Package gov.nih.mipav.model.algorithms

Class AlgorithmStandardDeviationThreshold

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.AlgorithmStandardDeviationThreshold

All Implemented Interfaces:

ActionListener, WindowListener, Runnable, EventListener

public class AlgorithmStandardDeviationThreshold
extends AlgorithmBase

The Standard Deviation Threshold works by first having an active VOI in which the standard deviation and other statistics are calculated. The dialog allows the user to enter the number of standard deviations and the values outside the range for the thersholding process. The theresholding can be done on the whole image or alternatively, on other VOIS that are not active that might be on the image. The destination can either be a new image or paint in existing image except if the src image is a color image.

Author:

pandyan

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 BitSet	bitset	bitset for src image
private boolean	inverseThreshold	flags for destination, threshold, inverse, and color image
private boolean	isColorImage	flags for destination, threshold, inverse, and color image
private int	length	dimensions and length
private BitSet	mask	bitset of vois mask
private float	maxIntensity	max intensities for threshold
private float	maxIntensityB	max intensities for threshold
private float	maxIntensityG	max intensities for threshold
private float	maxIntensityR	max intensities for threshold
private float	minIntensity	min intensities for threshold
private float	minIntensityB	min intensities for threshold
private float	minIntensityG	min intensities for threshold
private float	minIntensityR	min intensities for threshold
private boolean	newImageDestination	flags for destination, threshold, inverse, and color image
private int	numPixels	num pixels in threshold
private int	numPixelsB	num pixels in threshold
private int	numPixelsG	num pixels in threshold
private int	numPixelsR	num pixels in threshold
private ModelImage	resultImage	src image, result image
private ModelImage	srcImage	src image, result image
private float	sumIntensities	total volume in threshold
private float	sumIntensitiesB	total volume in threshold
private float	sumIntensitiesG	total volume in threshold
private float	sumIntensitiesR	total volume in threshold
private float	totalArea	total volume in threshold
private float	totalAreaB	total volume in threshold
private float	totalAreaG	total volume in threshold
private float	totalAreaR	total volume in threshold
private float	totalVolume	total volume in threshold
private float	totalVolumeB	total volume in threshold
private float	totalVolumeG	total volume in threshold
private float	totalVolumeR	total volume in threshold
private float	valuesOutside	values outside intensities for threshold
private float	valuesOutsideB	values outside intensities for threshold
private float	valuesOutsideG	values outside intensities for threshold
private float	valuesOutsideR	values outside intensities for threshold
private boolean	wholeImageThreshold	flags for destination, threshold, inverse, and color image
private int	xDim	dimensions and length
private float	xRes	resolutions
private int	yDim	dimensions and length
private float	yRes	resolutions
private int	zDim	dimensions and length
private float	zRes	resolutions

Fields inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase

destFlag, destImage, image25D, maxProgressValue, minProgressValue, multiThreadingEnabled, nthreads, progress, progressModulus, progressStep, runningInSeparateThread, separable, threadStopped

Fields inherited from class java.lang.Thread

MAX_PRIORITY, MIN_PRIORITY, NORM_PRIORITY

Constructor Summary

Constructors

Constructor	Description
AlgorithmStandardDeviationThreshold(ModelImage srcImage, float minIntensity, float maxIntensity, float valuesOutside, boolean newImageDestination, boolean wholeImageThreshold, boolean inverseThreshold)	constructor for grey scale image
AlgorithmStandardDeviationThreshold(ModelImage srcImage, float minIntensityR, float minIntensityG, float minIntensityB, float maxIntensityR, float maxIntensityG, float maxIntensityB, float valuesOutsideR, float valuesOutsideG, float valuesOutsideB, boolean newImageDestination, boolean wholeImageThreshold, boolean inverseThreshold)	constructor for color image

Method Summary

Modifier and Type	Method	Description
int	getNumPixels()	getNumPixels
int	getNumPixelsB()	getNumPixelsB
int	getNumPixelsG()	getNumPixelsG
int	getNumPixelsR()	getNumPixelsR
ModelImage	getResultImage()	getResultImage
float	getSumIntensities()	get sum intensities
float	getSumIntensitiesB()	get sum intensities B
float	getSumIntensitiesG()	get sum intensities G
float	getSumIntensitiesR()	get sum intensities R
float	getTotalArea()	getTotalArea
float	getTotalAreaB()	getTotalAreaB
float	getTotalAreaG()	getTotalAreaG
float	getTotalAreaR()	getTotalAreaR
float	getTotalVolume()	getTotalVolume
float	getTotalVolumeB()	getTotalVolumeB
float	getTotalVolumeG()	getTotalVolumeG
float	getTotalVolumeR()	getTotalVolumeR
void	runAlgorithm()	run algorithm

Methods inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase

actionPerformed, addListener, addProgressChangeListener, calculateImageSize, calculatePrincipleAxis, computeElapsedTime, computeElapsedTime, convertIntoFloat, delinkProgressToAlgorithm, delinkProgressToAlgorithmMulti, displayError, errorCleanUp, finalize, 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

maxIntensity

private float maxIntensity

max intensities for threshold

maxIntensityR

private float maxIntensityR

max intensities for threshold

maxIntensityG

private float maxIntensityG

max intensities for threshold

maxIntensityB

private float maxIntensityB

max intensities for threshold

minIntensity

private float minIntensity

min intensities for threshold

minIntensityR

private float minIntensityR

min intensities for threshold

minIntensityG

private float minIntensityG

min intensities for threshold

minIntensityB

private float minIntensityB

min intensities for threshold

srcImage

private ModelImage srcImage

src image, result image

resultImage

private ModelImage resultImage

src image, result image

valuesOutside

private float valuesOutside

values outside intensities for threshold

valuesOutsideR

private float valuesOutsideR

values outside intensities for threshold

valuesOutsideG

private float valuesOutsideG

values outside intensities for threshold

valuesOutsideB

private float valuesOutsideB

values outside intensities for threshold

xDim

private int xDim

dimensions and length

yDim

private int yDim

dimensions and length

zDim

private int zDim

dimensions and length

length

private int length

dimensions and length

numPixels

private int numPixels

num pixels in threshold

numPixelsR

private int numPixelsR

num pixels in threshold

numPixelsG

private int numPixelsG

num pixels in threshold

numPixelsB

private int numPixelsB

num pixels in threshold

totalVolume

private float totalVolume

total volume in threshold

totalArea

private float totalArea

total volume in threshold

totalVolumeR

private float totalVolumeR

total volume in threshold

totalVolumeG

private float totalVolumeG

total volume in threshold

totalVolumeB

private float totalVolumeB

total volume in threshold

totalAreaR

private float totalAreaR

total volume in threshold

totalAreaG

private float totalAreaG

total volume in threshold

totalAreaB

private float totalAreaB

total volume in threshold

sumIntensities

private float sumIntensities

total volume in threshold

sumIntensitiesR

private float sumIntensitiesR

total volume in threshold

sumIntensitiesG

private float sumIntensitiesG

total volume in threshold

sumIntensitiesB

private float sumIntensitiesB

total volume in threshold

xRes

private float xRes

resolutions

yRes

private float yRes

resolutions

zRes

private float zRes

resolutions

bitset

private BitSet bitset

bitset for src image

newImageDestination

private boolean newImageDestination

flags for destination, threshold, inverse, and color image

wholeImageThreshold

private boolean wholeImageThreshold

flags for destination, threshold, inverse, and color image

inverseThreshold

private boolean inverseThreshold

flags for destination, threshold, inverse, and color image

isColorImage

private boolean isColorImage

flags for destination, threshold, inverse, and color image

mask

private BitSet mask

bitset of vois mask

Constructor Details

AlgorithmStandardDeviationThreshold

public AlgorithmStandardDeviationThreshold(ModelImage srcImage,
 float minIntensity,
 float maxIntensity,
 float valuesOutside,
 boolean newImageDestination,
 boolean wholeImageThreshold,
 boolean inverseThreshold)

constructor for grey scale image

Parameters:

srcImage -

minIntensity -

maxIntensity -

valuesOutside -

newImageDestination -

wholeImageThreshold -

inverseThreshold -

AlgorithmStandardDeviationThreshold

public AlgorithmStandardDeviationThreshold(ModelImage srcImage,
 float minIntensityR,
 float minIntensityG,
 float minIntensityB,
 float maxIntensityR,
 float maxIntensityG,
 float maxIntensityB,
 float valuesOutsideR,
 float valuesOutsideG,
 float valuesOutsideB,
 boolean newImageDestination,
 boolean wholeImageThreshold,
 boolean inverseThreshold)

constructor for color image

Parameters:

srcImage -

minIntensityR -

minIntensityG -

minIntensityB -

maxIntensityR -

maxIntensityG -

maxIntensityB -

valuesOutsideR -

valuesOutsideG -

valuesOutsideB -

newImageDestination -

wholeImageThreshold -

inverseThreshold -

Method Details

runAlgorithm

public void runAlgorithm()

run algorithm

Specified by:

runAlgorithm in class AlgorithmBase

getResultImage

public ModelImage getResultImage()

getResultImage

Returns:

getTotalArea

public float getTotalArea()

getTotalArea

Returns:

getTotalVolume

public float getTotalVolume()

getTotalVolume

Returns:

getNumPixels

public int getNumPixels()

getNumPixels

Returns:

getNumPixelsB

public int getNumPixelsB()

getNumPixelsB

Returns:

getNumPixelsG

public int getNumPixelsG()

getNumPixelsG

Returns:

getNumPixelsR

public int getNumPixelsR()

getNumPixelsR

Returns:

getTotalAreaB

public float getTotalAreaB()

getTotalAreaB

Returns:

getTotalAreaG

public float getTotalAreaG()

getTotalAreaG

Returns:

getTotalAreaR

public float getTotalAreaR()

getTotalAreaR

Returns:

getTotalVolumeB

public float getTotalVolumeB()

getTotalVolumeB

Returns:

getTotalVolumeG

public float getTotalVolumeG()

getTotalVolumeG

Returns:

getTotalVolumeR

public float getTotalVolumeR()

getTotalVolumeR

Returns:

getSumIntensities

public float getSumIntensities()

get sum intensities

Returns:

getSumIntensitiesB

public float getSumIntensitiesB()

get sum intensities B

Returns:

getSumIntensitiesG

public float getSumIntensitiesG()

get sum intensities G

Returns:

getSumIntensitiesR

public float getSumIntensitiesR()

get sum intensities R

Returns: