loci.formats.out

Class TiffWriter

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatWriter

loci.formats.out.TiffWriter

All Implemented Interfaces:

Closeable, AutoCloseable, IFormatHandler, IFormatWriter, IMetadataConfigurable

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 long	BIG_TIFF_CUTOFF Number of bytes at which to automatically switch to BigTIFF This is approximately 3.9 GB instead of 4 GB, to allow space for the IFDs.
private static String[]	BIG_TIFF_SUFFIXES
protected boolean	checkParams Whether or not to check the parameters passed to saveBytes.
static String	COMPRESSION_J2K
static String	COMPRESSION_J2K_LOSSY
static String	COMPRESSION_JPEG
static String	COMPRESSION_LZW
static String	COMPRESSION_UNCOMPRESSED
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.

Fields inherited from class loci.formats.FormatWriter

cm, compression, compressionTypes, fps, initialized, interleaved, metadataRetrieve, options, out, 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(String format, String[] exts)

Method Summary

Methods

Modifier and Type	Method and Description
boolean	canDoStacks() Reports whether the writer can save multiple images to a single file.
void	close()
private void	formatCompression(IFD ifd) Sets the compression code for the specified IFD.
int[]	getPixelTypes(String codec) Gets the supported pixel types for the given codec.
int	getPlaneCount() Retrieve the total number of planes in the current series.
protected int	getPlaneCount(int series) Retrieve the total number of planes in given series.
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	setBigTiff(boolean bigTiff) Sets whether or not BigTIFF files should be written.
void	setId(String id) Initializes a writer from the input file name.
protected void	setupTiffSaver()

Methods inherited from class loci.formats.FormatWriter

changeOutputFile, checkParams, getColorModel, getCompression, getCompressionTypes, getFramesPerSecond, getMetadataRetrieve, getPixelTypes, getSamplesPerPixel, getSamplesPerPixel, getSeries, isFullPlane, isInterleaved, isSupportedType, saveBytes, saveBytes, savePlane, savePlane, savePlane, seekToPlaneOffset, setCodecOptions, setColorModel, setCompression, setFramesPerSecond, setInterleaved, setMetadataRetrieve, 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 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

BIG_TIFF_SUFFIXES

private static final String[] BIG_TIFF_SUFFIXES

BIG_TIFF_CUTOFF

private static final long BIG_TIFF_CUTOFF

Number of bytes at which to automatically switch to BigTIFF This is approximately 3.9 GB instead of 4 GB, to allow space for the IFDs.

See Also:

Constant Field Values

isBigTiff

protected boolean isBigTiff

Whether or not the output file is a BigTIFF file.

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.

Constructor Detail

TiffWriter

public TiffWriter()

TiffWriter

public TiffWriter(String format,
          String[] exts)

Method Detail

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

setId

public void setId(String id)
           throws FormatException,
                  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

IOException

saveBytes

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

Throws:

IOException

FormatException

saveBytes

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

Throws:

IOException

FormatException

prepareToWriteImage

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

IOException

FormatException

close

public void close()
           throws IOException

Specified by:

close in interface Closeable

Specified by:

close in interface AutoCloseable

Overrides:

close in class FormatWriter

Throws:

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

getPlaneCount

protected int getPlaneCount(int series)

Description copied from class: FormatWriter

Retrieve the total number of planes in given series.

Overrides:

getPlaneCount in class FormatWriter

saveBytes

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

Description copied from interface: IFormatWriter

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

Parameters:

no - the image index within the current file, starting from 0.

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.

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(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.

setupTiffSaver

protected void setupTiffSaver()
                       throws IOException

Throws:

IOException