loci.formats.out

Class TiffWriter

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatWriter

loci.formats.out.TiffWriter

All Implemented Interfaces:

java.io.Closeable, java.lang.AutoCloseable, ICompressedTileWriter, IFormatHandler, IFormatWriter, IMetadataConfigurable, IPyramidHandler

Direct Known Subclasses:

OMETiffWriter

public class TiffWriter
extends FormatWriter

TiffWriter is the file format writer for TIFF files.

Field Summary

Fields

Modifier and Type	Field and Description
private static java.lang.String[]	BIG_TIFF_SUFFIXES
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 java.lang.String	COMPRESSION_J2K
static java.lang.String	COMPRESSION_J2K_LOSSY
static java.lang.String	COMPRESSION_JPEG
static java.lang.String	COMPRESSION_LZW
static java.lang.String	COMPRESSION_UNCOMPRESSED
static java.lang.String	COMPRESSION_ZLIB
protected loci.common.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.
private static int	TILE_GRANULARITY TIFF tiles must be of a height and width divisible by 16.
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 and Description
TiffWriter()
TiffWriter(java.lang.String format, java.lang.String[] exts)

Method Summary

Modifier and Type	Method and Description
boolean	canDoStacks() Reports whether the writer can save multiple images to a single file.
void	close()
protected loci.common.RandomAccessInputStream	createInputStream()
protected TiffSaver	createTiffSaver()
private void	formatCompression(IFD ifd) Sets the compression code for the specified IFD.
Codec	getCodec()
int[]	getPixelTypes(java.lang.String codec) Gets the supported pixel types for the given codec.
int	getPlaneCount() Retrieve the total number of planes in the current series.
private TiffCompression	getTIFFCompression() Get the TIFF compression enum value that corresponds to the current compression type.
private byte[]	getTile(byte[] buf, loci.common.Region tileParams, loci.common.Region srcParams)
int	getTileSizeX() Retrieves the current tile width Defaults to 0 if not supported
int	getTileSizeY() Retrieves the current tile height Defaults to 0 if not supported
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, 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	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	saveCompressedBytes(int no, byte[] buf, int x, int y, int w, int h) Save a compressed tile to the current output file.
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(java.lang.String id) Initializes a writer from the input file name.
int	setTileSizeX(int tileSize) Will attempt to set the tile width to the desired value and return the actual value which will be used
int	setTileSizeY(int tileSize) Will attempt to set the tile height to the desired value and return the actual value which will be used
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 Detail

COMPRESSION_UNCOMPRESSED

public static final java.lang.String COMPRESSION_UNCOMPRESSED

COMPRESSION_LZW

public static final java.lang.String COMPRESSION_LZW

COMPRESSION_J2K

public static final java.lang.String COMPRESSION_J2K

COMPRESSION_J2K_LOSSY

public static final java.lang.String COMPRESSION_J2K_LOSSY

COMPRESSION_JPEG

public static final java.lang.String COMPRESSION_JPEG

COMPRESSION_ZLIB

public static final java.lang.String COMPRESSION_ZLIB

BIG_TIFF_SUFFIXES

private static final java.lang.String[] BIG_TIFF_SUFFIXES

TILE_GRANULARITY

private static final int TILE_GRANULARITY

TIFF tiles must be of a height and width divisible by 16.

See Also:

Constant Field Values

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 loci.common.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 Detail

TiffWriter

public TiffWriter()

TiffWriter

public TiffWriter(java.lang.String format,
                  java.lang.String[] exts)

Method Detail

getTIFFCompression

private TiffCompression getTIFFCompression()

Get the TIFF compression enum value that corresponds to the current compression type.

formatCompression

private void formatCompression(IFD ifd)
                        throws FormatException

Sets the compression code for the specified IFD.

Parameters:

ifd - The IFD table to handle.

Throws:

FormatException

getCodec

public Codec getCodec()

Returns:

the codec that can be used to compress tiles

saveCompressedBytes

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

Description copied from interface: ICompressedTileWriter

Save a compressed tile to the current output file. The compression type of the tile should match the compression type set in the writer.

Parameters:

no - plane index

buf - compressed tile bytes

x - pixel X coordinate of the upper-left corner of the tile

y - pixel Y coordinate of the upper-left corner of the tile

w - width in pixels of the compressed tile

h - height in pixels of the compressed tile

Throws:

FormatException

java.io.IOException

makeIFD

protected IFD makeIFD()
               throws FormatException,
                      java.io.IOException

Throws:

FormatException

java.io.IOException

setId

public void setId(java.lang.String id)
           throws FormatException,
                  java.io.IOException

Description copied from class: FormatWriter

Initializes a writer from the input file name. Initializes a RandomAccessOutputStream for the output file and initializes the metadata for all the series using FormatWriter.setSeries(int).

Specified by:

setId in interface IFormatHandler

Overrides:

setId in class FormatWriter

Parameters:

id - a String specifying the path to the file

Throws:

FormatException

java.io.IOException

saveBytes

public void saveBytes(int no,
                      byte[] buf,
                      IFD ifd)
               throws java.io.IOException,
                      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:

java.io.IOException

FormatException

saveBytes

public void saveBytes(int no,
                      byte[] buf,
                      IFD ifd,
                      int x,
                      int y,
                      int w,
                      int h)
               throws java.io.IOException,
                      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:

java.io.IOException

FormatException

prepareToWriteImage

protected int prepareToWriteImage(int no,
                                  byte[] buf,
                                  IFD ifd,
                                  int x,
                                  int y,
                                  int w,
                                  int h)
                           throws java.io.IOException,
                                  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:

java.io.IOException

FormatException

close

public void close()
           throws java.io.IOException

Specified by:

close in interface java.io.Closeable

Specified by:

close in interface java.lang.AutoCloseable

Overrides:

close in class FormatWriter

Throws:

java.io.IOException

getPlaneCount

public int getPlaneCount()

Description copied from class: FormatWriter

Retrieve the total number of planes in the current series.

Overrides:

getPlaneCount in class FormatWriter

saveBytes

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

Description copied from interface: IFormatWriter

Saves the given image tile to the current series in the current file.

Parameters:

no - the plane index within the series.

buf - the byte array that represents the image tile.

x - the X coordinate of the upper-left corner of the image tile.

y - the Y coordinate of the upper-left corner of the image tile.

w - the width (in pixels) of the image tile.

h - the height (in pixels) of the image tile.

Throws:

FormatException - if one of the parameters is invalid.

java.io.IOException - if there was a problem writing to the file.

See Also:

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

canDoStacks

public boolean canDoStacks()

Description copied from interface: IFormatWriter

Reports whether the writer can save multiple images to a single file.

Specified by:

canDoStacks in interface IFormatWriter

Overrides:

canDoStacks in class FormatWriter

getPixelTypes

public int[] getPixelTypes(java.lang.String codec)

Description copied from interface: IFormatWriter

Gets the supported pixel types for the given codec.

Specified by:

getPixelTypes in interface IFormatWriter

Overrides:

getPixelTypes in class 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 java.io.IOException

Throws:

java.io.IOException

getTileSizeX

public int getTileSizeX()
                 throws FormatException

Description copied from interface: IFormatWriter

Retrieves the current tile width Defaults to 0 if not supported

Specified by:

getTileSizeX in interface IFormatWriter

Overrides:

getTileSizeX in class FormatWriter

Returns:

The current tile width being used

Throws:

FormatException - Image metadata including Pixels Size X must be set prior to calling getTileSizeX()

setTileSizeX

public int setTileSizeX(int tileSize)
                 throws FormatException

Description copied from interface: IFormatWriter

Will attempt to set the tile width to the desired value and return the actual value which will be used

Specified by:

setTileSizeX in interface IFormatWriter

Overrides:

setTileSizeX in class FormatWriter

Parameters:

tileSize - The tile width you wish to use. Setting to 0 will disable tiling

Returns:

The tile width which will actually be used, this may differ from the value requested. If the requested value is not supported the writer will return and use the closest appropriate value.

Throws:

FormatException - Tile size must be greater than or equal to 0 and less than the image width

getTileSizeY

public int getTileSizeY()
                 throws FormatException

Description copied from interface: IFormatWriter

Retrieves the current tile height Defaults to 0 if not supported

Specified by:

getTileSizeY in interface IFormatWriter

Overrides:

getTileSizeY in class FormatWriter

Returns:

The current tile height being used

Throws:

FormatException - Image metadata including Pixels Size Y must be set prior to calling getTileSizeY()

setTileSizeY

public int setTileSizeY(int tileSize)
                 throws FormatException

Description copied from interface: IFormatWriter

Will attempt to set the tile height to the desired value and return the actual value which will be used

Specified by:

setTileSizeY in interface IFormatWriter

Overrides:

setTileSizeY in class FormatWriter

Parameters:

tileSize - The tile height you wish to use. Setting to 0 will disable tiling

Returns:

The tile height which will actually be used, this may differ from the value requested. If the requested value is not supported the writer will return and use the closest appropriate value.

Throws:

FormatException - Tile size must be greater than or equal to 0 and less than the image height

getTile

private byte[] getTile(byte[] buf,
                       loci.common.Region tileParams,
                       loci.common.Region srcParams)

createInputStream

protected loci.common.RandomAccessInputStream createInputStream()
                                                         throws java.io.IOException

Throws:

java.io.IOException

createTiffSaver

protected TiffSaver createTiffSaver()