Package gov.nih.mipav.model.algorithms

Class AlgorithmGrayScaleMorphology3D

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.AlgorithmGrayScaleMorphology3D

All Implemented Interfaces:

ActionListener, WindowListener, Runnable, EventListener

public class AlgorithmGrayScaleMorphology3D
extends AlgorithmBase

Three-Dimensional mathematical morphology class applied to Gray scale images.

Version:

1.0 Aug 1999

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
private int	algorithm	algorithm type (i.e. erode, dilate)
static final int	BG_DISTANCE_MAP	DOCUMENT ME!
static final int	BOTTOM_HAT
static final int	CLOSE	DOCUMENT ME!
static final int	CLOSING_BY_RECONSTRUCTION
static final int	CONNECTED24	DOCUMENT ME!
static final int	CONNECTED26
static final int	CONNECTED6	DOCUMENT ME!
static final int	DELETE_OBJECTS	DOCUMENT ME!
static final int	DILATE	DOCUMENT ME!
static final int	DISTANCE_MAP	DOCUMENT ME!
static final int	DISTANCE_MAP_FOR_SHAPE_INTERPOLATION	DOCUMENT ME!
private int	edgingType	Edge type.
private boolean	entireImage	if true, indicates that the VOIs should NOT be used and that entire image should be processed.
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	imgBuffer that hold voxel value for the 3D slices.
private double[]	imgBuffer2
static final int	INNER_EDGING	Parameter used in Find_Edges.
private int	iterationsD	Dilation iteration times.
private int	iterationsE	Erosion iteration times.
private int	kDimXY	Kernel dimension.
private int	kDimZ	DOCUMENT ME!
private BitSet	kernel	Kernel for both erosion and dilation.
private int	kernelType	kernel size (i.e. connectedness)
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
private int	max	maximum, minimum size of objects.
private int	min	maximum, minimum size of objects.
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	Parameter used in Find_Edges.
static final int	PARTICLE_ANALYSIS	DOCUMENT ME!
private float	pixDist
private double[]	processBuffer	intermediate processing buffer, same size with imgBuffer.
static final int	SIZED_SPHERE	DOCUMENT ME!
static final int	SKELETONIZE	DOCUMENT ME!
private float	sphereDiameter	kernel diameter.
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
AlgorithmGrayScaleMorphology3D(ModelImage srcImg, int kernelType, float sphereDiameter, int method, int iterD, int iterE, int pruningPix, int edType, boolean entireImage)	Creates a new AlgorithmMorphology3D object.
AlgorithmGrayScaleMorphology3D(ModelImage srcImg, ModelImage destImg, int kernelType, float sphereDiameter, int method, int iterD, int iterE, int pruningPix, int edType, boolean entireImage)	Creates a new AlgorithmMorphology3D object.
AlgorithmGrayScaleMorphology3D(ModelImage srcImg, ModelImage destImg, ModelImage maskImage, int kernelType, float sphereDiameter, int method, int geodesicSize, int iterD, int iterE, boolean entireImage)	Creates a new AlgorithmGrayScaleMorphology3D 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 iterations.
private void	erode(boolean returnFlag, int iters)	Erodes an image using the indicated kernel and the indicated number of iterations.
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	makeKernel(int kernelType)	Generates a kernel of the indicated type.
private void	makeSphericalKernel()	Generates a spherical kernel of a specific diameter.
void	runAlgorithm()	Starts the program.
void	setAlgorithm(int method)	Sets the algorithm type (i.e. erode, dilate)
void	setImage(ModelImage img)	Sets new source image.
void	setKernel(BitSet kernel, int dimXY, int dimZ)	Sets user defined square kernels.
void	setMinMax(int _min, int _max)	Sets the bounds of object size used to delete objects.
void	setPixDistance(float dist)	Used in the ultimate erode function to remove all eroded points less than the distance specified in pixel units.
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

FILL_HOLES

public static final int FILL_HOLES

DOCUMENT ME!

See Also:

• Constant Field Values

DISTANCE_MAP_FOR_SHAPE_INTERPOLATION

public static final int DISTANCE_MAP_FOR_SHAPE_INTERPOLATION

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_SPHERE

public static final int SIZED_SPHERE

DOCUMENT ME!

See Also:

• Constant Field Values

CONNECTED6

public static final int CONNECTED6

DOCUMENT ME!

See Also:

• Constant Field Values

CONNECTED24

public static final int CONNECTED24

DOCUMENT ME!

See Also:

• Constant Field Values

CONNECTED26

public static final int CONNECTED26

See Also:

• Constant Field Values

OUTER_EDGING

public static final int OUTER_EDGING

Parameter used in Find_Edges. Indicates that the edge extracted is formed from the voxels that are directly adjacient to the ojbect.

See Also:

• Constant Field Values

INNER_EDGING

public static final int INNER_EDGING

Parameter used in Find_Edges. Indicates that the edge extracted is formed from the voxels that overlay the edge voxels of the object.

See Also:

• Constant Field Values

algorithm

private int algorithm

algorithm type (i.e. erode, dilate)

edgingType

private int edgingType

Edge type.

entireImage

private boolean entireImage

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

imgBuffer

private double[] imgBuffer

imgBuffer that hold voxel value for the 3D slices.

imgBuffer2

private double[] imgBuffer2

maskBuffer

private double[] maskBuffer

iterationsD

private int iterationsD

Dilation iteration times.

iterationsE

private int iterationsE

Erosion iteration times.

kDimXY

private int kDimXY

Kernel dimension.

kDimZ

private int kDimZ

DOCUMENT ME!

kernel

private BitSet kernel

Kernel for both erosion and dilation.

kernelType

private int kernelType

kernel size (i.e. connectedness)

min

private int min

maximum, minimum size of objects.

max

private int max

maximum, minimum size of objects.

numPruningPixels

private int numPruningPixels

Number pixels to prune.

pixDist

private float pixDist

processBuffer

private double[] processBuffer

intermediate processing buffer, same size with imgBuffer.

sphereDiameter

private float sphereDiameter

kernel diameter.

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

AlgorithmGrayScaleMorphology3D

public AlgorithmGrayScaleMorphology3D(ModelImage srcImg,
 int kernelType,
 float sphereDiameter,
 int method,
 int iterD,
 int iterE,
 int pruningPix,
 int edType,
 boolean entireImage)

Creates a new AlgorithmMorphology3D object.

Parameters:

srcImg - source image model

kernelType - kernel size (i.e. connectedness)

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

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

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 - flag that indicates if the VOIs should NOT be used and entire image should be processed

AlgorithmGrayScaleMorphology3D

public AlgorithmGrayScaleMorphology3D(ModelImage srcImg,
 ModelImage destImg,
 int kernelType,
 float sphereDiameter,
 int method,
 int iterD,
 int iterE,
 int pruningPix,
 int edType,
 boolean entireImage)

Creates a new AlgorithmMorphology3D object.

Parameters:

srcImg - source image model

destImg - destination image model

kernelType - kernel size (i.e. connectedness)

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

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

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 - flag that indicates if the VOIs should NOT be used and entire image should be processed

AlgorithmGrayScaleMorphology3D

public AlgorithmGrayScaleMorphology3D(ModelImage srcImg,
 ModelImage destImg,
 ModelImage maskImage,
 int kernelType,
 float sphereDiameter,
 int method,
 int geodesicSize,
 int iterD,
 int iterE,
 boolean entireImage)

Creates a new AlgorithmGrayScaleMorphology3D object.

Parameters:

srcImg - source image model

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

sphereDiameter - dilation only valid if kernelType == SIZED_SPHERE 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 new source image.

Parameters:

img - image model

setKernel

public void setKernel(BitSet kernel,
 int dimXY,
 int dimZ)

Sets user defined square kernels.

Parameters:

kernel - user defined kernel

dimXY - length of x and y dimensions

dimZ - length of z dimension

setMinMax

public void setMinMax(int _min,
 int _max)

Sets the bounds of object size used to delete objects.

Parameters:

_min - minimum size of objects

_max - maximum size of objects

setPixDistance

public void setPixDistance(float dist)

Used in the ultimate erode function to remove all eroded points less than the distance specified in pixel units.

Parameters:

dist - distance in pixels.

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 iterations. 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 dilation iterations

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 -

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 -

erode

private void erode(boolean returnFlag,
 int iters)

Erodes an image using the indicated kernel and the indicated number of iterations. 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

makeKernel

private void makeKernel(int kernelType)

Generates a kernel of the indicated type.

Parameters:

kernelType - type of kernel to be generated.

makeSphericalKernel

private void makeSphericalKernel()

Generates a spherical kernel of a specific diameter. Most importantly it normalizes the kernel based on the resolution in the z-dimension. This in effect accounts for the anisotrophy in the z-dimension of typical 3D medical images. The resultant data is stored in the kernel class variable.