| 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 |
Package containing Bio-Formats compression and decompression logic.
|
| 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.
|
| loci.tests |
Base package for automated and manual testing of the Bio-Formats software packages.
|
| loci.tests.testng |
Package for automated testing of the Bio-Formats software packages using TestNG.
|
| 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 |
IFormatWriter.changeOutputFile(String id)
Switch the output file for the current dataset.
|
void |
FormatWriter.changeOutputFile(String id) |
void |
WriterWrapper.changeOutputFile(String id) |
void |
ImageWriter.changeOutputFile(String id) |
static void |
FormatTools.checkBufferSize(IFormatReader r,
int len) |
static void |
FormatTools.checkBufferSize(IFormatReader r,
int len,
int w,
int h)
Checks that the given buffer size is large enough to hold a w * h
image as returned by the given reader.
|
protected void |
FormatWriter.checkParams(int no,
byte[] buf,
int x,
int y,
int w,
int h)
Ensure that the arguments that are being passed to saveBytes(...) are
valid.
|
static void |
FormatTools.checkPlaneNumber(IFormatReader r,
int no)
Checks that the given plane number is valid for the given reader.
|
static void |
FormatTools.checkPlaneParameters(IFormatReader r,
int no,
int bufLength,
int x,
int y,
int w,
int h)
Convenience method for checking that the plane number, tile size and
buffer sizes are all valid for the given reader.
|
static void |
FormatTools.checkTileSize(IFormatReader r,
int x,
int y,
int w,
int h)
Checks that the given tile size is valid for the given reader.
|
protected void |
FileStitcher.computeAxisLengths()
Computes axis length arrays, and total axis lengths.
|
protected int[] |
FileStitcher.computeIndices(int no)
Gets the file index, and image index into that file,
corresponding to the given global image index.
|
static void |
FormatTools.convert(IFormatReader input,
IFormatWriter output,
String outputFile)
Convenience method for writing all of the images and metadata obtained
from the specified IFormatReader into the specified IFormatWriter.
|
static void |
FormatTools.convert(String input,
String output)
Convenience method for converting the specified input file to the
specified output file.
|
ReaderWrapper |
ReaderWrapper.duplicate(Class<? extends IFormatReader> imageReaderClass)
Performs a deep copy of the reader, including nested wrapped readers.
|
WriterWrapper |
WriterWrapper.duplicate(Class<? extends IFormatWriter> imageWriterClass)
Performs a deep copy of the writer, including nested wrapped writers.
|
int |
ReaderWrapper.fileGroupOption(String id) |
int |
IFormatReader.fileGroupOption(String id)
Returns an int indicating that we cannot, must, or might group the files
in a given dataset.
|
int |
ImageReader.fileGroupOption(String id) |
int |
FormatReader.fileGroupOption(String id) |
short[][] |
ChannelFiller.get16BitLookupTable() |
short[][] |
FileStitcher.get16BitLookupTable() |
short[][] |
ReaderWrapper.get16BitLookupTable() |
short[][] |
IFormatReader.get16BitLookupTable()
Gets the 16-bit color lookup table associated with
the most recently opened image.
|
short[][] |
ImageReader.get16BitLookupTable() |
short[][] |
FormatReader.get16BitLookupTable() |
short[][] |
DelegateReader.get16BitLookupTable() |
byte[][] |
ChannelFiller.get8BitLookupTable() |
byte[][] |
FileStitcher.get8BitLookupTable() |
byte[][] |
ReaderWrapper.get8BitLookupTable() |
byte[][] |
IFormatReader.get8BitLookupTable()
Gets the 8-bit color lookup table associated with
the most recently opened image.
|
byte[][] |
ImageReader.get8BitLookupTable() |
byte[][] |
FormatReader.get8BitLookupTable() |
byte[][] |
DelegateReader.get8BitLookupTable() |
protected AcquisitionMode |
FormatReader.getAcquisitionMode(String value)
Retrieves an
AcquisitionMode enumeration
value for the given String. |
int |
FileStitcher.getAdjustedIndex(int no)
Gets the local reader index for use with the given image plane.
|
protected ArcType |
FormatReader.getArcType(String value)
Retrieves an
ArcType enumeration
value for the given String. |
protected Binning |
FormatReader.getBinning(String value)
Retrieves an
Binning enumeration
value for the given String. |
Double |
MinMaxCalculator.getChannelGlobalMaximum(int theC)
Retrieves a specified channel's global maximum.
|
Double |
MinMaxCalculator.getChannelGlobalMinimum(int theC)
Retrieves a specified channel's global minimum.
|
Double |
MinMaxCalculator.getChannelKnownMaximum(int theC)
Retrieves the specified channel's maximum based on the images that
have been read.
|
Double |
MinMaxCalculator.getChannelKnownMinimum(int theC)
Retrieves the specified channel's minimum based on the images that have
been read.
|
protected Compression |
FormatReader.getCompression(String value)
Retrieves an
Compression enumeration
value for the given String. |
protected ContrastMethod |
FormatReader.getContrastMethod(String value)
Retrieves an
ContrastMethod enumeration
value for the given String. |
protected Correction |
FormatReader.getCorrection(String value)
Retrieves an
Correction enumeration
value for the given String. |
protected DetectorType |
FormatReader.getDetectorType(String value)
Retrieves an
DetectorType enumeration
value for the given String. |
protected DimensionOrder |
FormatReader.getDimensionOrder(String value)
Retrieves an
DimensionOrder enumeration
value for the given String. |
protected ExperimentType |
FormatReader.getExperimentType(String value)
Retrieves an
ExperimentType enumeration
value for the given String. |
protected FilamentType |
FormatReader.getFilamentType(String value)
Retrieves an
FilamentType enumeration
value for the given String. |
static String |
FormatTools.getFilename(int series,
int image,
IFormatReader r,
String pattern) |
static String[] |
FormatTools.getFilenames(String pattern,
IFormatReader r) |
protected FillRule |
FormatReader.getFillRule(String value)
Retrieves an
FillRule enumeration
value for the given String. |
protected FilterType |
FormatReader.getFilterType(String value)
Retrieves an
FilterType enumeration
value for the given String. |
protected FontFamily |
FormatReader.getFontFamily(String value)
Retrieves an
FontFamily enumeration
value for the given String. |
protected FontStyle |
FormatReader.getFontStyle(String value)
Retrieves an
FontStyle enumeration
value for the given String. |
String |
ImageReader.getFormat(String id)
Gets a string describing the file format for the given file.
|
String |
ImageWriter.getFormat(String id)
Gets a string describing the file format for the given file.
|
protected IlluminationType |
FormatReader.getIlluminationType(String value)
Retrieves an
IlluminationType enumeration
value for the given String. |
static int |
FormatTools.getImagesPerFile(String pattern,
IFormatReader r) |
protected Immersion |
FormatReader.getImmersion(String value)
Retrieves an
Immersion enumeration
value for the given String. |
protected LaserMedium |
FormatReader.getLaserMedium(String value)
Retrieves an
LaserMedium enumeration
value for the given String. |
protected LaserType |
FormatReader.getLaserType(String value)
Retrieves an
LaserType enumeration
value for the given String. |
protected LineCap |
FormatReader.getLineCap(String value)
Retrieves an
LineCap enumeration
value for the given String. |
protected Marker |
FormatReader.getMarker(String value)
Retrieves an
Marker enumeration
value for the given String. |
protected Medium |
FormatReader.getMedium(String value)
Retrieves an
Medium enumeration
value for the given String. |
protected MicrobeamManipulationType |
FormatReader.getMicrobeamManipulationType(String value)
Retrieves an
MicrobeamManipulationType
enumeration value for the given String. |
protected MicroscopeType |
FormatReader.getMicroscopeType(String value)
Retrieves an
MicroscopeType enumeration
value for the given String. |
protected NamingConvention |
FormatReader.getNamingConvention(String value)
Retrieves an
NamingConvention enumeration
value for the given String. |
int |
ChannelMerger.getOriginalIndex(int no)
Returns the image number in the original dataset that corresponds to the
given image number.
|
protected PixelType |
FormatReader.getPixelType(String value)
Retrieves an
PixelType enumeration
value for the given String. |
Double[] |
MinMaxCalculator.getPlaneMaximum(int no)
Retrieves the maximum pixel value for the specified plane.
|
Double[] |
MinMaxCalculator.getPlaneMinimum(int no)
Retrieves the minimum pixel value for the specified plane.
|
String[] |
ReaderWrapper.getPossibleDomains(String id) |
String[] |
IFormatReader.getPossibleDomains(String id)
Returns a list of scientific domains in which this format is used.
|
String[] |
ImageReader.getPossibleDomains(String id) |
String[] |
FormatReader.getPossibleDomains(String id) |
protected Pulse |
FormatReader.getPulse(String value)
Retrieves an
Pulse enumeration
value for the given String. |
IFormatReader |
FileStitcher.getReader(int no)
Gets the reader appropriate for use with the given image plane.
|
IFormatReader |
ImageReader.getReader(String id)
Gets the reader used to open the given file.
|
static int |
FormatTools.getReorderedIndex(IFormatReader reader,
String newOrder,
int newIndex)
Converts index from the given dimension order to the reader's native one.
|
int |
ReaderWrapper.getRequiredDirectories(String[] files) |
int |
IFormatReader.getRequiredDirectories(String[] files)
Returns the number of parent directories that are important when
processing the given list of files.
|
int |
ImageReader.getRequiredDirectories(String[] files) |
int |
FormatReader.getRequiredDirectories(String[] files) |
IFormatWriter |
ImageWriter.getWriter(String id)
Gets the writer used to save the given file.
|
protected void |
FileStitcher.initFile(String id)
Initializes the given file or file pattern.
|
protected void |
FormatReader.initFile(String id)
Initializes the given file (parsing header information, etc.).
|
protected void |
MinMaxCalculator.initMinMax()
Ensures internal min/max variables are initialized properly.
|
boolean |
MinMaxCalculator.isMinMaxPopulated()
Returns true if the values returned by
getChannelGlobalMinimum/Maximum can be trusted.
|
boolean |
ReaderWrapper.isSingleFile(String id) |
boolean |
IFormatReader.isSingleFile(String id)
Returns true if this is a single-file format.
|
boolean |
ImageReader.isSingleFile(String id) |
boolean |
FormatReader.isSingleFile(String id) |
IFormatReader |
Memoizer.loadMemo() |
static void |
AxisGuesser.main(String[] args)
Method for testing pattern guessing logic.
|
byte[] |
TileStitcher.openBytes(int no) |
byte[] |
DimensionSwapper.openBytes(int no) |
byte[] |
ChannelFiller.openBytes(int no) |
byte[] |
ChannelSeparator.openBytes(int no) |
byte[] |
ChannelMerger.openBytes(int no) |
byte[] |
FileStitcher.openBytes(int no) |
byte[] |
MinMaxCalculator.openBytes(int no) |
byte[] |
ReaderWrapper.openBytes(int no) |
byte[] |
IFormatReader.openBytes(int no)
Obtains the specified image plane from the current file as a byte array.
|
byte[] |
ImageReader.openBytes(int no) |
byte[] |
FormatReader.openBytes(int no) |
byte[] |
TileStitcher.openBytes(int no,
byte[] buf) |
byte[] |
DimensionSwapper.openBytes(int no,
byte[] buf) |
byte[] |
ChannelFiller.openBytes(int no,
byte[] buf) |
byte[] |
ChannelSeparator.openBytes(int no,
byte[] buf) |
byte[] |
ChannelMerger.openBytes(int no,
byte[] buf) |
byte[] |
FileStitcher.openBytes(int no,
byte[] buf) |
byte[] |
MinMaxCalculator.openBytes(int no,
byte[] buf) |
byte[] |
ReaderWrapper.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[] |
ImageReader.openBytes(int no,
byte[] buf) |
byte[] |
FormatReader.openBytes(int no,
byte[] buf) |
byte[] |
TileStitcher.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[] |
ChannelFiller.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[] |
FileStitcher.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[] |
ReaderWrapper.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.
|
byte[] |
ImageReader.openBytes(int no,
byte[] buf,
int x,
int y,
int w,
int h) |
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[] |
DimensionSwapper.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[] |
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[] |
FileStitcher.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[] |
ReaderWrapper.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[] |
ImageReader.openBytes(int no,
int x,
int y,
int w,
int h) |
byte[] |
FormatReader.openBytes(int no,
int x,
int y,
int w,
int h) |
Object |
FileStitcher.openPlane(int no,
int x,
int y,
int w,
int h) |
Object |
ReaderWrapper.openPlane(int no,
int x,
int y,
int w,
int h) |
Object |
IFormatReader.openPlane(int no,
int x,
int y,
int w,
int h)
Obtains the specified image plane (or sub-image thereof) in the reader's
native data structure.
|
Object |
ImageReader.openPlane(int no,
int x,
int y,
int w,
int h) |
Object |
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[] |
DimensionSwapper.openThumbBytes(int no) |
byte[] |
ChannelSeparator.openThumbBytes(int no) |
byte[] |
FileStitcher.openThumbBytes(int no) |
byte[] |
ReaderWrapper.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[] |
ImageReader.openThumbBytes(int no) |
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 |
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) |
void |
ImageWriter.saveBytes(int no,
byte[] buf) |
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,
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,
Region tile)
Saves the given image tile to the current series in the current file.
|
void |
FormatWriter.saveBytes(int no,
byte[] buf,
Region tile) |
void |
WriterWrapper.saveBytes(int no,
byte[] buf,
Region tile) |
void |
ImageWriter.saveBytes(int no,
byte[] buf,
Region tile) |
void |
IFormatWriter.savePlane(int no,
Object plane)
Saves the given image plane to the current series in the current file.
|
void |
FormatWriter.savePlane(int no,
Object plane) |
void |
WriterWrapper.savePlane(int no,
Object plane) |
void |
ImageWriter.savePlane(int no,
Object plane) |
void |
IFormatWriter.savePlane(int no,
Object plane,
int x,
int y,
int w,
int h)
Saves the given image plane to the current series in the current file.
|
void |
FormatWriter.savePlane(int no,
Object plane,
int x,
int y,
int w,
int h) |
void |
WriterWrapper.savePlane(int no,
Object plane,
int x,
int y,
int w,
int h) |
void |
ImageWriter.savePlane(int no,
Object plane,
int x,
int y,
int w,
int h) |
void |
IFormatWriter.savePlane(int no,
Object plane,
Region tile)
Saves the given image plane to the current series in the current file.
|
void |
FormatWriter.savePlane(int no,
Object plane,
Region tile) |
void |
WriterWrapper.savePlane(int no,
Object plane,
Region tile) |
void |
ImageWriter.savePlane(int no,
Object plane,
Region tile) |
void |
FileStitcher.setAxisTypes(int[] axes)
Sets the axis type for each dimensional block.
|
void |
IFormatWriter.setCompression(String compress)
Sets the current compression type.
|
void |
FormatWriter.setCompression(String compress) |
void |
WriterWrapper.setCompression(String compress) |
void |
ImageWriter.setCompression(String compress) |
void |
TileStitcher.setId(String id) |
void |
DimensionSwapper.setId(String id) |
void |
ChannelFiller.setId(String id) |
void |
ChannelSeparator.setId(String id) |
void |
Memoizer.setId(String id) |
void |
FileStitcher.setId(String id) |
void |
ReaderWrapper.setId(String id) |
void |
ImageReader.setId(String id) |
void |
IFormatHandler.setId(String id)
Sets the current file name.
|
void |
FormatWriter.setId(String id) |
void |
WriterWrapper.setId(String id) |
void |
FormatReader.setId(String id) |
void |
DelegateReader.setId(String id) |
void |
ImageWriter.setId(String id) |
void |
IFormatWriter.setSeries(int series)
Sets the current series.
|
void |
FormatWriter.setSeries(int series) |
void |
WriterWrapper.setSeries(int series) |
void |
ImageWriter.setSeries(int series) |
IFormatReader |
ReaderWrapper.unwrap()
Unwraps nested wrapped readers until the core reader (i.e., not
a
ReaderWrapper or ImageReader) is found. |
IFormatWriter |
WriterWrapper.unwrap()
Unwraps nested wrapped writers until the core writer (i.e., not
a
WriterWrapper or ImageWriter) is found. |
IFormatReader |
ReaderWrapper.unwrap(Class<? extends IFormatReader> readerClass,
String id)
Unwraps nested wrapped readers until the given reader class is found.
|
IFormatWriter |
WriterWrapper.unwrap(Class<? extends IFormatWriter> writerClass,
String id)
Unwraps nested wrapped writers until the given writer class is found.
|
IFormatReader |
ReaderWrapper.unwrap(String id)
Unwraps nested wrapped readers until the core reader (i.e., not
a
ReaderWrapper or ImageReader) is found. |
IFormatWriter |
WriterWrapper.unwrap(String id)
Unwraps nested wrapped writers until the core writer (i.e., not
a
WriterWrapper or ImageWriter) is found. |
protected void |
MinMaxCalculator.updateMinMax(int no,
byte[] buf,
int len)
Updates min/max values based on the given byte array.
|
static void |
MetadataTools.verifyMinimumPopulated(MetadataRetrieve src)
Checks whether the given metadata object has the minimum metadata
populated to successfully describe an Image.
|
static void |
MetadataTools.verifyMinimumPopulated(MetadataRetrieve src,
int n)
Checks whether the given metadata object has the minimum metadata
populated to successfully describe the nth Image.
|
| 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 |
|---|---|
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[] |
JPEG2000Codec.compress(byte[] data,
CodecOptions options)
The CodecOptions parameter should have the following fields set:
width
height
bitsPerSample
channels
interleaved
littleEndian
lossless |
byte[] |
LosslessJPEGCodec.compress(byte[] data,
CodecOptions options) |
byte[] |
LZOCodec.compress(byte[] data,
CodecOptions options) |
byte[] |
NikonCodec.compress(byte[] data,
CodecOptions options) |
byte[] |
LZWCodec.compress(byte[] input,
CodecOptions options) |
byte[] |
MSRLECodec.compress(byte[] data,
CodecOptions options) |
byte[] |
Base64Codec.compress(byte[] input,
CodecOptions options) |
byte[] |
MJPBCodec.compress(byte[] data,
CodecOptions options) |
byte[] |
JPEGCodec.compress(byte[] data,
CodecOptions options)
The CodecOptions parameter should have the following fields set:
width
height
channels
bitsPerSample
interleaved
littleEndian
signed |
byte[] |
HuffmanCodec.compress(byte[] data,
CodecOptions options) |
byte[] |
QTRLECodec.compress(byte[] data,
CodecOptions options) |
byte[] |
ZlibCodec.compress(byte[] data,
CodecOptions options) |
byte[] |
PackbitsCodec.compress(byte[] data,
CodecOptions options) |
byte[] |
MSVideoCodec.compress(byte[] data,
CodecOptions options) |
byte[] |
LuraWaveCodec.compress(byte[] data,
CodecOptions options) |
byte[] |
PassthroughCodec.compress(byte[] data,
CodecOptions options) |
byte[] |
RPZACodec.compress(byte[] input,
CodecOptions options) |
byte[] |
TargaRLECodec.compress(byte[] data,
CodecOptions options) |
byte[] |
Codec.compress(byte[] data,
CodecOptions options)
Compresses a block of data.
|
byte[] |
BaseCodec.decompress(byte[] data) |
byte[] |
Codec.decompress(byte[] data)
Decompresses a block of data.
|
byte[] |
BaseCodec.decompress(byte[][] data) |
byte[] |
Codec.decompress(byte[][] data)
Decompresses a block of data.
|
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[] |
JPEG2000Codec.decompress(byte[] buf,
CodecOptions options)
The CodecOptions parameter should have the following fields set:
interleaved
littleEndian |
byte[] |
BaseCodec.decompress(byte[] data,
CodecOptions options) |
byte[] |
QTRLECodec.decompress(byte[] data,
CodecOptions options)
The CodecOptions parameter should have the following fields set:
width
height
bitsPerSample
previousImage |
byte[] |
LuraWaveCodec.decompress(byte[] buf,
CodecOptions options)
The CodecOptions parameter should have the following fields set:
maxBytes |
byte[] |
PassthroughCodec.decompress(byte[] data,
CodecOptions options) |
byte[] |
Codec.decompress(byte[] data,
CodecOptions options)
Decompresses a block of data.
|
byte[] |
JPEG2000Codec.decompress(RandomAccessInputStream in,
CodecOptions options)
The CodecOptions parameter should have the following fields set:
interleaved
littleEndian |
abstract byte[] |
BaseCodec.decompress(RandomAccessInputStream in,
CodecOptions options) |
byte[] |
LosslessJPEGCodec.decompress(RandomAccessInputStream in,
CodecOptions options)
The CodecOptions parameter should have the following fields set:
interleaved
littleEndian |
byte[] |
LZOCodec.decompress(RandomAccessInputStream in,
CodecOptions options) |
byte[] |
NikonCodec.decompress(RandomAccessInputStream in,
CodecOptions options)
The CodecOptions parameter must be an instance of
NikonCodecOptions, and should have the following fields set:
lossy
vPredictor
curve
split
bitsPerSample
maxBytes
width
height |
byte[] |
LZWCodec.decompress(RandomAccessInputStream in,
CodecOptions options)
The CodecOptions parameter should have the following fields set:
maxBytes |
byte[] |
MSRLECodec.decompress(RandomAccessInputStream in,
CodecOptions options)
|
byte[] |
Base64Codec.decompress(RandomAccessInputStream in,
CodecOptions options) |
byte[] |
MJPBCodec.decompress(RandomAccessInputStream in,
CodecOptions options)
The CodecOptions parameter must be an instance of
MJPBCodecOptions,
and should have the following fields set:
interlaced
width
height
bitsPerSample
littleEndian
interleaved |
byte[] |
JPEGCodec.decompress(RandomAccessInputStream in,
CodecOptions options)
The CodecOptions parameter should have the following fields set:
interleaved
littleEndian |
byte[] |
HuffmanCodec.decompress(RandomAccessInputStream in,
CodecOptions options)
The CodecOptions parameter must be an instance of
HuffmanCodecOptions, and should have the following fields set:
table
bitsPerSample
maxBytes |
byte[] |
QTRLECodec.decompress(RandomAccessInputStream in,
CodecOptions options) |
byte[] |
ZlibCodec.decompress(RandomAccessInputStream in,
CodecOptions options) |
byte[] |
PackbitsCodec.decompress(RandomAccessInputStream in,
CodecOptions options)
The CodecOptions parameter should have the following fields set:
maxBytes |
byte[] |
MSVideoCodec.decompress(RandomAccessInputStream in,
CodecOptions options)
The CodecOptions parameter should have the following fields set:
width
height
bitsPerSample
previousImage |
byte[] |
LuraWaveCodec.decompress(RandomAccessInputStream in,
CodecOptions options) |
byte[] |
PassthroughCodec.decompress(RandomAccessInputStream in,
CodecOptions options) |
byte[] |
RPZACodec.decompress(RandomAccessInputStream in,
CodecOptions options)
|
byte[] |
TargaRLECodec.decompress(RandomAccessInputStream in,
CodecOptions options)
The CodecOptions parameter should have the following fields set:
maxBytes
CodecOptions.bitsPerSample |
byte[] |
Codec.decompress(RandomAccessInputStream in,
CodecOptions options)
Decompresses data from the given RandomAccessInputStream.
|
int |
HuffmanCodec.getSample(BitBuffer bb,
CodecOptions options) |
void |
BaseCodec.test()
Main testing method default implementation.
|
| Modifier and Type | Method and Description |
|---|---|
Dimension |
LegacyQTTools.getPictDimensions(byte[] bytes)
Gets width and height for the given PICT bytes.
|
static BufferedImage |
AWTImageTools.makeImage(byte[] data,
boolean interleaved,
MetadataRetrieve meta,
int series)
Creates an image from the given raw byte array, obtaining the
dimensional parameters from the specified metadata object.
|
static BufferedImage |
AWTImageTools.openImage(byte[] buf,
IFormatReader r,
int w,
int h)
Creates an image from the given byte array, using the given
IFormatReader to retrieve additional information.
|
BufferedImage |
BufferedImageReader.openImage(int no)
Obtains the specified image from the current file.
|
BufferedImage |
BufferedImageReader.openImage(int no,
int x,
int y,
int w,
int h)
Obtains a sub-image of the specified image, whose upper-left corner is
given by (x, y).
|
BufferedImage |
BufferedImageReader.openThumbImage(int no)
Obtains a thumbnail for the specified image from the current file.
|
Image |
LegacyQTTools.pictToImage(byte[] bytes)
Converts the given byte array in PICT format to a Java image.
|
void |
BufferedImageWriter.saveImage(int no,
BufferedImage image)
Saves the given BufferedImage to the current file.
|
void |
BufferedImageWriter.saveImage(int no,
BufferedImage image,
int x,
int y,
int w,
int h)
Saves the given BufferedImage to the current file.
|
| Modifier and Type | Method and Description |
|---|---|
static void |
FlexReader.appendServerMap(String alias,
String realName)
Add the path 'realName' to the mapping for the server named 'alias'.
|
protected loci.formats.in.ZeissTIFFReader.TIFFInfo |
ZeissTIFFReader.evalFile(String id)
Evaluate the metadata of a TIFF/XML file collection, and return this to the user.
|
int |
CellomicsReader.fileGroupOption(String id) |
int |
PerkinElmerReader.fileGroupOption(String id) |
int |
LeicaReader.fileGroupOption(String id) |
int |
FV1000Reader.fileGroupOption(String id) |
int |
OperettaReader.fileGroupOption(String id) |
int |
TrestleReader.fileGroupOption(String id) |
int |
TillVisionReader.fileGroupOption(String id) |
int |
BrukerReader.fileGroupOption(String id) |
int |
NDPISReader.fileGroupOption(String id) |
int |
ScreenReader.fileGroupOption(String id) |
int |
MIASReader.fileGroupOption(String id) |
int |
NiftiReader.fileGroupOption(String id) |
int |
MetamorphReader.fileGroupOption(String id) |
int |
ScanrReader.fileGroupOption(String id) |
int |
CellVoyagerReader.fileGroupOption(String id) |
int |
CellSensReader.fileGroupOption(String id) |
int |
FlexReader.fileGroupOption(String id) |
int |
SVSReader.fileGroupOption(String id) |
int |
NDPIReader.fileGroupOption(String id) |
int |
VisitechReader.fileGroupOption(String id) |
int |
ZeissLSMReader.fileGroupOption(String id) |
int |
InCellReader.fileGroupOption(String id) |
int |
ZeissTIFFReader.fileGroupOption(String id) |
int |
FujiReader.fileGroupOption(String id) |
int |
PrairieReader.fileGroupOption(String id) |
int |
BDReader.fileGroupOption(String id) |
int |
ImagicReader.fileGroupOption(String id) |
int |
L2DReader.fileGroupOption(String id) |
int |
TCSReader.fileGroupOption(String id) |
int |
HitachiReader.fileGroupOption(String id) |
int |
BioRadReader.fileGroupOption(String id) |
int |
AFIReader.fileGroupOption(String id) |
int |
APLReader.fileGroupOption(String id) |
int |
AnalyzeReader.fileGroupOption(String id) |
int |
DicomReader.fileGroupOption(String id) |
int |
ICSReader.fileGroupOption(String id) |
int |
NRRDReader.fileGroupOption(String id) |
int |
MicromanagerReader.fileGroupOption(String id) |
protected void |
ZeissZVIReader.fillMetadataPass1(MetadataStore store) |
protected void |
BaseZeissReader.fillMetadataPass1(MetadataStore store)
Read and store basic dimensions in model
|
protected void |
ZeissTIFFReader.fillMetadataPass1(MetadataStore store) |
protected void |
BaseZeissReader.fillMetadataPass2(MetadataStore store)
Read and store basic dimensions in model
|
protected void |
ZeissTIFFReader.fillMetadataPass2(MetadataStore store) |
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 |
BaseZeissReader.fillMetadataPass5(MetadataStore store)
Read and store basic dimensions in model
|
protected void |
ZeissTIFFReader.fillMetadataPass5(MetadataStore store) |
protected void |
BaseZeissReader.fillMetadataPass6(MetadataStore store)
Read and store basic dimensions in model
|
protected void |
BaseZeissReader.fillMetadataPass7(MetadataStore store)
Store basic dimensions in model
|
short[][] |
PerkinElmerReader.get16BitLookupTable() |
short[][] |
LeicaReader.get16BitLookupTable() |
short[][] |
ZeissCZIReader.get16BitLookupTable() |
short[][] |
ScreenReader.get16BitLookupTable() |
short[][] |
MIASReader.get16BitLookupTable() |
short[][] |
BaseZeissReader.get16BitLookupTable() |
short[][] |
SlidebookTiffReader.get16BitLookupTable() |
short[][] |
PDSReader.get16BitLookupTable() |
short[][] |
ZeissLSMReader.get16BitLookupTable() |
short[][] |
InCellReader.get16BitLookupTable() |
short[][] |
TCSReader.get16BitLookupTable() |
short[][] |
ImprovisionTiffReader.get16BitLookupTable() |
short[][] |
ZipReader.get16BitLookupTable() |
short[][] |
OMETiffReader.get16BitLookupTable() |
short[][] |
MinimalTiffReader.get16BitLookupTable() |
short[][] |
FakeReader.get16BitLookupTable() |
byte[][] |
PerkinElmerReader.get8BitLookupTable() |
byte[][] |
LeicaReader.get8BitLookupTable() |
byte[][] |
ZeissCZIReader.get8BitLookupTable() |
byte[][] |
ScreenReader.get8BitLookupTable() |
byte[][] |
KhorosReader.get8BitLookupTable() |
byte[][] |
MIASReader.get8BitLookupTable() |
byte[][] |
BaseZeissReader.get8BitLookupTable() |
byte[][] |
SlidebookTiffReader.get8BitLookupTable() |
byte[][] |
ZeissLSMReader.get8BitLookupTable() |
byte[][] |
InCellReader.get8BitLookupTable() |
byte[][] |
IPWReader.get8BitLookupTable() |
byte[][] |
TargaReader.get8BitLookupTable() |
byte[][] |
TCSReader.get8BitLookupTable() |
byte[][] |
ImprovisionTiffReader.get8BitLookupTable() |
byte[][] |
PictReader.get8BitLookupTable() |
byte[][] |
ZipReader.get8BitLookupTable() |
byte[][] |
OMETiffReader.get8BitLookupTable() |
byte[][] |
BMPReader.get8BitLookupTable() |
byte[][] |
MinimalTiffReader.get8BitLookupTable() |
byte[][] |
FakeReader.get8BitLookupTable() |
byte[][] |
GIFReader.get8BitLookupTable() |
int |
OperettaReader.getRequiredDirectories(String[] files) |
int |
BrukerReader.getRequiredDirectories(String[] files) |
int |
MIASReader.getRequiredDirectories(String[] files) |
int |
CellVoyagerReader.getRequiredDirectories(String[] files) |
int |
L2DReader.getRequiredDirectories(String[] files) |
protected void |
LeicaSCNReader.initCoreMetadata(int s) |
protected void |
DeltavisionReader.initExtraMetadata() |
protected void |
LIMReader.initFile(String id) |
protected void |
CellomicsReader.initFile(String id) |
protected void |
ZeissZVIReader.initFile(String id) |
protected void |
PovrayReader.initFile(String id) |
protected void |
NikonReader.initFile(String id) |
protected void |
SeikoReader.initFile(String id) |
protected void |
PerkinElmerReader.initFile(String id) |
protected void |
SMCameraReader.initFile(String id) |
protected void |
ARFReader.initFile(String id) |
protected void |
LeicaReader.initFile(String id) |
protected void |
FV1000Reader.initFile(String id) |
protected void |
OperettaReader.initFile(String id) |
protected void |
ZeissCZIReader.initFile(String id) |
protected void |
VolocityReader.initFile(String id) |
protected void |
TrestleReader.initFile(String id) |
protected void |
TillVisionReader.initFile(String id) |
protected void |
WATOPReader.initFile(String id) |
protected void |
BrukerReader.initFile(String id) |
protected void |
VarianFDFReader.initFile(String id) |
protected void |
NDPISReader.initFile(String id) |
protected void |
ScreenReader.initFile(String id) |
protected void |
KhorosReader.initFile(String id) |
protected void |
MIASReader.initFile(String id) |
protected void |
NiftiReader.initFile(String id) |
protected void |
LiFlimReader.initFile(String id) |
protected void |
MetamorphReader.initFile(String id) |
protected void |
OpenlabRawReader.initFile(String id) |
protected void |
PSDReader.initFile(String id) |
protected void |
ScanrReader.initFile(String id) |
protected void |
DeltavisionReader.initFile(String id) |
protected void |
CellWorxReader.initFile(String id) |
protected void |
SDTReader.initFile(String id) |
protected void |
KodakReader.initFile(String id) |
protected void |
CellVoyagerReader.initFile(String id) |
protected void |
ImspectorReader.initFile(String id) |
protected void |
CellSensReader.initFile(String id) |
protected void |
IvisionReader.initFile(String id) |
protected void |
SBIGReader.initFile(String id) |
protected void |
NAFReader.initFile(String id) |
protected void |
SlidebookReader.initFile(String id) |
protected void |
FlexReader.initFile(String id) |
protected void |
AIMReader.initFile(String id) |
protected void |
IMODReader.initFile(String id) |
protected void |
NDPIReader.initFile(String id) |
protected void |
WlzReader.initFile(String id) |
protected void |
JPXReader.initFile(String id) |
protected void |
GatanDM2Reader.initFile(String id) |
protected void |
InCell3000Reader.initFile(String id) |
protected void |
OxfordInstrumentsReader.initFile(String id) |
protected void |
VisitechReader.initFile(String id) |
protected void |
IPLabReader.initFile(String id) |
protected void |
Ecat7Reader.initFile(String id) |
protected void |
PCIReader.initFile(String id) |
protected void |
FEIReader.initFile(String id) |
protected void |
INRReader.initFile(String id) |
protected void |
NativeND2Reader.initFile(String id) |
protected void |
MetamorphTiffReader.initFile(String id) |
protected void |
PhotoshopTiffReader.initFile(String id) |
protected void |
PQBinReader.initFile(String id) |
protected void |
ImarisReader.initFile(String id) |
protected void |
PDSReader.initFile(String id) |
protected void |
BioRadSCNReader.initFile(String id) |
protected void |
HRDGDFReader.initFile(String id) |
protected void |
ZeissLSMReader.initFile(String id) |
protected void |
InCellReader.initFile(String id) |
protected void |
QuesantReader.initFile(String id) |
protected void |
MINCReader.initFile(String id) |
protected void |
IPWReader.initFile(String id) |
protected void |
GatanReader.initFile(String id) |
protected void |
UnisokuReader.initFile(String id) |
protected void |
ZeissTIFFReader.initFile(String id) |
protected void |
InveonReader.initFile(String id) |
protected void |
MolecularImagingReader.initFile(String id) |
protected void |
SpiderReader.initFile(String id) |
protected void |
FujiReader.initFile(String id) |
protected void |
VolocityClippingReader.initFile(String id) |
protected void |
CanonRawReader.initFile(String id) |
protected void |
PrairieReader.initFile(String id) |
protected void |
BurleighReader.initFile(String id) |
protected void |
BDReader.initFile(String id) |
void |
MRCReader.initFile(String id) |
protected void |
ImagicReader.initFile(String id) |
protected void |
VGSAMReader.initFile(String id) |
protected void |
L2DReader.initFile(String id) |
protected void |
TargaReader.initFile(String id) |
protected void |
BioRadGelReader.initFile(String id) |
protected void |
HISReader.initFile(String id) |
protected void |
LegacyND2Reader.initFile(String id) |
protected void |
MRWReader.initFile(String id) |
protected void |
TCSReader.initFile(String id) |
protected void |
UBMReader.initFile(String id) |
protected void |
OpenlabReader.initFile(String id) |
protected void |
HitachiReader.initFile(String id) |
protected void |
AliconaReader.initFile(String id) |
protected void |
RHKReader.initFile(String id) |
protected void |
ImarisHDFReader.initFile(String id) |
protected void |
HamamatsuVMSReader.initFile(String id) |
protected void |
AmiraReader.initFile(String id) |
protected void |
ImarisTiffReader.initFile(String id) |
protected void |
TopometrixReader.initFile(String id) |
protected void |
BioRadReader.initFile(String id) |
protected void |
AFIReader.initFile(String id) |
protected void |
SIFReader.initFile(String id) |
protected void |
PCORAWReader.initFile(String id) |
protected void |
LIFReader.initFile(String id) |
protected void |
APLReader.initFile(String id) |
protected void |
AnalyzeReader.initFile(String id) |
protected void |
JEOLReader.initFile(String id) |
protected void |
DNGReader.initFile(String id) |
protected void |
OMEXMLReader.initFile(String id) |
protected void |
PictReader.initFile(String id) |
protected void |
MNGReader.initFile(String id) |
protected void |
ZipReader.initFile(String id) |
protected void |
LegacyQTReader.initFile(String id) |
protected void |
OBFReader.initFile(String id) |
protected void |
JPEG2000Reader.initFile(String id) |
void |
TileJPEGReader.initFile(String id) |
protected void |
DicomReader.initFile(String id) |
protected void |
PGMReader.initFile(String id) |
protected void |
OMETiffReader.initFile(String id) |
protected void |
FitsReader.initFile(String id) |
protected void |
BMPReader.initFile(String id) |
protected void |
APNGReader.initFile(String id) |
protected void |
ICSReader.initFile(String id) |
protected void |
BaseTiffReader.initFile(String id) |
protected void |
TiffJAIReader.initFile(String id) |
protected void |
PCXReader.initFile(String id) |
protected void |
EPSReader.initFile(String id) |
protected void |
NativeQTReader.initFile(String id) |
protected void |
AVIReader.initFile(String id) |
protected void |
ImageIOReader.initFile(String id) |
protected void |
NRRDReader.initFile(String id) |
protected void |
MinimalTiffReader.initFile(String id) |
protected void |
TextReader.initFile(String id) |
protected void |
FakeReader.initFile(String id) |
protected void |
GIFReader.initFile(String id) |
void |
MicromanagerReader.initFile(String id) |
protected void |
BaseZeissReader.initFileMain(String id) |
protected void |
ImageIOReader.initImage() |
protected void |
GelReader.initMetadata() |
protected void |
BaseTiffReader.initMetadata()
Populates the metadata hashtable and metadata store.
|
protected void |
ZeissLSMReader.initMetadata(int series) |
protected void |
LEOReader.initMetadataStore() |
protected void |
TrestleReader.initMetadataStore() |
protected void |
PyramidTiffReader.initMetadataStore() |
protected void |
NikonTiffReader.initMetadataStore() |
protected void |
FluoviewReader.initMetadataStore() |
protected void |
SVSReader.initMetadataStore() |
protected void |
ImaconReader.initMetadataStore() |
protected void |
NDPIReader.initMetadataStore() |
protected void |
SlidebookTiffReader.initMetadataStore() |
protected void |
SimplePCITiffReader.initMetadataStore() |
protected void |
SISReader.initMetadataStore() |
protected void |
LeicaSCNReader.initMetadataStore() |
protected void |
JPKReader.initMetadataStore() |
protected void |
ImprovisionTiffReader.initMetadataStore() |
protected void |
FEITiffReader.initMetadataStore() |
protected void |
NikonElementsTiffReader.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() |
protected void |
NikonReader.initStandardMetadata() |
protected void |
LEOReader.initStandardMetadata() |
protected void |
TrestleReader.initStandardMetadata() |
protected void |
PyramidTiffReader.initStandardMetadata() |
protected void |
MetamorphReader.initStandardMetadata() |
protected void |
NikonTiffReader.initStandardMetadata() |
protected void |
FluoviewReader.initStandardMetadata() |
protected void |
SVSReader.initStandardMetadata() |
protected void |
ImaconReader.initStandardMetadata() |
protected void |
NDPIReader.initStandardMetadata() |
protected void |
SlidebookTiffReader.initStandardMetadata() |
protected void |
SimplePCITiffReader.initStandardMetadata() |
protected void |
SISReader.initStandardMetadata() |
protected void |
LeicaSCNReader.initStandardMetadata() |
protected void |
JPKReader.initStandardMetadata() |
protected void |
ImprovisionTiffReader.initStandardMetadata() |
protected void |
FEITiffReader.initStandardMetadata() |
protected void |
SEQReader.initStandardMetadata() |
protected void |
NikonElementsTiffReader.initStandardMetadata() |
protected void |
DNGReader.initStandardMetadata() |
protected void |
TiffReader.initStandardMetadata() |
protected void |
BaseTiffReader.initStandardMetadata()
Parses standard metadata.
|
protected void |
ZeissZVIReader.initVars(String id) |
protected void |
BaseZeissReader.initVars(String id) |
protected void |
ZeissTIFFReader.initVars(String id) |
boolean |
PerkinElmerReader.isSingleFile(String id) |
boolean |
LeicaReader.isSingleFile(String id) |
boolean |
FV1000Reader.isSingleFile(String id) |
boolean |
OperettaReader.isSingleFile(String id) |
boolean |
TillVisionReader.isSingleFile(String id) |
boolean |
BrukerReader.isSingleFile(String id) |
boolean |
NDPISReader.isSingleFile(String id) |
boolean |
ScreenReader.isSingleFile(String id) |
boolean |
MIASReader.isSingleFile(String id) |
boolean |
NiftiReader.isSingleFile(String id) |
boolean |
MetamorphReader.isSingleFile(String id) |
boolean |
ScanrReader.isSingleFile(String id) |
boolean |
DeltavisionReader.isSingleFile(String id) |
boolean |
CellVoyagerReader.isSingleFile(String id) |
boolean |
CellSensReader.isSingleFile(String id) |
boolean |
FlexReader.isSingleFile(String id) |
boolean |
VisitechReader.isSingleFile(String id) |
boolean |
ZeissLSMReader.isSingleFile(String id) |
boolean |
InCellReader.isSingleFile(String id) |
boolean |
ZeissTIFFReader.isSingleFile(String id) |
boolean |
FujiReader.isSingleFile(String id) |
boolean |
PrairieReader.isSingleFile(String id) |
boolean |
BDReader.isSingleFile(String id) |
boolean |
ImagicReader.isSingleFile(String id) |
boolean |
L2DReader.isSingleFile(String id) |
boolean |
TCSReader.isSingleFile(String id) |
boolean |
HitachiReader.isSingleFile(String id) |
boolean |
BioRadReader.isSingleFile(String id) |
boolean |
AFIReader.isSingleFile(String id) |
boolean |
APLReader.isSingleFile(String id) |
boolean |
AnalyzeReader.isSingleFile(String id) |
boolean |
OMETiffReader.isSingleFile(String id) |
boolean |
ICSReader.isSingleFile(String id) |
boolean |
NRRDReader.isSingleFile(String id) |
boolean |
FakeReader.isSingleFile(String id) |
boolean |
MicromanagerReader.isSingleFile(String id) |
static void |
CellVoyagerReader.main(String[] args) |
static void |
FlexReader.mapServersFromConfigurationFile(String configFile)
Read a configuration file with lines of the form:
<server alias>=<real server name>
and call mapServer(String, String) accordingly.
|
protected BufferedImage |
TiffJAIReader.openBufferedImage(int no)
Obtains a BufferedImage from the given data source using JAI.
|
byte[] |
LIMReader.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[] |
ZeissZVIReader.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[] |
NikonReader.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[] |
PerkinElmerReader.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[] |
ARFReader.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[] |
FV1000Reader.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[] |
ZeissCZIReader.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[] |
TrestleReader.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[] |
WATOPReader.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[] |
VarianFDFReader.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[] |
ScreenReader.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[] |
MIASReader.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[] |
NiftiReader.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[] |
MetamorphReader.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[] |
PSDReader.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[] |
DeltavisionReader.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[] |
SDTReader.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[] |
CellVoyagerReader.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[] |
FluoviewReader.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[] |
IvisionReader.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[] |
NAFReader.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[] |
FlexReader.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[] |
SVSReader.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[] |
IMODReader.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[] |
WlzReader.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[] |
GatanDM2Reader.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[] |
OxfordInstrumentsReader.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[] |
IPLabReader.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[] |
PCIReader.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[] |
INRReader.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[] |
MetamorphTiffReader.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[] |
PQBinReader.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[] |
SimplePCITiffReader.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[] |
PDSReader.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[] |
HRDGDFReader.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[] |
InCellReader.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[] |
QuesantReader.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[] |
IPWReader.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[] |
UnisokuReader.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[] |
InveonReader.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[] |
SpiderReader.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[] |
VolocityClippingReader.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[] |
PrairieReader.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[] |
BDReader.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[] |
ImagicReader.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[] |
L2DReader.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[] |
BioRadGelReader.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[] |
GelReader.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[] |
LegacyND2Reader.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[] |
TCSReader.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[] |
OpenlabReader.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[] |
ImprovisionTiffReader.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[] |
RHKReader.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[] |
HamamatsuVMSReader.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[] |
TopometrixReader.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[] |
AFIReader.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[] |
PCORAWReader.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[] |
APLReader.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[] |
JEOLReader.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[] |
OMEXMLReader.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[] |
ZipReader.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[] |
JPEG2000Reader.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[] |
DicomReader.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[] |
OMETiffReader.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[] |
BMPReader.openBytes(int no,
byte[] buf,
int x,
int y,
int w,
int h) |
byte[] |
APNGReader.openBytes(int no,
byte[] buf,
int x,
int y,
int w,
int h) |
byte[] |
ICSReader.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[] |
EPSReader.openBytes(int no,
byte[] buf,
int x,
int y,
int w,
int h) |
byte[] |
NativeQTReader.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[] |
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[] |
BIFormatReader.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[] |
FakeReader.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[] |
MicromanagerReader.openBytes(int no,
byte[] buf,
int x,
int y,
int w,
int h) |
Object |
MNGReader.openPlane(int no,
int x,
int y,
int w,
int h) |
Object |
LegacyQTReader.openPlane(int no,
int x,
int y,
int w,
int h) |
Object |
TiffJAIReader.openPlane(int no,
int x,
int y,
int w,
int h) |
Object |
ImageIOReader.openPlane(int no,
int x,
int y,
int w,
int h) |
Object |
TextReader.openPlane(int no,
int x,
int y,
int w,
int h) |
byte[] |
CellSensReader.openThumbBytes(int no) |
byte[] |
SVSReader.openThumbBytes(int no) |
byte[] |
NDPIReader.openThumbBytes(int no) |
byte[] |
LeicaSCNReader.openThumbBytes(int no) |
byte[] |
AFIReader.openThumbBytes(int no) |
byte[] |
MinimalTiffReader.openThumbBytes(int no) |
void |
MIASReader.parseMasks(MetadataStore overlayStore)
Parse masks into a separate overlay-specific MetadataStore.
|
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.
|
void |
MicromanagerReader.populateMetadataStore(String[] jsonData) |
protected void |
ZeissLSMReader.populateMetadataStore(loci.formats.in.ZeissLSMReader.SubBlock block,
MetadataStore store,
int series) |
void |
MIASReader.setAutomaticallyParseMasks(boolean parse)
Toggle whether or not Mask pixel data should be parsed in setId.
|
void |
JPEGReader.setId(String id) |
protected void |
BaseZeissReader.storeROIs(MetadataStore store)
Store basic dimensions in model
|
| Modifier and Type | Method and Description |
|---|---|
byte[] |
JPEG2000Writer.compressBuffer(int no,
byte[] buf,
int x,
int y,
int w,
int h)
Compresses the buffer.
|
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 |
TiffWriter.saveBytes(int no,
byte[] buf,
IFD ifd)
Saves the given image to the specified (possibly already open) file.
|
void |
OMETiffWriter.saveBytes(int no,
byte[] buf,
IFD ifd,
int x,
int y,
int w,
int h) |
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 |
WlzWriter.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 |
EPSWriter.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 |
OMETiffWriter.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 |
AVIWriter.saveBytes(int no,
byte[] buf,
int x,
int y,
int w,
int h) |
void |
ImageIOWriter.saveBytes(int no,
byte[] buf,
int x,
int y,
int w,
int h) |
void |
JavaWriter.saveBytes(int no,
byte[] buf,
int x,
int y,
int w,
int h) |
void |
JPEG2000Writer.saveBytes(int no,
byte[] buf,
int x,
int y,
int w,
int h) |
void |
ICSWriter.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 |
TiffWriter.saveBytes(int no,
byte[] buf,
int x,
int y,
int w,
int h) |
void |
LegacyQTWriter.savePlane(int no,
Object plane,
int x,
int y,
int w,
int h) |
void |
ImageIOWriter.savePlane(int no,
Object plane,
int x,
int y,
int w,
int h) |
void |
WlzWriter.setId(String id) |
void |
QTWriter.setId(String id) |
void |
OMETiffWriter.setId(String id) |
void |
APNGWriter.setId(String id) |
void |
AVIWriter.setId(String id) |
void |
JavaWriter.setId(String id) |
void |
ICSWriter.setId(String id) |
void |
OMEXMLWriter.setId(String id) |
void |
TiffWriter.setId(String id) |
| Modifier and Type | Method and Description |
|---|---|
void |
WlzServiceImpl.open(String file,
String rw) |
void |
WlzService.open(String file,
String rw)
Initializes the service for the given file path.
|
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.
|
String |
IFD.getIFDStringValue(int tag)
Gets the given directory entry value as a string from this IFD,
performing some error checking.
|
Object |
IFD.getIFDValue(int tag,
Class checkClass)
Gets the given directory entry value from this IFD,
performing some error checking.
|
long |
IFD.getImageLength()
Retrieves the image's length (TIFF tag ImageLength) from a given TIFF IFD.
|
long |
IFD.getImageWidth()
Retrieves the image's width (TIFF tag ImageWidth) from a given TIFF IFD.
|
OnDemandLongArray |
IFD.getOnDemandStripOffsets() |
PhotoInterp |
IFD.getPhotometricInterpretation()
Retrieves the image's photometric interpretation (TIFF tag
PhotometricInterpretation) from this IFD.
|
int |
IFD.getPixelType()
Retrieves the image's pixel type based on the BitsPerSample tag.
|
int |
IFD.getPlanarConfiguration()
Retrieves the image's planar configuration (TIFF tag PlanarConfiguration)
from this IFD.
|
long[] |
IFD.getRowsPerStrip()
Retrieves the number of rows per strip for image (TIFF tag RowsPerStrip)
from this IFD.
|
byte[] |
TiffParser.getSamples(IFD ifd,
byte[] buf) |
byte[] |
TiffParser.getSamples(IFD ifd,
byte[] buf,
int x,
int y,
long width,
long height) |
byte[] |
TiffParser.getSamples(IFD ifd,
byte[] buf,
int x,
int y,
long width,
long height,
int overlapX,
int overlapY) |
int |
IFD.getSamplesPerPixel()
Retrieves the number of samples per pixel for the image (TIFF tag
SamplesPerPixel) from this IFD.
|
long[] |
IFD.getStripByteCounts()
Retrieves strip byte counts for the image (TIFF tag StripByteCounts) from
this IFD.
|
long[] |
IFD.getStripOffsets()
Retrieves the strip offsets for the image (TIFF tag StripOffsets) from
this IFD.
|
byte[] |
TiffParser.getTile(IFD ifd,
byte[] buf,
int row,
int col) |
long |
IFD.getTileLength()
Returns the length of an image tile.
|
long |
IFD.getTilesPerColumn()
Returns the number of image tiles per column.
|
long |
IFD.getTilesPerRow()
Returns the number of image tiles per row.
|
long |
IFD.getTileWidth()
Returns the width of an image tile.
|
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(RandomAccessInputStream in,
Object value)
Convenience method for overwriting a file's first ImageDescription.
|
void |
TiffSaver.overwriteIFDValue(RandomAccessInputStream raf,
int ifd,
int tag,
Object value)
Surgically overwrites an existing IFD value with the given one.
|
void |
TiffSaver.overwriteLastIFDOffset(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) |
void |
TiffSaver.writeIFDValue(RandomAccessOutputStream extraOut,
long offset,
int tag,
Object value)
Writes the given IFD value to the given output object.
|
void |
TiffSaver.writeImage(byte[][] buf,
IFDList ifds,
int pixelType) |
void |
TiffSaver.writeImage(byte[] buf,
IFD ifd,
int no,
int pixelType,
boolean last) |
void |
TiffSaver.writeImage(byte[] buf,
IFD ifd,
int no,
int pixelType,
int x,
int y,
int w,
int h,
boolean last)
Writes to any rectangle from the passed block.
|
void |
TiffSaver.writeImage(byte[] buf,
IFD ifd,
int no,
int pixelType,
int x,
int y,
int w,
int h,
boolean last,
Integer nChannels,
boolean copyDirectly) |
| Modifier and Type | Method and Description |
|---|---|
static String |
AmiraParameters.entryToString(Object object,
String indent) |
protected void |
AmiraParameters.extractCoreMetaData() |
static void |
CacheConsole.main(String[] args)
Interactive interpreter for testing Bio-Formats caching implementation.
|
static void |
TiffComment.main(String[] args) |
static void |
MakeTestOmeTiff.main(String[] args) |
int |
MakeTestOmeTiff.makeOmeTiff(String... args) |
void |
MakeTestOmeTiff.makeOmeTiff(String name,
CoreMetadata info) |
void |
MakeTestOmeTiff.makeSamples() |
protected Double[] |
AmiraParameters.readDoubleArray(int count) |
protected void |
AmiraParameters.readFile(RandomAccessInputStream inputStream) |
protected void |
AmiraParameters.readFile(String path) |
protected Integer[] |
AmiraParameters.readIntArray() |
protected Integer[] |
AmiraParameters.readIntArray(int count) |
protected Map |
AmiraParameters.readMap() |
protected Number |
AmiraParameters.readNumber() |
protected Number[] |
AmiraParameters.readNumberArray() |
protected String |
AmiraParameters.readQuotedString() |
protected void |
AmiraParameters.readTopLevel() |
protected void |
AmiraParameters.syntaxError(String message) |
static String |
AmiraParameters.toString(Map map,
String indent) |
| Constructor and Description |
|---|
AmiraParameters(RandomAccessInputStream inputStream) |
AmiraParameters(String path) |
| Modifier and Type | Method and Description |
|---|---|
static ImagePlus[] |
BF.openImagePlus(ImporterOptions options) |
static ImagePlus[] |
BF.openImagePlus(String path) |
static ImagePlus[] |
BF.openThumbImagePlus(ImporterOptions options) |
static ImagePlus[] |
BF.openThumbImagePlus(String path) |
| Modifier and Type | Method and Description |
|---|---|
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.
|
ImagePlus[] |
ImagePlusReader.openImagePlus()
Opens one or more
ImagePlus objects
corresponding to the reader's associated options. |
ImagePlus[] |
ImagePlusReader.openThumbImagePlus() |
ImagePlus[] |
Importer.readPixels(ImagePlusReader reader,
ImporterOptions options,
DisplayHandler displayHandler) |
void |
Importer.showDialogs(ImportProcess process) |
| Modifier and Type | Method and Description |
|---|---|
void |
LociFunctions.fileGroupOption(String id,
String[] fileGroupOption) |
void |
LociFunctions.getFormat(String id,
String[] format) |
void |
LociFunctions.openImage(String title,
Double no) |
void |
LociFunctions.openSubImage(String title,
Double no,
Double x,
Double y,
Double w,
Double h) |
void |
LociFunctions.openThumbImage(String title,
Double no) |
void |
LociFunctions.setId(String id) |
| 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 |
|---|---|
protected static int |
BFVirtualStack.getHeight(IFormatReader r,
String path,
int series) |
protected static int |
BFVirtualStack.getWidth(IFormatReader r,
String path,
int series) |
Object |
ImageProcessorReader.openPlane(int no,
int x,
int y,
int w,
int h) |
ImageProcessor[] |
ImageProcessorReader.openProcessors(int no)
Creates an ImageJ image processor object
for the image plane at the given position.
|
ImageProcessor[] |
ImageProcessorReader.openProcessors(int no,
int x,
int y,
int w,
int h)
Returns an array of ImageProcessors that represent the given slice.
|
ImageProcessor[] |
ImageProcessorReader.openThumbProcessors(int no) |
| Constructor and Description |
|---|
BFVirtualStack(String path,
IFormatReader r,
boolean colorize,
boolean merge,
boolean record) |
| Modifier and Type | Method and Description |
|---|---|
static void |
SingularityTest.main(String[] args) |
static void |
ZipTester.main(String[] args) |
static void |
ZipTester.time(String id) |
| Modifier and Type | Method and Description |
|---|---|
void |
SubResolutionTest.init(String id) |
void |
FileHandleTest.testHandleCount() |
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