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

Class AlgorithmCorrectSpacing

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.utilities.AlgorithmCorrectSpacing

All Implemented Interfaces:

ActionListener, WindowListener, Runnable, EventListener

public class AlgorithmCorrectSpacing
extends AlgorithmBase

Algorithm to adjust image volume for cases when the slice spacing is not equal to the slice thickness. When spacing > thickness: repeat images from original image set insert blank images (so that in the final image volume, all images will have the same slice thickness and the image volume will be to proper scale. When spacing invalid input: '<' thickness: set thickness = spacing.

Nested Class Summary

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

Thread.Builder, Thread.State, Thread.UncaughtExceptionHandler

Field Summary

Fields

Modifier and Type	Field	Description
private int	colorFactor
private int	DIM	The number of dimensions in the image.
private int	newTimeStepVolume	Volume for each time step.
private int	newZdim	New Z dimension.
private int	numBlanks	Number of blank images, to make up gap.
private int	numRepIm	Number of repeated images, to compensate for gap.
private int	oldTimeStepVolume	Volume for each time step.
private int	oldZdim	Original Z dimension of the image.
private ModelImage	resultImage	Result Image.
private int	sliceArea	Area of a slice (Xdim * Ydim).
private int	Tdim	Time dimension of the image.
private int	Xdim	X dimension of the image.
private int	Ydim	Y dimension of the 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
AlgorithmCorrectSpacing(ModelImage srcImage, ModelImage resultImage, int numRepIm, int numBlanks)	Import source image into the class.

Method Summary

Modifier and Type	Method	Description
void	disposeLocal()	Dispose of local variables that may be taking up lots of room.
void	finalize()	Prepares this class for destruction.
ModelImage	getResultImage()	Returns corrected image.
void	runAlgorithm()	Runs algorithm.

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, isVirtual, join, join, join, join, ofPlatform, ofVirtual, onSpinWait, resume, setContextClassLoader, setDaemon, setDefaultUncaughtExceptionHandler, setName, setPriority, setUncaughtExceptionHandler, sleep, sleep, sleep, start, startVirtualThread, stop, suspend, threadId, toString, yield

Methods inherited from class java.lang.Object

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

Field Details

DIM

private int DIM

The number of dimensions in the image.

newZdim

private int newZdim

New Z dimension.

numBlanks

private int numBlanks

Number of blank images, to make up gap.

numRepIm

private int numRepIm

Number of repeated images, to compensate for gap.

oldTimeStepVolume

private int oldTimeStepVolume

Volume for each time step.

newTimeStepVolume

private int newTimeStepVolume

Volume for each time step.

oldZdim

private int oldZdim

Original Z dimension of the image.

resultImage

private ModelImage resultImage

Result Image.

sliceArea

private int sliceArea

Area of a slice (Xdim * Ydim).

Tdim

private int Tdim

Time dimension of the image.

Xdim

private int Xdim

X dimension of the image.

Ydim

private int Ydim

Y dimension of the image.

colorFactor

private int colorFactor

Constructor Details

AlgorithmCorrectSpacing

public AlgorithmCorrectSpacing(ModelImage srcImage,
 ModelImage resultImage,
 int numRepIm,
 int numBlanks)

Import source image into the class.

Parameters:

srcImage - source image (image to clip from)

resultImage - corrected image

numRepIm - number of times to repeat each of original images

numBlanks - number of blank images to insert

Method Details

disposeLocal

public void disposeLocal()

Dispose of local variables that may be taking up lots of room.

finalize

public void finalize()

Prepares this class for destruction.

Overrides:

finalize in class AlgorithmBase

getResultImage

public ModelImage getResultImage()

Returns corrected image.

Returns:

resultImage

runAlgorithm

public void runAlgorithm()

Runs algorithm.

Specified by:

runAlgorithm in class AlgorithmBase