Package WildMagic.LibImagics.Extraction

Class ExtractSurfaceTetra

  • All Implemented Interfaces:
    java.io.Serializable
    public class ExtractSurfaceTetra
extends java.lang.Object
implements java.io.Serializable
    A level surface extractor that is based on decomposing voxels into tetrahedra, assuming a linear interpolation on the tetrahedra, and extracting triangular level sets for those tetrahedra. The resulting level surface is a triangle mesh. A detailed discussion of the algorithm is found in Level Set Extraction
    See Also:
    Serialized Form

    • Field Summary

      Fields 
      Modifier and Type Field Description
      protected int[] m_aiData
      data
      protected int m_iNextIndex
      for unique indexing of vertices.
      protected int m_iXBound
      bounds on each dimension of 3D data set and data itself.
      protected int m_iXYProduct
      ??
      protected int m_iXYZProduct
      ??
      protected int m_iYBound
      bounds on each dimension of 3D data set and data itself.
      protected int m_iZBound
      bounds on each dimension of 3D data set and data itself.
      protected Vector3f m_kCentroid
      temporary variables to eliminate 'new' calls for Vector3f.
      protected Vector3f m_kE0
      temporary variables to eliminate 'new' calls for Vector3f
      protected Vector3f m_kE1
      temporary variables to eliminate 'new' calls for Vector3f
      protected Vector3f m_kGradient
      temporary variables to eliminate 'new' calls for Vector3f
      protected Vector3f m_kN
      temporary variables to eliminate 'new' calls for Vector3f
      protected java.util.HashSet<ExtractSurfaceTetra.Triangle> m_kTSet
      set of
      protected Vector3f m_kV0
      temporary variables to eliminate 'new' calls for Vector3f.
      protected Vector3f m_kV1
      temporary variables to eliminate 'new' calls for Vector3f.
      protected Vector3f m_kV2
      temporary variables to eliminate 'new' calls for Vector3f.
      protected java.util.HashMap<ExtractSurfaceTetra.Vertex,​java.lang.Integer> m_kVMap
      temporary storage for use in extraction.
      private static long serialVersionUID  

    • Constructor Summary

      Constructors 
      Constructor Description
      ExtractSurfaceTetra​(int iXBound, int iYBound, int iZBound, int[] aiData)
      Create a level surface extractor for a 3D image.

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      protected void addTriangle​(int iXN0, int iXD0, int iYN0, int iYD0, int iZN0, int iZD0, int iXN1, int iXD1, int iYN1, int iYD1, int iZN1, int iZD1, int iXN2, int iXD2, int iYN2, int iYD2, int iZN2, int iZD2)
      Add a level set triangle that was found in processTetrahedron.
      protected int addVertex​(int iXN, int iXD, int iYN, int iYD, int iZN, int iZD)
      Add a level set vertex that was found in processTetrahedron.
      void ExtractContour​(int iLevel, java.util.HashMap<ExtractSurfaceTetra.Vertex,​java.lang.Integer> kVMap, java.util.HashSet<ExtractSurfaceTetra.Triangle> kTSet)
      Construct a level surface from the 3D image managed by the extractor.
      void ExtractContour​(int iLevel, java.util.Vector<int[]> kTriTable, java.util.HashMap<ExtractSurfaceTetra.Vertex,​java.lang.Integer> kVMap, java.util.HashSet<ExtractSurfaceTetra.Triangle> kTSet)
      Construct a level surface from the 3D image managed by the extractor.
      float getFunction​(Vector3f kP)
      Interpolation of the image.
      Vector3f getGradient​(Vector3f kP)
      Interpolation of the gradient vector of the image.
      protected void processTetrahedron​(float iLevel, int iX0, int iY0, int iZ0, int iF0, int iX1, int iY1, int iZ1, int iF1, int iX2, int iY2, int iZ2, int iF2, int iX3, int iY3, int iZ3, int iF3)
      Find the triangles that are the level set for a linear function defined on a single tetrahedron.

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Field Detail

      • m_aiData

        protected int[] m_aiData
        data

      • m_iNextIndex

        protected int m_iNextIndex
        for unique indexing of vertices.

      • m_iXBound

        protected int m_iXBound
        bounds on each dimension of 3D data set and data itself.

      • m_iYBound

        protected int m_iYBound
        bounds on each dimension of 3D data set and data itself.

      • m_iZBound

        protected int m_iZBound
        bounds on each dimension of 3D data set and data itself.

      • m_iXYProduct

        protected int m_iXYProduct
        ??

      • m_iXYZProduct

        protected int m_iXYZProduct
        ??

      • m_kE0

        protected Vector3f m_kE0
        temporary variables to eliminate 'new' calls for Vector3f

      • m_kE1

        protected Vector3f m_kE1
        temporary variables to eliminate 'new' calls for Vector3f

      • m_kN

        protected Vector3f m_kN
        temporary variables to eliminate 'new' calls for Vector3f

      • m_kGradient

        protected Vector3f m_kGradient
        temporary variables to eliminate 'new' calls for Vector3f

      • m_kV0

        protected Vector3f m_kV0
        temporary variables to eliminate 'new' calls for Vector3f.

      • m_kV1

        protected Vector3f m_kV1
        temporary variables to eliminate 'new' calls for Vector3f.

      • m_kV2

        protected Vector3f m_kV2
        temporary variables to eliminate 'new' calls for Vector3f.

      • m_kCentroid

        protected Vector3f m_kCentroid
        temporary variables to eliminate 'new' calls for Vector3f.

      • m_kVMap

        protected java.util.HashMap<ExtractSurfaceTetra.Vertex,​java.lang.Integer> m_kVMap
        temporary storage for use in extraction.

    • Constructor Detail

      • ExtractSurfaceTetra

        public ExtractSurfaceTetra​(int iXBound,
                           int iYBound,
                           int iZBound,
                           int[] aiData)
        Create a level surface extractor for a 3D image. The delta input values are important when the voxels are not cubic. For example, a typical MRI might have z-slice spacing about 5 times that of the x and y spacing. In this case, dx = 1, dy = 1, and dz = 5. The idea is that 1 is a 'voxel unit' and the z-slices are spaced by 5 voxel units.
        Parameters:
        iXBound - the number of columns in the 3D image
        iYBound - the number of rows in the 3D image
        iZBound - the number of slices in the 3D image
        aiData - The image data stored in order of slice indices, each slice stored in row-major order. That is, slice z=0 is stored first, slice z=1 is stored next, and so on. In slice z=0, the y=0 row is stored first, the y=1 row is stored next, and so on.
        fXDelta - the relative voxel x-size (in voxel units)
        fYDelta - the relative voxel y-size (in voxel units)
        fZDelta - the relative voxel z-size (in voxel units)
        direction - array of direction factors == 1 or -1.
        startLocation - array of startLocation
        dicomMatrix - DOCUMENT ME!

    • Method Detail

      • ExtractContour

        public void ExtractContour​(int iLevel,
                           java.util.Vector<int[]> kTriTable,
                           java.util.HashMap<ExtractSurfaceTetra.Vertex,​java.lang.Integer> kVMap,
                           java.util.HashSet<ExtractSurfaceTetra.Triangle> kTSet)
        Construct a level surface from the 3D image managed by the extractor.

      • getFunction

        public float getFunction​(Vector3f kP)
        Interpolation of the image. The voxel containing the input point is determined. Within that voxel, the correct tetrahedron containing the point is determined. A barycentric combination of the function values at the vertices of the tetrahedron is used for the interpolated value. The barycentric coordinates are those of the input point relative to the vertices of the tetrahedron.
        Parameters:
        kP - - (x,y,z) the point to be interpolated
        Returns:
        the interpolated function value

      • getGradient

        public Vector3f getGradient​(Vector3f kP)
        Interpolation of the gradient vector of the image. The voxel containing the input point is determined. Within that voxel, the correct tetrahedron containing the point is determined. A barycentric combination of the gradient values at the vertices of the tetrahedron is used for the interpolated value. The barycentric coordinates are those of the input point relative to the vertices of the tetrahedron.
        This vector is used to determine consistent normals for the triangles in the mesh representing the level surface. This is faster than using ModelSurfaceTopology.getConsistentComponents(), but may fail on some pathological cases. These cases are rare in 3D images from real applications.
        Parameters:
        kP - the point to be interpolated
        Returns:
        the gradient at the input point

      • addTriangle

        protected void addTriangle​(int iXN0,
                           int iXD0,
                           int iYN0,
                           int iYD0,
                           int iZN0,
                           int iZD0,
                           int iXN1,
                           int iXD1,
                           int iYN1,
                           int iYD1,
                           int iZN1,
                           int iZD1,
                           int iXN2,
                           int iXD2,
                           int iYN2,
                           int iYD2,
                           int iZN2,
                           int iZD2)
        Add a level set triangle that was found in processTetrahedron.
        Parameters:
        iXN0 - a vertex in rational form
        iXD0 - a vertex in rational form
        iYN0 - a vertex in rational form
        iYD0 - DOCUMENT ME!
        iZN0 - DOCUMENT ME!
        iZD0 - DOCUMENT ME!
        iXN1 - DOCUMENT ME!
        iXD1 - DOCUMENT ME!
        iYN1 - DOCUMENT ME!
        iYD1 - DOCUMENT ME!
        iZN1 - DOCUMENT ME!
        iZD1 - DOCUMENT ME!
        iXN2 - DOCUMENT ME!
        iXD2 - DOCUMENT ME!
        iYN2 - DOCUMENT ME!
        iYD2 - DOCUMENT ME!
        iZN2 - DOCUMENT ME!
        iZD2 - DOCUMENT ME!

      • addVertex

        protected int addVertex​(int iXN,
                        int iXD,
                        int iYN,
                        int iYD,
                        int iZN,
                        int iZD)
        Add a level set vertex that was found in processTetrahedron.
        Parameters:
        iXN - the vertex in rational form
        iXD - DOCUMENT ME!
        iYN - DOCUMENT ME!
        iYD - DOCUMENT ME!
        iZN - DOCUMENT ME!
        iZD - DOCUMENT ME!
        Returns:
        the index of that added vertex, used in addTriangle

      • processTetrahedron

        protected void processTetrahedron​(float iLevel,
                                  int iX0,
                                  int iY0,
                                  int iZ0,
                                  int iF0,
                                  int iX1,
                                  int iY1,
                                  int iZ1,
                                  int iF1,
                                  int iX2,
                                  int iY2,
                                  int iZ2,
                                  int iF2,
                                  int iX3,
                                  int iY3,
                                  int iZ3,
                                  int iF3)
        Find the triangles that are the level set for a linear function defined on a single tetrahedron.
        Parameters:
        iLevel - the desired level value
        iX0 - a tetrahedron vertex and function value
        iY0 - a tetrahedron vertex and function value
        iZ0 - a tetrahedron vertex and function value
        iF0 - a tetrahedron vertex and function value
        iX1 - DOCUMENT ME!
        iY1 - DOCUMENT ME!
        iZ1 - DOCUMENT ME!
        iF1 - DOCUMENT ME!
        iX2 - DOCUMENT ME!
        iY2 - DOCUMENT ME!
        iZ2 - DOCUMENT ME!
        iF2 - DOCUMENT ME!
        iX3 - DOCUMENT ME!
        iY3 - DOCUMENT ME!
        iZ3 - DOCUMENT ME!
        iF3 - DOCUMENT ME!