Package gov.nih.mipav.model.algorithms

Class AlgorithmGrayScaleMorphology25D

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.AlgorithmGrayScaleMorphology25D

All Implemented Interfaces:

ActionListener, WindowListener, Runnable, EventListener

public class AlgorithmGrayScaleMorphology25D
extends AlgorithmBase

2.5D mathematical morphology class applied to Gray scale images. (2D morphology on 3D volumes). Kernels of 3x3 (4 or 8 connected) and 5x5 (12 connected) are available or user defined kernels can be supplied.

Supported methods include:

• Bottom hat
• close
• dilate
• erode
• Morphological gradient
• Morphological laplacian
• open
• Top hat

Adapted from AlgoritmMorphology2D by Matthew J. McAuliffe, Ph.D.

Version:

1.0 June 8, 2004

Author:

Evan McCreedy

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	algorithm	DOCUMENT ME!
static final int	BG_DISTANCE_MAP	DOCUMENT ME!
static final int	BOTTOM_HAT
private float	circleDiameter	DOCUMENT ME!
static final int	CLOSE	DOCUMENT ME!
static final int	CLOSING_BY_RECONSTRUCTION
static final int	CONNECTED12	DOCUMENT ME!
static final int	CONNECTED4	DOCUMENT ME!
static final int	CONNECTED8	DOCUMENT ME!
static final int	DELETE_OBJECTS	DOCUMENT ME!
static final int	DILATE	DOCUMENT ME!
static final int	DISTANCE_MAP	DOCUMENT ME!
private boolean	entireImage	DOCUMENT ME!
static final int	ERODE	DOCUMENT ME!
static final int	FILL_HOLES	DOCUMENT ME!
static final int	FIND_EDGES	DOCUMENT ME!
static final int	GEODESIC_DILATION
static final int	GEODESIC_EROSION
private int	geodesicSize	Size of geodesic erosions and dilations
static final int	ID_OBJECTS	DOCUMENT ME!
private double[]	imgBuffer	DOCUMENT ME!
private double[]	imgBuffer2
private int	imgLength	DOCUMENT ME!
static final int	INNER_EDGING	DOCUMENT ME!
private int	iterationsD	DOCUMENT ME!
private int	iterationsE	DOCUMENT ME!
private int	kDim	DOCUMENT ME!
private BitSet	kernel	DOCUMENT ME!
private int	kernelType
private double[]	maskBuffer
private ModelImage	maskImage	Used in geodesic dilation, geodesic erosion, morphological reconstruction by dilation, and morphological reconstruction by erosion Not used in opening by reconstruction and closing by reconstruction
static final int	MORPHOLOGICAL_GRADIENT
static final int	MORPHOLOGICAL_LAPLACIAN
static final int	MORPHOLOGICAL_RECONSTRUCTION_BY_DILATION
static final int	MORPHOLOGICAL_RECONSTRUCTION_BY_EROSION
private int	numPruningPixels	Number pixels to prune.
static final int	OPEN	DOCUMENT ME!
static final int	OPENING_BY_RECONSTRUCTION
static final int	OUTER_EDGING	DOCUMENT ME!
static final int	PARTICLE_ANALYSIS	DOCUMENT ME!
static final int	PARTICLE_ANALYSIS_NEW	DOCUMENT ME!
private double[]	processBuffer	DOCUMENT ME!
static final int	SIZED_CIRCLE	DOCUMENT ME!
static final int	SKELETONIZE	DOCUMENT ME!
private int	sliceLength	DOCUMENT ME!
static final int	TOP_HAT
static final int	ULTIMATE_ERODE	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
AlgorithmGrayScaleMorphology25D(ModelImage srcImg, int kernelType, float circleDiameter, int method, int iterD, int iterE, int pruningPix, int edType, boolean entireImage)	Creates a new AlgorithmMorphology25D object.
AlgorithmGrayScaleMorphology25D(ModelImage srcImg, ModelImage maskImage, int kernelType, float circleDiameter, int method, int geodesicSize, int iterD, int iterE, boolean entireImage)	Creates a new AlgorithmGrayScaleMorphology25D object.

Method Summary

Modifier and Type	Method	Description
private void	dilate(boolean returnFlag, int iters)	Dilates an image using the indicated kernel and the indicated number of executions.
private void	dilate2D(int indexZ, int iters)	Dilates an image slice using the indicated kernel and the indicated number of executions.
private void	erode(boolean returnFlag, int iters)	Erodes an image using the indicated kernel and the indicated number of executions.
private void	erode2D(int indexZ, int iters)	Erodes an image slice using the indicated kernel and the indicated number of executions.
void	finalize()	Prepares this class for destruction.
private void	geodesicDilation(boolean returnFlag, int geodesicSize)	geodesic dilation of a boolean, unsigned byte or unsigned short image using the indicated kernel and the indicated number of executions.
private void	geodesicErosion(boolean returnFlag, int geodesicSize)	geodesic erosion of a boolean, unsigned byte or unsigned short image using the indicated kernel and the indicated number of executions.
private void	makeCircularKernel(float circDiameter)	Generates a circular kernel of a specific diameter.
private void	makeKernel(int kernelType)	Generates a kernel of the indicated type.
void	runAlgorithm()	Starts the program.
void	setAlgorithm(int method)	Sets the algorithm type (i.e. erode, dilate)
void	setImage(ModelImage img)	Sets the algorithm to new image of boolean type.
void	setIterations(int itersD, int itersE)	Sets number of iterations for closing or opening.
void	setKernel(BitSet kernel, int dim)	Sets user defined square kernels.
void	showKernel()	display kernel as 1 or 0 in the debug 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, 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

ERODE

public static final int ERODE

DOCUMENT ME!

See Also:

• Constant Field Values

DILATE

public static final int DILATE

DOCUMENT ME!

See Also:

• Constant Field Values

CLOSE

public static final int CLOSE

DOCUMENT ME!

See Also:

• Constant Field Values

OPEN

public static final int OPEN

DOCUMENT ME!

See Also:

• Constant Field Values

ID_OBJECTS

public static final int ID_OBJECTS

DOCUMENT ME!

See Also:

• Constant Field Values

DELETE_OBJECTS

public static final int DELETE_OBJECTS

DOCUMENT ME!

See Also:

• Constant Field Values

DISTANCE_MAP

public static final int DISTANCE_MAP

DOCUMENT ME!

See Also:

• Constant Field Values

BG_DISTANCE_MAP

public static final int BG_DISTANCE_MAP

DOCUMENT ME!

See Also:

• Constant Field Values

ULTIMATE_ERODE

public static final int ULTIMATE_ERODE

DOCUMENT ME!

See Also:

• Constant Field Values

PARTICLE_ANALYSIS

public static final int PARTICLE_ANALYSIS

DOCUMENT ME!

See Also:

• Constant Field Values

SKELETONIZE

public static final int SKELETONIZE

DOCUMENT ME!

See Also:

• Constant Field Values

FIND_EDGES

public static final int FIND_EDGES

DOCUMENT ME!

See Also:

• Constant Field Values

PARTICLE_ANALYSIS_NEW

public static final int PARTICLE_ANALYSIS_NEW

DOCUMENT ME!

See Also:

• Constant Field Values

FILL_HOLES

public static final int FILL_HOLES

DOCUMENT ME!

See Also:

• Constant Field Values

MORPHOLOGICAL_GRADIENT

public static final int MORPHOLOGICAL_GRADIENT

See Also:

• Constant Field Values

TOP_HAT

public static final int TOP_HAT

See Also:

• Constant Field Values

BOTTOM_HAT

public static final int BOTTOM_HAT

See Also:

• Constant Field Values

MORPHOLOGICAL_LAPLACIAN

public static final int MORPHOLOGICAL_LAPLACIAN

See Also:

• Constant Field Values

GEODESIC_DILATION

public static final int GEODESIC_DILATION

See Also:

• Constant Field Values

GEODESIC_EROSION

public static final int GEODESIC_EROSION

See Also:

• Constant Field Values

MORPHOLOGICAL_RECONSTRUCTION_BY_DILATION

public static final int MORPHOLOGICAL_RECONSTRUCTION_BY_DILATION

See Also:

• Constant Field Values

MORPHOLOGICAL_RECONSTRUCTION_BY_EROSION

public static final int MORPHOLOGICAL_RECONSTRUCTION_BY_EROSION

See Also:

• Constant Field Values

OPENING_BY_RECONSTRUCTION

public static final int OPENING_BY_RECONSTRUCTION

See Also:

• Constant Field Values

CLOSING_BY_RECONSTRUCTION

public static final int CLOSING_BY_RECONSTRUCTION

See Also:

• Constant Field Values

SIZED_CIRCLE

public static final int SIZED_CIRCLE

DOCUMENT ME!

See Also:

• Constant Field Values

CONNECTED4

public static final int CONNECTED4

DOCUMENT ME!

See Also:

• Constant Field Values

CONNECTED8

public static final int CONNECTED8

DOCUMENT ME!

See Also:

• Constant Field Values

CONNECTED12

public static final int CONNECTED12

DOCUMENT ME!

See Also:

• Constant Field Values

OUTER_EDGING

public static final int OUTER_EDGING

DOCUMENT ME!

See Also:

• Constant Field Values

INNER_EDGING

public static final int INNER_EDGING

DOCUMENT ME!

See Also:

• Constant Field Values

algorithm

private int algorithm

DOCUMENT ME!

circleDiameter

private float circleDiameter

DOCUMENT ME!

entireImage

private boolean entireImage

DOCUMENT ME!

imgBuffer

private double[] imgBuffer

DOCUMENT ME!

imgBuffer2

private double[] imgBuffer2

maskBuffer

private double[] maskBuffer

imgLength

private int imgLength

DOCUMENT ME!

iterationsD

private int iterationsD

DOCUMENT ME!

iterationsE

private int iterationsE

DOCUMENT ME!

kDim

private int kDim

DOCUMENT ME!

kernel

private BitSet kernel

DOCUMENT ME!

kernelType

private int kernelType

numPruningPixels

private int numPruningPixels

Number pixels to prune.

processBuffer

private double[] processBuffer

DOCUMENT ME!

sliceLength

private int sliceLength

DOCUMENT ME!

maskImage

private ModelImage maskImage

Used in geodesic dilation, geodesic erosion, morphological reconstruction by dilation, and morphological reconstruction by erosion Not used in opening by reconstruction and closing by reconstruction

geodesicSize

private int geodesicSize

Size of geodesic erosions and dilations

Constructor Details

AlgorithmGrayScaleMorphology25D

public AlgorithmGrayScaleMorphology25D(ModelImage srcImg,
 int kernelType,
 float circleDiameter,
 int method,
 int iterD,
 int iterE,
 int pruningPix,
 int edType,
 boolean entireImage)

Creates a new AlgorithmMorphology25D object.

Parameters:

srcImg - source image model

kernelType - kernel size (i.e. connectedness)

circleDiameter - only valid if kernelType == SIZED_CIRCLE and represents the width of a circle in the resolution of the image

method - setup the algorithm method (i.e. erode, dilate)

iterD - number of times to dilate

iterE - number of times to erode

pruningPix - the number of pixels to prune

edType - the type of edging to perform (inner or outer)

entireImage - if true, indicates that the VOIs should NOT be used and that entire image should be processed

AlgorithmGrayScaleMorphology25D

public AlgorithmGrayScaleMorphology25D(ModelImage srcImg,
 ModelImage maskImage,
 int kernelType,
 float circleDiameter,
 int method,
 int geodesicSize,
 int iterD,
 int iterE,
 boolean entireImage)

Creates a new AlgorithmGrayScaleMorphology25D object.

Parameters:

srcImg - source image model

kernelType - dilation kernel size (i.e. connectedness)

circleDiameter - dilation only valid if kernelType == SIZED_CIRCLE and represents the width of a circle in the resolution of the image

method - setup the algorithm method (i.e. erode, dilate)

geodesicSize -

iterD - number of times to dilate

iterE - number of times to erode

entireImage - if true, indicates that the VOIs should NOT be used and that entire image should be processed

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

setAlgorithm

public void setAlgorithm(int method)

Sets the algorithm type (i.e. erode, dilate)

Parameters:

method - algorithm type

setImage

public void setImage(ModelImage img)

Sets the algorithm to new image of boolean type.

Parameters:

img - image model of boolean type

setIterations

public void setIterations(int itersD,
 int itersE)

Sets number of iterations for closing or opening.

Parameters:

itersD - number of dilations

itersE - number of erosions

setKernel

public void setKernel(BitSet kernel,
 int dim)

Sets user defined square kernels.

Parameters:

kernel - user defined kernel

dim - length of one dimension (kernel should be square)

showKernel

public void showKernel()

display kernel as 1 or 0 in the debug window.

dilate

private void dilate(boolean returnFlag,
 int iters)

Dilates an image using the indicated kernel and the indicated number of executions. The grayscale dilation is the maximum value over the reflected kernel region. For symmetric kernels the reflected kernel is the same as the kernel.

Parameters:

returnFlag - if true then this operation is a step in the morph process (i.e. close)

iters - number of dilations

geodesicDilation

private void geodesicDilation(boolean returnFlag,
 int geodesicSize)

geodesic dilation of a boolean, unsigned byte or unsigned short image using the indicated kernel and the indicated number of executions.

Parameters:

returnFlag - if true then this operation is a step in the morph process (i.e. close)

geodesicSize -

dilate2D

private void dilate2D(int indexZ,
 int iters)

Dilates an image slice using the indicated kernel and the indicated number of executions. The grayscale dilation is the maximum value over the reflected kernel region. For symmetric kernels the reflected kernel is the same as the kernel.

Parameters:

indexZ -

iters - number of dilations

geodesicErosion

private void geodesicErosion(boolean returnFlag,
 int geodesicSize)

geodesic erosion of a boolean, unsigned byte or unsigned short image using the indicated kernel and the indicated number of executions.

Parameters:

returnFlag - if true then this operation is a step in the morph process (i.e. close)

geodesicSize -

erode2D

private void erode2D(int indexZ,
 int iters)

Erodes an image slice using the indicated kernel and the indicated number of executions. The grayscale erosion is the minimum value over the kernel region.

Parameters:

indexZ -

iters - number of erosion iterations.

erode

private void erode(boolean returnFlag,
 int iters)

Erodes an image using the indicated kernel and the indicated number of executions. The grayscale erosion is the minimum value over the kernel region.

Parameters:

returnFlag - if true then this operation is a step in the morph process (i.e. open)

iters - number of erosion iterations.

makeCircularKernel

private void makeCircularKernel(float circDiameter)

Generates a circular kernel of a specific diameter.

Parameters:

circDiameter - represents the width of a circle in the resolution of the image

makeKernel

private void makeKernel(int kernelType)

Generates a kernel of the indicated type.

Parameters:

kernelType - type of kernel to be generated.