| 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.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.
|
| Modifier and Type | Class and Description |
|---|---|
class |
MissingLibraryException
MissingLibraryException is the exception thrown when a particular data
stream or filename requires a library that is not present on the system.
|
class |
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.
|
| Modifier and Type | Method and Description |
|---|---|
void |
WriterWrapper.changeOutputFile(java.lang.String id) |
void |
ImageWriter.changeOutputFile(java.lang.String id) |
void |
IFormatWriter.changeOutputFile(java.lang.String id)
Switch the output file for the current dataset.
|
void |
FormatWriter.changeOutputFile(java.lang.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(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 void |
FormatTools.convert(java.lang.String input,
java.lang.String output)
Convenience method for converting the specified input file to the
specified output file.
|
ReaderWrapper |
ReaderWrapper.duplicate(java.lang.Class<? extends IFormatReader> imageReaderClass)
Performs a deep copy of the reader, including nested wrapped readers.
|
WriterWrapper |
WriterWrapper.duplicate(java.lang.Class<? extends IFormatWriter> imageWriterClass)
Performs a deep copy of the writer, including nested wrapped writers.
|
private ReaderWrapper |
ReaderWrapper.duplicateRecurse(java.lang.Class<? extends IFormatReader> imageReaderClass) |
private WriterWrapper |
WriterWrapper.duplicateRecurse(java.lang.Class<? extends IFormatWriter> imageWriterClass) |
int |
ReaderWrapper.fileGroupOption(java.lang.String id) |
int |
ImageReader.fileGroupOption(java.lang.String id) |
int |
IFormatReader.fileGroupOption(java.lang.String id)
Returns an indication of whether the files in a multi-file dataset can
be handled individually.
|
int |
FormatReader.fileGroupOption(java.lang.String id) |
short[][] |
FileStitcher.get16BitLookupTable() |
short[][] |
ChannelFiller.get16BitLookupTable() |
short[][] |
WrappedReader.get16BitLookupTable() |
short[][] |
ReaderWrapper.get16BitLookupTable() |
short[][] |
ImageReader.get16BitLookupTable() |
short[][] |
IFormatReader.get16BitLookupTable()
Gets the 16-bit color lookup table associated with
the most recently opened image.
|
short[][] |
FormatReader.get16BitLookupTable() |
short[][] |
DelegateReader.get16BitLookupTable() |
byte[][] |
FileStitcher.get8BitLookupTable() |
byte[][] |
ChannelFiller.get8BitLookupTable() |
byte[][] |
WrappedReader.get8BitLookupTable() |
byte[][] |
ReaderWrapper.get8BitLookupTable() |
byte[][] |
ImageReader.get8BitLookupTable() |
byte[][] |
IFormatReader.get8BitLookupTable()
Gets the 8-bit color lookup table associated with
the most recently opened image.
|
byte[][] |
FormatReader.get8BitLookupTable() |
byte[][] |
DelegateReader.get8BitLookupTable() |
static ome.xml.model.enums.AcquisitionMode |
MetadataTools.getAcquisitionMode(java.lang.String value)
Retrieves an
AcquisitionMode enumeration
value for the given String. |
protected ome.xml.model.enums.AcquisitionMode |
FormatReader.getAcquisitionMode(java.lang.String value)
Deprecated.
|
int |
FileStitcher.getAdjustedIndex(int no)
Gets the local reader index for use with the given image plane.
|
static ome.xml.model.enums.ArcType |
MetadataTools.getArcType(java.lang.String value)
Retrieves an
ArcType enumeration
value for the given String. |
protected ome.xml.model.enums.ArcType |
FormatReader.getArcType(java.lang.String value)
Deprecated.
|
static ome.xml.model.enums.Binning |
MetadataTools.getBinning(java.lang.String value)
Retrieves an
Binning enumeration
value for the given String. |
protected ome.xml.model.enums.Binning |
FormatReader.getBinning(java.lang.String value)
Deprecated.
|
java.lang.Double |
MinMaxCalculator.getChannelGlobalMaximum(int theC)
Retrieves a specified channel's global maximum.
|
java.lang.Double |
MinMaxCalculator.getChannelGlobalMinimum(int theC)
Retrieves a specified channel's global minimum.
|
java.lang.Double |
MinMaxCalculator.getChannelKnownMaximum(int theC)
Retrieves the specified channel's maximum based on the images that
have been read.
|
java.lang.Double |
MinMaxCalculator.getChannelKnownMinimum(int theC)
Retrieves the specified channel's minimum based on the images that have
been read.
|
static ome.xml.model.enums.Compression |
MetadataTools.getCompression(java.lang.String value)
Retrieves an
Compression enumeration
value for the given String. |
protected ome.xml.model.enums.Compression |
FormatReader.getCompression(java.lang.String value)
Deprecated.
|
static ome.xml.model.enums.ContrastMethod |
MetadataTools.getContrastMethod(java.lang.String value)
Retrieves an
ContrastMethod enumeration
value for the given String. |
protected ome.xml.model.enums.ContrastMethod |
FormatReader.getContrastMethod(java.lang.String value)
Deprecated.
|
static ome.xml.model.enums.Correction |
MetadataTools.getCorrection(java.lang.String value)
Retrieves an
Correction enumeration
value for the given String. |
protected ome.xml.model.enums.Correction |
FormatReader.getCorrection(java.lang.String value)
Deprecated.
|
static ome.xml.model.enums.DetectorType |
MetadataTools.getDetectorType(java.lang.String value)
Retrieves an
DetectorType enumeration
value for the given String. |
protected ome.xml.model.enums.DetectorType |
FormatReader.getDetectorType(java.lang.String value)
Deprecated.
|
static ome.xml.model.enums.DimensionOrder |
MetadataTools.getDimensionOrder(java.lang.String value)
Retrieves an
DimensionOrder enumeration
value for the given String. |
protected ome.xml.model.enums.DimensionOrder |
FormatReader.getDimensionOrder(java.lang.String value)
Deprecated.
|
static ome.xml.model.enums.ExperimentType |
MetadataTools.getExperimentType(java.lang.String value)
Retrieves an
ExperimentType enumeration
value for the given String. |
protected ome.xml.model.enums.ExperimentType |
FormatReader.getExperimentType(java.lang.String value)
Deprecated.
|
static ome.xml.model.enums.FilamentType |
MetadataTools.getFilamentType(java.lang.String value)
Retrieves an
FilamentType enumeration
value for the given String. |
protected ome.xml.model.enums.FilamentType |
FormatReader.getFilamentType(java.lang.String value)
Deprecated.
|
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.getFilename(int series,
int image,
MetadataRetrieve retrieve,
java.lang.String pattern,
boolean padded) |
static java.lang.String[] |
FormatTools.getFilenames(java.lang.String pattern,
IFormatReader r) |
static ome.xml.model.enums.FillRule |
MetadataTools.getFillRule(java.lang.String value)
Retrieves an
FillRule enumeration
value for the given String. |
protected ome.xml.model.enums.FillRule |
FormatReader.getFillRule(java.lang.String value)
Deprecated.
|
static ome.xml.model.enums.FilterType |
MetadataTools.getFilterType(java.lang.String value)
Retrieves an
FilterType enumeration
value for the given String. |
protected ome.xml.model.enums.FilterType |
FormatReader.getFilterType(java.lang.String value)
Deprecated.
|
static ome.xml.model.enums.FontFamily |
MetadataTools.getFontFamily(java.lang.String value)
Retrieves an
FontFamily enumeration
value for the given String. |
protected ome.xml.model.enums.FontFamily |
FormatReader.getFontFamily(java.lang.String value)
Deprecated.
|
static ome.xml.model.enums.FontStyle |
MetadataTools.getFontStyle(java.lang.String value)
Retrieves an
FontStyle enumeration
value for the given String. |
protected ome.xml.model.enums.FontStyle |
FormatReader.getFontStyle(java.lang.String value)
Deprecated.
|
java.lang.String |
ImageWriter.getFormat(java.lang.String id)
Gets a string describing the file format for the given file.
|
java.lang.String |
ImageReader.getFormat(java.lang.String id)
Gets a string describing the file format for the given file.
|
static ome.xml.model.enums.IlluminationType |
MetadataTools.getIlluminationType(java.lang.String value)
Retrieves an
IlluminationType enumeration
value for the given String. |
protected ome.xml.model.enums.IlluminationType |
FormatReader.getIlluminationType(java.lang.String value)
Deprecated.
|
static int |
FormatTools.getImagesPerFile(java.lang.String pattern,
IFormatReader r) |
static ome.xml.model.enums.Immersion |
MetadataTools.getImmersion(java.lang.String value)
Retrieves an
Immersion enumeration
value for the given String. |
protected ome.xml.model.enums.Immersion |
FormatReader.getImmersion(java.lang.String value)
Deprecated.
|
static ome.xml.model.enums.LaserMedium |
MetadataTools.getLaserMedium(java.lang.String value)
Retrieves an
LaserMedium enumeration
value for the given String. |
protected ome.xml.model.enums.LaserMedium |
FormatReader.getLaserMedium(java.lang.String value)
Deprecated.
|
static ome.xml.model.enums.LaserType |
MetadataTools.getLaserType(java.lang.String value)
Retrieves an
LaserType enumeration
value for the given String. |
protected ome.xml.model.enums.LaserType |
FormatReader.getLaserType(java.lang.String value)
Deprecated.
|
private int |
ChannelFiller.getLookupTableComponentCount()
Gets the number of color components in the lookup table.
|
static ome.xml.model.enums.Marker |
MetadataTools.getMarker(java.lang.String value)
Retrieves an
Marker enumeration
value for the given String. |
protected ome.xml.model.enums.Marker |
FormatReader.getMarker(java.lang.String value)
Deprecated.
|
static ome.xml.model.enums.Medium |
MetadataTools.getMedium(java.lang.String value)
Retrieves an
Medium enumeration
value for the given String. |
protected ome.xml.model.enums.Medium |
FormatReader.getMedium(java.lang.String value)
Deprecated.
|
static ome.xml.model.enums.MicrobeamManipulationType |
MetadataTools.getMicrobeamManipulationType(java.lang.String value)
Retrieves an
MicrobeamManipulationType
enumeration value for the given String. |
protected ome.xml.model.enums.MicrobeamManipulationType |
FormatReader.getMicrobeamManipulationType(java.lang.String value)
Deprecated.
|
static ome.xml.model.enums.MicroscopeType |
MetadataTools.getMicroscopeType(java.lang.String value)
Retrieves an
MicroscopeType enumeration
value for the given String. |
protected ome.xml.model.enums.MicroscopeType |
FormatReader.getMicroscopeType(java.lang.String value)
Deprecated.
|
static ome.xml.model.enums.NamingConvention |
MetadataTools.getNamingConvention(java.lang.String value)
Retrieves an
NamingConvention enumeration
value for the given String. |
protected ome.xml.model.enums.NamingConvention |
FormatReader.getNamingConvention(java.lang.String value)
Deprecated.
|
int |
ChannelMerger.getOriginalIndex(int no)
Returns the image number in the original dataset that corresponds to the
given image number.
|
static ome.xml.model.enums.PixelType |
MetadataTools.getPixelType(java.lang.String value)
Retrieves an
PixelType enumeration
value for the given String. |
protected ome.xml.model.enums.PixelType |
FormatReader.getPixelType(java.lang.String value)
Deprecated.
|
java.lang.Double[] |
MinMaxCalculator.getPlaneMaximum(int no)
Retrieves the maximum pixel value for the specified plane.
|
java.lang.Double[] |
MinMaxCalculator.getPlaneMinimum(int no)
Retrieves the minimum pixel value for the specified plane.
|
java.lang.String[] |
WrappedReader.getPossibleDomains(java.lang.String id) |
java.lang.String[] |
ReaderWrapper.getPossibleDomains(java.lang.String id) |
java.lang.String[] |
ImageReader.getPossibleDomains(java.lang.String id) |
java.lang.String[] |
IFormatReader.getPossibleDomains(java.lang.String id)
Returns a list of scientific domains in which this format is used.
|
java.lang.String[] |
FormatReader.getPossibleDomains(java.lang.String id) |
static ome.xml.model.enums.Pulse |
MetadataTools.getPulse(java.lang.String value)
Retrieves an
Pulse enumeration
value for the given String. |
protected ome.xml.model.enums.Pulse |
FormatReader.getPulse(java.lang.String value)
Deprecated.
|
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.
|
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.
|
int |
FileStitcher.getRequiredDirectories(java.lang.String[] files) |
int |
ReaderWrapper.getRequiredDirectories(java.lang.String[] files) |
int |
ImageReader.getRequiredDirectories(java.lang.String[] files) |
int |
IFormatReader.getRequiredDirectories(java.lang.String[] files)
Returns the number of parent directories that are important when
processing the given list of files.
|
int |
FormatReader.getRequiredDirectories(java.lang.String[] files) |
protected int |
FormatWriter.getSizeX() |
protected int |
FormatWriter.getSizeY() |
int |
WriterWrapper.getTileSizeX() |
int |
ImageWriter.getTileSizeX() |
int |
IFormatWriter.getTileSizeX()
Retrieves the current tile width
Defaults to 0 if not supported
|
int |
FormatWriter.getTileSizeX() |
int |
WriterWrapper.getTileSizeY() |
int |
ImageWriter.getTileSizeY() |
int |
IFormatWriter.getTileSizeY()
Retrieves the current tile height
Defaults to 0 if not supported
|
int |
FormatWriter.getTileSizeY() |
IFormatWriter |
ImageWriter.getWriter(java.lang.String id)
Gets the writer used to save the given file.
|
protected void |
FileStitcher.initFile(java.lang.String id)
Initializes the given file or file pattern.
|
protected void |
SubResolutionFormatReader.initFile(java.lang.String id)
Initializes the given file (parsing header information, etc.).
|
protected void |
FormatReader.initFile(java.lang.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 |
WrappedReader.isSingleFile(java.lang.String id) |
boolean |
ReaderWrapper.isSingleFile(java.lang.String id) |
boolean |
ImageReader.isSingleFile(java.lang.String id) |
boolean |
IFormatReader.isSingleFile(java.lang.String id)
Returns true if the named file is expected to be the only
file in the dataset.
|
boolean |
FormatReader.isSingleFile(java.lang.String id) |
IFormatReader |
Memoizer.loadMemo()
Load a memo file if possible, returning a null if not.
|
byte[] |
TileStitcher.openBytes(int no) |
byte[] |
MinMaxCalculator.openBytes(int no) |
byte[] |
FileStitcher.openBytes(int no) |
byte[] |
DimensionSwapper.openBytes(int no) |
byte[] |
ChannelSeparator.openBytes(int no) |
byte[] |
ChannelMerger.openBytes(int no) |
byte[] |
ChannelFiller.openBytes(int no) |
byte[] |
WrappedReader.openBytes(int no) |
byte[] |
ReaderWrapper.openBytes(int no) |
byte[] |
ImageReader.openBytes(int no) |
byte[] |
IFormatReader.openBytes(int no)
Obtains the specified image plane from the current file as a byte array.
|
byte[] |
FormatReader.openBytes(int no) |
byte[] |
TileStitcher.openBytes(int no,
byte[] buf) |
byte[] |
MinMaxCalculator.openBytes(int no,
byte[] buf) |
byte[] |
FileStitcher.openBytes(int no,
byte[] buf) |
byte[] |
DimensionSwapper.openBytes(int no,
byte[] buf) |
byte[] |
ChannelSeparator.openBytes(int no,
byte[] buf) |
byte[] |
ChannelMerger.openBytes(int no,
byte[] buf) |
byte[] |
ChannelFiller.openBytes(int no,
byte[] buf) |
byte[] |
WrappedReader.openBytes(int no,
byte[] buf) |
byte[] |
ReaderWrapper.openBytes(int no,
byte[] buf) |
byte[] |
ImageReader.openBytes(int no,
byte[] buf) |
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[] |
FormatReader.openBytes(int no,
byte[] buf) |
byte[] |
TileStitcher.openBytes(int no,
byte[] buf,
int x,
int y,
int w,
int h) |
byte[] |
MinMaxCalculator.openBytes(int no,
byte[] buf,
int x,
int y,
int w,
int h) |
byte[] |
FileStitcher.openBytes(int no,
byte[] buf,
int x,
int y,
int w,
int h) |
byte[] |
DimensionSwapper.openBytes(int no,
byte[] buf,
int x,
int y,
int w,
int h) |
byte[] |
ChannelSeparator.openBytes(int no,
byte[] buf,
int x,
int y,
int w,
int h) |
byte[] |
ChannelMerger.openBytes(int no,
byte[] buf,
int x,
int y,
int w,
int h) |
byte[] |
ChannelFiller.openBytes(int no,
byte[] buf,
int x,
int y,
int w,
int h) |
byte[] |
WrappedReader.openBytes(int no,
byte[] buf,
int x,
int y,
int w,
int h) |
byte[] |
ReaderWrapper.openBytes(int no,
byte[] buf,
int x,
int y,
int w,
int h) |
byte[] |
ImageReader.openBytes(int no,
byte[] buf,
int x,
int y,
int w,
int h) |
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.
|
abstract byte[] |
FormatReader.openBytes(int no,
byte[] buf,
int x,
int y,
int w,
int h) |
byte[] |
DelegateReader.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[] |
MinMaxCalculator.openBytes(int no,
int x,
int y,
int w,
int h) |
byte[] |
FileStitcher.openBytes(int no,
int x,
int y,
int w,
int h) |
byte[] |
DimensionSwapper.openBytes(int no,
int x,
int y,
int w,
int h) |
byte[] |
ChannelSeparator.openBytes(int no,
int x,
int y,
int w,
int h) |
byte[] |
ChannelMerger.openBytes(int no,
int x,
int y,
int w,
int h) |
byte[] |
ChannelFiller.openBytes(int no,
int x,
int y,
int w,
int h) |
byte[] |
WrappedReader.openBytes(int no,
int x,
int y,
int w,
int h) |
byte[] |
ReaderWrapper.openBytes(int no,
int x,
int y,
int w,
int h) |
byte[] |
ImageReader.openBytes(int no,
int x,
int y,
int w,
int h) |
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[] |
FormatReader.openBytes(int no,
int x,
int y,
int w,
int h) |
java.lang.Object |
FileStitcher.openPlane(int no,
int x,
int y,
int w,
int h) |
java.lang.Object |
WrappedReader.openPlane(int no,
int x,
int y,
int w,
int h) |
java.lang.Object |
ReaderWrapper.openPlane(int no,
int x,
int y,
int w,
int h) |
java.lang.Object |
ImageReader.openPlane(int no,
int x,
int y,
int w,
int h) |
java.lang.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.
|
java.lang.Object |
FormatReader.openPlane(int no,
int x,
int y,
int w,
int h) |
static byte[] |
FormatTools.openThumbBytes(IFormatReader reader,
int no)
Default implementation for
IFormatReader.openThumbBytes(int). |
byte[] |
FileStitcher.openThumbBytes(int no) |
byte[] |
DimensionSwapper.openThumbBytes(int no) |
byte[] |
ChannelSeparator.openThumbBytes(int no) |
byte[] |
WrappedReader.openThumbBytes(int no) |
byte[] |
ReaderWrapper.openThumbBytes(int no) |
byte[] |
ImageReader.openThumbBytes(int no) |
byte[] |
IFormatReader.openThumbBytes(int no)
Obtains a thumbnail for the specified image plane from the current file,
as a byte array.
|
byte[] |
FormatReader.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 |
WriterWrapper.saveBytes(int no,
byte[] buf) |
void |
ImageWriter.saveBytes(int no,
byte[] buf) |
void |
IFormatWriter.saveBytes(int no,
byte[] buf)
Saves the given image to the current series in the current file.
|
void |
FormatWriter.saveBytes(int no,
byte[] buf) |
void |
WriterWrapper.saveBytes(int no,
byte[] buf,
int x,
int y,
int w,
int h) |
void |
ImageWriter.saveBytes(int no,
byte[] buf,
int x,
int y,
int w,
int h) |
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 |
WriterWrapper.saveBytes(int no,
byte[] buf,
loci.common.Region tile) |
void |
ImageWriter.saveBytes(int no,
byte[] buf,
loci.common.Region tile) |
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 |
FormatWriter.saveBytes(int no,
byte[] buf,
loci.common.Region tile) |
void |
WriterWrapper.savePlane(int no,
java.lang.Object plane) |
void |
ImageWriter.savePlane(int no,
java.lang.Object plane) |
void |
IFormatWriter.savePlane(int no,
java.lang.Object plane)
Saves the given image plane to the current series in the current file.
|
void |
FormatWriter.savePlane(int no,
java.lang.Object plane) |
void |
WriterWrapper.savePlane(int no,
java.lang.Object plane,
int x,
int y,
int w,
int h) |
void |
ImageWriter.savePlane(int no,
java.lang.Object plane,
int x,
int y,
int w,
int h) |
void |
IFormatWriter.savePlane(int no,
java.lang.Object plane,
int x,
int y,
int w,
int h)
Saves the given image plane to the current series in the current file.
|
void |
FormatWriter.savePlane(int no,
java.lang.Object plane,
int x,
int y,
int w,
int h) |
void |
WriterWrapper.savePlane(int no,
java.lang.Object plane,
loci.common.Region tile) |
void |
ImageWriter.savePlane(int no,
java.lang.Object plane,
loci.common.Region tile) |
void |
IFormatWriter.savePlane(int no,
java.lang.Object plane,
loci.common.Region tile)
Saves the given image plane to the current series in the current file.
|
void |
FormatWriter.savePlane(int no,
java.lang.Object plane,
loci.common.Region tile) |
void |
FileStitcher.setAxisTypes(int[] axes)
Sets the axis type for each dimensional block.
|
void |
WriterWrapper.setCompression(java.lang.String compress) |
void |
ImageWriter.setCompression(java.lang.String compress) |
void |
IFormatWriter.setCompression(java.lang.String compress)
Sets the current compression type.
|
void |
FormatWriter.setCompression(java.lang.String compress) |
void |
TileStitcher.setId(java.lang.String id) |
void |
Memoizer.setId(java.lang.String id) |
void |
FileStitcher.setId(java.lang.String id) |
void |
DimensionSwapper.setId(java.lang.String id) |
void |
ChannelSeparator.setId(java.lang.String id) |
void |
ChannelFiller.setId(java.lang.String id) |
void |
WriterWrapper.setId(java.lang.String id) |
void |
ReaderWrapper.setId(java.lang.String id) |
void |
ImageWriter.setId(java.lang.String id) |
void |
ImageReader.setId(java.lang.String id) |
void |
IFormatHandler.setId(java.lang.String id)
Sets the current file name.
|
void |
FormatWriter.setId(java.lang.String id)
Initializes a writer from the input file name.
|
void |
FormatReader.setId(java.lang.String id)
Initialize a reader from the input file name.
|
void |
DelegateReader.setId(java.lang.String id) |
void |
WriterWrapper.setSeries(int series) |
void |
ImageWriter.setSeries(int series) |
void |
IFormatWriter.setSeries(int series)
Sets the current series.
|
void |
FormatWriter.setSeries(int series) |
int |
WriterWrapper.setTileSizeX(int tileSize) |
int |
ImageWriter.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 |
FormatWriter.setTileSizeX(int tileSize) |
int |
WriterWrapper.setTileSizeY(int tileSize) |
int |
ImageWriter.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 |
FormatWriter.setTileSizeY(int tileSize) |
IFormatWriter |
WriterWrapper.unwrap()
Unwraps nested wrapped writers until the core writer (i.e., not
a
WriterWrapper or ImageWriter) is found. |
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.
|
IFormatWriter |
WriterWrapper.unwrap(java.lang.Class<? extends IFormatWriter> writerClass,
java.lang.String id)
Unwraps nested wrapped writers until the given writer class is found.
|
IFormatWriter |
WriterWrapper.unwrap(java.lang.String id)
Unwraps nested wrapped writers until the core writer (i.e., not
a
WriterWrapper or ImageWriter) 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. |
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.
|
| Constructor and Description |
|---|
ExternalSeries(FilePattern pattern) |
| Modifier and Type | Class and Description |
|---|---|
class |
CacheException
CacheException is the exception thrown when something
goes wrong performing a cache operation.
|
| Modifier and Type | Method and Description |
|---|---|
(package private) static FormatException |
WrappedCodec.unwrapCodecException(ome.codecs.CodecException e) |
| Modifier and Type | Method and Description |
|---|---|
byte[] |
WrappedCodec.compress(byte[][] data,
CodecOptions options) |
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[] |
WrappedCodec.compress(byte[] data,
CodecOptions options) |
byte[] |
TargaRLECodec.compress(byte[] data,
CodecOptions options) |
byte[] |
NikonCodec.compress(byte[] data,
CodecOptions options) |
byte[] |
JPEGXRCodec.compress(byte[] data,
CodecOptions options) |
byte[] |
Codec.compress(byte[] data,
CodecOptions options)
Compresses a block of data.
|
private static void |
WrappedCodec.copyOptions(CodecOptions src,
ome.codecs.CodecOptions dest) |
byte[] |
WrappedCodec.decompress(byte[] data) |
byte[] |
BaseCodec.decompress(byte[] data) |
byte[] |
Codec.decompress(byte[] data)
Decompresses a block of data.
|
byte[] |
WrappedCodec.decompress(byte[][] data) |
byte[] |
BaseCodec.decompress(byte[][] data) |
byte[] |
Codec.decompress(byte[][] data)
Decompresses a block of data.
|
byte[] |
WrappedCodec.decompress(byte[][] data,
CodecOptions options) |
byte[] |
BaseCodec.decompress(byte[][] data,
CodecOptions options)
2D data block decoding default implementation.
|
byte[] |
Codec.decompress(byte[][] data,
CodecOptions options)
Decompresses a block of data.
|
byte[] |
WrappedCodec.decompress(byte[] data,
CodecOptions options) |
byte[] |
JPEGXRCodec.decompress(byte[] buf,
CodecOptions options)
The CodecOptions parameter should have the following fields set:
maxBytes
interleaved
bitsPerSample
littleEndian
width
height |
byte[] |
BaseCodec.decompress(byte[] data,
CodecOptions options) |
byte[] |
Codec.decompress(byte[] data,
CodecOptions options)
Decompresses a block of data.
|
byte[] |
WrappedCodec.decompress(loci.common.RandomAccessInputStream in,
CodecOptions options) |
byte[] |
TargaRLECodec.decompress(loci.common.RandomAccessInputStream in,
CodecOptions options)
The CodecOptions parameter should have the following fields set:
maxBytes
CodecOptions.bitsPerSample |
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[] |
JPEGXRCodec.decompress(loci.common.RandomAccessInputStream in,
CodecOptions options) |
abstract byte[] |
BaseCodec.decompress(loci.common.RandomAccessInputStream in,
CodecOptions options) |
byte[] |
Codec.decompress(loci.common.RandomAccessInputStream in,
CodecOptions options)
Decompresses data from the given RandomAccessInputStream.
|
protected static ome.codecs.CodecOptions |
WrappedCodec.getOptions(CodecOptions options) |
int |
HuffmanCodec.getSample(BitBuffer bb,
CodecOptions options)
Deprecated.
|
int |
HuffmanCodec.getSample(loci.common.RandomAccessInputStream bb,
CodecOptions options) |
private void |
JPEGXRCodec.initialize()
Initializes the JPEG-XR dependency service.
|
void |
BaseCodec.test()
Main testing method default implementation.
|
| Modifier and Type | Method and Description |
|---|---|
private int |
DicomTag.getNextTag(loci.common.RandomAccessInputStream in)
Get the next 4 byte DICOM tag from the given input stream.
|
| Constructor and Description |
|---|
DicomFileInfo(java.lang.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.
|
| Modifier and Type | Method and Description |
|---|---|
java.awt.Dimension |
LegacyQTTools.getPictDimensions(byte[] bytes)
Gets width and height for the given PICT bytes.
|
static java.awt.image.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 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.
|
java.awt.image.BufferedImage |
BufferedImageReader.openImage(int no)
Obtains the specified image from the current file.
|
java.awt.image.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).
|
java.awt.image.BufferedImage |
BufferedImageReader.openThumbImage(int no)
Obtains a thumbnail for the specified image from the current file.
|
java.awt.Image |
LegacyQTTools.pictToImage(byte[] bytes)
Converts the given byte array in PICT format to a Java image.
|
void |
BufferedImageWriter.saveImage(int no,
java.awt.image.BufferedImage image)
Saves the given BufferedImage to the current file.
|
void |
BufferedImageWriter.saveImage(int no,
java.awt.image.BufferedImage image,
int x,
int y,
int w,
int h)
Saves the given BufferedImage to the current file.
|
| Modifier and Type | Method and Description |
|---|---|
private void |
DicomReader.addFileToList(java.lang.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(org.w3c.dom.Element imageNode,
int image) |
static void |
FlexReader.appendServerMap(java.lang.String alias,
java.lang.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 boolean |
ZeissCZIReader.checkPALM(java.lang.String xml) |
private void |
ZeissCZIReader.convertPixelType(CoreMetadata ms0,
int pixelType) |
private void |
KLBReader.convertPixelType(CoreMetadata ms0,
int pixelType) |
private void |
ZeissCZIReader.convertPixelType(int pixelType) |
private int |
TillVisionReader.convertPixelType(int type) |
private int |
CellSensReader.convertPixelType(int pixelType) |
private DicomFileInfo |
DicomReader.createFileInfo(java.lang.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) |
private boolean |
PictReader.drivePictDecoder(int opcode)
Handles the opcodes in the PICT file.
|
protected ZeissTIFFReader.TIFFInfo |
ZeissTIFFReader.evalFile(java.lang.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 java.lang.String |
BDVReader.fetchXMLId() |
int |
ZeissTIFFReader.fileGroupOption(java.lang.String id) |
int |
ZeissLSMReader.fileGroupOption(java.lang.String id) |
int |
VisitechReader.fileGroupOption(java.lang.String id) |
int |
VentanaReader.fileGroupOption(java.lang.String id) |
int |
TrestleReader.fileGroupOption(java.lang.String id) |
int |
TillVisionReader.fileGroupOption(java.lang.String id) |
int |
TecanReader.fileGroupOption(java.lang.String id) |
int |
TCSReader.fileGroupOption(java.lang.String id) |
int |
ScanrReader.fileGroupOption(java.lang.String id) |
int |
SVSReader.fileGroupOption(java.lang.String id) |
int |
SPCReader.fileGroupOption(java.lang.String id) |
int |
PrairieReader.fileGroupOption(java.lang.String id) |
int |
PerkinElmerReader.fileGroupOption(java.lang.String id) |
int |
OperettaReader.fileGroupOption(java.lang.String id) |
int |
OlympusTileReader.fileGroupOption(java.lang.String id) |
int |
OIRReader.fileGroupOption(java.lang.String id) |
int |
NiftiReader.fileGroupOption(java.lang.String id) |
int |
NDPISReader.fileGroupOption(java.lang.String id) |
int |
NDPIReader.fileGroupOption(java.lang.String id) |
int |
MicroCTReader.fileGroupOption(java.lang.String id) |
int |
MetamorphReader.fileGroupOption(java.lang.String id) |
int |
MIASReader.fileGroupOption(java.lang.String id) |
int |
LeicaReader.fileGroupOption(java.lang.String id) |
int |
L2DReader.fileGroupOption(java.lang.String id) |
int |
InCellReader.fileGroupOption(java.lang.String id) |
int |
ImagicReader.fileGroupOption(java.lang.String id) |
int |
HitachiReader.fileGroupOption(java.lang.String id) |
int |
FujiReader.fileGroupOption(java.lang.String id) |
int |
FlexReader.fileGroupOption(java.lang.String id) |
int |
FV1000Reader.fileGroupOption(java.lang.String id) |
int |
ColumbusReader.fileGroupOption(java.lang.String id) |
int |
CellomicsReader.fileGroupOption(java.lang.String id) |
int |
CellWorxReader.fileGroupOption(java.lang.String id) |
int |
CellVoyagerReader.fileGroupOption(java.lang.String id) |
int |
CellSensReader.fileGroupOption(java.lang.String id) |
int |
CV7000Reader.fileGroupOption(java.lang.String id) |
int |
BrukerReader.fileGroupOption(java.lang.String id) |
int |
BioRadReader.fileGroupOption(java.lang.String id) |
int |
BDReader.fileGroupOption(java.lang.String id) |
int |
AnalyzeReader.fileGroupOption(java.lang.String id) |
int |
APLReader.fileGroupOption(java.lang.String id) |
int |
AFIReader.fileGroupOption(java.lang.String id) |
int |
NRRDReader.fileGroupOption(java.lang.String id) |
int |
MicromanagerReader.fileGroupOption(java.lang.String id) |
int |
KLBReader.fileGroupOption(java.lang.String id) |
int |
ICSReader.fileGroupOption(java.lang.String id) |
int |
DicomReader.fileGroupOption(java.lang.String id) |
protected void |
ZeissZVIReader.fillMetadataPass1(MetadataStore store) |
protected void |
ZeissTIFFReader.fillMetadataPass1(MetadataStore store) |
protected void |
BaseZeissReader.fillMetadataPass1(MetadataStore store)
Read and store basic dimensions in model
|
protected void |
ZeissTIFFReader.fillMetadataPass2(MetadataStore store) |
protected void |
BaseZeissReader.fillMetadataPass2(MetadataStore store)
Read and store basic dimensions in model
|
protected void |
ZeissZVIReader.fillMetadataPass3(MetadataStore store) |
protected void |
BaseZeissReader.fillMetadataPass3(MetadataStore store)
Read and store basic dimensions in model
|
protected void |
BaseZeissReader.fillMetadataPass4(MetadataStore store)
Read and store basic dimensions in model
|
protected void |
ZeissZVIReader.fillMetadataPass5(MetadataStore store) |
protected void |
ZeissTIFFReader.fillMetadataPass5(MetadataStore store) |
protected void |
BaseZeissReader.fillMetadataPass5(MetadataStore store)
Read and store basic dimensions in model
|
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 java.lang.String |
LeicaReader.findLEIFile(java.lang.String baseFile)
Find the .lei file that belongs to the same dataset as the given file.
|
private java.lang.String |
FV1000Reader.findOIFFile(java.lang.String baseFile) |
protected void |
MetaxpressTiffReader.findPixelsFiles() |
protected void |
CellWorxReader.findPixelsFiles() |
short[][] |
ZeissLSMReader.get16BitLookupTable() |
short[][] |
ZeissCZIReader.get16BitLookupTable() |
short[][] |
VentanaReader.get16BitLookupTable() |
short[][] |
TCSReader.get16BitLookupTable() |
short[][] |
SlidebookTiffReader.get16BitLookupTable() |
short[][] |
PerkinElmerReader.get16BitLookupTable() |
short[][] |
PDSReader.get16BitLookupTable() |
short[][] |
OIRReader.get16BitLookupTable() |
short[][] |
MIASReader.get16BitLookupTable() |
short[][] |
LeicaReader.get16BitLookupTable() |
short[][] |
InCellReader.get16BitLookupTable() |
short[][] |
ImprovisionTiffReader.get16BitLookupTable() |
short[][] |
BaseZeissReader.get16BitLookupTable() |
short[][] |
ZipReader.get16BitLookupTable() |
short[][] |
OMETiffReader.get16BitLookupTable() |
short[][] |
MinimalTiffReader.get16BitLookupTable() |
short[][] |
FilePatternReader.get16BitLookupTable() |
short[][] |
FakeReader.get16BitLookupTable() |
byte[][] |
ZeissLSMReader.get8BitLookupTable() |
byte[][] |
ZeissCZIReader.get8BitLookupTable() |
byte[][] |
VentanaReader.get8BitLookupTable() |
byte[][] |
TargaReader.get8BitLookupTable() |
byte[][] |
TCSReader.get8BitLookupTable() |
byte[][] |
SlidebookTiffReader.get8BitLookupTable() |
byte[][] |
PerkinElmerReader.get8BitLookupTable() |
byte[][] |
OIRReader.get8BitLookupTable() |
byte[][] |
MIASReader.get8BitLookupTable() |
byte[][] |
LeicaReader.get8BitLookupTable() |
byte[][] |
KhorosReader.get8BitLookupTable() |
byte[][] |
InCellReader.get8BitLookupTable() |
byte[][] |
ImprovisionTiffReader.get8BitLookupTable() |
byte[][] |
IPWReader.get8BitLookupTable() |
byte[][] |
BaseZeissReader.get8BitLookupTable() |
byte[][] |
ZipReader.get8BitLookupTable() |
byte[][] |
PictReader.get8BitLookupTable() |
byte[][] |
OMETiffReader.get8BitLookupTable() |
byte[][] |
MinimalTiffReader.get8BitLookupTable() |
byte[][] |
GIFReader.get8BitLookupTable() |
byte[][] |
FilePatternReader.get8BitLookupTable() |
byte[][] |
FakeReader.get8BitLookupTable() |
byte[][] |
BMPReader.get8BitLookupTable() |
protected ome.xml.model.enums.AcquisitionMode |
OperettaReader.getAcquisitionMode(java.lang.String mode) |
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(java.lang.String file)
Get the color associated with the given file's channel.
|
private boolean |
OBFReader.getCompression(int compression) |
private loci.common.RandomAccessInputStream |
ZeissLSMReader.getCZTag(IFD ifd) |
private loci.common.RandomAccessInputStream |
CellomicsReader.getDecompressedStream(java.lang.String filename) |
private int |
ZeissLSMReader.getExtraSeries(java.lang.String file) |
private loci.common.RandomAccessInputStream |
FV1000Reader.getFile(java.lang.String name) |
private java.lang.String |
SlidebookTiffReader.getFirstChannel(java.lang.String path) |
private java.lang.Object |
CellH5Reader.getImageData(int no,
int y,
int height) |
private java.lang.Object |
ImarisHDFReader.getImageData(int no,
int x,
int y,
int width,
int height)
Retrieve an array corresponding to the specified image tile.
|
private java.lang.Object |
BDVReader.getImageData(int no,
int x,
int y,
int width,
int height) |
private loci.common.IniList |
FV1000Reader.getIniFile(java.lang.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) |
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(java.util.Map materials) |
private java.lang.String |
ZeissLSMReader.getMDBFile(java.lang.String id) |
private org.w3c.dom.Element |
OlympusTileReader.getMetadataRoot(java.lang.String xml) |
private org.w3c.dom.Element |
LIFReader.getMetadataRoot(java.lang.String xml) |
private int |
OBFReader.getPixelType(int type) |
private int |
LiFlimReader.getPixelTypeFromString(java.lang.String type) |
protected IFormatReader |
MetaxpressTiffReader.getReader(java.lang.String file,
boolean omexml) |
protected IFormatReader |
CellWorxReader.getReader(java.lang.String file,
boolean omexml) |
int |
TecanReader.getRequiredDirectories(java.lang.String[] files) |
int |
OperettaReader.getRequiredDirectories(java.lang.String[] files) |
int |
MicroCTReader.getRequiredDirectories(java.lang.String[] files) |
int |
MIASReader.getRequiredDirectories(java.lang.String[] files) |
int |
ColumbusReader.getRequiredDirectories(java.lang.String[] files) |
int |
CellVoyagerReader.getRequiredDirectories(java.lang.String[] files) |
int |
CV7000Reader.getRequiredDirectories(java.lang.String[] files) |
int |
BrukerReader.getRequiredDirectories(java.lang.String[] files) |
int |
OMETiffReader.getRequiredDirectories(java.lang.String[] files) |
int |
DicomReader.getRequiredDirectories(java.lang.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
|
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.
|
java.lang.String |
SPEReader.SpeHeader.getString(SPEReader.SpeHeaderEntry entry)
Method used to retrieve data values for String entries into the SPE header table
|
private java.lang.String[] |
MetaxpressTiffReader.getTiffFiles(java.lang.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) |
private java.lang.String |
SlidebookTiffReader.getTimestamp(java.lang.String path) |
private long |
BDReader.getTimestamp(java.lang.String file) |
private java.lang.String |
ImprovisionTiffReader.getUUID(java.lang.String path) |
private void |
TCSReader.groupFiles() |
private void |
FlexReader.groupFiles(java.lang.String[] fileList,
MetadataStore store) |
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() |
private void |
LiFlimReader.initCoreMetadata() |
protected void |
LeicaSCNReader.initCoreMetadata(int series,
int resolution) |
protected void |
DeltavisionReader.initExtraMetadata() |
protected void |
ZeissZVIReader.initFile(java.lang.String id) |
protected void |
ZeissTIFFReader.initFile(java.lang.String id) |
protected void |
ZeissLSMReader.initFile(java.lang.String id) |
void |
ZeissLMSReader.initFile(java.lang.String id) |
protected void |
ZeissCZIReader.initFile(java.lang.String id) |
protected void |
WlzReader.initFile(java.lang.String id) |
protected void |
WATOPReader.initFile(java.lang.String id) |
protected void |
VolocityReader.initFile(java.lang.String id) |
protected void |
VolocityClippingReader.initFile(java.lang.String id) |
protected void |
VisitechReader.initFile(java.lang.String id) |
protected void |
VeecoReader.initFile(java.lang.String id) |
protected void |
VarianFDFReader.initFile(java.lang.String id) |
protected void |
VGSAMReader.initFile(java.lang.String id) |
protected void |
UnisokuReader.initFile(java.lang.String id) |
protected void |
UBMReader.initFile(java.lang.String id) |
protected void |
TrestleReader.initFile(java.lang.String id) |
protected void |
TopometrixReader.initFile(java.lang.String id) |
protected void |
TillVisionReader.initFile(java.lang.String id) |
protected void |
TecanReader.initFile(java.lang.String id) |
protected void |
TargaReader.initFile(java.lang.String id) |
protected void |
TCSReader.initFile(java.lang.String id) |
protected void |
SpiderReader.initFile(java.lang.String id) |
protected void |
SlidebookReader.initFile(java.lang.String id) |
protected void |
SeikoReader.initFile(java.lang.String id) |
protected void |
ScanrReader.initFile(java.lang.String id) |
protected void |
SPEReader.initFile(java.lang.String id) |
protected void |
SPCReader.initFile(java.lang.String id) |
protected void |
SMCameraReader.initFile(java.lang.String id) |
protected void |
SIFReader.initFile(java.lang.String id) |
protected void |
SEQReader.initFile(java.lang.String id) |
protected void |
SDTReader.initFile(java.lang.String id) |
protected void |
SBIGReader.initFile(java.lang.String id) |
protected void |
RHKReader.initFile(java.lang.String id) |
protected void |
QuesantReader.initFile(java.lang.String id) |
protected void |
PrairieReader.initFile(java.lang.String id) |
protected void |
PovrayReader.initFile(java.lang.String id) |
protected void |
PhotoshopTiffReader.initFile(java.lang.String id) |
protected void |
PerkinElmerReader.initFile(java.lang.String id) |
protected void |
PSDReader.initFile(java.lang.String id) |
protected void |
PQBinReader.initFile(java.lang.String id) |
protected void |
PDSReader.initFile(java.lang.String id) |
protected void |
PCORAWReader.initFile(java.lang.String id) |
protected void |
PCIReader.initFile(java.lang.String id) |
protected void |
OxfordInstrumentsReader.initFile(java.lang.String id) |
protected void |
OperettaReader.initFile(java.lang.String id) |
protected void |
OpenlabReader.initFile(java.lang.String id) |
protected void |
OpenlabRawReader.initFile(java.lang.String id) |
protected void |
OlympusTileReader.initFile(java.lang.String id) |
protected void |
OIRReader.initFile(java.lang.String id) |
protected void |
NikonReader.initFile(java.lang.String id) |
protected void |
NiftiReader.initFile(java.lang.String id) |
protected void |
NativeND2Reader.initFile(java.lang.String id) |
protected void |
NDPISReader.initFile(java.lang.String id) |
protected void |
NDPIReader.initFile(java.lang.String id) |
protected void |
NAFReader.initFile(java.lang.String id) |
protected void |
MolecularImagingReader.initFile(java.lang.String id) |
protected void |
MicroCTReader.initFile(java.lang.String id) |
protected void |
MetamorphTiffReader.initFile(java.lang.String id) |
protected void |
MetamorphReader.initFile(java.lang.String id) |
protected void |
MRWReader.initFile(java.lang.String id) |
void |
MRCReader.initFile(java.lang.String id) |
protected void |
MINCReader.initFile(java.lang.String id) |
protected void |
MIASReader.initFile(java.lang.String id) |
protected void |
LiFlimReader.initFile(java.lang.String id) |
protected void |
LeicaReader.initFile(java.lang.String id) |
protected void |
LegacyND2Reader.initFile(java.lang.String id) |
protected void |
LIMReader.initFile(java.lang.String id) |
protected void |
LIFReader.initFile(java.lang.String id) |
protected void |
L2DReader.initFile(java.lang.String id) |
protected void |
KodakReader.initFile(java.lang.String id) |
protected void |
KhorosReader.initFile(java.lang.String id) |
protected void |
JPXReader.initFile(java.lang.String id) |
protected void |
JEOLReader.initFile(java.lang.String id) |
protected void |
IvisionReader.initFile(java.lang.String id) |
protected void |
InveonReader.initFile(java.lang.String id) |
protected void |
InCellReader.initFile(java.lang.String id) |
protected void |
InCell3000Reader.initFile(java.lang.String id) |
protected void |
ImspectorReader.initFile(java.lang.String id) |
protected void |
ImarisTiffReader.initFile(java.lang.String id) |
protected void |
ImarisReader.initFile(java.lang.String id) |
protected void |
ImarisHDFReader.initFile(java.lang.String id) |
protected void |
ImagicReader.initFile(java.lang.String id) |
protected void |
IPWReader.initFile(java.lang.String id) |
protected void |
IPLabReader.initFile(java.lang.String id) |
protected void |
INRReader.initFile(java.lang.String id) |
protected void |
IMODReader.initFile(java.lang.String id) |
void |
I2IReader.initFile(java.lang.String id) |
protected void |
HitachiReader.initFile(java.lang.String id) |
protected void |
HamamatsuVMSReader.initFile(java.lang.String id) |
protected void |
HRDGDFReader.initFile(java.lang.String id) |
protected void |
HISReader.initFile(java.lang.String id) |
protected void |
GatanReader.initFile(java.lang.String id) |
protected void |
GatanDM2Reader.initFile(java.lang.String id) |
protected void |
FujiReader.initFile(java.lang.String id) |
protected void |
FlexReader.initFile(java.lang.String id) |
protected void |
FV1000Reader.initFile(java.lang.String id) |
protected void |
FEIReader.initFile(java.lang.String id) |
protected void |
Ecat7Reader.initFile(java.lang.String id) |
protected void |
DeltavisionReader.initFile(java.lang.String id) |
protected void |
DNGReader.initFile(java.lang.String id) |
protected void |
ColumbusReader.initFile(java.lang.String id) |
protected void |
CellomicsReader.initFile(java.lang.String id) |
protected void |
CellWorxReader.initFile(java.lang.String id) |
protected void |
CellVoyagerReader.initFile(java.lang.String id) |
protected void |
CellSensReader.initFile(java.lang.String id) |
protected void |
CanonRawReader.initFile(java.lang.String id) |
protected void |
CV7000Reader.initFile(java.lang.String id) |
protected void |
BurleighReader.initFile(java.lang.String id) |
protected void |
BrukerReader.initFile(java.lang.String id) |
protected void |
BioRadSCNReader.initFile(java.lang.String id) |
protected void |
BioRadReader.initFile(java.lang.String id) |
protected void |
BioRadGelReader.initFile(java.lang.String id) |
protected void |
BDReader.initFile(java.lang.String id) |
protected void |
AnalyzeReader.initFile(java.lang.String id) |
protected void |
AmiraReader.initFile(java.lang.String id) |
protected void |
AliconaReader.initFile(java.lang.String id) |
protected void |
ARFReader.initFile(java.lang.String id) |
protected void |
APLReader.initFile(java.lang.String id) |
protected void |
AIMReader.initFile(java.lang.String id) |
protected void |
AFIReader.initFile(java.lang.String id) |
protected void |
ZipReader.initFile(java.lang.String id) |
void |
TileJPEGReader.initFile(java.lang.String id) |
protected void |
TiffJAIReader.initFile(java.lang.String id) |
protected void |
TextReader.initFile(java.lang.String id) |
protected void |
PictReader.initFile(java.lang.String id) |
protected void |
PGMReader.initFile(java.lang.String id) |
protected void |
PCXReader.initFile(java.lang.String id) |
protected void |
OMEXMLReader.initFile(java.lang.String id) |
protected void |
OMETiffReader.initFile(java.lang.String id) |
protected void |
OBFReader.initFile(java.lang.String id) |
protected void |
NativeQTReader.initFile(java.lang.String id) |
protected void |
NRRDReader.initFile(java.lang.String id) |
protected void |
MinimalTiffReader.initFile(java.lang.String id) |
void |
MicromanagerReader.initFile(java.lang.String id) |
protected void |
MNGReader.initFile(java.lang.String id) |
protected void |
LegacyQTReader.initFile(java.lang.String id) |
protected void |
KLBReader.initFile(java.lang.String id) |
protected void |
JPEGReader.DefaultJPEGReader.initFile(java.lang.String id) |
protected void |
JPEG2000Reader.initFile(java.lang.String id) |
protected void |
ImageIOReader.initFile(java.lang.String id) |
protected void |
IM3Reader.initFile(java.lang.String id) |
protected void |
ICSReader.initFile(java.lang.String id) |
protected void |
GIFReader.initFile(java.lang.String id) |
protected void |
FlowSightReader.initFile(java.lang.String id) |
protected void |
FitsReader.initFile(java.lang.String id) |
protected void |
FilePatternReader.initFile(java.lang.String id) |
protected void |
FakeReader.initFile(java.lang.String id) |
protected void |
EPSReader.initFile(java.lang.String id) |
protected void |
DicomReader.initFile(java.lang.String id) |
protected void |
CellH5Reader.initFile(java.lang.String id) |
protected void |
BaseTiffReader.initFile(java.lang.String id) |
protected void |
BMPReader.initFile(java.lang.String id) |
protected void |
BDVReader.initFile(java.lang.String id) |
protected void |
AVIReader.initFile(java.lang.String id) |
protected void |
APNGReader.initFile(java.lang.String id) |
protected void |
BaseZeissReader.initFileMain(java.lang.String id) |
private void |
FlexReader.initFlexFile(java.lang.String id) |
private void |
OMETiffReader.initializeReader(IFormatReader r,
java.lang.String file) |
protected void |
ImageIOReader.initImage() |
private void |
FlexReader.initMeaFile(java.lang.String id)
Initialize the dataset from a .mea file.
|
protected void |
GelReader.initMetadata() |
protected void |
BaseTiffReader.initMetadata()
Populates the metadata hashtable and metadata store.
|
protected void |
ZeissLSMReader.initMetadata(int series) |
private void |
LIFReader.initMetadata(java.lang.String xml)
Parses a string of XML and puts the values in a Hashtable.
|
protected void |
VentanaReader.initMetadataStore() |
protected void |
VectraReader.initMetadataStore() |
protected void |
TrestleReader.initMetadataStore() |
protected void |
SlidebookTiffReader.initMetadataStore() |
protected void |
SimplePCITiffReader.initMetadataStore() |
protected void |
SVSReader.initMetadataStore() |
protected void |
SISReader.initMetadataStore() |
protected void |
PyramidTiffReader.initMetadataStore() |
protected void |
NikonTiffReader.initMetadataStore() |
protected void |
NikonElementsTiffReader.initMetadataStore() |
protected void |
NDPIReader.initMetadataStore() |
protected void |
LeicaSCNReader.initMetadataStore() |
protected void |
LEOReader.initMetadataStore() |
protected void |
JPKReader.initMetadataStore() |
protected void |
IonpathMIBITiffReader.initMetadataStore() |
protected void |
ImprovisionTiffReader.initMetadataStore() |
protected void |
ImaconReader.initMetadataStore() |
protected void |
FluoviewReader.initMetadataStore() |
protected void |
FEITiffReader.initMetadataStore() |
protected void |
TiffReader.initMetadataStore() |
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 |
DeltavisionReader.initPixels() |
private void |
ZeissZVIReader.initPOIService() |
private void |
PCIReader.initPOIService() |
private void |
IPWReader.initPOIService() |
private void |
FV1000Reader.initPOIService() |
protected void |
CellWorxReader.initReader(IFormatReader reader,
java.lang.String file,
boolean omexml) |
private void |
FlexReader.initResFile(java.lang.String id)
Initialize the dataset from a .res file.
|
private long |
OBFReader.initStack(long current) |
protected void |
VentanaReader.initStandardMetadata() |
protected void |
VectraReader.initStandardMetadata() |
protected void |
TrestleReader.initStandardMetadata() |
protected void |
SlidebookTiffReader.initStandardMetadata() |
protected void |
SimplePCITiffReader.initStandardMetadata() |
protected void |
SVSReader.initStandardMetadata() |
protected void |
SISReader.initStandardMetadata() |
protected void |
SEQReader.initStandardMetadata() |
protected void |
PyramidTiffReader.initStandardMetadata() |
protected void |
NikonTiffReader.initStandardMetadata() |
protected void |
NikonReader.initStandardMetadata() |
protected void |
NikonElementsTiffReader.initStandardMetadata() |
protected void |
NDPIReader.initStandardMetadata() |
protected void |
MetamorphReader.initStandardMetadata() |
protected void |
LeicaSCNReader.initStandardMetadata() |
protected void |
LEOReader.initStandardMetadata() |
protected void |
JPKReader.initStandardMetadata() |
protected void |
IonpathMIBITiffReader.initStandardMetadata() |
protected void |
ImprovisionTiffReader.initStandardMetadata() |
protected void |
ImaconReader.initStandardMetadata() |
protected void |
FluoviewReader.initStandardMetadata() |
protected void |
FEITiffReader.initStandardMetadata() |
protected void |
DNGReader.initStandardMetadata() |
protected void |
TiffReader.initStandardMetadata() |
protected void |
BaseTiffReader.initStandardMetadata()
Parses standard metadata.
|
protected void |
ZeissZVIReader.initVars(java.lang.String id) |
protected void |
ZeissTIFFReader.initVars(java.lang.String id) |
protected void |
BaseZeissReader.initVars(java.lang.String id) |
boolean |
ZeissTIFFReader.isSingleFile(java.lang.String id) |
boolean |
ZeissLSMReader.isSingleFile(java.lang.String id) |
boolean |
VisitechReader.isSingleFile(java.lang.String id) |
boolean |
TillVisionReader.isSingleFile(java.lang.String id) |
boolean |
TecanReader.isSingleFile(java.lang.String id) |
boolean |
TCSReader.isSingleFile(java.lang.String id) |
boolean |
ScanrReader.isSingleFile(java.lang.String id) |
boolean |
SPCReader.isSingleFile(java.lang.String id) |
boolean |
PrairieReader.isSingleFile(java.lang.String id) |
boolean |
PerkinElmerReader.isSingleFile(java.lang.String id) |
boolean |
OperettaReader.isSingleFile(java.lang.String id) |
boolean |
OlympusTileReader.isSingleFile(java.lang.String id) |
boolean |
OIRReader.isSingleFile(java.lang.String id) |
boolean |
NiftiReader.isSingleFile(java.lang.String id) |
boolean |
NDPISReader.isSingleFile(java.lang.String id) |
boolean |
MicroCTReader.isSingleFile(java.lang.String id) |
boolean |
MetamorphReader.isSingleFile(java.lang.String id) |
boolean |
MIASReader.isSingleFile(java.lang.String id) |
boolean |
LeicaReader.isSingleFile(java.lang.String id) |
boolean |
L2DReader.isSingleFile(java.lang.String id) |
boolean |
InCellReader.isSingleFile(java.lang.String id) |
boolean |
ImagicReader.isSingleFile(java.lang.String id) |
boolean |
HitachiReader.isSingleFile(java.lang.String id) |
boolean |
FujiReader.isSingleFile(java.lang.String id) |
boolean |
FlexReader.isSingleFile(java.lang.String id) |
boolean |
FV1000Reader.isSingleFile(java.lang.String id) |
boolean |
DeltavisionReader.isSingleFile(java.lang.String id) |
boolean |
ColumbusReader.isSingleFile(java.lang.String id) |
boolean |
CellVoyagerReader.isSingleFile(java.lang.String id) |
boolean |
CellSensReader.isSingleFile(java.lang.String id) |
boolean |
CV7000Reader.isSingleFile(java.lang.String id) |
boolean |
BrukerReader.isSingleFile(java.lang.String id) |
boolean |
BioRadReader.isSingleFile(java.lang.String id) |
boolean |
BDReader.isSingleFile(java.lang.String id) |
boolean |
AnalyzeReader.isSingleFile(java.lang.String id) |
boolean |
APLReader.isSingleFile(java.lang.String id) |
boolean |
AFIReader.isSingleFile(java.lang.String id) |
boolean |
OMETiffReader.isSingleFile(java.lang.String id) |
boolean |
NRRDReader.isSingleFile(java.lang.String id) |
boolean |
MicromanagerReader.isSingleFile(java.lang.String id) |
boolean |
ICSReader.isSingleFile(java.lang.String id) |
boolean |
FilePatternReader.isSingleFile(java.lang.String id) |
boolean |
FakeReader.isSingleFile(java.lang.String id) |
void |
DynamicMetadataOptions.loadOptions(java.lang.String optionsFile,
java.util.ArrayList<java.lang.String> availableOptionKeys) |
private java.lang.String |
BDReader.locateExperimentFile(java.lang.String id) |
private void |
DicomReader.makeFileList()
Build a list of files that belong with the current file.
|
private java.lang.String |
FV1000Reader.mapOIBFiles() |
static void |
FlexReader.mapServersFromConfigurationFile(java.lang.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 java.awt.image.BufferedImage |
TiffJAIReader.openBufferedImage(int no)
Obtains a BufferedImage from the given data source using JAI.
|
byte[] |
ZeissZVIReader.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[] |
ZeissLSMReader.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[] |
ZeissCZIReader.openBytes(int no,
byte[] buf,
int x,
int y,
int w,
int h) |
byte[] |
WlzReader.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[] |
VolocityReader.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[] |
VisitechReader.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[] |
VeecoReader.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[] |
VarianFDFReader.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[] |
UnisokuReader.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[] |
TrestleReader.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[] |
TillVisionReader.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[] |
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[] |
SpiderReader.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[] |
SlidebookReader.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[] |
SeikoReader.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[] |
SVSReader.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[] |
SPCReader.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[] |
SIFReader.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[] |
SDTReader.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[] |
RHKReader.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[] |
PyramidTiffReader.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[] |
PovrayReader.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[] |
PerkinElmerReader.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[] |
PQBinReader.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[] |
PCORAWReader.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[] |
OxfordInstrumentsReader.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[] |
OpenlabReader.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[] |
OlympusTileReader.openBytes(int no,
byte[] buf,
int x,
int y,
int w,
int h) |
byte[] |
OIRReader.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[] |
NiftiReader.openBytes(int no,
byte[] buf,
int x,
int y,
int w,
int h) |
byte[] |
NativeND2Reader.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[] |
NDPIReader.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[] |
MolecularImagingReader.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[] |
MetamorphTiffReader.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[] |
MRWReader.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[] |
MINCReader.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[] |
LiFlimReader.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[] |
LeicaReader.openBytes(int no,
byte[] buf,
int x,
int y,
int w,
int h) |
byte[] |
LegacyND2Reader.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[] |
LIFReader.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[] |
KodakReader.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[] |
JPXReader.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[] |
JEOLReader.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[] |
IonpathMIBITiffReader.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[] |
InCellReader.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[] |
ImspectorReader.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[] |
ImarisReader.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[] |
ImagicReader.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[] |
IPWReader.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[] |
INRReader.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[] |
I2IReader.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[] |
HamamatsuVMSReader.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[] |
HISReader.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[] |
GatanReader.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[] |
FujiReader.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[] |
FlexReader.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[] |
FEIReader.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[] |
DeltavisionReader.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[] |
ColumbusReader.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[] |
CellWorxReader.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[] |
CellSensReader.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[] |
CV7000Reader.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[] |
BrukerReader.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[] |
BioRadReader.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[] |
BDReader.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[] |
AmiraReader.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[] |
ARFReader.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[] |
AIMReader.openBytes(int no,
byte[] buf,
int x,
int y,
int w,
int h) |
byte[] |
AFIReader.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) |
byte[] |
TileJPEGReader.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[] |
TextReader.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[] |
PGMReader.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[] |
OMEXMLReader.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[] |
OBFReader.openBytes(int no,
byte[] buffer,
int x,
int y,
int w,
int h) |
byte[] |
NativeQTReader.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[] |
MinimalTiffReader.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[] |
KLBReader.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[] |
IM3Reader.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[] |
GIFReader.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[] |
FitsReader.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[] |
EPSReader.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[] |
CellH5Reader.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[] |
BIFormatReader.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[] |
AVIReader.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) |
private byte[] |
FlowSightReader.openGreyscaleBytes(IFD ifd,
int imageWidth,
int imageHeight)
Decode the whole IFD plane using greyscale compression
|
java.lang.Object |
TiffJAIReader.openPlane(int no,
int x,
int y,
int w,
int h) |
java.lang.Object |
TextReader.openPlane(int no,
int x,
int y,
int w,
int h) |
java.lang.Object |
MNGReader.openPlane(int no,
int x,
int y,
int w,
int h) |
java.lang.Object |
LegacyQTReader.openPlane(int no,
int x,
int y,
int w,
int h) |
java.lang.Object |
ImageIOReader.openPlane(int no,
int x,
int y,
int w,
int h) |
byte[] |
VentanaReader.openThumbBytes(int no) |
byte[] |
VectraReader.openThumbBytes(int no) |
byte[] |
SVSReader.openThumbBytes(int no) |
byte[] |
NDPIReader.openThumbBytes(int no) |
byte[] |
LeicaSCNReader.openThumbBytes(int no) |
byte[] |
CellSensReader.openThumbBytes(int no) |
byte[] |
AFIReader.openThumbBytes(int no) |
byte[] |
MinimalTiffReader.openThumbBytes(int no) |
private void |
NativeQTReader.parse(int depth,
long offset,
long length)
Parse all of the atoms in the file.
|
private void |
TiffReader.parseCommentImageJ(java.lang.String comment) |
private void |
LeicaReader.parseDimensionTag(int seriesIndex) |
private void |
CellSensReader.parseETSFile(loci.common.RandomAccessInputStream etsFile,
java.lang.String file,
int s) |
private void |
VarianFDFReader.parseFDF(java.lang.String file) |
private int |
TextReader.parseFileHeader(java.util.List<java.lang.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(org.w3c.dom.Element root) |
protected void |
CellWorxReader.parseHTD() |
private void |
OIRReader.parseImageProperties(org.w3c.dom.Element root) |
private void |
ColumbusReader.parseImageXML(java.lang.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(org.w3c.dom.Element root,
java.lang.String uid) |
(package private) void |
BaseZeissReader.parseMainTags(int image,
MetadataStore store,
java.util.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,
java.lang.String overlayTiff)
Parse Mask ROIs from the given TIFF and place them in the given
MetadataStore.
|
private java.lang.String[] |
ZeissLSMReader.parseMDB(java.lang.String mdbFile)
Parse a .mdb file and return a list of referenced .lsm files.
|
private boolean |
BioRadReader.parseNotes(MetadataStore store) |
private void |
ZeissCZIReader.parseObjectives(org.w3c.dom.NodeList objectives) |
private void |
MicromanagerReader.parsePosition(int posIndex) |
private void |
MicromanagerReader.parsePosition(java.lang.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(java.lang.String filename,
MetadataStore store,
int nextROI,
int plane) |
private void |
TrestleReader.parseROIs(MetadataStore store) |
private void |
CellH5Reader.parseStructure() |
private void |
BDVReader.parseStructure() |
private void |
ZeissZVIReader.parseTags(int image,
java.lang.String file,
MetadataStore store)
Parse all of the tags in a stream.
|
private void |
GatanReader.parseTags(int numTags,
java.lang.String parent,
java.lang.String indent)
Parses Gatan DM3 tags.
|
private void |
IPLabReader.parseTags(MetadataStore store) |
private void |
OIRReader.parseXML(loci.common.RandomAccessInputStream s,
java.lang.String xml,
long startFilePointer) |
private void |
PrairieReader.populateCoreMetadata()
This step populates the
CoreMetadata by extracting relevant values
from the parsed PrairieReader.meta structure. |
private void |
FlexReader.populateCoreMetadata(int wellRow,
int wellCol,
int field,
java.util.List<java.lang.String> imageNames)
Populate core metadata using the given list of image names.
|
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 |
TillVisionReader.populateMetadataStore() |
private void |
FlexReader.populateMetadataStore(MetadataStore store) |
private void |
FV1000Reader.populateMetadataStore(MetadataStore store,
java.lang.String path) |
private void |
NativeND2Reader.populateMetadataStore(ND2Handler handler) |
void |
MicromanagerReader.populateMetadataStore(java.lang.String[] jsonData) |
protected void |
ZeissLSMReader.populateMetadataStore(ZeissLSMReader.SubBlock block,
MetadataStore store,
int series) |
protected void |
RCPNLReader.populateObjective(MetadataStore store,
int lensID) |
protected void |
DeltavisionReader.populateObjective(MetadataStore store,
int lensID)
Populate an Objective based upon the lens ID.
|
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.
|
(package private) void |
AmiraReader.HxRLE.read(byte[] buf,
int len) |
byte[] |
AmiraReader.PlaneReader.read(int no,
byte[] buf) |
byte[] |
AmiraReader.ASCII.read(int no,
byte[] buf) |
byte[] |
AmiraReader.HxZip.read(int no,
byte[] buf) |
byte[] |
AmiraReader.HxRLE.read(int no,
byte[] buf) |
private void |
ZeissCZIReader.readAttachments() |
private void |
AVIReader.readChunk() |
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(org.w3c.dom.Document msDocument,
org.w3c.dom.Document omeDocument) |
private int[] |
GIFReader.readLut(int size)
Read a color lookup table of the specified size.
|
private void |
OlympusTileReader.readMetadata(java.lang.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(java.lang.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(java.lang.String file,
loci.common.RandomAccessInputStream s) |
private void |
KLBReader.reCalculateBlockOffsets(int no) |
private long |
OBFReader.remainingBytesInChunk(OBFReader.Stack stack) |
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(java.lang.String pattern,
java.lang.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 |
TiffDelegateReader.setId(java.lang.String id) |
void |
JPEGReader.setId(java.lang.String id) |
private void |
OMETiffReader.setupService() |
private void |
OBFReader.skipBytes(OBFReader.Stack stack,
long byteCount) |
protected void |
BaseZeissReader.storeROIs(MetadataStore store)
Store basic dimensions in model
|
private void |
OBFReader.switchChunk(OBFReader.Stack stack,
int chunkIndex) |
private void |
LIFReader.translateAttachmentNodes(org.w3c.dom.Element imageNode,
int image) |
private void |
LIFReader.translateDetectors(org.w3c.dom.Element imageNode,
int image) |
private void |
ZeissCZIReader.translateDisplaySettings(org.w3c.dom.Element root) |
private void |
ZeissCZIReader.translateExperiment(org.w3c.dom.Element root) |
private void |
LIFReader.translateFilterSettings(org.w3c.dom.Element imageNode,
int image) |
private void |
ZeissCZIReader.translateHardwareSettings(org.w3c.dom.Element root) |
private void |
LIFReader.translateImageNodes(org.w3c.dom.Element imageNode,
int i) |
private void |
ZeissCZIReader.translateInformation(org.w3c.dom.Element root) |
private void |
LIFReader.translateLaserLines(org.w3c.dom.Element imageNode,
int image) |
private void |
LIFReader.translateMetadata(org.w3c.dom.Element root) |
private void |
ZeissCZIReader.translateMetadata(java.lang.String xml) |
private void |
LIFReader.translateROIs(org.w3c.dom.Element imageNode,
int image) |
private void |
LIFReader.translateScannerSettings(org.w3c.dom.Element imageNode,
int image) |
private void |
LIFReader.translateSingleROIs(org.w3c.dom.Element imageNode,
int image) |
private void |
LIFReader.translateTimestamps(org.w3c.dom.Element imageNode,
int image) |
private byte[] |
NativeQTReader.uncompress(byte[] pixs,
java.lang.String code)
Uncompresses an image plane according to the the codec identifier.
|
private byte[] |
AVIReader.uncompress(int no,
byte[] buf) |
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) |
| Modifier and Type | Method and Description |
|---|---|
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 java.lang.String |
OMETiffWriter.getBinaryOnlyOMEXML(java.lang.String file,
java.lang.String companion,
java.lang.String companionUUID) |
private java.lang.String |
OMETiffWriter.getOMEXML(java.lang.String file) |
int |
TiffWriter.getTileSizeX() |
int |
TiffWriter.getTileSizeY() |
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 |
CellH5Writer.saveBytes(int no,
byte[] buf)
Saves the given image to the specified (possibly already open) file.
|
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 |
PyramidOMETiffWriter.saveBytes(int no,
byte[] buf,
IFD ifd,
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 |
WlzWriter.saveBytes(int no,
byte[] buf,
int x,
int y,
int w,
int h) |
void |
V3DrawWriter.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 |
QTWriter.saveBytes(int no,
byte[] buf,
int x,
int y,
int w,
int h) |
void |
OMEXMLWriter.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 |
LegacyQTWriter.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 |
ImageIOWriter.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 |
EPSWriter.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 |
CellH5Writer.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 |
APNGWriter.saveBytes(int no,
byte[] buf,
int x,
int y,
int w,
int h) |
void |
LegacyQTWriter.savePlane(int no,
java.lang.Object plane,
int x,
int y,
int w,
int h) |
void |
ImageIOWriter.savePlane(int no,
java.lang.Object plane,
int x,
int y,
int w,
int h) |
void |
WlzWriter.setId(java.lang.String id) |
void |
V3DrawWriter.setId(java.lang.String id) |
void |
TiffWriter.setId(java.lang.String id) |
void |
QTWriter.setId(java.lang.String id) |
void |
OMEXMLWriter.setId(java.lang.String id) |
void |
OMETiffWriter.setId(java.lang.String id) |
void |
JavaWriter.setId(java.lang.String id) |
void |
ICSWriter.setId(java.lang.String id) |
void |
DicomWriter.setId(java.lang.String id) |
void |
CellH5Writer.setId(java.lang.String id) |
void |
AVIWriter.setId(java.lang.String id) |
void |
APNGWriter.setId(java.lang.String id) |
void |
DicomWriter.setSeries(int s) |
int |
TiffWriter.setTileSizeX(int tileSize) |
int |
DicomWriter.setTileSizeX(int tileSize) |
int |
TiffWriter.setTileSizeY(int tileSize) |
int |
DicomWriter.setTileSizeY(int tileSize) |
private void |
APNGWriter.writePixels(java.lang.String chunk,
byte[] stream,
int x,
int y,
int width,
int height) |
| Modifier and Type | Method and Description |
|---|---|
byte[] |
JPEGXRServiceImpl.decompress(byte[] compressed) |
byte[] |
JPEGXRService.decompress(byte[] compressed)
Decompress the given JPEG-XR compressed byte array and return as a byte array.
|
private short[] |
JPEGXRServiceImpl.getPixelFormat(byte[] stream) |
void |
WlzServiceImpl.open(java.lang.String file,
java.lang.String rw) |
void |
WlzService.open(java.lang.String file,
java.lang.String rw)
Initializes the service for the given file path.
|
private void |
WlzServiceImpl.openRead(java.lang.String file) |
private void |
WlzServiceImpl.openWrite(java.lang.String file) |
byte[] |
WlzServiceImpl.readBytes(int no,
byte[] buf,
int x,
int y,
int w,
int h) |
byte[] |
WlzService.readBytes(int no,
byte[] buf,
int x,
int y,
int w,
int h)
Reads a rectangle of bytes in an x-y plane from the opened Woolz
object.
|
void |
WlzServiceImpl.saveBytes(int no,
byte[] buf,
int x,
int y,
int w,
int h) |
void |
WlzService.saveBytes(int no,
byte[] buf,
int x,
int y,
int w,
int h)
Adds a rectangle of bytes in an x-y plane to the opened Woolz object.
|
void |
WlzServiceImpl.setupWrite(int orgX,
int orgY,
int orgZ,
int pixSzX,
int pixSzY,
int pixSzZ,
int pixSzC,
int pixSzT,
double voxSzX,
double voxSzY,
double voxSzZ,
int gType) |
void |
WlzService.setupWrite(int orgX,
int orgY,
int orgZ,
int pixSzX,
int pixSzY,
int pixSzZ,
int pixSzC,
int pixSzT,
double voxSzX,
double voxSzY,
double voxSzZ,
int gType)
Sets up the service, which must have already been opened for writing.
|
| Modifier and Type | Method and 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.
|
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.
|
java.lang.String |
IFD.getIFDStringValue(int tag)
Gets the given directory entry value as a string from this IFD,
performing some error checking.
|
java.lang.Object |
IFD.getIFDValue(int tag,
java.lang.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.
|
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,
java.lang.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,
java.lang.Object value)
Surgically overwrites an existing IFD value with the given one.
|
void |
TiffSaver.overwriteIFDValue(loci.common.RandomAccessInputStream raf,
long ifdOffset,
int tag,
java.lang.Object value)
Surgically overwrites an existing IFD value with the given one.
|
void |
TiffSaver.overwriteIFDValue(loci.common.RandomAccessInputStream raf,
long ifdOffset,
int tag,
java.lang.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) |
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,
java.lang.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,
java.lang.Integer nChannels,
boolean copyDirectly) |
private 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.
|
| Modifier and Type | Method and Description |
|---|---|
private OMETiffWriter |
MakeTestOmeTiff.createWriter(java.lang.String name,
CoreMetadata info,
java.lang.String id) |
static java.lang.String |
AmiraParameters.entryToString(java.lang.Object object,
java.lang.String indent) |
protected void |
AmiraParameters.extractCoreMetaData() |
static void |
MakeTestOmeTiff.main(java.lang.String[] args) |
static void |
CacheConsole.main(java.lang.String[] args)
Interactive interpreter for testing Bio-Formats caching implementation.
|
int |
MakeTestOmeTiff.makeOmeTiff(java.lang.String... args) |
void |
MakeTestOmeTiff.makeOmeTiff(java.lang.String name,
CoreMetadata info) |
void |
MakeTestOmeTiff.makeOmeTiffExtensions(java.lang.String... args) |
void |
MakeTestOmeTiff.makeSamples() |
protected java.lang.Double[] |
AmiraParameters.readDoubleArray(int count) |
protected void |
AmiraParameters.readFile(loci.common.RandomAccessInputStream inputStream) |
protected void |
AmiraParameters.readFile(java.lang.String path) |
protected java.lang.Integer[] |
AmiraParameters.readIntArray() |
protected java.lang.Integer[] |
AmiraParameters.readIntArray(int count) |
protected java.util.Map |
AmiraParameters.readMap() |
protected java.lang.Number |
AmiraParameters.readNumber() |
protected java.lang.Number[] |
AmiraParameters.readNumberArray() |
protected java.lang.String |
AmiraParameters.readQuotedString() |
protected void |
AmiraParameters.readTopLevel() |
protected void |
AmiraParameters.syntaxError(java.lang.String message) |
static java.lang.String |
AmiraParameters.toString(java.util.Map map,
java.lang.String indent) |
private void |
MakeTestOmeTiff.writeData(java.lang.String name,
CoreMetadata info,
java.lang.String id,
OMETiffWriter out) |
| Constructor and Description |
|---|
AmiraParameters(loci.common.RandomAccessInputStream inputStream) |
AmiraParameters(java.lang.String path) |
| Modifier and Type | Method and Description |
|---|---|
static ij.ImagePlus[] |
BF.openImagePlus(ImporterOptions options) |
static ij.ImagePlus[] |
BF.openImagePlus(java.lang.String path) |
static ij.ImagePlus[] |
BF.openThumbImagePlus(ImporterOptions options) |
static ij.ImagePlus[] |
BF.openThumbImagePlus(java.lang.String path) |
| Modifier and Type | Method and Description |
|---|---|
private void |
ImportProcess.createBaseReader()
Initializes an
IFormatReader
according to the current configuration. |
private ij.ImageStack |
ImagePlusReader.createVirtualStack(ImportProcess process,
int s,
java.util.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 java.util.List<ij.ImagePlus> |
ImagePlusReader.readImages() |
private java.util.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,
java.util.List<ij.process.LUT> luts,
boolean thumbnail) |
private ij.process.ImageProcessor[] |
ImagePlusReader.readProcessors(ImportProcess process,
int no,
loci.common.Region r,
boolean thumbnail)
HACK: This method mainly exists to prompt the user for a missing
LuraWave license code, in the case of LWF-compressed Flex.
|
private java.util.List<ij.ImagePlus> |
ImagePlusReader.readThumbImages() |
private void |
ImportProcess.setId()
HACK: This method mainly exists to prompt the user for a missing
LuraWave license code, in the case of LWF-compressed Flex.
|
void |
Importer.showDialogs(ImportProcess process) |
| Modifier and Type | Method and Description |
|---|---|
void |
LociFunctions.fileGroupOption(java.lang.String id,
java.lang.String[] fileGroupOption) |
void |
LociFunctions.getFormat(java.lang.String id,
java.lang.String[] format) |
void |
LociFunctions.openImage(java.lang.String title,
java.lang.Double no) |
void |
LociFunctions.openSubImage(java.lang.String title,
java.lang.Double no,
java.lang.Double x,
java.lang.Double y,
java.lang.Double w,
java.lang.Double h) |
void |
LociFunctions.openThumbImage(java.lang.String title,
java.lang.Double no) |
void |
LociFunctions.setId(java.lang.String id) |
| Modifier and Type | Method and Description |
|---|---|
static boolean |
LuraWave.isLicenseCodeException(FormatException exc)
Returns true if the given exception was cause
by a missing or invalid LuraWave license code.
|
| Modifier and Type | Method and Description |
|---|---|
private ij.process.LUT |
ImageProcessorReader.createColorModel() |
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) |
java.lang.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) |
| Constructor and Description |
|---|
BFVirtualStack(java.lang.String path,
IFormatReader r,
boolean colorize,
boolean merge,
boolean record) |
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