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

Class StackReader

Object

AnchorBean<StackReader>

StackReader

Direct Known Subclasses:

BranchExtension, FlattenAsChannel, ImposeResolution, MultiFileReader, OpenCVReader, ReadVoxelExtentXml, RejectIfConditionXYResolution, StackReaderOrientationCorrection

public abstract class StackReader
extends AnchorBean<StackReader>

Reads an image-Stack from the file-system.

Author:

Owen Feehan

Constructor Summary

Constructors

Constructor	Description
StackReader()

Method Summary

Modifier and Type	Method	Description
abstract OpenedImageFile	openFile(Path path, ExecutionTimeRecorder executionTimeRecorder)	Opens a file containing one or more images.
Stack	readStack(Path path, OperationContext context)	Opens a file at path that should contain only a single-stack.

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

StackReader

public StackReader()

Method Details

readStack

public Stack readStack(Path path,
 OperationContext context)
                throws ImageIOException

Opens a file at path that should contain only a single-stack.

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

Parameters:

path - the path of the image-file to open.

context - context parameters.

Returns:

the stack that has been read.

Throws:

ImageIOException - if there is a series of stacks in the file, or if anything else goes wrong.

openFile

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

Opens a file containing one or more images.

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

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.