ome.io.bioformats
Class OmeroPixelsPyramidWriter

java.lang.Object
  extended by loci.formats.FormatHandler
      extended by loci.formats.FormatWriter
          extended by loci.formats.out.TiffWriter
              extended by ome.io.bioformats.OmeroPixelsPyramidWriter
All Implemented Interfaces:
loci.formats.IFormatHandler, loci.formats.IFormatWriter

public class OmeroPixelsPyramidWriter
extends loci.formats.out.TiffWriter

File format writer for OMERO pixels pyramid files.

Since:
Beta4.3
Author:
Chris Allan, callan at blackcat dot ca

Field Summary
static int IFD_TAG_PLANE_NUMBER
          TIFF tag we're using to store the Bio-Formats plane number.
static int IFD_TAG_SERIES
          TIFF tag we're using to store the Bio-Formats series.
static String IMAGE_DESCRIPTION
          Current TIFF image comment for OMERO pixels pyramid TIFFs.
 
Fields inherited from class loci.formats.out.TiffWriter
COMPRESSION_J2K, COMPRESSION_J2K_LOSSY, COMPRESSION_JPEG, COMPRESSION_LZW, COMPRESSION_UNCOMPRESSED, in, isBigTiff, tiffSaver
 
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, suffixes
 
Constructor Summary
OmeroPixelsPyramidWriter()
           
 
Method Summary
 void close()
           
protected  void postProcess()
          Performs re-compression post processing on the pixel pyramid.
protected  void recompressSeries(loci.formats.in.TiffReader source, int series)
          Re-compresses a source series, that is JPEG 2000 compressed, via its resolution level.
 void setId(String id)
           
 
Methods inherited from class loci.formats.out.TiffWriter
canDoStacks, getPixelTypes, getPlaneCount, saveBytes, saveBytes, saveBytes, setBigTiff
 
Methods inherited from class loci.formats.FormatWriter
changeOutputFile, checkParams, getColorModel, getCompression, getCompressionTypes, getFramesPerSecond, getMetadataRetrieve, getPixelTypes, getSamplesPerPixel, getSeries, isFullPlane, isInterleaved, isSupportedType, saveBytes, saveBytes, saveBytes, savePlane, savePlane, savePlane, savePlane, seekToPlaneOffset, setCodecOptions, setColorModel, setCompression, setFramesPerSecond, setInterleaved, setMetadataRetrieve, setSeries, setValidBitsPerPixel, setWriteSequentially
 
Methods inherited from class loci.formats.FormatHandler
checkSuffix, checkSuffix, getFormat, getNativeDataType, getSuffixes, isThisType
 
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
 

Field Detail

IMAGE_DESCRIPTION

public static final String IMAGE_DESCRIPTION
Current TIFF image comment for OMERO pixels pyramid TIFFs.

See Also:
Constant Field Values

IFD_TAG_SERIES

public static final int IFD_TAG_SERIES
TIFF tag we're using to store the Bio-Formats series.

See Also:
Constant Field Values

IFD_TAG_PLANE_NUMBER

public static final int IFD_TAG_PLANE_NUMBER
TIFF tag we're using to store the Bio-Formats plane number.

See Also:
Constant Field Values
Constructor Detail

OmeroPixelsPyramidWriter

public OmeroPixelsPyramidWriter()
Method Detail

close

public void close()
           throws IOException
Specified by:
close in interface loci.formats.IFormatHandler
Overrides:
close in class loci.formats.out.TiffWriter
Throws:
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.out.TiffWriter
Throws:
loci.formats.FormatException
IOException

postProcess

protected void postProcess()
                    throws IOException,
                           loci.formats.FormatException
Performs re-compression post processing on the pixel pyramid.

Throws:
IOException
loci.formats.FormatException

recompressSeries

protected void recompressSeries(loci.formats.in.TiffReader source,
                                int series)
                         throws loci.formats.FormatException,
                                IOException
Re-compresses a source series, that is JPEG 2000 compressed, via its resolution level.

Parameters:
source - Reader created of ourselves.
series - Target series for the re-compressed data which is the inverse of the source resolution level.
Throws:
loci.formats.FormatException
IOException


OmeroJava Api

Version: 4.3.4-dbcbce5a-b4

Copyright © 2009 The University of Dundee. All Rights Reserved.