Package gov.nih.mipav.model.algorithms

Class AlgorithmThresholdDual

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.AlgorithmThresholdDual

All Implemented Interfaces:

ActionListener, WindowListener, Runnable, EventListener

public class AlgorithmThresholdDual
extends AlgorithmBase

This algorithm has two modes of operation:

1. Generates binary image based on threshold values passed in by the constructor. Inside the volume of interest: If the image intensity is greater than or equal to the threshold[0] and less than or equal to the threshold[1], the binary image is set to one. Otherwise, it is set to zero. Outside the volume of interest: The binary image is set equal to zero.

2. Inside the volume of interest: Preserves all grey scale values from threshold[0] to threshold[1] and sets all values less than the lower threshold and all values greater than the upper threshold to the fillValue supplied to this algorithm via the constructor. Outside the volume of interest: Sets all gray scale values to the fill value.

Version:

1.0 March 8, 2000

Author:

Matthew J. McAuliffe, Ph.D.

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
static final int	BINARY_TYPE	DOCUMENT ME!
private boolean	entireImage	Flag, if true, indicates that the whole image should be processed.
private float	fillValue	All values outside the thresholds are set to this value.
private boolean	isInverse	Inverse threshold: false means turn all pixels outside of the lower and upper thresholds to the given fill value, true means turn all data within the lower and upper thresholds to the fill value (fill value can also be binary (0)).
static final int	ORIGINAL_TYPE	DOCUMENT ME!
private int	outputType	Type of output (same type, binary, or unsigned byte).
private int	pixelsInRange	Variable that will store the total number of pixels in thresholding range
private float[]	threshold	Array of two thresholds. threshold[0] = Minimum threshold, threshold[1] = Maximum threshold.
static final int	UNSIGNED_BYTE_TYPE	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
AlgorithmThresholdDual(ModelImage srcImg, float[] threshold, float fillValue, int output_type, boolean maskFlag, boolean isInverse)	Creates a new AlgorithmThresholdDual object.
AlgorithmThresholdDual(ModelImage destImg, ModelImage srcImg, float[] threshold, float fillValue, int output_type, boolean maskFlag, boolean isInverse)	Creates a new AlgorithmThresholdDual object.

Method Summary

Modifier and Type	Method	Description
private void	calcInPlace2D()	Replace 2D source image with the thresholded image.
private void	calcInPlace34D()	Replace 3D or 4D source image with the thresholded image.
private void	calcStoreInDest2D()	Stores the thresholded image into the destination image.
private void	calcStoreInDest34D()	Stores the thresholded image into the destination image.
void	finalize()	Prepares this class for destruction.
void	runAlgorithm()	Starts the program.
private void	setThresholdStatistics()

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

ORIGINAL_TYPE

public static final int ORIGINAL_TYPE

DOCUMENT ME!

See Also:

• Constant Field Values

BINARY_TYPE

public static final int BINARY_TYPE

DOCUMENT ME!

See Also:

• Constant Field Values

UNSIGNED_BYTE_TYPE

public static final int UNSIGNED_BYTE_TYPE

DOCUMENT ME!

See Also:

• Constant Field Values

entireImage

private boolean entireImage

Flag, if true, indicates that the whole image should be processed. If false on process the image over the mask areas.

fillValue

private float fillValue

All values outside the thresholds are set to this value.

isInverse

private boolean isInverse

Inverse threshold: false means turn all pixels outside of the lower and upper thresholds to the given fill value, true means turn all data within the lower and upper thresholds to the fill value (fill value can also be binary (0)).

outputType

private int outputType

Type of output (same type, binary, or unsigned byte).

threshold

private float[] threshold

Array of two thresholds. threshold[0] = Minimum threshold, threshold[1] = Maximum threshold.

pixelsInRange

private int pixelsInRange

Variable that will store the total number of pixels in thresholding range

Constructor Details

AlgorithmThresholdDual

public AlgorithmThresholdDual(ModelImage srcImg,
 float[] threshold,
 float fillValue,
 int output_type,
 boolean maskFlag,
 boolean isInverse)

Creates a new AlgorithmThresholdDual object.

Parameters:

srcImg - source image model

threshold - array of two thresholds

fillValue - all values outside the thresholds are set to this value

output_type - same type, binary, or unsigned byte

maskFlag - true indicates that the whole image should be processed

isInverse - false means turn all pixels outside of the lower and upper thresholds to the given fill value, true means turn all data within the lower and upper thresholds to the fill value

AlgorithmThresholdDual

public AlgorithmThresholdDual(ModelImage destImg,
 ModelImage srcImg,
 float[] threshold,
 float fillValue,
 int output_type,
 boolean maskFlag,
 boolean isInverse)

Creates a new AlgorithmThresholdDual object.

Parameters:

destImg - image model where result image is to be stored

srcImg - source image model

threshold - array of two thresholds

fillValue - all values outside the thresholds are set to this value

output_type - same type, binary, or unsigned byte

maskFlag - true indicates that the whole image should be processed

isInverse - false means turn all pixels outside of the lower and upper thresholds to the given fill value, true means turn all data within the lower and upper thresholds to the fill value

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

calcInPlace2D

private void calcInPlace2D()

Replace 2D source image with the thresholded image.

calcInPlace34D

private void calcInPlace34D()

Replace 3D or 4D source image with the thresholded image.

calcStoreInDest2D

private void calcStoreInDest2D()

Stores the thresholded image into the destination image.

calcStoreInDest34D

private void calcStoreInDest34D()

Stores the thresholded image into the destination image.

setThresholdStatistics

private void setThresholdStatistics()