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

Class AlgorithmExtractSlicesVolumes

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.utilities.AlgorithmExtractSlicesVolumes

All Implemented Interfaces:

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

public class AlgorithmExtractSlicesVolumes
extends AlgorithmBase

Title: AlgorithmExtractIndividualSlices

Description: Extracts individual slices from 3D or 4D images and opens each slice in its own Frame

Version:

1.0

Author:

Justin Senseney

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[]	extract	List of slices to remove from source image.
private java.util.Vector<ModelImage>	extractedImages	DOCUMENT ME!
(package private) FileInfoDicom[]	fileInfoDicom
private int	oldZdim	Original Z dimension of the 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
AlgorithmExtractSlicesVolumes(ModelImage srcImage, boolean[] removeSlices)	Import source and destination images into the class.

Method Summary

Modifier and Type	Method	Description
private void	extractSlices()	Calculates the final output and stores it in the source image.
void	finalize()	Prepares this class for destruction.
protected int	getColorFactor()	Calculates and returns the color factor based on the srcImage.
ModelImage[]	getExtractedImages()	Return the images extracted from the source image.
private int	getOffset(ModelImage img, int colorFactor, int t)	Calculate and return the offset for the given image and time slice.
void	runAlgorithm()	Calculates the final output.
void	updateFileInfo(ModelImage image, ModelImage resultImage, int slice)	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, 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

extract

private boolean[] extract

List of slices to remove from source image.

extractedImages

private java.util.Vector<ModelImage> extractedImages

DOCUMENT ME!

oldZdim

private int oldZdim

Original Z dimension of the 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.

fileInfoDicom

FileInfoDicom[] fileInfoDicom

Constructor Detail

AlgorithmExtractSlicesVolumes

public AlgorithmExtractSlicesVolumes(ModelImage srcImage,
                                     boolean[] removeSlices)

Import source and destination images into the class.

Parameters:

srcImage - source image (image to extract from)

removeSlices - list of booleans for slices that should be extracted

Method Detail

finalize

public void finalize()

Prepares this class for destruction.

Overrides:

finalize in class AlgorithmBase

getExtractedImages

public ModelImage[] getExtractedImages()

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

updateFileInfo

public void updateFileInfo(ModelImage image,
                           ModelImage resultImage,
                           int slice)

Copy important file information to resultant image structure.

Parameters:

image - Source image.

resultImage - Resultant image.

slice - DOCUMENT ME!

getColorFactor

protected int getColorFactor()

Calculates and returns the color factor based on the srcImage.

Returns:

DOCUMENT ME!

extractSlices

private void extractSlices()

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

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