Package gov.nih.mipav.model.algorithms

Class AlgorithmSubtractVOI

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.AlgorithmSubtractVOI

All Implemented Interfaces:

ActionListener, WindowListener, Runnable, EventListener

public class AlgorithmSubtractVOI
extends AlgorithmBase

Algorithm that subtracts the mean or median value of a VOI from the image. If only 1 contour is present, that contour is used whether or not it is selected. If multiple contours are present, at least 1 contour must be selected, and only selected contours are used. Note that under MIPAV all selected contours must belong to the same VOI. If the new image exceeds the range that can be stored in an image of that type the data is either clipped and stored in the original image. Or a new image of a type (int, float...) that can store the range of new data is generated. For color the dialog currently disables promotion for color because MIPAV cannot handle negative color values.

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 double	average	DOCUMENT ME!
private float	averageB	DOCUMENT ME!
private float	averageG	DOCUMENT ME!
private int	averageMode	DOCUMENT ME!
private float	averageR	DOCUMENT ME!
static final int	CLIP	DOCUMENT ME!
private double	clipMax	Maximum clipping modes if data result value exceeds the capacity of image's data type.
private float	clipMaxC	DOCUMENT ME!
private double	clipMin	Minimum clipping modes if data result value exceeds the capacity of image's data type.
private float	clipMinC	DOCUMENT ME!
private int	clipMode	Clipping mode.
private double	max	Used to store the image maximum.
static final int	MEAN	DOCUMENT ME!
static final int	MEDIAN	DOCUMENT ME!
private double	min	Used to store the image minimum.
private double	minB	DOCUMENT ME!
private double	minG	DOCUMENT ME!
private double	minR	DOCUMENT ME!
static final int	PROMOTE	DOCUMENT ME!

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
AlgorithmSubtractVOI(ModelImage srcImg, int _averageMode, int _clipMode)	Creates a new AlgorithmSubtractVOI object.
AlgorithmSubtractVOI(ModelImage destImg, ModelImage srcImg, int _averageMode, int _clipMode)	Creates a new AlgorithmSubtractVOI object.

Method Summary

Modifier and Type	Method	Description
private void	calcInPlace()	Generates the new data and places in the source image.
private void	calcInPlaceColor()	Generates the new data and places in the source image.
private void	calcStoreInDest()	Generates the new data and places in a new (destination) image.
private void	calcStoreInDestColor()	Generates the new data and places in a new (destination) image.
void	finalize()	Prepares this class for destruction.
private int	findType(int stType)	Find the type able to contain the full range of the data.
private void	getAverage()	DOCUMENT ME!
private int	promoteType(int presentType)	DOCUMENT ME!
void	runAlgorithm()	Starts the program.
private void	setClipValues()	Sets clipMin and clipMax.
private boolean	testType(int type, double minVal, double maxVal)	Determine if the min and max values are in the image types range.

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

MEAN

public static final int MEAN

DOCUMENT ME!

See Also:

• Constant Field Values

MEDIAN

public static final int MEDIAN

DOCUMENT ME!

See Also:

• Constant Field Values

CLIP

public static final int CLIP

DOCUMENT ME!

See Also:

• Constant Field Values

PROMOTE

public static final int PROMOTE

DOCUMENT ME!

See Also:

• Constant Field Values

average

private double average

DOCUMENT ME!

averageB

private float averageB

DOCUMENT ME!

averageG

private float averageG

DOCUMENT ME!

averageMode

private int averageMode

DOCUMENT ME!

averageR

private float averageR

DOCUMENT ME!

clipMax

private double clipMax

Maximum clipping modes if data result value exceeds the capacity of image's data type.

clipMaxC

private float clipMaxC

DOCUMENT ME!

clipMin

private double clipMin

Minimum clipping modes if data result value exceeds the capacity of image's data type.

clipMinC

private float clipMinC

DOCUMENT ME!

clipMode

private int clipMode

Clipping mode.

                          CLIP          = 0;   clamp result data to the bounds of the input image type
                          PROMOTE       = 1;   promote image type so that the range of the result fits into
                                               the new image type. ( ie. byte to short).
                   

max

private double max

Used to store the image maximum.

min

private double min

Used to store the image minimum.

minR

private double minR

DOCUMENT ME!

minG

private double minG

DOCUMENT ME!

minB

private double minB

DOCUMENT ME!

Constructor Details

AlgorithmSubtractVOI

public AlgorithmSubtractVOI(ModelImage srcImg,
 int _averageMode,
 int _clipMode)

Creates a new AlgorithmSubtractVOI object.

Parameters:

srcImg - source image model

_averageMode - mean or median of VOI

_clipMode - clamp data to image type range or promote image type to hold new data range.

AlgorithmSubtractVOI

public AlgorithmSubtractVOI(ModelImage destImg,
 ModelImage srcImg,
 int _averageMode,
 int _clipMode)

Creates a new AlgorithmSubtractVOI object.

Parameters:

destImg - image model where result image is to stored

srcImg - source image model

_averageMode - mean or median of VOI

_clipMode - clamp data to image type range or promote image type to hold new data range.

Method Details

finalize

public void finalize()

Prepares this class for destruction.

Overrides:

finalize in class AlgorithmBase

runAlgorithm

public void runAlgorithm()

Starts the program.

Specified by:

runAlgorithm in class AlgorithmBase

calcInPlace

private void calcInPlace()

Generates the new data and places in the source image.

note that if this method is canceled part-way through a multi-sliced image, it will almost certainly be partially adjusted. This is because to save memory buffer-space, it returns an adjusted slice back to the source image after processing it; it then takes out the next slice to alter it. Canceling a job causes the current slice will not be affected, but all previous slices will be.

calcInPlaceColor

private void calcInPlaceColor()

Generates the new data and places in the source image.

note that if this method is canceled part-way through a multi-sliced image, it will almost certainly be partially adjusted. This is because to save memory buffer-space, it returns an adjusted slice back to the source image after processing it; it then takes out the next slice to alter it. Canceling a job causes the current slice will not be affected, but all previous slices will be.

calcStoreInDest

private void calcStoreInDest()

Generates the new data and places in a new (destination) image.

This method checks for thread halting actions more infrequently than the in-place method.

calcStoreInDestColor

private void calcStoreInDestColor()

Generates the new data and places in a new (destination) image.

This method checks for thread halting actions more infrequently than the in-place method.

findType

private int findType(int stType)

Find the type able to contain the full range of the data.

Parameters:

stType - starting type of image. Image will be promoted above this type if needed.

Returns:

type capable of storing full range of data. See ModelStorageBase for image types.

getAverage

private void getAverage()

DOCUMENT ME!

promoteType

private int promoteType(int presentType)

DOCUMENT ME!

Parameters:

presentType - DOCUMENT ME!

Returns:

DOCUMENT ME!

setClipValues

private void setClipValues()

Sets clipMin and clipMax.

testType

private boolean testType(int type,
 double minVal,
 double maxVal)

Determine if the min and max values are in the image types range.

Parameters:

type - image type

minVal - min value of the image

maxVal - max value of the image

Returns:

true if min and max are within the image type specified