ome.io.bioformats

Class OmeroPixelsPyramidWriter

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatWriter

loci.formats.out.TiffWriter

ome.io.bioformats.OmeroPixelsPyramidWriter

All Implemented Interfaces:

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

public class OmeroPixelsPyramidWriter
extends TiffWriter

File format writer for OMERO pixels pyramid files.

Since:

Beta4.3

Author:

Chris Allan, callan at blackcat dot ca

Field Summary

Fields

Modifier and Type	Field and Description
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 java.lang.String	IMAGE_DESCRIPTION Current TIFF image comment for OMERO pixels pyramid TIFFs.

Fields inherited from class loci.formats.out.TiffWriter

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, sequential, series, validBits

Fields inherited from class loci.formats.FormatHandler

COMPRESSION_SUFFIXES, currentId, format, LOGGER, metadataOptions, suffixes

Constructor Summary

Constructors

Constructor and Description
OmeroPixelsPyramidWriter()

Method Summary

Modifier and Type	Method and Description
void	close()
protected void	postProcess() Performs re-compression post processing on the pixel pyramid.
protected void	recompressSeries(TiffReader source, int series) Re-compresses a source series, that is JPEG 2000 compressed, via its resolution level.
void	setId(java.lang.String id)

Methods inherited from class loci.formats.out.TiffWriter

canDoStacks, createInputStream, createTiffSaver, getPixelTypes, getPlaneCount, getTileSizeX, getTileSizeY, prepareToWriteImage, saveBytes, saveBytes, saveBytes, setBigTiff, setTileSizeX, setTileSizeY, setupTiffSaver

Methods inherited from class loci.formats.FormatWriter

changeOutputFile, checkParams, createOutputStream, getColorModel, getCompression, getCompressionTypes, getFramesPerSecond, getMetadataRetrieve, getPixelTypes, getPlaneCount, 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

IMAGE_DESCRIPTION

public static final java.lang.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 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

setId

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

Specified by:

setId in interface IFormatHandler

Overrides:

setId in class TiffWriter

Throws:

FormatException

java.io.IOException

postProcess

protected void postProcess()
                    throws java.io.IOException,
                           FormatException

Performs re-compression post processing on the pixel pyramid.

Throws:

java.io.IOException

FormatException

recompressSeries

protected void recompressSeries(TiffReader source,
                                int series)
                         throws FormatException,
                                java.io.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:

FormatException

java.io.IOException