loci.formats.out

Class OMEXMLWriter

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatWriter

loci.formats.out.OMEXMLWriter

All Implemented Interfaces:

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

public class OMEXMLWriter
extends FormatWriter

OMEXMLWriter is the file format writer for OME-XML files.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
(package private) class	OMEXMLWriter.OMEHandler

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	CREATOR_KEY
private java.lang.String	currentFragment
private OMEXMLService	service
private java.util.List<java.lang.String>	xmlFragments

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
OMEXMLWriter()

Method Summary

Modifier and Type	Method and Description
boolean	canDoStacks() Reports whether the writer can save multiple images to a single file.
void	close()
private byte[]	compress(byte[] b) Compress the given byte array using the current codec.
int[]	getPixelTypes(java.lang.String codec) Gets the supported pixel types for the given codec.
boolean	preserveCreator() Get the value of the CREATOR_KEY option.
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	setId(java.lang.String id) Initializes a writer from the input file name.

Methods inherited from class loci.formats.FormatWriter

changeOutputFile, checkParams, createOutputStream, getCodecOptions, getColorModel, getCompression, getCompressionTypes, getFramesPerSecond, getMetadataRetrieve, getPixelTypes, getPlaneCount, getPlaneCount, getResolution, getResolutionCount, getResolutions, getSamplesPerPixel, getSamplesPerPixel, getSeries, getSizeX, getSizeY, getTileSizeX, getTileSizeY, hasResolutions, isFullPlane, isInterleaved, isSupportedType, saveBytes, saveBytes, savePlane, savePlane, savePlane, seekToPlaneOffset, setCodecOptions, setColorModel, setCompression, setFramesPerSecond, setInterleaved, setMetadataRetrieve, setResolution, setResolutions, setSeries, setTileSizeX, setTileSizeY, 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

CREATOR_KEY

public static final java.lang.String CREATOR_KEY

See Also:

Constant Field Values

xmlFragments

private java.util.List<java.lang.String> xmlFragments

currentFragment

private java.lang.String currentFragment

service

private OMEXMLService service

Constructor Detail

OMEXMLWriter

public OMEXMLWriter()

Method Detail

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 FormatWriter

Parameters:

id - a String specifying the path to the file

Throws:

FormatException

java.io.IOException

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 FormatWriter

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.

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)

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(java.lang.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

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)

compress

private byte[] compress(byte[] b)
                 throws FormatException,
                        java.io.IOException

Compress the given byte array using the current codec. The compressed data is then base64-encoded.

Throws:

FormatException

java.io.IOException