java.lang.Object
- java.lang.Thread
- - gov.nih.mipav.model.algorithms.AlgorithmBase
  - - gov.nih.mipav.model.algorithms.AlgorithmGrayScaleMorphology3D

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.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
  java.lang.Thread.State, java.lang.Thread.UncaughtExceptionHandler

Field Summary

Fields
Modifier and Type	Field	Description
`private int`	`algorithm`	algorithm type (i.e. erode, dilate)
`static int`	`BG_DISTANCE_MAP`	DOCUMENT ME!
`static int`	`BOTTOM_HAT`
`static int`	`CLOSE`	DOCUMENT ME!
`static int`	`CLOSING_BY_RECONSTRUCTION`
`static int`	`CONNECTED24`	DOCUMENT ME!
`static int`	`CONNECTED26`
`static int`	`CONNECTED6`	DOCUMENT ME!
`static int`	`DELETE_OBJECTS`	DOCUMENT ME!
`static int`	`DILATE`	DOCUMENT ME!
`static int`	`DISTANCE_MAP`	DOCUMENT ME!
`static 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 int`	`ERODE`	DOCUMENT ME!
`static int`	`FILL_HOLES`	DOCUMENT ME!
`static int`	`FIND_EDGES`	DOCUMENT ME!
`static int`	`GEODESIC_DILATION`
`static int`	`GEODESIC_EROSION`
`private int`	`geodesicSize`	Size of geodesic erosions and dilations
`static int`	`ID_OBJECTS`	DOCUMENT ME!
`private double[]`	`imgBuffer`	imgBuffer that hold voxel value for the 3D slices.
`private double[]`	`imgBuffer2`
`static 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 java.util.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 int`	`MORPHOLOGICAL_GRADIENT`
`static int`	`MORPHOLOGICAL_LAPLACIAN`
`static int`	`MORPHOLOGICAL_RECONSTRUCTION_BY_DILATION`
`static int`	`MORPHOLOGICAL_RECONSTRUCTION_BY_EROSION`
`private int`	`numPruningPixels`	Number pixels to prune.
`static int`	`OPEN`	DOCUMENT ME!
`static int`	`OPENING_BY_RECONSTRUCTION`
`static int`	`OUTER_EDGING`	Parameter used in Find_Edges.
`static int`	`PARTICLE_ANALYSIS`	DOCUMENT ME!
`private float`	`pixDist`
`private double[]`	`processBuffer`	intermediate processing buffer, same size with imgBuffer.
`static int`	`SIZED_SPHERE`	DOCUMENT ME!
`static int`	`SKELETONIZE`	DOCUMENT ME!
`private float`	`sphereDiameter`	kernel diameter.
`static int`	`TOP_HAT`
`static 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

All Methods Instance Methods Concrete Methods
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(java.util.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, join, join, join, onSpinWait, resume, setContextClassLoader, setDaemon, setDefaultUncaughtExceptionHandler, setName, setPriority, setUncaughtExceptionHandler, sleep, sleep, start, stop, suspend, toString, yield

Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Field Detail
  - 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 java.util.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 Detail
  - 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 Detail
  - 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(java.util.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.

Class AlgorithmGrayScaleMorphology3D

Nested Class Summary

Nested classes/interfaces inherited from class java.lang.Thread

Field Summary

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

Fields inherited from class java.lang.Thread

Constructor Summary

Method Summary

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

Methods inherited from class java.lang.Thread

Methods inherited from class java.lang.Object

Field Detail

ERODE

DILATE

CLOSE

OPEN

ID_OBJECTS

DELETE_OBJECTS

DISTANCE_MAP

BG_DISTANCE_MAP

ULTIMATE_ERODE

PARTICLE_ANALYSIS

SKELETONIZE

FIND_EDGES

FILL_HOLES

DISTANCE_MAP_FOR_SHAPE_INTERPOLATION

MORPHOLOGICAL_GRADIENT

TOP_HAT

BOTTOM_HAT

MORPHOLOGICAL_LAPLACIAN

GEODESIC_DILATION

GEODESIC_EROSION

MORPHOLOGICAL_RECONSTRUCTION_BY_DILATION

MORPHOLOGICAL_RECONSTRUCTION_BY_EROSION

OPENING_BY_RECONSTRUCTION

CLOSING_BY_RECONSTRUCTION

SIZED_SPHERE

CONNECTED6

CONNECTED24

CONNECTED26

OUTER_EDGING

INNER_EDGING

algorithm

edgingType

entireImage

imgBuffer

imgBuffer2

maskBuffer

iterationsD

iterationsE

kDimXY

kDimZ

kernel

kernelType

min

max

numPruningPixels

pixDist

processBuffer

sphereDiameter

maskImage

geodesicSize

Constructor Detail

AlgorithmGrayScaleMorphology3D

AlgorithmGrayScaleMorphology3D

AlgorithmGrayScaleMorphology3D

Method Detail

finalize

runAlgorithm

setAlgorithm

setImage

setKernel

setMinMax

setPixDistance

showKernel

dilate

geodesicDilation

geodesicErosion

erode

makeKernel