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

Class BioformatsWriter

Object

AnchorBean<StackWriter>

StackWriter

BioformatsWriter

Direct Known Subclasses:

OMETiff, OMEXML, Tiff

public abstract class BioformatsWriter
extends StackWriter

Base class for writing a stack to the filesystem using the Bioformats library.

The following formats are supported with a variety of number of channels and stacks:

• unsigned 8-bit
• unsigned 16-bit
• unsigned 32-bit
• float

Note that not all implementations support writing as RGB. When they do, it insists on three channels, and only supported unsigned 8-bit or unsigned-16 bit as channel types.

If a stack has heterogeneous channel types (i.e. not all channels have the same type) then it writes all channels with the most generic type (e.g. most bits).

Author:

Owen Feehan

Constructor Summary

Constructors

Constructor	Description
BioformatsWriter(boolean supportsRGB)	Creates a new BioformatsWriter instance.

Method Summary

Modifier and Type	Method	Description
protected abstract loci.formats.IFormatWriter	createWriter()	Creates or gets an instance of IFormatWriter which dictates the file format to use for writing.
void	writeStack(Stack stack, Path filePath, StackWriteOptions options)	Writes a stack to the filesystem at a particular path.

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

fileFormat, 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

BioformatsWriter

public BioformatsWriter(boolean supportsRGB)

Creates a new BioformatsWriter instance.

Parameters:

supportsRGB - Whether the writer supports writing RGB images or not.

Method Details

writeStack

public void writeStack(Stack stack,
 Path filePath,
 StackWriteOptions options)
                throws ImageIOException

Description copied from class: StackWriter

Writes a stack to the filesystem at a particular path.

Specified by:

writeStack in class StackWriter

Parameters:

stack - the stack to write.

filePath - the path to write the file to.

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

Throws:

ImageIOException - if anything goes wrong while writing.

createWriter

protected abstract loci.formats.IFormatWriter createWriter()
                                                    throws ImageIOException

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

Returns:

a newly created writer.

Throws:

ImageIOException - if a writer cannot be created successfully.