Package gov.nih.mipav.model.algorithms.utilities

Class AlgorithmMatchImages

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.utilities.AlgorithmMatchImages

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener

public class AlgorithmMatchImages
extends AlgorithmBase

Matches two ModelImages. The output of this Algorithm is two ModelImages that have the same units of measure, the same resolutions, and the same extents. If the user chooses, the image orientations (left-to-right, anterior-to-posterior, inferior-to-superior, etc) will be matched. If the user chooses, the image origins will be matched. Either imageA, imageB or sometimes neither will be different after the algorithm completes. The result images are returned with the getImageA() and getImageB() functions.

Nested Class Summary

Nested classes/interfaces inherited from class java.lang.Thread

java.lang.Thread.State, java.lang.Thread.UncaughtExceptionHandler

Field Summary

Fields

Modifier and Type	Field	Description
private boolean	doOrients	flag for turning on/off using the image orientations to match the images
private boolean	doOrigins	flag for turning on/off using the image origins to match the images
private float[]	padValue	image values to use for padding the images, if necessary
private ModelImage	srcImageB	srcImageB: image to match to srcImage
private boolean	useReferenceResolutions	When true resolution matching defaults to the reference image.

Fields inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase

destFlag, destImage, image25D, mask, maxProgressValue, minProgressValue, multiThreadingEnabled, nthreads, progress, progressModulus, progressStep, runningInSeparateThread, separable, srcImage, threadStopped

Fields inherited from class java.lang.Thread

MAX_PRIORITY, MIN_PRIORITY, NORM_PRIORITY

Constructor Summary

Constructors

Constructor	Description
AlgorithmMatchImages(ModelImage kImageA, ModelImage kImageB, boolean doOrigins, boolean doOrients)	Create an AlgorithmMatchImages to match the two input images.
AlgorithmMatchImages(ModelImage kImageA, ModelImage kImageB, boolean doOrigins, boolean doOrients, boolean useReferenceResolutions)	Create an AlgorithmMatchImages to match the two input images.

Method Summary

Modifier and Type	Method	Description
private ModelImage	changeResolutions(ModelImage kImage, float[] afNewRes)	Changes the resolutions of the input image.
void	disposeLocal()	remove local memory
void	finalize()	Prepares this class for destruction.
ModelImage	getImageA()	Returns imageA, which may have changed during the match.
ModelImage	getImageB()	Returns imageB, which may have changed during the match.
private boolean	matchOriginsExtents(ModelImage imageA, ModelImage imageB, int[] padAFront, int[] padABack, int[] padBFront, int[] padBBack)	Matches the origins and extents of the two input images.
private float[]	matchResolutions(ModelImage imageA, ModelImage imageB)	Match the resolutions of the two images.
private void	matchUnits(ModelImage imageA, ModelImage imageB)	Matches the units of measure for the two input images.
private ModelImage	padImage(ModelImage kImage, int[] padFront, int[] padBack)	Adds or removes margins to the input image.
void	runAlgorithm()	Actually runs the algorithm.
void	setPadValue(float value)	Sets the pad value for single-channel images.
void	setPadValue(float red, float green, float blue)	Sets the pad value for color images

Methods inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase

actionPerformed, addListener, addProgressChangeListener, calculateImageSize, calculatePrincipleAxis, computeElapsedTime, computeElapsedTime, convertIntoFloat, delinkProgressToAlgorithm, delinkProgressToAlgorithmMulti, displayError, errorCleanUp, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, generateProgressValues, getDestImage, getElapsedTime, getMask, getMaxProgressValue, getMinProgressValue, getNumberOfThreads, getProgress, getProgressChangeListener, getProgressChangeListeners, getProgressModulus, getProgressStep, getProgressValues, getSrcImage, isCompleted, isImage25D, isMultiThreadingEnabled, isRunningInSeparateThread, isThreadStopped, linkProgressToAlgorithm, linkProgressToAlgorithm, makeProgress, notifyListeners, removeListener, removeProgressChangeListener, run, setCompleted, setImage25D, setMask, setMaxProgressValue, setMinProgressValue, setMultiThreadingEnabled, setNumberOfThreads, setProgress, setProgressModulus, setProgressStep, setProgressValues, setProgressValues, setRunningInSeparateThread, setSrcImage, setStartTime, setThreadStopped, startMethod, windowActivated, windowClosed, windowClosing, windowDeactivated, windowDeiconified, windowIconified, windowOpened

Methods inherited from class java.lang.Thread

activeCount, checkAccess, clone, countStackFrames, currentThread, dumpStack, enumerate, getAllStackTraces, getContextClassLoader, getDefaultUncaughtExceptionHandler, getId, getName, getPriority, getStackTrace, getState, getThreadGroup, getUncaughtExceptionHandler, holdsLock, interrupt, interrupted, isAlive, isDaemon, isInterrupted, join, join, join, onSpinWait, resume, setContextClassLoader, setDaemon, setDefaultUncaughtExceptionHandler, setName, setPriority, setUncaughtExceptionHandler, sleep, sleep, start, stop, suspend, toString, yield

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

srcImageB

private ModelImage srcImageB

srcImageB: image to match to srcImage

doOrigins

private boolean doOrigins

flag for turning on/off using the image origins to match the images

doOrients

private boolean doOrients

flag for turning on/off using the image orientations to match the images

useReferenceResolutions

private boolean useReferenceResolutions

When true resolution matching defaults to the reference image.

padValue

private float[] padValue

image values to use for padding the images, if necessary

Constructor Detail

AlgorithmMatchImages

public AlgorithmMatchImages(ModelImage kImageA,
                            ModelImage kImageB,
                            boolean doOrigins,
                            boolean doOrients)

Create an AlgorithmMatchImages to match the two input images.

Parameters:

kImageA - target image to match to

kImageB - image that is changing to match to imageA

doOrigins - flag for turning on/off using the image origins to match the images

doOrients - flag for turning on/off using the image orientations to match the images

AlgorithmMatchImages

public AlgorithmMatchImages(ModelImage kImageA,
                            ModelImage kImageB,
                            boolean doOrigins,
                            boolean doOrients,
                            boolean useReferenceResolutions)

Create an AlgorithmMatchImages to match the two input images.

Parameters:

kImageA - target image to match to

kImageB - image that is changing to match to imageA

doOrigins - flag for turning on/off using the image origins to match the images

doOrients - flag for turning on/off using the image orientations to match the images

Method Detail

disposeLocal

public void disposeLocal()

remove local memory

finalize

public void finalize()

Prepares this class for destruction.

Overrides:

finalize in class AlgorithmBase

getImageA

public ModelImage getImageA()

Returns imageA, which may have changed during the match.

Returns:

imageA

getImageB

public ModelImage getImageB()

Returns imageB, which may have changed during the match.

Returns:

imageB

setPadValue

public void setPadValue(float value)

Sets the pad value for single-channel images.

Parameters:

value - value used to pad images.

setPadValue

public void setPadValue(float red,
                        float green,
                        float blue)

Sets the pad value for color images

Parameters:

red - red pad value

green - green pad value

blue - blue pad value

runAlgorithm

public void runAlgorithm()

Description copied from class: AlgorithmBase

Actually runs the algorithm. Implemented by inheriting algorithms.

Specified by:

runAlgorithm in class AlgorithmBase

matchUnits

private void matchUnits(ModelImage imageA,
                        ModelImage imageB)

Matches the units of measure for the two input images.

Parameters:

imageA - target image to match to.

imageB - image that is being changed.

matchResolutions

private float[] matchResolutions(ModelImage imageA,
                                 ModelImage imageB)

Match the resolutions of the two images. Determines the lowest resolution of either image along each dimension. If useReferenceResolutions is true, the reference image (imageA) resolutions are used.

Parameters:

imageA -

imageB -

Returns:

new resolutions that will be applied to both images.

changeResolutions

private ModelImage changeResolutions(ModelImage kImage,
                                     float[] afNewRes)

Changes the resolutions of the input image.

Parameters:

kImage - input image.

afNewRes - new resolutions.

Returns:

new ModelImage, or the input image if unchanged.

matchOriginsExtents

private boolean matchOriginsExtents(ModelImage imageA,
                                    ModelImage imageB,
                                    int[] padAFront,
                                    int[] padABack,
                                    int[] padBFront,
                                    int[] padBBack)

Matches the origins and extents of the two input images. Matching origins is an option the user sets.

Parameters:

imageA - input image A.

imageB - input image B.

padAFront - output values for adding or removing voxels to the front of imageA [left,top,front,time]

padABack - output values for adding or removing voxels to the back of imageA [right,bottom,back,time]

padBFront - output values for adding or removing voxels to the front of imageB [left,top,front,time]

padBBack - output values for adding or removing voxels to the back of imageB [right,bottom,back,time]

Returns:

true if either image requires changing to match the two images, false if neither image requires changing.

padImage

private ModelImage padImage(ModelImage kImage,
                            int[] padFront,
                            int[] padBack)

Adds or removes margins to the input image.

Parameters:

kImage - input images.

padFront - margins to add or remove to the front of the image [left,top,front,time]

padBack - margins to add or remove to the end of the image [right,bottom,back,time]

Returns:

new image or the original input image if no change.