java.lang.Object
- java.lang.Thread
- - gov.nih.mipav.model.algorithms.AlgorithmBase
  - - gov.nih.mipav.model.algorithms.AlgorithmGrayScaleMorphology2D

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener
```
public class AlgorithmGrayScaleMorphology2D
extends AlgorithmBase
```
Two-Dimensional mathematical morphology class applied to Gray scale images. Kernels of 3x3 (4 or 8 connected) and 5x5 (12 connected) are available or user defined kernels can be supplied.

Version:

1.0 March 15, 1998

Author:

Matthew J. McAuliffe, Ph.D.

Nested Class Summary

Nested Classes
Modifier and Type Class Description

private class AlgorithmGrayScaleMorphology2D.intObject
Simple class to temporarily store the object's size, ID and seed index value.
- 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`
`private float`	`circleDiameter`	kernel diameter.
`private float`	`circleDiameterErode`	Erosion kernel diameter.
`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!
`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 pixel value for the 2D slice.
`private double[]`	`imgBuffer2`
`static int`	`INNER_EDGING`	DOCUMENT ME!
`private int`	`iterationsD`	Dilation iteration times.
`private int`	`iterationsE`	Erosion iteration times.
`private int`	`iterationsOpen`
`private int`	`kDim`	Kernel dimension.
`private java.util.BitSet`	`kernel`	Kernel for both erosion and dilation.
`private int`	`kernelType`	kernel size (i.e. connectedness)
`private int`	`kernelTypeErode`	Erosion kernel type.
`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.
`private java.util.Vector<AlgorithmGrayScaleMorphology2D.intObject>`	`objects`	Vector that holding the current available objects in the 2D image.
`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 float`	`pixDist`
`private double[]`	`processBuffer`	intermediate processing buffer, same size with imgBuffer.
`private boolean`	`showFrame`	Flag to show frame during each algorithm method call.
`static int`	`SIZED_CIRCLE`	DOCUMENT ME!
`static int`	`SKELETONIZE`	DOCUMENT ME!
`static int`	`TOP_HAT`
`private java.awt.Point[]`	`ultErodeObjects`	DOCUMENT ME!
`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
`AlgorithmGrayScaleMorphology2D(ModelImage srcImg, int kernelType, float circleDiameter, int kernelTypeErode, float circleDiameterErode, int method, int iterOpen, int iterE, int pruningPix, int edType, boolean entireImage, boolean _showFrame)`	Creates a new AlgorithmGrayScaleMorphology2D object.
`AlgorithmGrayScaleMorphology2D(ModelImage srcImg, int kernelType, float circleDiameter, int method, int iterD, int iterE, int pruningPix, int edType, boolean entireImage)`	Creates a new AlgorithmMorphology2D object.
`AlgorithmGrayScaleMorphology2D(ModelImage srcImg, ModelImage maskImage, int kernelType, float circleDiameter, int method, int geodesicSize, int iterD, int iterE, boolean entireImage, boolean _showFrame)`	Creates a new AlgorithmGrayScaleMorphology2D object.

Method Summary

All Methods Static 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`	`erode(boolean returnFlag, int iters)`	Erodes an image using the indicated kernel and the indicated number of executions.
`void`	`finalize()`	Prepares this class for destruction.
`private int`	`floodFill(short[] idBuffer, int stIndex, short floodValue, short objValue)`	2D flood fill that forms a short mask.
`static java.awt.Polygon`	`genContour(int xDimE, int yDimE, java.awt.Point startPt, java.util.BitSet maskA)`	Static method that generates a boundary of a general object.
`static java.awt.Polygon`	`genContour(short[] image, int xDim, int yDim, java.awt.Point startPt, short objectValue)`	Static method that generates a boundary of a general object.
`static java.awt.Polygon`	`genContour(ModelImage image, int xDim, int yDim, java.awt.Point startPt)`	Static method that generates a boundary of a binary object.
`static java.awt.Polygon`	`genContour(java.util.BitSet image, int xDim, int yDim, java.awt.Point startPt)`	Static method that generates a boundary of a binary object.
`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 boolean`	`isEndpoint(int pix, short[] tmpBuffer)`	This method returns whether or not pix is the index of an endpoint in tmpBuffer (it is assumed that location pix is not the intensity of the background in tmpBuffer).
`private boolean`	`isNeighbor(int index, int pixNeighbor)`	Check the neighbor pix.
`private boolean`	`isSinglePoint(int index, short[] tmpBuffer)`	Check if the given pix is a single point or not.
`private void`	`makeCircularKernel(float circDiameter)`	Generates a cicular kernel of a specific diameter.
`private void`	`makeKernel(int kernelType)`	Generates a kernel of the indicated type.
`private boolean`	`onePixel(short[] buffer, int index, int xDim)`	Used by ultimate erode to simplify code a little.
`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`	`setMinMax(int _min, int _max)`	Sets 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`	`setShowFrame(boolean showFrame)`	DOCUMENT ME!
`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
  - 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_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
```
    algorithm type (i.e. erode, dilate)
  - circleDiameter
```
private float circleDiameter
```
    kernel diameter.
  - circleDiameterErode
```
private float circleDiameterErode
```
    Erosion kernel diameter.
  - 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 pixel value for the 2D slice.
  - imgBuffer2
```
private double[] imgBuffer2
```
  - maskBuffer
```
private double[] maskBuffer
```
  - iterationsD
```
private int iterationsD
```
    Dilation iteration times.
  - iterationsE
```
private int iterationsE
```
    Erosion iteration times.
  - iterationsOpen
```
private int iterationsOpen
```
  - kDim
```
private int kDim
```
    Kernel dimension.
  - kernel
```
private java.util.BitSet kernel
```
    Kernel for both erosion and dilation.
  - kernelType
```
private int kernelType
```
    kernel size (i.e. connectedness)
  - kernelTypeErode
```
private int kernelTypeErode
```
    Erosion kernel type.
  - 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.
  - objects
```
private java.util.Vector<AlgorithmGrayScaleMorphology2D.intObject> objects
```
    Vector that holding the current available objects in the 2D image.
  - pixDist
```
private float pixDist
```
  - processBuffer
```
private double[] processBuffer
```
    intermediate processing buffer, same size with imgBuffer.
  - showFrame
```
private boolean showFrame
```
    Flag to show frame during each algorithm method call.
  - ultErodeObjects
```
private java.awt.Point[] ultErodeObjects
```
    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
  - AlgorithmGrayScaleMorphology2D
```
public AlgorithmGrayScaleMorphology2D(ModelImage srcImg,
                                      int kernelType,
                                      float circleDiameter,
                                      int method,
                                      int iterD,
                                      int iterE,
                                      int pruningPix,
                                      int edType,
                                      boolean entireImage)
```
    Creates a new AlgorithmMorphology2D 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
  - AlgorithmGrayScaleMorphology2D
```
public AlgorithmGrayScaleMorphology2D(ModelImage srcImg,
                                      int kernelType,
                                      float circleDiameter,
                                      int kernelTypeErode,
                                      float circleDiameterErode,
                                      int method,
                                      int iterOpen,
                                      int iterE,
                                      int pruningPix,
                                      int edType,
                                      boolean entireImage,
                                      boolean _showFrame)
```
    Creates a new AlgorithmGrayScaleMorphology2D 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
    
    kernelTypeErode - kernel size (i.e. connectedness) of erosion
    
    circleDiameterErode - Erosion 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)
    
    iterOpen - 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
    
    _showFrame - if true, indicates that show image frame after each algorithm be processed
  - AlgorithmGrayScaleMorphology2D
```
public AlgorithmGrayScaleMorphology2D(ModelImage srcImg,
                                      ModelImage maskImage,
                                      int kernelType,
                                      float circleDiameter,
                                      int method,
                                      int geodesicSize,
                                      int iterD,
                                      int iterE,
                                      boolean entireImage,
                                      boolean _showFrame)
```
    Creates a new AlgorithmGrayScaleMorphology2D 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
    
    _showFrame - if true, indicates that show image frame after each algorithm be processed
- Method Detail
  - genContour
```
public static final java.awt.Polygon genContour(java.util.BitSet image,
                                                int xDim,
                                                int yDim,
                                                java.awt.Point startPt)
```
    Static method that generates a boundary of a binary object. (aka. turtle algorithm: if 1 turn left, step if 0 turn right, step)
    
    Parameters:
    
    image - input image where binary object is located.
    
    xDim - the x dimension of the image
    
    yDim - the y dimension of the image
    
    startPt - starting point
    
    Returns:
    
    returns boundary of the object as Polygon
  - genContour
```
public static final java.awt.Polygon genContour(ModelImage image,
                                                int xDim,
                                                int yDim,
                                                java.awt.Point startPt)
```
    Static method that generates a boundary of a binary object. (aka. turtle algorithm: if 1 turn left, step if 0 turn right, step)
    
    Parameters:
    
    image - input image (Boolean) where binary object is located.
    
    xDim - the x dimension of the image
    
    yDim - the y dimension of the image
    
    startPt - starting point
    
    Returns:
    
    returns boundary of the object as Polygon
  - genContour
```
public static final java.awt.Polygon genContour(int xDimE,
                                                int yDimE,
                                                java.awt.Point startPt,
                                                java.util.BitSet maskA)
```
    Static method that generates a boundary of a general object. (aka. turtle algorithm: if 1 turn left, step if 0 turn right, step)
    
    Parameters:
    
    xDimE - the x dimension of the image
    
    yDimE - the y dimension of the image
    
    startPt - starting point
    
    maskA - mask of the object
    
    Returns:
    
    returns boundary of the object as Polygon
  - genContour
```
public static final java.awt.Polygon genContour(short[] image,
                                                int xDim,
                                                int yDim,
                                                java.awt.Point startPt,
                                                short objectValue)
```
    Static method that generates a boundary of a general object. (aka. turtle algorithm: if 1 turn left, step if 0 turn right, step)
    
    Parameters:
    
    image - input image where > object is located.
    
    xDim - the x dimension of the image
    
    yDim - the y dimension of the image
    
    startPt - starting point
    
    objectValue - value of the object
    
    Returns:
    
    returns boundary of the object as Polygon
  - 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)
  - setMinMax
```
public void setMinMax(int _min,
                      int _max)
```
    Sets 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. Default = 0 (i.e. do not remove any points)
  - setShowFrame
```
public void setShowFrame(boolean showFrame)
```
    DOCUMENT ME!
    
    Parameters:
    
    showFrame - DOCUMENT ME!
  - 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 -
  - 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 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.
  - floodFill
```
private int floodFill(short[] idBuffer,
                      int stIndex,
                      short floodValue,
                      short objValue)
```
    2D flood fill that forms a short mask.
    
    Parameters:
    
    idBuffer - buffer used to hold flood value
    
    stIndex - the starting index of the seed point
    
    floodValue - the value to flood the region with
    
    objValue - object ID value that idenditifies the flood region.
    
    Returns:
    
    DOCUMENT ME!
  - isEndpoint
```
private boolean isEndpoint(int pix,
                           short[] tmpBuffer)
```
    This method returns whether or not pix is the index of an endpoint in tmpBuffer (it is assumed that location pix is not the intensity of the background in tmpBuffer).
    
    Parameters:
    
    pix - the index of a non-zero pixel in tmpBuffer
    
    tmpBuffer - the image
    
    Returns:
    
    DOCUMENT ME!
  - isNeighbor
```
private boolean isNeighbor(int index,
                           int pixNeighbor)
```
    Check the neighbor pix.
    
    Parameters:
    
    index - pixel in center
    
    pixNeighbor - neighbor pix
    
    Returns:
    
    boolean is connected neighbor or not
  - isSinglePoint
```
private boolean isSinglePoint(int index,
                              short[] tmpBuffer)
```
    Check if the given pix is a single point or not.
    
    Parameters:
    
    index - index
    
    tmpBuffer - short[]
    
    Returns:
    
    boolean
  - makeCircularKernel
```
private void makeCircularKernel(float circDiameter)
```
    Generates a cicular 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.
  - onePixel
```
private boolean onePixel(short[] buffer,
                         int index,
                         int xDim)
```
    Used by ultimate erode to simplify code a little.
    
    Parameters:
    
    buffer - reference to the mask data
    
    index - pointer into the array
    
    xDim - the width of image
    
    Returns:
    
    DOCUMENT ME!

Class AlgorithmGrayScaleMorphology2D

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

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_CIRCLE

CONNECTED4

CONNECTED8

CONNECTED12

OUTER_EDGING

INNER_EDGING

algorithm

circleDiameter

circleDiameterErode

edgingType

entireImage

imgBuffer

imgBuffer2

maskBuffer

iterationsD

iterationsE

iterationsOpen

kDim

kernel

kernelType

kernelTypeErode

min

max

numPruningPixels

objects

pixDist

processBuffer

showFrame

ultErodeObjects

maskImage

geodesicSize

Constructor Detail

AlgorithmGrayScaleMorphology2D

AlgorithmGrayScaleMorphology2D

AlgorithmGrayScaleMorphology2D

Method Detail

genContour

genContour

genContour

genContour

finalize

runAlgorithm

setAlgorithm