mpicbg.imglib.algorithm

Class ROIAlgorithm<T extends RealType<T>,S extends RealType<S>>

java.lang.Object

mpicbg.imglib.algorithm.ROIAlgorithm<T,S>

Type Parameters:

T -

S -

All Implemented Interfaces:

Algorithm, Benchmark, OutputAlgorithm<S>

Direct Known Subclasses:

DirectConvolution, StatisticalOperation

public abstract class ROIAlgorithm<T extends RealType<T>,S extends RealType<S>>
extends Object
implements OutputAlgorithm<S>, Benchmark

ROIAlgorithm implements a framework against which to build operations of one image against another, like convolution, cross-correlation, or morphological operations. It operates by creating a RegionOfInterestCursor from the input image, and an output image, which is assumed to be of the same size as the input. The process() method curses over the output image, and at each step calls the abstract method patchOperation(), giving it the current location in the output and input images, as well as the RegionOfInterestCursor, which will curse over a patch of a given size in the input image. patchOperation() is responsible for setting the value of the pixel at the given position in the output image.

Author:

Larry Lindsey

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	ROIAlgorithm(S type, Image<T> imageIn, int[] patchSize) Creates an ROIAlgorithm with default OutOfBoundsStrategyValueFactory, with value Zero.
protected	ROIAlgorithm(S type, Image<T> imageIn, int[] patchSize, OutOfBoundsStrategyFactory<T> inOutFactory)

Method Summary

Modifier and Type	Method and Description
boolean	checkInput()
void	close()
String	getErrorMessage()
String	getName()
protected Image<S>	getOutputImage() Returns the Image that will eventually become the result of this OutputAlgorithm, and creates it if it has not yet been created.
int[]	getPatchSize()
long	getProcessingTime()
Image<S>	getResult()
protected abstract boolean	patchOperation(int[] position, RegionOfInterestCursor<T> cursor) Performs this algorithm's operation on the patch represented by a RegionOfInterestCursor
protected int[]	positionOffset(int[] position, int[] offsetPosition) Offsets the given position to reflect the origin of the patch being in its center, rather than at the top-left corner as is usually the case.
boolean	process()
protected void	setErrorMessage(String message)
void	setImageFactory(ImageFactory<S> factory) Set the ImageFactory used to create the output Image
void	setName(String inName) Set the name given to the output image.

Methods inherited from class java.lang.Object

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

Constructor Detail

ROIAlgorithm

protected ROIAlgorithm(S type,
                       Image<T> imageIn,
                       int[] patchSize)

Creates an ROIAlgorithm with default OutOfBoundsStrategyValueFactory, with value Zero.

Parameters:

type - a representative type for the output image.

imageIn - the image over which to iterate.

patchSize - the size of the patch that will be examined at each iteration.

ROIAlgorithm

protected ROIAlgorithm(S type,
                       Image<T> imageIn,
                       int[] patchSize,
                       OutOfBoundsStrategyFactory<T> inOutFactory)

Parameters:

type - a representative type for the output image.

imageIn - the image over which to iterate.

patchSize - the size of the patch that will be examined at each iteration.

inOutFactory - an OutOfBoundsStrategyFactory to handle the border phenomenon.

Method Detail

patchOperation

protected abstract boolean patchOperation(int[] position,
                                          RegionOfInterestCursor<T> cursor)

Performs this algorithm's operation on the patch represented by a RegionOfInterestCursor

Parameters:

position - the position in the input image at the center of the patch represented by the RegionOfInterestCursor

cursor - a RegionOfInterestCursor that iterates over the given patch-of-interest

Returns:

true if the operation on the given patch was successful, false otherwise. If false is returned by this method, process() will abort.

setImageFactory

public void setImageFactory(ImageFactory<S> factory)

Set the ImageFactory used to create the output Image

Parameters:

factory - the ImageFactory used to create the output Image

setName

public void setName(String inName)

Set the name given to the output image.

Parameters:

inName - the name to give to the output image.

getName

public String getName()

getPatchSize

public int[] getPatchSize()

getOutputImage

protected Image<S> getOutputImage()

Returns the Image that will eventually become the result of this OutputAlgorithm, and creates it if it has not yet been created.

Returns:

the Image that will eventually become the result of this OutputAlgorithm.

getResult

public Image<S> getResult()

Specified by:

getResult in interface OutputAlgorithm<S extends RealType<S>>

getErrorMessage

public String getErrorMessage()

Specified by:

getErrorMessage in interface Algorithm

setErrorMessage

protected void setErrorMessage(String message)

positionOffset

protected int[] positionOffset(int[] position,
                               int[] offsetPosition)

Offsets the given position to reflect the origin of the patch being in its center, rather than at the top-left corner as is usually the case.

Parameters:

position - the position to be offset

offsetPosition - an int array to contain the newly offset position coordinates

Returns:

offsetPosition, for convenience.

process

public boolean process()

Specified by:

process in interface Algorithm

checkInput

public boolean checkInput()

Specified by:

checkInput in interface Algorithm

close

public void close()

getProcessingTime

public long getProcessingTime()

Specified by:

getProcessingTime in interface Benchmark