java.lang.Object
- java.lang.Thread
- - gov.nih.mipav.model.algorithms.AlgorithmBase
  - - gov.nih.mipav.model.algorithms.AlgorithmMorphology2D

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener
```
public class AlgorithmMorphology2D
extends AlgorithmBase
```
Two-Dimensional mathmatical morphology class. Kernels of 3x3 (4 or 8 connected) and 5x5 (12 connected) are available or user defined kernels can be supplied.
Methods include:
- Background Distance Map
- close
- Delete objects
- dilate
- Distance Map
- erode
- fill holes
- find edges
- Identify objects
- Morphological gradient
- open
- Particle Analysis
- Skeletonize with pruning option
- ultimate erode
- Border clearing
- Geodesic dilation
- Geodesic erosion
- Morphological reconstruction by dilation
- Morphological reconstruction by erosion
- Opening by reconstruction
- Closing by reconstruction
Version:

1.0 March 15, 1998

Author:

Matthew J. McAuliffe, Ph.D.

Nested Class Summary

Nested Classes
Modifier and Type Class Description

private class AlgorithmMorphology2D.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`	`BORDER_CLEARING`
`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`	`CONNECTED80`
`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 float[]`	`distanceMap`	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 short[]`	`imgBuffer`	imgBuffer that hold pixel value for the 2D slice.
`private short[]`	`imgBuffer2`
`static int`	`INNER_EDGING`	DOCUMENT ME!
`private int`	`iterationsD`	Dilation iteration times.
`private int`	`iterationsE`	Erosion iteration times.
`private int`	`iterationsErodeDilate`	DOCUMENT ME!
`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 short[]`	`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_RECONSTRUCTION_BY_DILATION`
`static int`	`MORPHOLOGICAL_RECONSTRUCTION_BY_EROSION`
`private int`	`numPruningPixels`	Number pixels to prune.
`private java.util.Vector<AlgorithmMorphology2D.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`	DOCUMENT ME!
`private short[]`	`processBuffer`	intermediate processing buffer, same size with imgBuffer.
`private java.util.Vector<java.lang.Integer>`	`pruneSeeds`	Vector that hold the prune seeding pixels.
`private boolean`	`showFrame`	Flag to show frame during each algorithm method call.
`static int`	`SIZED_CIRCLE`	DOCUMENT ME!
`static int`	`SKELETONIZE`	DOCUMENT ME!
`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
`AlgorithmMorphology2D()`
`AlgorithmMorphology2D(ModelImage srcImg, int kernelType, float circleDiameter, int kernelTypeErode, float circleDiameterErode, int method, int iterErodeDilate, int iterE, int pruningPix, int edType, boolean entireImage, boolean _showFrame)`	Creates a new AlgorithmMorphology2D object.
`AlgorithmMorphology2D(ModelImage srcImg, int kernelType, float circleDiameter, int method, int iterD, int iterE, int pruningPix, int edType, boolean entireImage)`	Creates a new AlgorithmMorphology2D object.
`AlgorithmMorphology2D(ModelImage srcImg, ModelImage maskImage, int kernelType, float circleDiameter, int method, int geodesicSize, int iterD, int iterE, boolean entireImage, boolean _showFrame)`	Creates a new AlgorithmMorphology2D object.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`private void`	`backgroundDistanceMap(boolean returnFlag)`	Euclidian distance map of the background.
`private void`	`borderClearing(boolean returnFlag)`	Removes objects that touch (i.e., are connected to) the border
`private void`	`deleteObjects(int min, int max, boolean returnFlag)`	Deletes objects larger than maximum size indicated and objects smaller than the indicated minimum size.
`private void`	`dilate(boolean returnFlag, int iters)`	Dilates a boolean, unsigned byte or unsigned short image using the indicated kernel and the indicated number of executions.
`private void`	`distanceMap(boolean returnFlag)`	Euclidian distance map.
`private void`	`distanceMapForShapeInterpolation(boolean returnFlag)`
`private void`	`erode(boolean returnFlag, int iters)`	Erodes a boolean or unsigned byte or unsigned short image using the indicated kernel and the indicated number of executions.
`private void`	`fillHoles(boolean returnFlag)`	Fill the holes inside the cell region blocks.
`private void`	`fillHolesRegion(int stIndex, short floodValue, short objValue)`	2D flood fill that fill the holes insize the cell region block.
`void`	`finalize()`	Prepares this class for destruction.
`private void`	`findEdges(int edgingType, boolean returnFlag)`	Finds the edges of the objects in an image.
`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.
`void`	`identifyObjects(boolean returnFlag)`	Labels each object in an image with a different integer value.
`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.
`private void`	`particleAnalysis()`	DOCUMENT ME!
`private void`	`particleAnalysisNew(boolean returnFlag)`	particleAnalysis = Ult erode & (bg dist map AND orig image) => watershed(ultErodePts, ANDED Bg Dist) => IDobjects.
`void`	`prune(int iter, boolean returnFlag)`	This method is to be applied on skeletonized images: it removes all branches which are iter or less pixels in length.
`void`	`pruneAuto(boolean returnFlag)`	This method is to be applied on skeletonized images: it skeletonized each branches into a point.
`void`	`runAlgorithm()`	Starts the program.
`void`	`runGeodesicDilationTest()`
`void`	`runGeodesicErosionTest()`
`void`	`runMorphologicalReconstructionByDilationTest()`
`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.
`void`	`skeletonize(int pruningPixels, boolean returnFlag)`	Skeletonizes the image by using a lookup table to repeatedly remove pixels from the edges of objects in a binary image, reducing them to single pixel wide skeletons.
`private int`	`thin(int pass, int[] table)`	This a thinning algorithm used to do half of one layer of thinning (which layer is dictated by whether pass is even or odd).
`private void`	`ultimateErode(boolean returnFlag)`	Ultimate erodes objects down to a single pixel (almost).

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
  - BORDER_CLEARING
```
public static final int BORDER_CLEARING
```
    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
  - CONNECTED80
```
public static final int CONNECTED80
```
    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.
  - distanceMap
```
private float[] distanceMap
```
    DOCUMENT ME!
  - 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 short[] imgBuffer
```
    imgBuffer that hold pixel value for the 2D slice.
  - imgBuffer2
```
private short[] imgBuffer2
```
  - maskBuffer
```
private short[] maskBuffer
```
  - iterationsD
```
private int iterationsD
```
    Dilation iteration times.
  - iterationsE
```
private int iterationsE
```
    Erosion iteration times.
  - iterationsErodeDilate
```
private int iterationsErodeDilate
```
    DOCUMENT ME!
  - 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<AlgorithmMorphology2D.intObject> objects
```
    Vector that holding the current available objects in the 2D image.
  - pixDist
```
private float pixDist
```
    DOCUMENT ME!
  - processBuffer
```
private short[] processBuffer
```
    intermediate processing buffer, same size with imgBuffer.
  - pruneSeeds
```
private java.util.Vector<java.lang.Integer> pruneSeeds
```
    Vector that hold the prune seeding pixels.
  - 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
  - AlgorithmMorphology2D
```
public AlgorithmMorphology2D(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
  - AlgorithmMorphology2D
```
public AlgorithmMorphology2D(ModelImage srcImg,
                             int kernelType,
                             float circleDiameter,
                             int kernelTypeErode,
                             float circleDiameterErode,
                             int method,
                             int iterErodeDilate,
                             int iterE,
                             int pruningPix,
                             int edType,
                             boolean entireImage,
                             boolean _showFrame)
```
    Creates a new AlgorithmMorphology2D 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)
    
    iterErodeDilate - number of times to erode and 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
  - AlgorithmMorphology2D
```
public AlgorithmMorphology2D(ModelImage srcImg,
                             ModelImage maskImage,
                             int kernelType,
                             float circleDiameter,
                             int method,
                             int geodesicSize,
                             int iterD,
                             int iterE,
                             boolean entireImage,
                             boolean _showFrame)
```
    Creates a new AlgorithmMorphology2D 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
  - AlgorithmMorphology2D
```
public AlgorithmMorphology2D()
```
- Method Detail
  - runGeodesicDilationTest
```
public void runGeodesicDilationTest()
```
  - runGeodesicErosionTest
```
public void runGeodesicErosionTest()
```
  - runMorphologicalReconstructionByDilationTest
```
public void runMorphologicalReconstructionByDilationTest()
```
  - 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
  - identifyObjects
```
public void identifyObjects(boolean returnFlag)
```
    Labels each object in an image with a different integer value.
    
    Parameters:
    
    returnFlag - if true then this operation is a step in the morph process (i.e. close)
  - prune
```
public void prune(int iter,
                  boolean returnFlag)
```
    This method is to be applied on skeletonized images: it removes all branches which are iter or less pixels in length.
    
    Parameters:
    
    iter - the threshold number of pixels for the maximum length of a removed branch to be
    
    returnFlag - if true then this operation is a step in the morph process (i.e. close)
  - pruneAuto
```
public void pruneAuto(boolean returnFlag)
```
    This method is to be applied on skeletonized images: it skeletonized each branches into a point.
    
    Parameters:
    
    returnFlag - if true then this operation is a step in the morph process (i.e. close)
  - 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.
  - skeletonize
```
public void skeletonize(int pruningPixels,
                        boolean returnFlag)
```
    Skeletonizes the image by using a lookup table to repeatedly remove pixels from the edges of objects in a binary image, reducing them to single pixel wide skeletons. Based on a thinning algorithm by Zhang and Suen. There is an entry in the table for each of the 256 possible 3x3 neighborhood configurations. An entry of '1' signifies to delete the indicated pixel on the first pass, '2' means to delete the indicated pixel on the second pass, and '3' indicates to delete the pixel on either pass.
    
    Parameters:
    
    pruningPixels - the number of pixels to prune after skeletonizing. (should be 0 if no pruning is to be done)
    
    returnFlag - if true then this operation is a step in the morph process (i.e. close)
  - distanceMapForShapeInterpolation
```
private void distanceMapForShapeInterpolation(boolean returnFlag)
```
  - backgroundDistanceMap
```
private void backgroundDistanceMap(boolean returnFlag)
```
    Euclidian distance map of the background.
    
    Parameters:
    
    returnFlag - if true then this operation is a step in the morph process
  - deleteObjects
```
private void deleteObjects(int min,
                           int max,
                           boolean returnFlag)
```
    Deletes objects larger than maximum size indicated and objects smaller than the indicated minimum size.
    
    Parameters:
    
    min - delete all objects smaller than the minimum value (pixels)
    
    max - delete all objects greater than the maximum value (pixels)
    
    returnFlag - if true then this operation is a step in the morph process (i.e. close)
  - borderClearing
```
private void borderClearing(boolean returnFlag)
```
    Removes objects that touch (i.e., are connected to) the border
    
    Parameters:
    
    returnFlag -
  - dilate
```
private void dilate(boolean returnFlag,
                    int iters)
```
    Dilates 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)
    
    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 -
  - distanceMap
```
private void distanceMap(boolean returnFlag)
```
    Euclidian distance map.
    
    Parameters:
    
    returnFlag - if true then this operation is a step in the morph process
  - erode
```
private void erode(boolean returnFlag,
                   int iters)
```
    Erodes a boolean or 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. open)
    
    iters - number of erosion iterations.
  - fillHoles
```
private void fillHoles(boolean returnFlag)
```
    Fill the holes inside the cell region blocks.
    
    Parameters:
    
    returnFlag - if true then this operation is a step in the morph process (i.e. close)
  - fillHolesRegion
```
private void fillHolesRegion(int stIndex,
                             short floodValue,
                             short objValue)
```
    2D flood fill that fill the holes insize the cell region block.
    
    Parameters:
    
    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.
  - findEdges
```
private void findEdges(int edgingType,
                       boolean returnFlag)
```
    Finds the edges of the objects in an image.
    
    Parameters:
    
    edgingType - DOCUMENT ME!
    
    returnFlag - if true then this operation is a step in the morph process (i.e. close)
  - 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!
  - particleAnalysis
```
private void particleAnalysis()
```
    DOCUMENT ME!
  - particleAnalysisNew
```
private void particleAnalysisNew(boolean returnFlag)
```
    particleAnalysis = Ult erode & (bg dist map AND orig image) => watershed(ultErodePts, ANDED Bg Dist) => IDobjects.
    
    Parameters:
    
    returnFlag - DOCUMENT ME!
  - thin
```
private int thin(int pass,
                 int[] table)
```
    This a thinning algorithm used to do half of one layer of thinning (which layer is dictated by whether pass is even or odd).
    
    Parameters:
    
    pass - the number pass this execution is on the image
    
    table - the table to lookup whether to delete the pixel or let it stay.
    
    Returns:
    
    DOCUMENT ME!
  - ultimateErode
```
private void ultimateErode(boolean returnFlag)
```
    Ultimate erodes objects down to a single pixel (almost). Sometimes depending on the shape of the object (bar bell) more than a single point. Most likely a good situation.
    
    Parameters:
    
    returnFlag - if true then this operation is a step in the morph process

Class AlgorithmMorphology2D

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

BORDER_CLEARING

GEODESIC_DILATION

GEODESIC_EROSION

MORPHOLOGICAL_RECONSTRUCTION_BY_DILATION

MORPHOLOGICAL_RECONSTRUCTION_BY_EROSION

OPENING_BY_RECONSTRUCTION

CLOSING_BY_RECONSTRUCTION

SIZED_CIRCLE

CONNECTED4

CONNECTED8

CONNECTED12

CONNECTED80

OUTER_EDGING

INNER_EDGING

algorithm

circleDiameter

circleDiameterErode

distanceMap

edgingType

entireImage

imgBuffer

imgBuffer2

maskBuffer

iterationsD

iterationsE

iterationsErodeDilate

kDim

kernel

kernelType

kernelTypeErode

min

max

numPruningPixels

objects

pixDist

processBuffer

pruneSeeds

showFrame

ultErodeObjects

maskImage

geodesicSize

Constructor Detail

AlgorithmMorphology2D

AlgorithmMorphology2D

AlgorithmMorphology2D

AlgorithmMorphology2D

Method Detail

runGeodesicDilationTest

runGeodesicErosionTest

runMorphologicalReconstructionByDilationTest

genContour

genContour