Package org.anchoranalysis.io.bioformats.bean

Class BioformatsReader

Object

AnchorBean<StackReader>

StackReader

StackReaderOrientationCorrection

BioformatsReader

public class BioformatsReader
extends StackReaderOrientationCorrection

Reads a stack using the Bioformats library.

Note that EXIF orientation information is not processed when reading JPEGs or PNGs.

Author:

Owen Feehan

Constructor Summary

Constructors

Constructor	Description
BioformatsReader()
BioformatsReader(ReadOptions options)	Create with particular options.

Method Summary

Modifier and Type	Method	Description
ReadOptions	getOptions()	Options that influence how stack is read.
OpenedImageFile	openFile(Path path, ExecutionTimeRecorder executionTimeRecorder)	Opens a file containing one or more images.
OpenedImageFile	openFile(Path filePath, CalculateOrientationChange orientationCorrection, ExecutionTimeRecorder executionTimeRecorder)	Opens a file containing one or more images but does not read an image.
void	setOptions(ReadOptions options)	Options that influence how stack is read.

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

BioformatsReader

public BioformatsReader(ReadOptions options)

Create with particular options.

Parameters:

options - options that influence how stack is read.

BioformatsReader

public BioformatsReader()

Method Details

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.

openFile

public OpenedImageFile openFile(Path filePath,
 CalculateOrientationChange orientationCorrection,
 ExecutionTimeRecorder executionTimeRecorder)
                         throws ImageIOException

Description copied from class: StackReaderOrientationCorrection

Opens a file containing one or more images but does not read an image.

Specified by:

openFile in class StackReaderOrientationCorrection

Parameters:

filePath - where the file is located.

orientationCorrection - calculates any needed correction applied to the orientation as the image is loaded.

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.

getOptions

public ReadOptions getOptions()

Options that influence how stack is read.

setOptions

public void setOptions(ReadOptions options)

Options that influence how stack is read.