Package gov.nih.mipav.model.algorithms

Class AlgorithmMorphology25D

java.lang.Object
java.lang.Thread
gov.nih.mipav.model.algorithms.AlgorithmBase
gov.nih.mipav.model.algorithms.AlgorithmMorphology25D
All Implemented Interfaces:
ActionListener, WindowListener, Runnable, EventListener
public class AlgorithmMorphology25D extends AlgorithmBase
2.5D mathmatical morphology class (2D morphology on 3D volumes). Kernels of 3x3 (4 or 8 connected) and 5x5 (12 connected) are available or user defined kernels can be supplied.

Supported methods include:

  • erode
  • dilate
  • open
  • close
  • Morphological gradient

Adapted from AlgoritmMorphology2D by Matthew J. McAuliffe, Ph.D.

Version:
1.0 June 8, 2004
Author:
Evan McCreedy

  • Field Details

    • ERODE

      public static final int ERODE
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    • DILATE

      public static final int DILATE
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    • CLOSE

      public static final int CLOSE
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    • OPEN

      public static final int OPEN
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    • ID_OBJECTS

      public static final int ID_OBJECTS
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    • DELETE_OBJECTS

      public static final int DELETE_OBJECTS
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    • DISTANCE_MAP

      public static final int DISTANCE_MAP
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    • BG_DISTANCE_MAP

      public static final int BG_DISTANCE_MAP
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    • ULTIMATE_ERODE

      public static final int ULTIMATE_ERODE
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    • PARTICLE_ANALYSIS

      public static final int PARTICLE_ANALYSIS
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    • SKELETONIZE

      public static final int SKELETONIZE
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    • FIND_EDGES

      public static final int FIND_EDGES
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    • PARTICLE_ANALYSIS_NEW

      public static final int PARTICLE_ANALYSIS_NEW
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    • FILL_HOLES

      public static final int FILL_HOLES
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    • MORPHOLOGICAL_GRADIENT

      public static final int MORPHOLOGICAL_GRADIENT
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    • BORDER_CLEARING

      public static final int BORDER_CLEARING
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    • GEODESIC_DILATION

      public static final int GEODESIC_DILATION
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    • GEODESIC_EROSION

      public static final int GEODESIC_EROSION
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    • MORPHOLOGICAL_RECONSTRUCTION_BY_DILATION

      public static final int MORPHOLOGICAL_RECONSTRUCTION_BY_DILATION
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    • MORPHOLOGICAL_RECONSTRUCTION_BY_EROSION

      public static final int MORPHOLOGICAL_RECONSTRUCTION_BY_EROSION
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    • OPENING_BY_RECONSTRUCTION

      public static final int OPENING_BY_RECONSTRUCTION
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    • CLOSING_BY_RECONSTRUCTION

      public static final int CLOSING_BY_RECONSTRUCTION
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    • SIZED_CIRCLE

      public static final int SIZED_CIRCLE
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    • CONNECTED4

      public static final int CONNECTED4
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    • CONNECTED8

      public static final int CONNECTED8
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    • CONNECTED12

      public static final int CONNECTED12
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    • OUTER_EDGING

      public static final int OUTER_EDGING
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    • INNER_EDGING

      public static final int INNER_EDGING
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    • algorithm

      private int algorithm
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    • circleDiameter

      private float circleDiameter
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    • entireImage

      private boolean entireImage
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    • imgBuffer

      private short[] imgBuffer
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    • imgBuffer2

      private short[] imgBuffer2

    • maskBuffer

      private short[] maskBuffer

    • imgLength

      private int imgLength
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    • iterationsD

      private int iterationsD
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    • iterationsE

      private int iterationsE
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    • kDim

      private int kDim
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    • kernel

      private BitSet kernel
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    • kernelType

      private int kernelType

    • numPruningPixels

      private int numPruningPixels
      Number pixels to prune.

    • processBuffer

      private short[] processBuffer
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    • sliceLength

      private int sliceLength
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    • 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 Details

    • AlgorithmMorphology25D

      public AlgorithmMorphology25D(ModelImage srcImg, int kernelType, float circleDiameter, int method, int iterD, int iterE, int pruningPix, int edType, boolean entireImage)
      Creates a new AlgorithmMorphology25D object.
      Parameters:
      srcImg - source image model
      kernelType - kernel size (i.e. connectedness)
      circleDiameter - only valid if kernelType == SIZED_CIRCLE and represents the width of a circle in the resolution of the image
      method - setup the algorithm method (i.e. erode, dilate)
      iterD - number of times to dilate
      iterE - number of times to erode
      pruningPix - the number of pixels to prune
      edType - the type of edging to perform (inner or outer)
      entireImage - if true, indicates that the VOIs should NOT be used and that entire image should be processed

    • AlgorithmMorphology25D

      public AlgorithmMorphology25D(ModelImage srcImg, ModelImage maskImage, int kernelType, float circleDiameter, int method, int geodesicSize, int iterD, int iterE, boolean entireImage)
      Creates a new AlgorithmMorphology25D 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 Details

    • finalize

      public void finalize()
      Prepares this class for destruction.
      Overrides:
      finalize in class AlgorithmBase

    • 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 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(BitSet kernel, int dim)
      Sets user defined square kernels.
      Parameters:
      kernel - user defined kernel
      dim - length of one dimension (kernel should be square)

    • showKernel

      public void showKernel()
      display kernel as 1 or 0 in the debug window.

    • 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)

    • 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 -

    • dilate2D

      private void dilate2D(int indexZ, int iters)
      Dilates a boolean, unsigned byte or unsigned short image slice using the indicated kernel and the indicated number of executions.
      Parameters:
      indexZ -
      iters - number of dilations

    • geodesicErosion

      private void geodesicErosion(boolean returnFlag, int geodesicSize)
      geodesic erosion of a boolean, unsigned byte or unsigned short image using the indicated kernel and the indicated number of executions.
      Parameters:
      returnFlag - if true then this operation is a step in the morph process (i.e. close)
      geodesicSize -

    • erode2D

      private void erode2D(int indexZ, int iters)
      Erodes a boolean or unsigned byte or unsigned short image slice using the indicated kernel and the indicated number of executions.
      Parameters:
      indexZ -
      iters - number of erosion iterations.

    • 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.

    • borderClearing

      private void borderClearing(boolean returnFlag)
      Removes objects that touch (i.e., are connected to) the border
      Parameters:
      returnFlag -

    • 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:
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    • 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.

    • 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:
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