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Packages that use IFormatReader | |
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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 |
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Classes in loci.formats that implement IFormatReader | |
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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 | |
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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 | |
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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 | |
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static void |
FormatTools.checkBufferSize(IFormatReader r,
int len)
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static void |
FormatTools.checkBufferSize(IFormatReader r,
int len)
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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 | |
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ChannelFiller(IFormatReader r)
Constructs a ChannelFiller with a given reader. |
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ChannelFiller(IFormatReader r)
Constructs a ChannelFiller with a given reader. |
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ChannelMerger(IFormatReader r)
Constructs a ChannelMerger with the given reader. |
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ChannelMerger(IFormatReader r)
Constructs a ChannelMerger with the given reader. |
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ChannelSeparator(IFormatReader r)
Constructs a ChannelSeparator with the given reader. |
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ChannelSeparator(IFormatReader r)
Constructs a ChannelSeparator with the given reader. |
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DimensionSwapper(IFormatReader r)
Constructs a DimensionSwapper with the given reader. |
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DimensionSwapper(IFormatReader r)
Constructs a DimensionSwapper with the given reader. |
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FileStitcher(IFormatReader r)
Constructs a FileStitcher with the given reader. |
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FileStitcher(IFormatReader r)
Constructs a FileStitcher with the given reader. |
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FileStitcher(IFormatReader r,
boolean patternIds)
Constructs a FileStitcher with the given reader. |
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FileStitcher(IFormatReader r,
boolean patternIds)
Constructs a FileStitcher with the given reader. |
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MinMaxCalculator(IFormatReader r)
Constructs a MinMaxCalculator with the given reader. |
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MinMaxCalculator(IFormatReader r)
Constructs a MinMaxCalculator with the given reader. |
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ReaderWrapper(IFormatReader r)
Constructs a reader wrapper around the given reader. |
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ReaderWrapper(IFormatReader r)
Constructs a reader wrapper around the given reader. |
Uses of IFormatReader in loci.formats.gui |
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Fields in loci.formats.gui declared as IFormatReader | |
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protected IFormatReader |
ImageViewer.in
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protected IFormatReader |
ImageViewer.in
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protected IFormatReader |
ImageViewer.myReader
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protected IFormatReader |
ImageViewer.myReader
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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 | |
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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 | |
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FormatFileFilter(IFormatReader reader)
Constructs a new filter that accepts files of the given reader's type. |
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FormatFileFilter(IFormatReader reader)
Constructs a new filter that accepts files of the given reader's type. |
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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. |
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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 |
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Classes in loci.formats.in that implement IFormatReader | |
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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 |
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Fields in visad.data.bio declared as IFormatReader | |
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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 | |
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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 | |
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LociForm(IFormatReader reader)
Constructs a new LociForm that handles the given reader. |
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LociForm(IFormatReader reader)
Constructs a new LociForm that handles the given reader. |
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LociForm(IFormatReader reader,
IFormatWriter writer)
Constructs a new LociForm that handles the given reader/writer pair. |
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LociForm(IFormatReader reader,
IFormatWriter writer)
Constructs a new LociForm that handles the given reader/writer pair. |
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