Package org.anchoranalysis.plugin.io.bean.stack.reader

Class ReadVoxelExtentXml

Object

AnchorBean<StackReader>

StackReader

ReadVoxelExtentXml

public class ReadVoxelExtentXml
extends StackReader

Reads Resolution from an XML file associated an image.

Any existing Resolution is replaced.

The XML file is expected at the file path of the image, with .xml appended. e.g. someImage.tif would have metadata at someImage.tif.xml

The format of the XML is described in ResolutionAsXML.

Author:

Owen Feehan

Constructor Summary

Constructors

Constructor	Description
ReadVoxelExtentXml()

Method Summary

Modifier and Type	Method	Description
StackReader	getStackReader()	Reads an image before a resolution is imposed.
boolean	isAcceptNoResolution()	If false, an exception is thrown if the resolution file is missing for a particular image.
OpenedImageFile	openFile(Path path, ExecutionTimeRecorder executionTimeRecorder)	Opens a file containing one or more images.
static Optional<Resolution>	readMetadata(Path filePath, boolean acceptNoResolution)	Looks for a metadata file describing the resolution
void	setAcceptNoResolution(boolean acceptNoResolution)	If false, an exception is thrown if the resolution file is missing for a particular image.
void	setStackReader(StackReader stackReader)	Reads an image before a resolution is imposed.

Methods inherited from class org.anchoranalysis.image.io.bean.stack.reader.StackReader

readStack

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

ReadVoxelExtentXml

public ReadVoxelExtentXml()

Method Details

readMetadata

public static Optional<Resolution> readMetadata(Path filePath,
 boolean acceptNoResolution)
                                         throws ImageIOException

Looks for a metadata file describing the resolution

Given an existing image filepath, the filePath.xml is checked e.g. given /somePath/stackReader.tif it will look for /somePath/RasterRader.tif.xml

Parameters:

filePath - the filepath of the image

acceptNoResolution - if false, an exception is thrown if the resolution file is missing for a particular image.

Returns:

the scene res if the metadata file exists and was parsed. null otherwise.

Throws:

ImageIOException

openFile

public OpenedImageFile openFile(Path path,
 ExecutionTimeRecorder executionTimeRecorder)
                         throws ImageIOException

Description copied from class: StackReader

Opens a file containing one or more images.

This method should run as computationally quicky as possible. Image voxels should not yet be read.

Specified by:

openFile in class StackReader

Parameters:

path - where the file is located.

executionTimeRecorder - records the execution-times of certain operations.

Returns:

an interface to the opened file that should be closed when no longer in use.

Throws:

ImageIOException - if the file cannot be read.

getStackReader

public StackReader getStackReader()

Reads an image before a resolution is imposed.

setStackReader

public void setStackReader(StackReader stackReader)

Reads an image before a resolution is imposed.

isAcceptNoResolution

public boolean isAcceptNoResolution()

If false, an exception is thrown if the resolution file is missing for a particular image.

setAcceptNoResolution

public void setAcceptNoResolution(boolean acceptNoResolution)

If false, an exception is thrown if the resolution file is missing for a particular image.