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

Class AlgorithmMaximumIntensityProjection

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.utilities.AlgorithmMaximumIntensityProjection

All Implemented Interfaces:

ActionListener, WindowListener, Runnable, EventListener

public class AlgorithmMaximumIntensityProjection
extends AlgorithmBase

Computes the maximum or the minimum intensity along each projection of a 3D image. The user can specify theshold values in image intensity for the calculation, as well as which projection to compute along (X,Y, or Z), the start and end slice used in the calculation, the size of a sliding 'window' in number of slices to use in the calculation, and whether to calculate the minimum, maximum or both projections. When the sliding window size is not equal to the number of slices used in the calculation the output is a 3D image, where each slice of the output image is computed using the number of slices in the sliding window. When the sliding window size is equal to the number of slices used in the calculation the output image is a 2D image.

Author:

joshim2

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	colorFactor	When the image is a color image, the colorFactor is set to 4, otherwise it defaults to 1.
private boolean	computeMaximum	When true, computes the maximum intensity projection.
private boolean	computeMinimum	When true, computes the minimum intensity projection.
(package private) float[]	imResolutions	Source Image Resolutions
(package private) int[]	imUnitsOfMeasure	Source Image Units of Measure
private double[]	maxIntensity	Maximum intensity threshold value.
private double[]	minIntensity	Minimum intensity threshold value.
private int	projectionDirection	Default Projection is along the z-Axis.
private boolean	quiet
private Vector<ModelImage>	resultImages	Array of Result Images
private int	startSlice	The first slice in the intensity projection calculation:
private int	stopSlice	The last slice in the intensity projection calculation:
private int	window	The number of slices used in the intensity projection, represents a sliding window.
static final int	X_PROJECTION	Project along the X-Axis.
static final int	Y_PROJECTION	Project along the Y-Axis.
static final int	Z_PROJECTION	Project along the Z-Axis.

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
AlgorithmMaximumIntensityProjection(ModelImage srcImg, int _startSlice, int _stopSlice, int _window, double _minIntensity, double _maxIntensity, boolean _computeMaximum, boolean _computeMinimum, int _projectionDirection)	Estimates the maximum intensity projection in each direction of a 3D black and white image
AlgorithmMaximumIntensityProjection(ModelImage srcImg, int _startSlice, int _stopSlice, int _window, double _minR, double _maxR, double _minG, double _maxG, double _minB, double _maxB, boolean _computeMaximum, boolean _computeMinimum, int _projectionDirection)	Estimates the maximum intensity projection of a 3D color image

Method Summary

Modifier and Type	Method	Description
private void	calcXProjection()	Calculates the X Projection for color or black and white images.
private void	calcYProjection()	Calculates the Y Projection for color or black and white images.
private void	calcZProjection()	Calculates the Z Projection for color or black and white images.
void	finalize()	Prepares this class for destruction.
double[]	getMaxIntensity()
double[]	getMinIntensity()
int	getProjectionDirection()
Vector<ModelImage>	getResultImage()	This method returns the projection images in a Vector.
int	getStartSlice()
int	getStopSlice()
int	getWindow()
boolean	isComputeMaximum()
boolean	isComputeMinimum()
void	runAlgorithm()	Runs the Intensity Projection algorithm.
void	setComputeMaximum(boolean computeMaximum)
void	setComputeMinimum(boolean computeMinimum)
void	setMaxIntensity(double[] maxIntensity)
void	setMinIntensity(double[] minIntensity)
void	setProjectionDirection(int projectionDirection)
void	setQuiet(boolean quiet)
void	setSrcImage(ModelImage srcImage)	Sets the source image of the algorithm
void	setStartSlice(int startSlice)
void	setStopSlice(int stopSlice)
void	setWindow(int window)

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, 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

resultImages

private Vector<ModelImage> resultImages

Array of Result Images

imResolutions

float[] imResolutions

Source Image Resolutions

imUnitsOfMeasure

int[] imUnitsOfMeasure

Source Image Units of Measure

startSlice

private int startSlice

The first slice in the intensity projection calculation:

stopSlice

private int stopSlice

The last slice in the intensity projection calculation:

window

private int window

The number of slices used in the intensity projection, represents a sliding window. When this number is not the difference between the stop and start slices, the output image is a 3D that is a collection of projections. Otherwise the output image is a single 2D projection.

minIntensity

private double[] minIntensity

Minimum intensity threshold value.

maxIntensity

private double[] maxIntensity

Maximum intensity threshold value.

computeMaximum

private boolean computeMaximum

When true, computes the maximum intensity projection.

computeMinimum

private boolean computeMinimum

When true, computes the minimum intensity projection.

X_PROJECTION

public static final int X_PROJECTION

Project along the X-Axis.

See Also:

• Constant Field Values

Y_PROJECTION

public static final int Y_PROJECTION

Project along the Y-Axis.

See Also:

• Constant Field Values

Z_PROJECTION

public static final int Z_PROJECTION

Project along the Z-Axis.

See Also:

• Constant Field Values

projectionDirection

private int projectionDirection

Default Projection is along the z-Axis.

colorFactor

private int colorFactor

When the image is a color image, the colorFactor is set to 4, otherwise it defaults to 1.

quiet

private boolean quiet

Constructor Details

AlgorithmMaximumIntensityProjection

public AlgorithmMaximumIntensityProjection(ModelImage srcImg,
 int _startSlice,
 int _stopSlice,
 int _window,
 double _minIntensity,
 double _maxIntensity,
 boolean _computeMaximum,
 boolean _computeMinimum,
 int _projectionDirection)

Estimates the maximum intensity projection in each direction of a 3D black and white image

Parameters:

srcImg - source image

_startSlice - the first slice used in the projection calculation.

_stopSlice - the last slice used in the projection calculation.

_window - the number of slices to use in the projection.

_minIntensity - minimum intensity threshold.

_maxIntensity - maximum intensity threshold.

_computeMaximum - when true compute the maximum intensity projection.

_computeMinimum - when true compute the minimum intensity projection.

_projectionDirection - image axis to project along (X, Y, or Z).

AlgorithmMaximumIntensityProjection

public AlgorithmMaximumIntensityProjection(ModelImage srcImg,
 int _startSlice,
 int _stopSlice,
 int _window,
 double _minR,
 double _maxR,
 double _minG,
 double _maxG,
 double _minB,
 double _maxB,
 boolean _computeMaximum,
 boolean _computeMinimum,
 int _projectionDirection)

Estimates the maximum intensity projection of a 3D color image

Parameters:

srcImg - source image

_startSlice - the first slice used in the projection calculation.

_stopSlice - the last slice used in the projection calculation.

_window - the number of slices to use in the projection.

_minR - minimum Red intensity threshold.

_maxR - maximum Red intensity threshold.

_minG - minimum Green intensity threshold.

_maxG - maximum Green intensity threshold.

_minB - minimum Blue intensity threshold.

_maxB - maximum Blue intensity threshold.

_computeMaximum - when true compute the maximum intensity projection.

_computeMinimum - when true compute the minimum intensity projection.

_projectionDirection - image axis to project along (X, Y, or Z).

Method Details

finalize

public void finalize()

Prepares this class for destruction.

Overrides:

finalize in class AlgorithmBase

setQuiet

public void setQuiet(boolean quiet)

Parameters:

quiet -

runAlgorithm

public void runAlgorithm()

Runs the Intensity Projection algorithm.

Specified by:

runAlgorithm in class AlgorithmBase

calcZProjection

private void calcZProjection()

Calculates the Z Projection for color or black and white images.

calcYProjection

private void calcYProjection()

Calculates the Y Projection for color or black and white images.

calcXProjection

private void calcXProjection()

Calculates the X Projection for color or black and white images.

getStartSlice

public int getStartSlice()

Returns:

the startSlice

getStopSlice

public int getStopSlice()

Returns:

the stopSlice

getMinIntensity

public double[] getMinIntensity()

Returns:

the minIntensity

getMaxIntensity

public double[] getMaxIntensity()

Returns:

the maxIntensity

isComputeMaximum

public boolean isComputeMaximum()

Returns:

the computeMaximum

isComputeMinimum

public boolean isComputeMinimum()

Returns:

the computeMinimum

getProjectionDirection

public int getProjectionDirection()

Returns:

the projectionDirection

getResultImage

public Vector<ModelImage> getResultImage()

This method returns the projection images in a Vector.

getWindow

public int getWindow()

Returns:

the window

setStartSlice

public void setStartSlice(int startSlice)

Parameters:

startSlice - the startSlice to set

setStopSlice

public void setStopSlice(int stopSlice)

Parameters:

stopSlice - the stopSlice to set

setMinIntensity

public void setMinIntensity(double[] minIntensity)

Parameters:

minIntensity - the minIntensity to set

setMaxIntensity

public void setMaxIntensity(double[] maxIntensity)

Parameters:

maxIntensity - the maxIntensity to set

setComputeMaximum

public void setComputeMaximum(boolean computeMaximum)

Parameters:

computeMaximum - the computeMaximum to set

setComputeMinimum

public void setComputeMinimum(boolean computeMinimum)

Parameters:

computeMinimum - the computeMinimum to set

setProjectionDirection

public void setProjectionDirection(int projectionDirection)

Parameters:

projectionDirection - the projectionDirection to set

setSrcImage

public void setSrcImage(ModelImage srcImage)

Description copied from class: AlgorithmBase

Sets the source image of the algorithm

Overrides:

setSrcImage in class AlgorithmBase

Parameters:

srcImage - the source image

setWindow

public void setWindow(int window)

Parameters:

window - the window to set