

Constructor and Description
ImporterMetadata(IFormatReader r, ImportProcess process, boolean usePrefix)
ThumbLoader(IFormatReader ir, java.awt.Panel[] p, java.awt.Dialog dialog) Constructs a new thumbnail loader.

Uses of IFormatReader in loci.plugins.macro

Methods in loci.plugins.macro with parameters of type IFormatReader

Modifier and Type	Method and Description
private static int	LociFunctions.getPlaneIndex(IFormatReader r, int no) Finds the Plane index corresponding to the given image plane number.

Uses of IFormatReader in loci.plugins.util

Classes in loci.plugins.util that implement IFormatReader

Modifier and Type	Class and Description
class	ImageProcessorReader A low-level reader for ImageProcessor objects.
class	VirtualReader TODO

Fields in loci.plugins.util declared as IFormatReader

Modifier and Type	Field and Description
private IFormatReader	VirtualImagePlus.r

Methods in loci.plugins.util with parameters of type IFormatReader

Modifier and Type	Method and Description
protected static int	BFVirtualStack.getHeight(IFormatReader r, java.lang.String path, int series)
protected static int	BFVirtualStack.getWidth(IFormatReader r, java.lang.String path, int series)
static boolean	LociPrefs.isWindowless(IFormatReader r) Gets whether windowless mode should be used when opening this reader's currently initialized dataset.
static ImageProcessorReader	ImageProcessorReader.makeImageProcessorReader(IFormatReader r) Converts the given reader into a ImageProcessorReader, wrapping if needed.
void	VirtualImagePlus.setReader(IFormatReader r)

Method parameters in loci.plugins.util with type arguments of type IFormatReader

Modifier and Type	Method and Description
private static boolean	LociPrefs.getPref(java.lang.String pref, java.lang.Class<? extends IFormatReader> c, boolean defaultValue)
static boolean	LociPrefs.isReaderEnabled(java.lang.Class<? extends IFormatReader> c)

Constructors in loci.plugins.util with parameters of type IFormatReader

Constructor and Description
BFVirtualStack(java.lang.String path, IFormatReader r, boolean colorize, boolean merge, boolean record)
ImageProcessorReader(IFormatReader r) Constructs an ImageProcessorReader with the given reader.
ImageProcessorSource(IFormatReader reader)
VirtualReader(IFormatReader r)