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

Class AlgorithmCrop

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.utilities.AlgorithmCrop

All Implemented Interfaces:

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

public class AlgorithmCrop
extends AlgorithmBase

Crops 2D and 3D images using a supplied VOI. Crops 4D images.

Version:

1.0 June 11, 1999

Author:

Matthew J. McAuliffe, Ph.D.

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 int	cushion	Extra space around VOI in x and y dimensions.
private boolean	RGBImage	Flag for color or noncolor image.
private int[]	x	Storage for VOI.
private int[]	y	Storage for VOI.
private int[]	z	Storage for VOI.

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
AlgorithmCrop(ModelImage destImg, ModelImage srcImg, int _cushion, int[] _x, int[] _y, int[] _z)	Creates new algorithms to crop image by specified bounds.

Method Summary

Modifier and Type	Method	Description
private void	calcStoreInDest2D()	This function produces a new image that has been cropped!
private void	calcStoreInDest3D()	This function produces a new image that has been cropped.
private void	calcStoreInDest4D()	This function produces a new image that has been cropped.
private void	calcStoreInPlace2D()	This function crops srcImage Must use getSrcImage after running.
private void	calcStoreInPlace3D()	This function crops srcImage Must use getSrcImage after running.
private void	calcStoreInPlace4D()	This function crops srcImage Must use getSrcImage after running.
void	finalize()	Prepares this class for destruction.
ModelImage	getSrcImage()	DOCUMENT ME!
private float[]	originImg2LPS(float[] origImg, ModelImage img)	Switch origin order from image order to LPS order.
private float[]	originLPS2Img(float[] origLPS, ModelImage img)	Switch origin order from LPS order to Img order.
void	runAlgorithm()	Starts the program.
private void	updateDICOM()	Update special case DICOM format tags.
private void	updateFileInfoData()	Updates important image attributes (start locations, orientation ) for the new cropped file by modifing the fileinfo fo the new ( destination ) image.

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, 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

cushion

private int cushion

Extra space around VOI in x and y dimensions.

RGBImage

private boolean RGBImage

Flag for color or noncolor image.

x

private int[] x

Storage for VOI.

y

private int[] y

Storage for VOI.

z

private int[] z

Storage for VOI.

Constructor Detail

AlgorithmCrop

public AlgorithmCrop(ModelImage destImg,
                     ModelImage srcImg,
                     int _cushion,
                     int[] _x,
                     int[] _y,
                     int[] _z)

Creates new algorithms to crop image by specified bounds. Stores in destImg.

Parameters:

destImg - image model where result image is to stored, use null to do in-place calculation

srcImg - source image model

_cushion - extra space around VOI in x and y dimensions.

_x - VOI xBounds: x[0] = min. bound and x[1] = max. bound

_y - VOI yBounds: y[0] = min. bound and y[1] = max. bound

_z - VOI zBounds: z[0] = min. bound and z[1] = max. bound

Method Detail

finalize

public void finalize()

Prepares this class for destruction.

Overrides:

finalize in class AlgorithmBase

getSrcImage

public ModelImage getSrcImage()

DOCUMENT ME!

Overrides:

getSrcImage in class AlgorithmBase

Returns:

ModelImage

runAlgorithm

public void runAlgorithm()

Starts the program.

Specified by:

runAlgorithm in class AlgorithmBase

calcStoreInDest2D

private void calcStoreInDest2D()

This function produces a new image that has been cropped!

calcStoreInDest3D

private void calcStoreInDest3D()

This function produces a new image that has been cropped.

calcStoreInDest4D

private void calcStoreInDest4D()

This function produces a new image that has been cropped.

calcStoreInPlace2D

private void calcStoreInPlace2D()

This function crops srcImage Must use getSrcImage after running.

calcStoreInPlace3D

private void calcStoreInPlace3D()

This function crops srcImage Must use getSrcImage after running.

calcStoreInPlace4D

private void calcStoreInPlace4D()

This function crops srcImage Must use getSrcImage after running.

originImg2LPS

private float[] originImg2LPS(float[] origImg,
                              ModelImage img)

Switch origin order from image order to LPS order.

Parameters:

origImg - DOCUMENT ME!

img - DOCUMENT ME!

Returns:

DOCUMENT ME!

originLPS2Img

private float[] originLPS2Img(float[] origLPS,
                              ModelImage img)

Switch origin order from LPS order to Img order.

Parameters:

origLPS - DOCUMENT ME!

img - DOCUMENT ME!

Returns:

DOCUMENT ME!

updateDICOM

private void updateDICOM()

Update special case DICOM format tags.

updateFileInfoData

private void updateFileInfoData()

Updates important image attributes (start locations, orientation ) for the new cropped file by modifing the fileinfo fo the new ( destination ) image.