Package loci.formats.out

Class TiffWriter

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatWriter

loci.formats.out.TiffWriter

All Implemented Interfaces:

Closeable, AutoCloseable, loci.formats.ICompressedTileWriter, loci.formats.IFormatHandler, loci.formats.IFormatWriter, loci.formats.IMetadataConfigurable, loci.formats.IPyramidHandler

Direct Known Subclasses:

OMETiffWriter

public class TiffWriter
extends loci.formats.FormatWriter

TiffWriter is the file format writer for TIFF files.

Field Summary

Fields

Modifier and Type	Field	Description
protected boolean	canDetectBigTiff	Whether or not BigTIFF can be used automatically.
protected boolean	checkParams	Whether or not to check the parameters passed to saveBytes.
static final String	COMPRESSION_J2K
static final String	COMPRESSION_J2K_LOSSY
static final String	COMPRESSION_JPEG
static final String	COMPRESSION_LZW
static final String	COMPRESSION_UNCOMPRESSED
static final String	COMPRESSION_ZLIB
protected RandomAccessInputStream	in	Input stream to use when overwriting data.
protected boolean	isBigTiff	Whether or not the output file is a BigTIFF file.
protected TiffSaver	tiffSaver	The TiffSaver that will do most of the writing.
protected int	tileSizeX	The tile width which will be used for writing.
protected int	tileSizeY	The tile height which will be used for writing.

Fields inherited from class loci.formats.FormatWriter

cm, compression, compressionTypes, fps, initialized, interleaved, metadataRetrieve, options, out, resolution, resolutionData, sequential, series, validBits

Fields inherited from class loci.formats.FormatHandler

COMPRESSION_SUFFIXES, currentId, format, LOGGER, metadataOptions, suffixes

Constructor Summary

Constructors

Constructor	Description
TiffWriter()
TiffWriter(String format, String[] exts)

Method Summary

Modifier and Type	Method	Description
boolean	canDoStacks()
void	close()
protected RandomAccessInputStream	createInputStream()
protected TiffSaver	createTiffSaver()
loci.formats.codec.Codec	getCodec()
int[]	getPixelTypes(String codec)
int	getPlaneCount()
int	getTileSizeX()
int	getTileSizeY()
protected IFD	makeIFD()
protected int	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	saveBytes(int no, byte[] buf, int x, int y, int w, int h)
void	saveBytes(int no, byte[] buf, IFD ifd)	Saves the given image to the specified (possibly already open) file.
void	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	saveCompressedBytes(int no, byte[] buf, int x, int y, int w, int h)
void	setBigTiff(boolean bigTiff)	Sets whether or not BigTIFF files should be written.
void	setCanDetectBigTiff(boolean detect)	Sets whether or not BigTIFF can be used automatically based upon the input data size (true by default).
void	setId(String id)
int	setTileSizeX(int tileSize)
int	setTileSizeY(int tileSize)
protected void	setupTiffSaver()

Methods inherited from class loci.formats.FormatWriter

changeOutputFile, checkParams, createOutputStream, getCodecOptions, getColorModel, getCompression, getCompressionTypes, getFramesPerSecond, getMetadataRetrieve, getPixelTypes, getPlaneCount, getResolution, getResolutionCount, getResolutions, getSamplesPerPixel, getSamplesPerPixel, getSeries, getSizeX, getSizeY, hasResolutions, isFullPlane, isInterleaved, isSupportedType, saveBytes, saveBytes, savePlane, savePlane, savePlane, seekToPlaneOffset, setCodecOptions, setColorModel, setCompression, setFramesPerSecond, setInterleaved, setMetadataRetrieve, setResolution, setResolutions, setSeries, setValidBitsPerPixel, setWriteSequentially

Methods inherited from class loci.formats.FormatHandler

checkSuffix, checkSuffix, getFormat, getMetadataOptions, getNativeDataType, getSuffixes, getSupportedMetadataLevels, isThisType, setMetadataOptions

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface loci.formats.IFormatHandler

getFormat, getNativeDataType, getSuffixes, isThisType

Methods inherited from interface loci.formats.IMetadataConfigurable

getMetadataOptions, getSupportedMetadataLevels, setMetadataOptions

Field Details

COMPRESSION_UNCOMPRESSED

public static final String COMPRESSION_UNCOMPRESSED

COMPRESSION_LZW

public static final String COMPRESSION_LZW

COMPRESSION_J2K

public static final String COMPRESSION_J2K

COMPRESSION_J2K_LOSSY

public static final String COMPRESSION_J2K_LOSSY

COMPRESSION_JPEG

public static final String COMPRESSION_JPEG

COMPRESSION_ZLIB

public static final String COMPRESSION_ZLIB

isBigTiff

protected boolean isBigTiff

Whether or not the output file is a BigTIFF file.

canDetectBigTiff

protected boolean canDetectBigTiff

Whether or not BigTIFF can be used automatically.

tiffSaver

protected TiffSaver tiffSaver

The TiffSaver that will do most of the writing.

in

protected RandomAccessInputStream in

Input stream to use when overwriting data.

checkParams

protected boolean checkParams

Whether or not to check the parameters passed to saveBytes.

tileSizeX

protected int tileSizeX

The tile width which will be used for writing.

tileSizeY

protected int tileSizeY

The tile height which will be used for writing.

Constructor Details

TiffWriter

public TiffWriter()

TiffWriter

public TiffWriter(String format,
 String[] exts)

Method Details

getCodec

public loci.formats.codec.Codec getCodec()

saveCompressedBytes

public void saveCompressedBytes(int no,
 byte[] buf,
 int x,
 int y,
 int w,
 int h)
                         throws loci.formats.FormatException,
IOException

Throws:

loci.formats.FormatException

IOException

makeIFD

protected IFD makeIFD()
               throws loci.formats.FormatException,
IOException

Throws:

loci.formats.FormatException

IOException

setId

public void setId(String id)
           throws loci.formats.FormatException,
IOException

Specified by:

setId in interface loci.formats.IFormatHandler

Overrides:

setId in class loci.formats.FormatWriter

Throws:

loci.formats.FormatException

IOException

saveBytes

public void saveBytes(int no,
 byte[] buf,
 IFD ifd)
               throws IOException,
loci.formats.FormatException

Saves the given image to the specified (possibly already open) file. The IFD hashtable allows specification of TIFF parameters such as bit depth, compression and units. Use one IFD instance per plane.

Throws:

IOException

loci.formats.FormatException

saveBytes

public void saveBytes(int no,
 byte[] buf,
 IFD ifd,
 int x,
 int y,
 int w,
 int h)
               throws IOException,
loci.formats.FormatException

Saves the given image to the specified series in the current file. The IFD hashtable allows specification of TIFF parameters such as bit depth, compression and units. Use one IFD instance per plane.

Throws:

IOException

loci.formats.FormatException

prepareToWriteImage

protected int prepareToWriteImage(int no,
 byte[] buf,
 IFD ifd,
 int x,
 int y,
 int w,
 int h)
                           throws IOException,
loci.formats.FormatException

Performs the preparation for work prior to the usage of the TIFF saver. This method is factored out from saveBytes() in an attempt to ensure thread safety.

Throws:

IOException

loci.formats.FormatException

close

public void close()
           throws IOException

Specified by:

close in interface AutoCloseable

Specified by:

close in interface Closeable

Overrides:

close in class loci.formats.FormatWriter

Throws:

IOException

getPlaneCount

public int getPlaneCount()

Overrides:

getPlaneCount in class loci.formats.FormatWriter

saveBytes

public void saveBytes(int no,
 byte[] buf,
 int x,
 int y,
 int w,
 int h)
               throws loci.formats.FormatException,
IOException

Throws:

loci.formats.FormatException

IOException

See Also:

• IFormatWriter.saveBytes(int, byte[], int, int, int, int)

canDoStacks

public boolean canDoStacks()

Specified by:

canDoStacks in interface loci.formats.IFormatWriter

Overrides:

canDoStacks in class loci.formats.FormatWriter

getPixelTypes

public int[] getPixelTypes(String codec)

Specified by:

getPixelTypes in interface loci.formats.IFormatWriter

Overrides:

getPixelTypes in class loci.formats.FormatWriter

setBigTiff

public void setBigTiff(boolean bigTiff)

Sets whether or not BigTIFF files should be written. This flag is not reset when close() is called.

setCanDetectBigTiff

public void setCanDetectBigTiff(boolean detect)

Sets whether or not BigTIFF can be used automatically based upon the input data size (true by default). This flag is not reset when close() is called.

setupTiffSaver

protected void setupTiffSaver()
                       throws IOException

Throws:

IOException

getTileSizeX

public int getTileSizeX()
                 throws loci.formats.FormatException

Specified by:

getTileSizeX in interface loci.formats.IFormatWriter

Overrides:

getTileSizeX in class loci.formats.FormatWriter

Throws:

loci.formats.FormatException

setTileSizeX

public int setTileSizeX(int tileSize)
                 throws loci.formats.FormatException

Specified by:

setTileSizeX in interface loci.formats.IFormatWriter

Overrides:

setTileSizeX in class loci.formats.FormatWriter

Throws:

loci.formats.FormatException

getTileSizeY

public int getTileSizeY()
                 throws loci.formats.FormatException

Specified by:

getTileSizeY in interface loci.formats.IFormatWriter

Overrides:

getTileSizeY in class loci.formats.FormatWriter

Throws:

loci.formats.FormatException

setTileSizeY

public int setTileSizeY(int tileSize)
                 throws loci.formats.FormatException

Specified by:

setTileSizeY in interface loci.formats.IFormatWriter

Overrides:

setTileSizeY in class loci.formats.FormatWriter

Throws:

loci.formats.FormatException

createInputStream

protected RandomAccessInputStream createInputStream()
                                             throws IOException

Throws:

IOException

createTiffSaver

protected TiffSaver createTiffSaver()