Package org.anchoranalysis.io.bioformats.bean.writer

Class OMEXML

Object

AnchorBean<StackWriter>

StackWriter

BioformatsWriter

OMEXML

public class OMEXML
extends BioformatsWriter

Writes a stack to the filesystem as an OME-XML using the Bioformats library.

This is particularly useful for stacks of images that have an unusual number of channels (neither 1 or 3 channels), and which most other file formats cannot support.

Note that OMEXML seems to struggle with reading/writing RGB files, so these files are not supported.

Author:

Owen Feehan

Constructor Summary

Constructors

Constructor	Description
OMEXML()	Default constructor.

Method Summary

Modifier and Type	Method	Description
protected loci.formats.IFormatWriter	createWriter()	Creates or gets an instance of IFormatWriter which dictates the file format to use for writing.
ImageFileFormat	fileFormat(StackWriteOptions writeOptions)	The file format that will be written by the generator.

Methods inherited from class org.anchoranalysis.io.bioformats.bean.writer.BioformatsWriter

writeStack

Methods inherited from class org.anchoranalysis.image.io.bean.stack.writer.StackWriter

fileFormatWarnUnexpected, writeStackWithExtension

Methods inherited from class org.anchoranalysis.bean.AnchorBean

checkMisconfigured, describeBean, describeChildren, duplicateBean, fields, findFieldsOfClass, getBeanName, getLocalPath, localise, toString

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Details

OMEXML

public OMEXML()

Default constructor.

Method Details

fileFormat

public ImageFileFormat fileFormat(StackWriteOptions writeOptions)

Description copied from class: StackWriter

The file format that will be written by the generator.

Specified by:

fileFormat in class StackWriter

Parameters:

writeOptions - options which may influence how a raster is written.

Returns:

the image file-format.

createWriter

protected loci.formats.IFormatWriter createWriter()
                                           throws ImageIOException

Description copied from class: BioformatsWriter

Creates or gets an instance of IFormatWriter which dictates the file format to use for writing.

Specified by:

createWriter in class BioformatsWriter

Returns:

a newly created writer.

Throws:

ImageIOException - if a writer cannot be created successfully.