Package gov.nih.mipav.model.algorithms

Class AlgorithmMorphology3D

java.lang.Object
java.lang.Thread
gov.nih.mipav.model.algorithms.AlgorithmBase
gov.nih.mipav.model.algorithms.AlgorithmMorphology3D
All Implemented Interfaces:
ActionListener, WindowListener, Runnable, 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.

  • Field Details

    • ERODE

      public static final int ERODE
      DOCUMENT ME!
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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
      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
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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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    • FILL_HOLES

      public static final int FILL_HOLES
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    • DISTANCE_MAP_FOR_SHAPE_INTERPOLATION

      public static final int DISTANCE_MAP_FOR_SHAPE_INTERPOLATION
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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_SPHERE

      public static final int SIZED_SPHERE
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    • CONNECTED6

      public static final int CONNECTED6
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    • CONNECTED24

      public static final int CONNECTED24
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    • CONNECTED26

      public static final int CONNECTED26
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    • 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.
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    • 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.
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    • 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 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 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:

    • 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 Details

    • 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)
      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
      circleDiameter - dilation only valid if kernelType == SIZED_CIRCLE and represents the width of a circle in the resolution of the image

  • Method Details

    • 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(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 invalid input: '&' (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)