java.lang.Object
- java.lang.Thread
- - gov.nih.mipav.model.algorithms.AlgorithmBase
  - - gov.nih.mipav.model.algorithms.AlgorithmGrayScaleMorphology25D

All Implemented Interfaces:

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

Field Summary

Fields
Modifier and Type	Field	Description
`private int`	`algorithm`	DOCUMENT ME!
`static int`	`BG_DISTANCE_MAP`	DOCUMENT ME!
`static int`	`BOTTOM_HAT`
`private float`	`circleDiameter`	DOCUMENT ME!
`static int`	`CLOSE`	DOCUMENT ME!
`static int`	`CLOSING_BY_RECONSTRUCTION`
`static int`	`CONNECTED12`	DOCUMENT ME!
`static int`	`CONNECTED4`	DOCUMENT ME!
`static int`	`CONNECTED8`	DOCUMENT ME!
`static int`	`DELETE_OBJECTS`	DOCUMENT ME!
`static int`	`DILATE`	DOCUMENT ME!
`static int`	`DISTANCE_MAP`	DOCUMENT ME!
`private boolean`	`entireImage`	DOCUMENT ME!
`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`	DOCUMENT ME!
`private double[]`	`imgBuffer2`
`private int`	`imgLength`	DOCUMENT ME!
`static int`	`INNER_EDGING`	DOCUMENT ME!
`private int`	`iterationsD`	DOCUMENT ME!
`private int`	`iterationsE`	DOCUMENT ME!
`private int`	`kDim`	DOCUMENT ME!
`private java.util.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 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`	DOCUMENT ME!
`static int`	`PARTICLE_ANALYSIS`	DOCUMENT ME!
`static int`	`PARTICLE_ANALYSIS_NEW`	DOCUMENT ME!
`private double[]`	`processBuffer`	DOCUMENT ME!
`static int`	`SIZED_CIRCLE`	DOCUMENT ME!
`static int`	`SKELETONIZE`	DOCUMENT ME!
`private int`	`sliceLength`	DOCUMENT ME!
`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
`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

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 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(java.util.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, 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
  - 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 java.util.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 Detail
  - 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 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 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(java.util.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.

Class AlgorithmGrayScaleMorphology25D

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

PARTICLE_ANALYSIS_NEW

FILL_HOLES

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_CIRCLE

CONNECTED4

CONNECTED8

CONNECTED12

OUTER_EDGING

INNER_EDGING

algorithm

circleDiameter

entireImage

imgBuffer

imgBuffer2

maskBuffer

imgLength

iterationsD

iterationsE

kDim

kernel

kernelType

numPruningPixels

processBuffer

sliceLength

maskImage

geodesicSize

Constructor Detail

AlgorithmGrayScaleMorphology25D

AlgorithmGrayScaleMorphology25D

Method Detail

finalize

runAlgorithm

setAlgorithm

setImage

setIterations

setKernel

showKernel

dilate

geodesicDilation

dilate2D

geodesicErosion

erode2D

erode

makeCircularKernel

makeKernel