Uses of Interface
loci.formats.IFormatReader

Packages that use IFormatReader
loci.formats Bio-Formats: a library for reading and writing popular microscopy file formats. 
loci.formats.gui   
loci.formats.in   
visad.data.bio Provides data forms for handling common microscopy formats. 
 

Uses of IFormatReader in loci.formats
 

Classes in loci.formats that implement IFormatReader
 class ChannelFiller
          Expands indexed color images to RGB.
 class ChannelMerger
          Logic to automatically merge channels in a file.
 class ChannelSeparator
          Logic to automatically separate the channels in a file.
 class DimensionSwapper
          Handles swapping the dimension order of a file.
 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 MinMaxCalculator
          Logic to compute minimum and maximum values for each channel.
 class ReaderWrapper
          Abstract superclass of reader logic that wraps other readers.
 

Fields in loci.formats declared as IFormatReader
protected  IFormatReader ReaderWrapper.reader
          FormatReader used to read the file.
protected  IFormatReader ReaderWrapper.reader
          FormatReader used to read the file.
 

Methods in loci.formats that return IFormatReader
 IFormatReader FileStitcher.getReader()
          Gets the wrapped reader prototype.
 IFormatReader ImageReader.getReader()
          Gets the reader used to open the current file.
 IFormatReader ReaderWrapper.getReader()
          Gets the wrapped reader.
 IFormatReader FileStitcher.getReader()
          Gets the wrapped reader prototype.
 IFormatReader ImageReader.getReader()
          Gets the reader used to open the current file.
 IFormatReader ReaderWrapper.getReader()
          Gets the wrapped reader.
 IFormatReader ImageReader.getReader(Class c)
          Gets the file format reader instance matching the given class.
 IFormatReader ImageReader.getReader(Class c)
          Gets the file format reader instance matching the given class.
 IFormatReader ImageReader.getReader(String id)
          Gets the reader used to open the given file.
 IFormatReader ImageReader.getReader(String id)
          Gets the reader used to open the given file.
 IFormatReader[] ImageReader.getReaders()
          Gets all constituent file format readers.
 IFormatReader[] ImageReader.getReaders()
          Gets all constituent file format readers.
 

Methods in loci.formats with parameters of type IFormatReader
static void FormatTools.checkBufferSize(IFormatReader r, int len)
           
static void FormatTools.checkBufferSize(IFormatReader r, int len)
           
static void FormatTools.checkPlaneNumber(IFormatReader r, int no)
          Checks that the given plane number is valid for the given reader.
static void FormatTools.checkPlaneNumber(IFormatReader r, int no)
          Checks that the given plane number is valid for the given reader.
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.
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.
static int FormatTools.getReorderedIndex(IFormatReader r, String order, int no)
          Converts indices from the given dimension order to the native one.
static int FormatTools.getReorderedIndex(IFormatReader r, String order, int no)
          Converts indices from the given dimension order to the native one.
static int[] FormatTools.getZCTCoords(IFormatReader reader, int index)
          Gets the Z, C and T coordinates corresponding to the given rasterized index value.
static int[] FormatTools.getZCTCoords(IFormatReader reader, int index)
          Gets the Z, C and T coordinates corresponding to the given rasterized index value.
static void FormatTools.populatePixels(MetadataStore store, IFormatReader r)
          Populates the 'pixels' element of the given metadata store, using core metadata from the given reader.
static void FormatTools.populatePixels(MetadataStore store, IFormatReader r)
          Populates the 'pixels' element of the given metadata store, using core metadata from the given reader.
 

Constructors in loci.formats with parameters of type IFormatReader
ChannelFiller(IFormatReader r)
          Constructs a ChannelFiller with a given reader.
ChannelFiller(IFormatReader r)
          Constructs a ChannelFiller with a given reader.
ChannelMerger(IFormatReader r)
          Constructs a ChannelMerger with the given reader.
ChannelMerger(IFormatReader r)
          Constructs a ChannelMerger with the given reader.
ChannelSeparator(IFormatReader r)
          Constructs a ChannelSeparator with the given reader.
ChannelSeparator(IFormatReader r)
          Constructs a ChannelSeparator with the given reader.
DimensionSwapper(IFormatReader r)
          Constructs a DimensionSwapper with the given reader.
DimensionSwapper(IFormatReader r)
          Constructs a DimensionSwapper with the given reader.
FileStitcher(IFormatReader r)
          Constructs a FileStitcher 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.
FileStitcher(IFormatReader r, boolean patternIds)
          Constructs a FileStitcher with the given reader.
MinMaxCalculator(IFormatReader r)
          Constructs a MinMaxCalculator with the given reader.
MinMaxCalculator(IFormatReader r)
          Constructs a MinMaxCalculator with the given reader.
ReaderWrapper(IFormatReader r)
          Constructs a reader wrapper around the given reader.
ReaderWrapper(IFormatReader r)
          Constructs a reader wrapper around the given reader.
 

Uses of IFormatReader in loci.formats.gui
 

Fields in loci.formats.gui declared as IFormatReader
protected  IFormatReader ImageViewer.in
           
protected  IFormatReader ImageViewer.in
           
protected  IFormatReader ImageViewer.myReader
           
protected  IFormatReader ImageViewer.myReader
           
protected  IFormatReader PreviewPane.reader
          Reader for use when loading thumbnails.
protected  IFormatReader PreviewPane.reader
          Reader for use when loading thumbnails.
 

Methods in loci.formats.gui with parameters of type IFormatReader
 void ImageViewer.setImages(IFormatReader reader, BufferedImage[] img)
          Sets the viewer to display the given images, obtaining corresponding core metadata from the specified format reader.
 void ImageViewer.setImages(IFormatReader reader, 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
FormatFileFilter(IFormatReader reader)
          Constructs a new filter that accepts files of the given reader's type.
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.
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
 class AliconaReader
          AliconaReader is the file format reader for Alicona AL3D files.
 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 BioRadReader
          BioRadReader is the file format reader for Bio-Rad PIC files.
 class BMPReader
          BMPReader is the file format reader for Microsoft Bitmap (BMP) files.
 class DeltavisionReader
          DeltavisionReader is the file format reader for Deltavision files.
 class DicomReader
          DicomReader is the file format reader for DICOM files.
 class EPSReader
          Reader is the file format reader for Encapsulated PostScript (EPS) files.
 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 FluoviewReader
          FluoviewReader is the file format reader for Olympus Fluoview TIFF files AND Andor Bio-imaging Division (ABD) TIFF 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 ICSReader
          ICSReader is the file format reader for ICS (Image Cytometry Standard) files.
 class ImageIOReader
          ImageIOReader is the superclass for file format readers that use the javax.imageio package.
 class ImarisReader
          ImarisReader is the file format reader for Bitplane Imaris files.
 class ImarisTiffReader
          ImarisTiffReader is the file format reader for Imaris 5 files (TIFF variant).
 class ImprovisionTiffReader
          ImprovisionTiffReader is the file format reader for Improvision 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 JPEGReader
          JPEGReader is the file format reader for JPEG images.
 class KhorosReader
          Reader for Khoros XV files.
 class LegacyPictReader
          LegacyPictReader is the old file format reader for Apple PICT files.
 class LegacyQTReader
          LegacyQTReader is a file format reader for QuickTime movie files.
 class LegacyZVIReader
          LegacyZVIReader is the legacy file format reader for Zeiss ZVI files.
 class LeicaReader
          LeicaReader is the file format reader for Leica 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 MicromanagerReader
          MicromanagerReader is the file format reader for Micro-Manager files.
 class MNGReader
          MNGReader is the file format reader for Multiple Network Graphics (MNG) files.
 class MRCReader
          MRCReader is the file format reader for MRC files.
 class ND2Reader
          ND2Reader is the file format reader for Nikon ND2 files.
 class NikonReader
          NikonReader is the file format reader for Nikon NEF (TIFF) files.
 class NRRDReader
          File format reader for NRRD files; see http://teem.sourceforge.net/nrrd.
 class OIBReader
          OIBReader is the file format reader for Fluoview FV1000 OIB files.
 class OIFReader
          OIFReader is the file format reader for Fluoview FV 1000 OIF 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 PCIReader
          PCIReader is the file format reader for SimplePCI (Compix) .cxd 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 PictReader
          PictReader is the file format reader for Apple PICT files.
 class PNGReader
          PNGReader is the file format reader for Portable Network Graphics (PNG) images.
 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 QTReader
          QTReader is the file format reader for QuickTime movie files.
 class SDTReader
          SDTReader is the file format reader for Becker & Hickl SPC-Image SDT files.
 class SEQReader
          SEQReader is the file format reader for Image-Pro Sequence files.
 class SlidebookReader
          SlidebookReader is the file format reader for 3I Slidebook files.
 class TCSReader
          TCSReader is the file format reader for Leica TCS TIFF files.
 class TiffReader
          TiffReader is the file format reader for TIFF files, including OME-TIFF.
 class VisitechReader
          VisitechReader is the file format reader for Visitech XYS files.
 class ZeissLSMReader
          ZeissLSMReader is the file format reader for Zeiss LSM files.
 class ZeissZVIReader
          ZeissZVIReader is the file format reader for Zeiss ZVI files.
 

Uses of IFormatReader in visad.data.bio
 

Fields in visad.data.bio declared as IFormatReader
protected  IFormatReader LociForm.reader
          Reader to use for open-related functions.
protected  IFormatReader LociForm.reader
          Reader to use for open-related functions.
 

Methods in visad.data.bio that return IFormatReader
 IFormatReader LociForm.getReader()
          Gets the IFormatReader backing this form's reading capabilities.
 IFormatReader LociForm.getReader()
          Gets the IFormatReader backing this form's reading capabilities.
 

Constructors in visad.data.bio with parameters of type IFormatReader
LociForm(IFormatReader reader)
          Constructs a new LociForm that handles the given reader.
LociForm(IFormatReader reader)
          Constructs a new LociForm that handles the given reader.
LociForm(IFormatReader reader, IFormatWriter writer)
          Constructs a new LociForm that handles the given reader/writer pair.
LociForm(IFormatReader reader, IFormatWriter writer)
          Constructs a new LociForm that handles the given reader/writer pair.