Package loci.formats.out

Class OMETiffWriter

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatWriter

loci.formats.out.TiffWriter

loci.formats.out.OMETiffWriter

All Implemented Interfaces:

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

Direct Known Subclasses:

PyramidOMETiffWriter

public class OMETiffWriter
extends TiffWriter

OMETiffWriter is the file format writer for OME-TIFF files.

Field Summary

Fields

Modifier and Type	Field	Description
static final String	COMPANION_KEY
static final String	CREATOR_KEY

Fields inherited from class loci.formats.out.TiffWriter

canDetectBigTiff, checkParams, COMPRESSION_J2K, COMPRESSION_J2K_LOSSY, COMPRESSION_JPEG, COMPRESSION_LZW, COMPRESSION_UNCOMPRESSED, COMPRESSION_ZLIB, in, isBigTiff, tiffSaver, tileSizeX, tileSizeY

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
OMETiffWriter()

Method Summary

Modifier and Type	Method	Description
void	close()
String	getCompanion()	Get the value of the COMPANION_KEY option.
boolean	preserveCreator()	Get the value of the CREATOR_KEY option.
void	saveBytes(int no, byte[] buf, int x, int y, int w, int h)
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	setId(String id)

Methods inherited from class loci.formats.out.TiffWriter

canDoStacks, createInputStream, createTiffSaver, getCodec, getPixelTypes, getPlaneCount, getTileSizeX, getTileSizeY, makeIFD, prepareToWriteImage, saveBytes, setBigTiff, setCanDetectBigTiff, setTileSizeX, setTileSizeY, 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

COMPANION_KEY

public static final String COMPANION_KEY

See Also:

• Constant Field Values

CREATOR_KEY

public static final String CREATOR_KEY

See Also:

• Constant Field Values

Constructor Details

OMETiffWriter

public OMETiffWriter()

Method Details

close

public void close()
           throws IOException

Specified by:

close in interface AutoCloseable

Specified by:

close in interface Closeable

Overrides:

close in class TiffWriter

Throws:

IOException

saveCompressedBytes

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

Specified by:

saveCompressedBytes in interface loci.formats.ICompressedTileWriter

Overrides:

saveCompressedBytes in class TiffWriter

Throws:

loci.formats.FormatException

IOException

saveBytes

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

Specified by:

saveBytes in interface loci.formats.IFormatWriter

Overrides:

saveBytes in class TiffWriter

Throws:

loci.formats.FormatException

IOException

See Also:

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

saveBytes

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

Description copied from class: TiffWriter

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.

Overrides:

saveBytes in class TiffWriter

Throws:

loci.formats.FormatException

IOException

See Also:

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

setId

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

Specified by:

setId in interface loci.formats.IFormatHandler

Overrides:

setId in class TiffWriter

Throws:

loci.formats.FormatException

IOException

getCompanion

public String getCompanion()

Get the value of the COMPANION_KEY option.

Returns:

path to the companion file, or null if a companion file is not used

preserveCreator

public boolean preserveCreator()

Get the value of the CREATOR_KEY option. This toggles whether or not the OME Creator attribute will be overwritten with the current Bio-Formats version. For input data that does not have a Creator attribute defined, this makes no difference. By default, returns false, i.e. the Creator will be overwritten if it exists.

Returns:

true if the Creator attribute should be preserved (if it exists)