org.anchoranalysis.plugin.opencv.bean.stack

Class OpenCVReader

Object

AnchorBean<StackReader>

StackReader

OpenCVReader

public class OpenCVReader
extends StackReader

Reads a stack from the file-system using OpenCV.

Depending on whether the file-path is ASCII-encoded or not-ASCII encoded, this occurs via two different implementations.

The non-ASCII method seems to be approximately 4 times slower empirically.

See this Stack Overflow post for more details on the problem/

Note that when reading image metadata only, this is computionally slow, as the entire image must be loaded into memory to determine the width and height. Users are recommended to use another library for this purpose.

However, unlike many other libraries, OpenCV has the advantage of automatically correcting the orientation (to give correct widths and heights) where EXIF rotation information is present - but only for the ASCII-mathod.

Author:

Owen Feehan

Constructor Summary

Constructors

Constructor and Description
OpenCVReader()

Method Summary

Modifier and Type	Method and Description
void	checkMisconfigured(BeanInstanceMap defaultInstances) Checks that a bean's properties conform to expectations.
OpenedImageFile	openFile(Path path, ExecutionTimeRecorder executionTimeRecorder) Opens a file containing one or more images.

Methods inherited from class StackReader

readStack

Methods inherited from class AnchorBean

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

Methods inherited from class Object

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

Constructor Detail

OpenCVReader

public OpenCVReader()

Method Detail

checkMisconfigured

public void checkMisconfigured(BeanInstanceMap defaultInstances)
                        throws BeanMisconfiguredException

Description copied from class: AnchorBean

Checks that a bean's properties conform to expectations.

Overrides:

checkMisconfigured in class AnchorBean<StackReader>

Parameters:

defaultInstances - all available default instances if the DefaultInstance annotation is used

Throws:

BeanMisconfiguredException - if the bean has not been configured properly as XML

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.