java.lang.Object
- java.lang.Thread
- - gov.nih.mipav.model.algorithms.AlgorithmBase
  - - gov.nih.mipav.model.algorithms.AlgorithmMorphology3D

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener
```
public class AlgorithmMorphology3D
extends AlgorithmBase
```
Three-Dimensional mathmatical morphology class. 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 Aug 1999

Author:

Matthew J. McAuliffe, Ph.D.

Nested Class Summary

Nested Classes
Modifier and Type Class Description

private class AlgorithmMorphology3D.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`
`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 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 voxel value for the 3D slices.
`private short[]`	`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 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<AlgorithmMorphology3D.intObject>`	`objects`	Vector that holding the current available objects in the 3D image.
`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`	DOCUMENT ME!
`private short[]`	`processBuffer`	intermediate processing buffer, same size with imgBuffer.
`private boolean`	`showFrame`	Not used now.
`static int`	`SIZED_SPHERE`	DOCUMENT ME!
`static int`	`SKELETONIZE`	DOCUMENT ME!
`private float`	`sphereDiameter`	kernel diameter.
`private WildMagic.LibFoundation.Mathematics.Vector3f[]`	`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
`AlgorithmMorphology3D(ModelImage srcImg, int kernelType, float sphereDiameter, int method, int iterD, int iterE, int pruningPix, int edType, boolean entireImage)`	Creates a new AlgorithmMorphology3D object.
`AlgorithmMorphology3D(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.
`AlgorithmMorphology3D(ModelImage srcImg, ModelImage destImg, ModelImage maskImage, int kernelType, float sphereDiameter, int method, int geodesicSize, int iterD, int iterE, boolean entireImage)`	Creates a new AlgorithmMorphology3D object.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`private void`	`backgroundDistanceMap(boolean returnFlag)`	Generates a 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 iterations.
`private void`	`distanceMap(boolean returnFlag)`	Generates a Euclidian distance map.
`private void`	`distanceMapForShapeInterpolation(boolean returnFlag)`
`private void`	`erode(boolean returnFlag, int iters)`	Erodes a boolean, unsigned byte, or unsigned short image using the indicated kernel and the indicated number of iterations.
`private void`	`fillHoles(boolean returnFlag)`	Fill the holes inside the cell region blocks.
`private void`	`fillHolesRegion(int stIndex, short floodValue, short objValue)`	3D flood fill that fill the holes insize the cell region block.
`void`	`finalize()`	Prepares this class for destruction.
`void`	`findEdges(int edgeType, boolean returnFlag)`	Finds the edges of objects.
`private int`	`floodFill(short[] idBuffer, int stIndex, short floodValue, short objValue)`	3D flood fill that forms a short mask.
`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 void`	`makeKernel(int kernelType)`	Generates a kernel of the indicated type.
`private void`	`makeSphericalKernel()`	Generates a spherical kernel of a specific diameter.
`private boolean`	`onePixel(short[] buffer, int index, int sliceSize, int xDim)`	Used by ultimate erode to simplify code a little.
`private void`	`particleAnalysis()`	Take a mask like image and performs an analysis.
`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`	`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.
`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 slice, 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)`	Erodes to a single point.

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
  - 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_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)
  - 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 voxel value for the 3D slices.
  - imgBuffer2
```
private short[] imgBuffer2
```
  - maskBuffer
```
private short[] maskBuffer
```
  - iterationsD
```
private final int iterationsD
```
    Dilation iteration times.
  - iterationsE
```
private final 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 final 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.
  - objects
```
private java.util.Vector<AlgorithmMorphology3D.intObject> objects
```
    Vector that holding the current available objects in the 3D image.
  - pixDist
```
private float pixDist
```
    DOCUMENT ME!
  - processBuffer
```
private short[] processBuffer
```
    intermediate processing buffer, same size with imgBuffer.
  - showFrame
```
private final boolean showFrame
```
    Not used now. Flag to show frame during each algorithm method call.
    
    See Also:
    
    Constant Field Values
  - sphereDiameter
```
private float sphereDiameter
```
    kernel diameter.
  - ultErodeObjects
```
private WildMagic.LibFoundation.Mathematics.Vector3f[] 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
  - AlgorithmMorphology3D
```
public AlgorithmMorphology3D(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
  - AlgorithmMorphology3D
```
public AlgorithmMorphology3D(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
  - AlgorithmMorphology3D
```
public AlgorithmMorphology3D(ModelImage srcImg,
                             ModelImage destImg,
                             ModelImage maskImage,
                             int kernelType,
                             float sphereDiameter,
                             int method,
                             int geodesicSize,
                             int iterD,
                             int iterE,
                             boolean entireImage)
```
    Creates a new AlgorithmMorphology3D 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
  - findEdges
```
public void findEdges(int edgeType,
                      boolean returnFlag)
```
    Finds the edges of objects.
    
    Parameters:
    
    edgeType - Indicates that the edge extracted is formed from the voxels that are directly adjacient to the ojbect or from the voxels that overlay the edge voxels of the object.
    
    returnFlag - if true then this operation is a step in the morph process (i.e. close) see OUTER_EDGING see INNER_EDGE
  - 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)
  - 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.
  - 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)
```
    Generates a 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 iterations.
    
    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 -
  - distanceMap
```
private void distanceMap(boolean returnFlag)
```
    Generates a 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, unsigned byte, or unsigned short image using the indicated kernel and the indicated number of iterations.
    
    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)
```
    3D 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.
  - floodFill
```
private int floodFill(short[] idBuffer,
                      int stIndex,
                      short floodValue,
                      short objValue)
```
    3D flood fill that forms a short mask.
    
    Parameters:
    
    idBuffer - buffer to store flooding results
    
    stIndex - starting index indicating the starting location of the flood fill
    
    floodValue - the value to flood the area with
    
    objValue - DOCUMENT ME!
    
    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!
  - 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.
  - onePixel
```
private boolean onePixel(short[] buffer,
                         int index,
                         int sliceSize,
                         int xDim)
```
    Used by ultimate erode to simplify code a little. Checks to find a single pixels in the 27 neighborhood.
    
    Parameters:
    
    buffer - input data buffer
    
    index - index of interest
    
    sliceSize - number of voxels in the image plane
    
    xDim - dimension of the image in the x direction
    
    Returns:
    
    true if single pixel, false if not single pixel.
  - particleAnalysis
```
private void particleAnalysis()
```
    Take a mask like image and performs an analysis.
    1. Deletes objects that are too small (noise) and objects that are too big 2. Ultimate erode and remove points that are too close 3. Watershed using ultimate eroded points as seed points and distance map. 4. Delete objects that are too small (noise) and objects that are too big
    
    Ult erode & (bg dist map AND orig image) => watershed(ultErodePts, ANDED Bg Dist) => IDobjects
  - thin
```
private int thin(int pass,
                 int slice,
                 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
    
    slice - the slice number being worked on (starting with 0);
    
    table - the table to lookup whether to delete the pixel or let it stay.
    
    Returns:
    
    DOCUMENT ME!
  - ultimateErode
```
private void ultimateErode(boolean returnFlag)
```
    Erodes to a single point.
    
    Parameters:
    
    returnFlag - if true then this operation is a step in the morph process (i.e. open)

Class AlgorithmMorphology3D

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

BORDER_CLEARING

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

distanceMap

edgingType

entireImage

imgBuffer

imgBuffer2

maskBuffer

iterationsD

iterationsE

kDimXY

kDimZ

kernel

kernelType

min

max

numPruningPixels

objects

pixDist

processBuffer

showFrame

sphereDiameter

ultErodeObjects

maskImage

geodesicSize

Constructor Detail

AlgorithmMorphology3D

AlgorithmMorphology3D

AlgorithmMorphology3D

Method Detail

finalize

findEdges

identifyObjects

prune

runAlgorithm

setAlgorithm

setImage

setKernel

setMinMax

setPixDistance

showKernel