Package gov.nih.mipav.model.algorithms

Class AlgorithmMorphology2D

java.lang.Object
java.lang.Thread
gov.nih.mipav.model.algorithms.AlgorithmBase
gov.nih.mipav.model.algorithms.AlgorithmMorphology2D
All Implemented Interfaces:
ActionListener, WindowListener, Runnable, 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.

  • Field Details

    • ERODE

      public static final int ERODE
      DOCUMENT ME!
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    • DILATE

      public static final int DILATE
      DOCUMENT ME!
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    • CLOSE

      public static final int CLOSE
      DOCUMENT ME!
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    • OPEN

      public static final int OPEN
      DOCUMENT ME!
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    • ID_OBJECTS

      public static final int ID_OBJECTS
      DOCUMENT ME!
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    • DELETE_OBJECTS

      public static final int DELETE_OBJECTS
      DOCUMENT ME!
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    • DISTANCE_MAP

      public static final int DISTANCE_MAP
      DOCUMENT ME!
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    • BG_DISTANCE_MAP

      public static final int BG_DISTANCE_MAP
      DOCUMENT ME!
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    • ULTIMATE_ERODE

      public static final int ULTIMATE_ERODE
      DOCUMENT ME!
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    • PARTICLE_ANALYSIS

      public static final int PARTICLE_ANALYSIS
      DOCUMENT ME!
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    • SKELETONIZE

      public static final int SKELETONIZE
      DOCUMENT ME!
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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
      DOCUMENT ME!
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    • FILL_HOLES

      public static final int FILL_HOLES
      DOCUMENT ME!
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    • DISTANCE_MAP_FOR_SHAPE_INTERPOLATION

      public static final int DISTANCE_MAP_FOR_SHAPE_INTERPOLATION
      DOCUMENT ME!
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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
      DOCUMENT ME!
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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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    • CONNECTED80

      public static final int CONNECTED80
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    • OUTER_EDGING

      public static final int OUTER_EDGING
      DOCUMENT ME!
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    • INNER_EDGING

      public static final int INNER_EDGING
      DOCUMENT ME!
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    • 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 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 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 Vector<Integer> pruneSeeds
      Vector that hold the prune seeding pixels.

    • showFrame

      private boolean showFrame
      Flag to show frame during each algorithm method call.

    • ultErodeObjects

      private 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 Details

    • 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 Details

    • runGeodesicDilationTest

      public void runGeodesicDilationTest()

    • runGeodesicErosionTest

      public void runGeodesicErosionTest()

    • runMorphologicalReconstructionByDilationTest

      public void runMorphologicalReconstructionByDilationTest()

    • genContour

      public static final Polygon genContour(BitSet image, int xDim, int yDim, 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 Polygon genContour(ModelImage image, int xDim, int yDim, 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 Polygon genContour(int xDimE, int yDimE, Point startPt, 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 Polygon genContour(short[] image, int xDim, int yDim, 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 invalid input: '<'> 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(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 invalid input: '&' (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