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

Class AlgorithmSwapSlicesVolume

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.utilities.AlgorithmSwapSlicesVolume

All Implemented Interfaces:

ActionListener, WindowListener, Runnable, EventListener

public class AlgorithmSwapSlicesVolume
extends AlgorithmBase

Title: AlgorithmSwapSlicesVolume

Description: Allows user to re-slice/re-volume and associates fileInfo. This allows for slice/volume duplication, deletion, or insertion.

Version:

0.9

Author:

Justin Senseney

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	extentDest	Internal sorting variables for sorting slices on images of greater than 3 dimensions
private int	extentSrc	Internal sorting variables for sorting slices on images of greater than 3 dimensions
private JDialogSwapSlicesVolumes.SwapMode	mode	Swap mode, either 3D or 4D.
private int	nSlices	Number of slices in mode.
private int[][]	sliceRenum	Reordering of slices/volumes.
private int	sliceSize	Number of pixels used by a slice/volume, includes colorFactor.
private boolean[]	sliceTouched	Slices that have been examined in recursive structure for swapping slices.
private int[]	srcExtents	Original extents array
private FileInfoBase[]	srcFileInfos	Original FileInfoBase array.

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
AlgorithmSwapSlicesVolume(ModelImage destImage, JDialogSwapSlicesVolumes.SwapMode mode, int[][] sliceRenum, ModelImage srcImage)	Import source and destination images into the class.

Method Summary

Modifier and Type	Method	Description
private boolean	allSlicesTouched()
private FileInfoBase[]	collectFileInfos(int in, int tDim)	Gets the fileInfos from the specified position.
void	finalize()	Prepares this class for destruction.
protected int	getColorFactor()	Calculates and returns the color factor based on the srcImage.
ModelImage	getSwappedVolume()	Return the images extracted from the source image.
private void	importFileInfos(ModelImage destImage, FileInfoBase[] fileIn, int in, int tDim)	Inserts the fileInfos into the specified position.
private void	reallocate(ModelImage image)	Reallocate destImage so that fileInfo and buffer equal required length
void	runAlgorithm()	Calculates the final output.
private void	swapSlices()	Calculates the final output and stores it in the source image.
private boolean	transferIn(int in)	Starts method of file/image transferring
private boolean	transferIn(FileInfoBase[] fileIn, Number[] bufferIn, int in, int tDim)	Transfers the given buffer into the given location.

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

mode

private JDialogSwapSlicesVolumes.SwapMode mode

Swap mode, either 3D or 4D.

nSlices

private int nSlices

Number of slices in mode.

sliceRenum

private int[][] sliceRenum

Reordering of slices/volumes.

sliceSize

private int sliceSize

Number of pixels used by a slice/volume, includes colorFactor.

sliceTouched

private boolean[] sliceTouched

Slices that have been examined in recursive structure for swapping slices.

extentSrc

private int extentSrc

Internal sorting variables for sorting slices on images of greater than 3 dimensions

extentDest

private int extentDest

Internal sorting variables for sorting slices on images of greater than 3 dimensions

srcFileInfos

private FileInfoBase[] srcFileInfos

Original FileInfoBase array.

srcExtents

private int[] srcExtents

Original extents array

Constructor Details

AlgorithmSwapSlicesVolume

public AlgorithmSwapSlicesVolume(ModelImage destImage,
 JDialogSwapSlicesVolumes.SwapMode mode,
 int[][] sliceRenum,
 ModelImage srcImage)

Import source and destination images into the class.

Parameters:

destImage - destination image

mode - type of swapping operation

sliceRenum - list of locations for slices that should be extracted/moved

srcImage - source image (image to extract from)

Method Details

finalize

public void finalize()

Prepares this class for destruction.

Overrides:

finalize in class AlgorithmBase

getSwappedVolume

public ModelImage getSwappedVolume()

Return the images extracted from the source image.

Returns:

The extracted images.

runAlgorithm

public void runAlgorithm()

Calculates the final output.

Specified by:

runAlgorithm in class AlgorithmBase

getColorFactor

protected int getColorFactor()

Calculates and returns the color factor based on the srcImage.

Returns:

DOCUMENT ME!

allSlicesTouched

private boolean allSlicesTouched()

collectFileInfos

private FileInfoBase[] collectFileInfos(int in,
 int tDim)

Gets the fileInfos from the specified position.

importFileInfos

private void importFileInfos(ModelImage destImage,
 FileInfoBase[] fileIn,
 int in,
 int tDim)

Inserts the fileInfos into the specified position.

reallocate

private void reallocate(ModelImage image)

Reallocate destImage so that fileInfo and buffer equal required length

Parameters:

image - ModelImage

swapSlices

private void swapSlices()

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

transferIn

private boolean transferIn(int in)

Starts method of file/image transferring

Parameters:

in - location to import data

Returns:

whether import was successful

transferIn

private boolean transferIn(FileInfoBase[] fileIn,
 Number[] bufferIn,
 int in,
 int tDim)

Transfers the given buffer into the given location. Also recursively transfers all the old data to the location(s) where the old data is used.

Parameters:

bufferIn - relieves the symptoms of arthritis

in - location to import data

Returns:

whether import was successful