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:

java.io.Closeable, java.lang.AutoCloseable, ICompressedTileWriter, IFormatHandler, IFormatWriter, IMetadataConfigurable, 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 and Description
static java.lang.String	COMPANION_KEY
static java.lang.String	CREATOR_KEY
private java.util.Map<java.lang.String,java.lang.Integer>	ifdCounts
private java.lang.String[][]	imageLocations
private OMEXMLMetadata	omeMeta
private OMEXMLService	service
private java.util.Map<java.lang.String,java.lang.String>	uuids
private static java.lang.String	WARNING_COMMENT

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 and Description
OMETiffWriter()

Method Summary

Modifier and Type	Method and Description
void	close()
private java.lang.String	getBinaryOnlyOMEXML(java.lang.String file, java.lang.String companion, java.lang.String companionUUID)
java.lang.String	getCompanion() Get the value of the COMPANION_KEY option.
private java.lang.String	getOMEXML(java.lang.String file)
private java.lang.String	getUUID(java.lang.String filename) Gets the UUID corresponding to the given filename.
private java.lang.String	insertWarningComment(java.lang.String xml)
private int	planeCount()
private void	populateImage(OMEXMLMetadata omeMeta, int series)
private void	populateTiffData(OMEXMLMetadata omeMeta, int[] zct, int ifd, int series, int plane)
boolean	preserveCreator() Get the value of the CREATOR_KEY option.
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.
private void	saveComment(java.lang.String file, java.lang.String xml)
private void	setCreator(ome.xml.meta.OMEXMLMetadataRoot root) Set the Creator attribute on the given OME-XML root object.
void	setId(java.lang.String id) Initializes a writer from the input file name.
private void	setupServiceAndMetadata()

Methods inherited from class loci.formats.out.TiffWriter

canDoStacks, createInputStream, createTiffSaver, getPixelTypes, getPlaneCount, getTileSizeX, getTileSizeY, 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

Methods inherited from interface loci.formats.ICompressedTileWriter

getCodec, saveCompressedBytes

Field Detail

WARNING_COMMENT

private static final java.lang.String WARNING_COMMENT

See Also:

Constant Field Values

COMPANION_KEY

public static final java.lang.String COMPANION_KEY

See Also:

Constant Field Values

CREATOR_KEY

public static final java.lang.String CREATOR_KEY

See Also:

Constant Field Values

imageLocations

private java.lang.String[][] imageLocations

omeMeta

private OMEXMLMetadata omeMeta

service

private OMEXMLService service

ifdCounts

private java.util.Map<java.lang.String,java.lang.Integer> ifdCounts

uuids

private java.util.Map<java.lang.String,java.lang.String> uuids

Constructor Detail

OMETiffWriter

public OMETiffWriter()

Method Detail

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 TiffWriter

Throws:

java.io.IOException

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.

Specified by:

saveBytes in interface IFormatWriter

Overrides:

saveBytes in class TiffWriter

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)

saveBytes

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

FormatException

java.io.IOException

See Also:

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

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 TiffWriter

Parameters:

id - a String specifying the path to the file

Throws:

FormatException

java.io.IOException

getCompanion

public java.lang.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)

getUUID

private java.lang.String getUUID(java.lang.String filename)

Gets the UUID corresponding to the given filename.

setupServiceAndMetadata

private void setupServiceAndMetadata()
                              throws loci.common.services.DependencyException,
                                     loci.common.services.ServiceException

Throws:

loci.common.services.DependencyException

loci.common.services.ServiceException

insertWarningComment

private java.lang.String insertWarningComment(java.lang.String xml)

getOMEXML

private java.lang.String getOMEXML(java.lang.String file)
                            throws FormatException,
                                   java.io.IOException

Throws:

FormatException

java.io.IOException

getBinaryOnlyOMEXML

private java.lang.String getBinaryOnlyOMEXML(java.lang.String file,
                                             java.lang.String companion,
                                             java.lang.String companionUUID)
                                      throws FormatException,
                                             java.io.IOException,
                                             loci.common.services.DependencyException,
                                             loci.common.services.ServiceException

Throws:

FormatException

java.io.IOException

loci.common.services.DependencyException

loci.common.services.ServiceException

setCreator

private void setCreator(ome.xml.meta.OMEXMLMetadataRoot root)

Set the Creator attribute on the given OME-XML root object. If the Creator was not previously set, it will be set to the current Bio-Formats version. If the Creator has been set already, the CREATOR_KEY option (via preserveCreator) is used to determine whether to overwrite the existing value with the Bio-Formats version.

Parameters:

root - OME-XML root object

saveComment

private void saveComment(java.lang.String file,
                         java.lang.String xml)
                  throws java.io.IOException

Throws:

java.io.IOException

populateTiffData

private void populateTiffData(OMEXMLMetadata omeMeta,
                              int[] zct,
                              int ifd,
                              int series,
                              int plane)

populateImage

private void populateImage(OMEXMLMetadata omeMeta,
                           int series)

planeCount

private int planeCount()