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

Class AlgorithmRemoveSlices

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.utilities.AlgorithmRemoveSlices

All Implemented Interfaces:

ActionListener, WindowListener, Runnable, EventListener

public class AlgorithmRemoveSlices
extends AlgorithmBase

Algorithm verifies the z-th slice should be in included in the destination image, as defined in the list, remove. It copies the slice from the srcImage img to a buffer, and then from the buffer into the destination img. Copies the srcImage file info to a buffer and makes it conform to the new img, then copies it into the destImage file.

Note that an image is a set of slices; each slice is XxY, with Z slices.**(as of 1 Nov, does not yet process the more complicated DICOM images Completely)

Version:

v0.11 1 Nov 1999 (processes most images)

Author:

David Parsons (parsonsd@cbel.cit.nih.gov) (with vast help from M.McAuliffe)

See Also:

• JDialogRemoveSlices

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	oldZdim	Original Z dimension of the image.
private boolean[]	remove	List of slices to remove from source image.
private int	sliceArea	Area of a slice (Xdim * Ydim).
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
AlgorithmRemoveSlices(ModelImage srcImage, ModelImage destImage, boolean[] removeSlices)	Import source and destination images into the class.

Method Summary

Modifier and Type	Method	Description
void	calcInPlace()	Calculates the final output and stores it in the source image.
void	calcStoreInDest()	Calculates the final output and puts it in a destination image.
private int[]	computeNewExtents()	Calculates and returns the new extents based on the source image and the list of slices to be removed.
void	finalize()	Prepares this class for destruction.
protected int	getAxisOfChange()	Calculates and returns the axis of change based on the srcImage.
protected int	getColorFactor()	Calculates and returns the color factor based on the srcImage.
private int	getNumRemoved()	computes and returns the number of slices to remove.
private int	getOffset(int ndims, int[] extents, int colorFactor, int t)	Calculate and return the offset for the given image and time slice.
private int	getOffset(ModelImage img, int colorFactor, int t)	Calculate and return the offset for the given image and time slice.
private FileInfoBase	getSliceFileInfo(int srcSlice, int destSlice, int t, int[] newExtents)	Build and return the fileInfo for the current slice based on the source slice, the destination slice and time slice.
void	runAlgorithm()	Calculates the final output.
static void	updateFileInfo(ModelImage image, ModelImage resultImage)	Copy important file information to resultant image structure.

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

oldZdim

private int oldZdim

Original Z dimension of the image.

remove

private boolean[] remove

List of slices to remove from source image.

sliceArea

private int sliceArea

Area of a slice (Xdim * Ydim).

Xdim

private int Xdim

X dimension of the image.

Ydim

private int Ydim

Y dimension of the image.

Constructor Details

AlgorithmRemoveSlices

public AlgorithmRemoveSlices(ModelImage srcImage,
 ModelImage destImage,
 boolean[] removeSlices)

Import source and destination images into the class.

Parameters:

srcImage - source image (image to clip from)

destImage - destination image (image to paste to)

removeSlices - list of boolean indicating which slices in source should *not* be in the destination

Method Details

updateFileInfo

public static void updateFileInfo(ModelImage image,
 ModelImage resultImage)

Copy important file information to resultant image structure.

Parameters:

image - Source image.

resultImage - Resultant image.

calcInPlace

public void calcInPlace()

Calculates the final output and stores it in the source image.

calcStoreInDest

public void calcStoreInDest()

Calculates the final output and puts it in a destination image.

finalize

public void finalize()

Prepares this class for destruction.

Overrides:

finalize in class AlgorithmBase

runAlgorithm

public void runAlgorithm()

Calculates the final output.

Specified by:

runAlgorithm in class AlgorithmBase

getAxisOfChange

protected int getAxisOfChange()
                       throws Exception

Calculates and returns the axis of change based on the srcImage. The default (for most images) is 2. DICOM images need to be checked.

Returns:

DOCUMENT ME!

Throws:

Exception - DOCUMENT ME!

getColorFactor

protected int getColorFactor()

Calculates and returns the color factor based on the srcImage.

Returns:

DOCUMENT ME!

computeNewExtents

private int[] computeNewExtents()

Calculates and returns the new extents based on the source image and the list of slices to be removed.

Returns:

DOCUMENT ME!

getNumRemoved

private int getNumRemoved()

computes and returns the number of slices to remove.

Returns:

DOCUMENT ME!

getOffset

private int getOffset(ModelImage img,
 int colorFactor,
 int t)

Calculate and return the offset for the given image and time slice.

Parameters:

img - -- ModelImage whose offset is being computed

colorFactor - -- the image's colorFactor

t - -- current time slice

Returns:

-- the computed offset into the data buffer

getOffset

private int getOffset(int ndims,
 int[] extents,
 int colorFactor,
 int t)

Calculate and return the offset for the given image and time slice.

Parameters:

ndims - -- number of dimensions

extents - -- the extents for the image offset

colorFactor - -- the image's colorFactor

t - -- current time slice

Returns:

-- the computed offset into the data buffer

getSliceFileInfo

private FileInfoBase getSliceFileInfo(int srcSlice,
 int destSlice,
 int t,
 int[] newExtents)

Build and return the fileInfo for the current slice based on the source slice, the destination slice and time slice.

Parameters:

srcSlice - the current slice index for the src image

destSlice - the current slice index for the result (dest) image

t - current time slice

newExtents - the extents for the result (dest) image

Returns:

the fileInfo for destSlice