Package gov.nih.mipav.view.renderer.J3D.surfaceview.brainflattenerview

Class MjCorticalMesh

java.lang.Object
gov.nih.mipav.view.renderer.J3D.surfaceview.brainflattenerview.MjCorticalMesh
public class MjCorticalMesh extends Object
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  • Field Details

    • m_afAvrConvexity

      private float[] m_afAvrConvexity
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    • m_afMeanCurvature

      private float[] m_afMeanCurvature
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    • m_aiConnect

      private int[] m_aiConnect
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    • m_akColor

      private javax.vecmath.Color4f[] m_akColor
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    • m_akCylinder

      private javax.vecmath.Point3f[] m_akCylinder
      projection of sphere onto cylinder.

    • m_akEdge

      private MjCorticalMesh.Edge[] m_akEdge
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    • m_akNormal

      private MjVector3f[] m_akNormal
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    • m_akPlane

      private javax.vecmath.Point2f[] m_akPlane
      Conformal mapping to a plane. The (u,v) points correspond to the (x,y,z) mesh points.

    • m_akPoint

      private javax.vecmath.Point3f[] m_akPoint
      mesh attributes.

    • m_akSphere

      private javax.vecmath.Point3f[] m_akSphere
      Conformal mapping to a sphere. rho is the radius of the stereographic sphere.

    • m_akTriangle

      private MjCorticalMesh.Triangle[] m_akTriangle
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    • m_akVertex

      private MjCorticalMesh.Vertex[] m_akVertex
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    • m_fMaxAvrConvexity

      private float m_fMaxAvrConvexity
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    • m_fMaxDistance

      private float m_fMaxDistance
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    • m_fMaxMeanCurvature

      private float m_fMaxMeanCurvature
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    • m_fMinAvrConvexity

      private float m_fMinAvrConvexity
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    • m_fMinDistance

      private float m_fMinDistance
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    • m_fMinMeanCurvature

      private float m_fMinMeanCurvature
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    • m_fRho

      private float m_fRho
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    • m_fSurfaceArea

      private float m_fSurfaceArea
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    • m_iEQuantity

      private int m_iEQuantity
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    • m_iPunctureTri

      private int m_iPunctureTri
      The index of the puncture triangle for computing the conformal mapping:.

    • m_iTQuantity

      private int m_iTQuantity
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    • m_iVQuantity

      private int m_iVQuantity
      mesh topology.

    • m_kDistance

      private HashMap m_kDistance
      vertex-vertex distances measured along edge paths.

    • m_kInitDistance

      private HashMap m_kInitDistance
      surface inflation.

    • m_kPlaneMax

      private javax.vecmath.Point2f m_kPlaneMax
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    • m_kPlaneMin

      private javax.vecmath.Point2f m_kPlaneMin
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  • Constructor Details

    • MjCorticalMesh

      public MjCorticalMesh(int iVQuantity, javax.vecmath.Point3f[] akPoint, int iTQuantity, int[] aiConnect)
      Creates a new MjCorticalMesh object.
      Parameters:
      iVQuantity - DOCUMENT ME!
      akPoint - DOCUMENT ME!
      iTQuantity - DOCUMENT ME!
      aiConnect - DOCUMENT ME!

  • Method Details

    • computeConformalMapping

      public void computeConformalMapping()
      conformal mapping of mesh to plane and sphere, projection to cylinder.

    • computeDistances

      public void computeDistances(int iSize)
      Computes the distances of vertex pairs invalid input: '<'V0,V1> for which an edge-path exists with at most iSize edges.
      Parameters:
      iSize - DOCUMENT ME!

    • computeMeanCurvature

      public void computeMeanCurvature()
      mean curvature.

    • computeNormals

      public void computeNormals()
      compute vertex normals as averages of triangle normals.

    • computeSurfaceArea

      public void computeSurfaceArea()
      surface area of the mesh (input mesh is closed, manifold).

    • disposeLocal

      public void disposeLocal()
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    • doInflation

      public float doInflation(int iOperation)
      surface inflation operation 0 = initialize 1 = inflate 2 = terminate.
      Parameters:
      iOperation - DOCUMENT ME!
      Returns:
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    • getAvrConvexity

      public float[] getAvrConvexity()
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      Returns:
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    • getColorCopy

      public javax.vecmath.Color4f[] getColorCopy()
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      Returns:
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    • getColors

      public javax.vecmath.Color4f[] getColors()
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      Returns:
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    • getConnectivity

      public int[] getConnectivity()
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      Returns:
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    • getConnectivityCopy

      public int[] getConnectivityCopy()
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      Returns:
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    • getCylinderCoordinates

      public javax.vecmath.Point3f[] getCylinderCoordinates()
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      Returns:
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    • getDistance

      public float getDistance(int iV0, int iV1)
      Vertex-vertex distance measured along the shortest edge-path connecting the two vertices.
      Parameters:
      iV0 - DOCUMENT ME!
      iV1 - DOCUMENT ME!
      Returns:
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    • getDistanceMap

      public HashMap getDistanceMap()
      access to the distance map - stored in map from MjEdgeKey to Float.
      Returns:
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    • getEdges

      public MjCorticalMesh.Edge[] getEdges()
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      Returns:
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    • getEQuantity

      public int getEQuantity()
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      Returns:
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    • getLatitude

      public MjCorticalMesh.Polylines getLatitude(float fZNormal, float fMBias, float fSBias, float fPBias)
      Produce polylines that are superimposed on the input cortical mesh, sphere, and plane. The znormal value indicates the z-slice on the unit sphere that is mapped to the polyline on the mesh. This value is in (-1,1). The angle value indicates the theta-slice on the unit sphere, theta measured as a positive angle counterclockwise from the x-axis towards the y-axis. This value is in [0,2*pi]. The bias value adds a small amount to the polyline to raise it above the mesh surface to avoid z-buffer fighting.
      Parameters:
      fZNormal - DOCUMENT ME!
      fMBias - DOCUMENT ME!
      fSBias - DOCUMENT ME!
      fPBias - DOCUMENT ME!
      Returns:
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    • getLongitude

      public MjCorticalMesh.Polylines getLongitude(float fAngle, float fMBias, float fSBias, float fPBias)
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      Parameters:
      fAngle - DOCUMENT ME!
      fMBias - DOCUMENT ME!
      fSBias - DOCUMENT ME!
      fPBias - DOCUMENT ME!
      Returns:
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    • getMaxAvrConvexity

      public float getMaxAvrConvexity()
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      Returns:
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    • getMaxDistance

      public float getMaxDistance()
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      Returns:
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    • getMaxMeanCurvature

      public float getMaxMeanCurvature()
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      Returns:
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    • getMeanCurvature

      public float[] getMeanCurvature()
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      Returns:
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    • getMinAvrConvexity

      public float getMinAvrConvexity()
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      Returns:
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    • getMinDistance

      public float getMinDistance()
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      Returns:
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    • getMinMeanCurvature

      public float getMinMeanCurvature()
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      Returns:
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    • getNormalCopy

      public javax.vecmath.Vector3f[] getNormalCopy()
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      Returns:
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    • getNormals

      public MjVector3f[] getNormals()
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      Returns:
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    • getPlaneCoordinates

      public javax.vecmath.Point2f[] getPlaneCoordinates()
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      Returns:
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    • getPlaneMax

      public javax.vecmath.Point2f getPlaneMax()
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      Returns:
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    • getPlaneMin

      public javax.vecmath.Point2f getPlaneMin()
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      Returns:
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    • getPointCopy

      public javax.vecmath.Point3f[] getPointCopy()
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      Returns:
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    • getPoints

      public javax.vecmath.Point3f[] getPoints()
      attribute member access.
      Returns:
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    • getSphereCoordinates

      public javax.vecmath.Point3f[] getSphereCoordinates()
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      Returns:
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    • getSurfaceArea

      public float getSurfaceArea()
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      Returns:
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    • getTQuantity

      public int getTQuantity()
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      Returns:
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    • getTriangles

      public MjCorticalMesh.Triangle[] getTriangles()
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      Returns:
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    • getVertices

      public MjCorticalMesh.Vertex[] getVertices()
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      Returns:
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    • getVQuantity

      public int getVQuantity()
      topology member access.
      Returns:
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    • scaleToCube

      public float scaleToCube()
      uniformly scale points to [-1,1]^3, originally in [min,max]^3 returns 2D vector with (min,max) as the elements public Vector2f scaleToCube ().
      Returns:
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    • setPunctureTriangle

      public void setPunctureTriangle(int[] aiIndex)
      Set the index of the triangle used to "puncture" the mesh before the conformal mapping is computed. The triangle is found based on the three index values that describe the triangle:
      Parameters:
      aiIndex - DOCUMENT ME!

    • finalize

      protected void finalize() throws Throwable
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      Overrides:
      finalize in class Object
      Throws:
      Throwable - DOCUMENT ME!

    • contains

      private static boolean contains(javax.vecmath.Point2f[] akVertex, javax.vecmath.Point2f kP)
      support for point-in-triangle tests; The akVertex array must have length 3.
      Parameters:
      akVertex - DOCUMENT ME!
      kP - DOCUMENT ME!
      Returns:
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    • computeDistance

      private void computeDistance(int iSize, int iSource, boolean bInitiator)
      compute distances within specified neighborhood size (size >= 1).
      Parameters:
      iSize - DOCUMENT ME!
      iSource - DOCUMENT ME!
      bInitiator - DOCUMENT ME!

    • computeExtremes

      private void computeExtremes()
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    • computeRadius

      private float computeRadius(MjVector2f kV0, MjVector2f kV1, MjVector2f kV2, float fAreaFraction)
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      Parameters:
      kV0 - DOCUMENT ME!
      kV1 - DOCUMENT ME!
      kV2 - DOCUMENT ME!
      fAreaFraction - DOCUMENT ME!
      Returns:
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    • doInflationStep

      private float doInflationStep()
      surface inflation.
      Returns:
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    • getBarycentric

      private javax.vecmath.Point3f getBarycentric(javax.vecmath.Point2f kP, int i)
      Support for conformal mapping to planar triangle mesh. Once the containing triangle i is found, compute the barycentric coordinates of P relative to the triangle vertices V0, V1, and V2.
      Parameters:
      kP - DOCUMENT ME!
      i - DOCUMENT ME!
      Returns:
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    • getContainingTriangle

      private int getContainingTriangle(javax.vecmath.Point2f kP, int iStart)
      Support for conformal mapping to planar triangle mesh. Use a linear walk to locate a triangle containing P. The index of such a triangle is returned, unless there is no containing triangle in which case the return value is -1. The "start" index is the suggested starting triangle. When testing a lot of points that are ordered in some spatial manner, the chance that the triangle containing the previous test point will contain the next test point (or a neighbor might contain it). Taking advantage of spatial coherence should speed up the search in "batch mode".
      Parameters:
      kP - DOCUMENT ME!
      iStart - DOCUMENT ME!
      Returns:
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    • getStereographicRadius

      private float getStereographicRadius()
      support for unfolding.
      Returns:
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