java.lang.Object
- gov.nih.mipav.view.renderer.J3D.surfaceview.brainflattenerview.MjCorticalMesh

public class MjCorticalMesh
extends java.lang.Object

DOCUMENT ME!

Nested Class Summary

Nested Classes
Modifier and Type	Class	Description
`static class`	`MjCorticalMesh.Edge`	DOCUMENT ME!
`static class`	`MjCorticalMesh.Polylines`	DOCUMENT ME!
`static class`	`MjCorticalMesh.Triangle`	DOCUMENT ME!
`static class`	`MjCorticalMesh.Vertex`	DOCUMENT ME!

Field Summary

Fields
Modifier and Type	Field	Description
`private float[]`	`m_afAvrConvexity`	DOCUMENT ME!
`private float[]`	`m_afMeanCurvature`	DOCUMENT ME!
`private int[]`	`m_aiConnect`	DOCUMENT ME!
`private javax.vecmath.Color4f[]`	`m_akColor`	DOCUMENT ME!
`private javax.vecmath.Point3f[]`	`m_akCylinder`	projection of sphere onto cylinder.
`private MjCorticalMesh.Edge[]`	`m_akEdge`	DOCUMENT ME!
`private MjVector3f[]`	`m_akNormal`	DOCUMENT ME!
`private javax.vecmath.Point2f[]`	`m_akPlane`	Conformal mapping to a plane.
`private javax.vecmath.Point3f[]`	`m_akPoint`	mesh attributes.
`private javax.vecmath.Point3f[]`	`m_akSphere`	Conformal mapping to a sphere. rho is the radius of the stereographic sphere.
`private MjCorticalMesh.Triangle[]`	`m_akTriangle`	DOCUMENT ME!
`private MjCorticalMesh.Vertex[]`	`m_akVertex`	DOCUMENT ME!
`private float`	`m_fMaxAvrConvexity`	DOCUMENT ME!
`private float`	`m_fMaxDistance`	DOCUMENT ME!
`private float`	`m_fMaxMeanCurvature`	DOCUMENT ME!
`private float`	`m_fMinAvrConvexity`	DOCUMENT ME!
`private float`	`m_fMinDistance`	DOCUMENT ME!
`private float`	`m_fMinMeanCurvature`	DOCUMENT ME!
`private float`	`m_fRho`	DOCUMENT ME!
`private float`	`m_fSurfaceArea`	DOCUMENT ME!
`private int`	`m_iEQuantity`	DOCUMENT ME!
`private int`	`m_iPunctureTri`	The index of the puncture triangle for computing the conformal mapping:.
`private int`	`m_iTQuantity`	DOCUMENT ME!
`private int`	`m_iVQuantity`	mesh topology.
`private java.util.HashMap`	`m_kDistance`	vertex-vertex distances measured along edge paths.
`private java.util.HashMap`	`m_kInitDistance`	surface inflation.
`private javax.vecmath.Point2f`	`m_kPlaneMax`	DOCUMENT ME!
`private javax.vecmath.Point2f`	`m_kPlaneMin`	DOCUMENT ME!

Constructor Summary

Constructors
Constructor	Description
`MjCorticalMesh(int iVQuantity, javax.vecmath.Point3f[] akPoint, int iTQuantity, int[] aiConnect)`	Creates a new MjCorticalMesh object.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`computeConformalMapping()`	conformal mapping of mesh to plane and sphere, projection to cylinder.
`private void`	`computeDistance(int iSize, int iSource, boolean bInitiator)`	compute distances within specified neighborhood size (size >= 1).
`void`	`computeDistances(int iSize)`	Computes the distances of vertex pairs for which an edge-path exists with at most iSize edges.
`private void`	`computeExtremes()`	DOCUMENT ME!
`void`	`computeMeanCurvature()`	mean curvature.
`void`	`computeNormals()`	compute vertex normals as averages of triangle normals.
`private float`	`computeRadius(MjVector2f kV0, MjVector2f kV1, MjVector2f kV2, float fAreaFraction)`	DOCUMENT ME!
`void`	`computeSurfaceArea()`	surface area of the mesh (input mesh is closed, manifold).
`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.
`void`	`disposeLocal()`	DOCUMENT ME!
`float`	`doInflation(int iOperation)`	surface inflation operation 0 = initialize 1 = inflate 2 = terminate.
`private float`	`doInflationStep()`	surface inflation.
`protected void`	`finalize()`	DOCUMENT ME!
`float[]`	`getAvrConvexity()`	DOCUMENT ME!
`private javax.vecmath.Point3f`	`getBarycentric(javax.vecmath.Point2f kP, int i)`	Support for conformal mapping to planar triangle mesh.
`javax.vecmath.Color4f[]`	`getColorCopy()`	DOCUMENT ME!
`javax.vecmath.Color4f[]`	`getColors()`	DOCUMENT ME!
`int[]`	`getConnectivity()`	DOCUMENT ME!
`int[]`	`getConnectivityCopy()`	DOCUMENT ME!
`private int`	`getContainingTriangle(javax.vecmath.Point2f kP, int iStart)`	Support for conformal mapping to planar triangle mesh.
`javax.vecmath.Point3f[]`	`getCylinderCoordinates()`	DOCUMENT ME!
`float`	`getDistance(int iV0, int iV1)`	Vertex-vertex distance measured along the shortest edge-path connecting the two vertices.
`java.util.HashMap`	`getDistanceMap()`	access to the distance map - stored in map from MjEdgeKey to Float.
`MjCorticalMesh.Edge[]`	`getEdges()`	DOCUMENT ME!
`int`	`getEQuantity()`	DOCUMENT ME!
`MjCorticalMesh.Polylines`	`getLatitude(float fZNormal, float fMBias, float fSBias, float fPBias)`	Produce polylines that are superimposed on the input cortical mesh, sphere, and plane.
`MjCorticalMesh.Polylines`	`getLongitude(float fAngle, float fMBias, float fSBias, float fPBias)`	DOCUMENT ME!
`float`	`getMaxAvrConvexity()`	DOCUMENT ME!
`float`	`getMaxDistance()`	DOCUMENT ME!
`float`	`getMaxMeanCurvature()`	DOCUMENT ME!
`float[]`	`getMeanCurvature()`	DOCUMENT ME!
`float`	`getMinAvrConvexity()`	DOCUMENT ME!
`float`	`getMinDistance()`	DOCUMENT ME!
`float`	`getMinMeanCurvature()`	DOCUMENT ME!
`javax.vecmath.Vector3f[]`	`getNormalCopy()`	DOCUMENT ME!
`MjVector3f[]`	`getNormals()`	DOCUMENT ME!
`javax.vecmath.Point2f[]`	`getPlaneCoordinates()`	DOCUMENT ME!
`javax.vecmath.Point2f`	`getPlaneMax()`	DOCUMENT ME!
`javax.vecmath.Point2f`	`getPlaneMin()`	DOCUMENT ME!
`javax.vecmath.Point3f[]`	`getPointCopy()`	DOCUMENT ME!
`javax.vecmath.Point3f[]`	`getPoints()`	attribute member access.
`javax.vecmath.Point3f[]`	`getSphereCoordinates()`	DOCUMENT ME!
`private float`	`getStereographicRadius()`	support for unfolding.
`float`	`getSurfaceArea()`	DOCUMENT ME!
`int`	`getTQuantity()`	DOCUMENT ME!
`MjCorticalMesh.Triangle[]`	`getTriangles()`	DOCUMENT ME!
`MjCorticalMesh.Vertex[]`	`getVertices()`	DOCUMENT ME!
`int`	`getVQuantity()`	topology member access.
`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 ().
`void`	`setPunctureTriangle(int[] aiIndex)`	Set the index of the triangle used to "puncture" the mesh before the conformal mapping is computed.

Methods inherited from class java.lang.Object
clone, equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - m_afAvrConvexity
```
private float[] m_afAvrConvexity
```
    DOCUMENT ME!
  - m_afMeanCurvature
```
private float[] m_afMeanCurvature
```
    DOCUMENT ME!
  - m_aiConnect
```
private int[] m_aiConnect
```
    DOCUMENT ME!
  - m_akColor
```
private javax.vecmath.Color4f[] m_akColor
```
    DOCUMENT ME!
  - m_akCylinder
```
private javax.vecmath.Point3f[] m_akCylinder
```
    projection of sphere onto cylinder.
  - m_akEdge
```
private MjCorticalMesh.Edge[] m_akEdge
```
    DOCUMENT ME!
  - m_akNormal
```
private MjVector3f[] m_akNormal
```
    DOCUMENT ME!
  - 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
```
    DOCUMENT ME!
  - m_akVertex
```
private MjCorticalMesh.Vertex[] m_akVertex
```
    DOCUMENT ME!
  - m_fMaxAvrConvexity
```
private float m_fMaxAvrConvexity
```
    DOCUMENT ME!
  - m_fMaxDistance
```
private float m_fMaxDistance
```
    DOCUMENT ME!
  - m_fMaxMeanCurvature
```
private float m_fMaxMeanCurvature
```
    DOCUMENT ME!
  - m_fMinAvrConvexity
```
private float m_fMinAvrConvexity
```
    DOCUMENT ME!
  - m_fMinDistance
```
private float m_fMinDistance
```
    DOCUMENT ME!
  - m_fMinMeanCurvature
```
private float m_fMinMeanCurvature
```
    DOCUMENT ME!
  - m_fRho
```
private float m_fRho
```
    DOCUMENT ME!
  - m_fSurfaceArea
```
private float m_fSurfaceArea
```
    DOCUMENT ME!
  - m_iEQuantity
```
private int m_iEQuantity
```
    DOCUMENT ME!
  - m_iPunctureTri
```
private int m_iPunctureTri
```
    The index of the puncture triangle for computing the conformal mapping:.
  - m_iTQuantity
```
private int m_iTQuantity
```
    DOCUMENT ME!
  - m_iVQuantity
```
private int m_iVQuantity
```
    mesh topology.
  - m_kDistance
```
private java.util.HashMap m_kDistance
```
    vertex-vertex distances measured along edge paths.
  - m_kInitDistance
```
private java.util.HashMap m_kInitDistance
```
    surface inflation.
  - m_kPlaneMax
```
private javax.vecmath.Point2f m_kPlaneMax
```
    DOCUMENT ME!
  - m_kPlaneMin
```
private javax.vecmath.Point2f m_kPlaneMin
```
    DOCUMENT ME!
- Constructor Detail
  - 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 Detail
  - 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 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()
```
    DOCUMENT ME!
  - doInflation
```
public float doInflation(int iOperation)
```
    surface inflation operation 0 = initialize 1 = inflate 2 = terminate.
    
    Parameters:
    
    iOperation - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - getAvrConvexity
```
public float[] getAvrConvexity()
```
    DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - getColorCopy
```
public javax.vecmath.Color4f[] getColorCopy()
```
    DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - getColors
```
public javax.vecmath.Color4f[] getColors()
```
    DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - getConnectivity
```
public int[] getConnectivity()
```
    DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - getConnectivityCopy
```
public int[] getConnectivityCopy()
```
    DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - getCylinderCoordinates
```
public javax.vecmath.Point3f[] getCylinderCoordinates()
```
    DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - 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:
    
    DOCUMENT ME!
  - getDistanceMap
```
public java.util.HashMap getDistanceMap()
```
    access to the distance map - stored in map from MjEdgeKey to Float.
    
    Returns:
    
    DOCUMENT ME!
  - getEdges
```
public MjCorticalMesh.Edge[] getEdges()
```
    DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - getEQuantity
```
public int getEQuantity()
```
    DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - 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:
    
    DOCUMENT ME!
  - getLongitude
```
public MjCorticalMesh.Polylines getLongitude(float fAngle,
                                             float fMBias,
                                             float fSBias,
                                             float fPBias)
```
    DOCUMENT ME!
    
    Parameters:
    
    fAngle - DOCUMENT ME!
    
    fMBias - DOCUMENT ME!
    
    fSBias - DOCUMENT ME!
    
    fPBias - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - getMaxAvrConvexity
```
public float getMaxAvrConvexity()
```
    DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - getMaxDistance
```
public float getMaxDistance()
```
    DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - getMaxMeanCurvature
```
public float getMaxMeanCurvature()
```
    DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - getMeanCurvature
```
public float[] getMeanCurvature()
```
    DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - getMinAvrConvexity
```
public float getMinAvrConvexity()
```
    DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - getMinDistance
```
public float getMinDistance()
```
    DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - getMinMeanCurvature
```
public float getMinMeanCurvature()
```
    DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - getNormalCopy
```
public javax.vecmath.Vector3f[] getNormalCopy()
```
    DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - getNormals
```
public MjVector3f[] getNormals()
```
    DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - getPlaneCoordinates
```
public javax.vecmath.Point2f[] getPlaneCoordinates()
```
    DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - getPlaneMax
```
public javax.vecmath.Point2f getPlaneMax()
```
    DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - getPlaneMin
```
public javax.vecmath.Point2f getPlaneMin()
```
    DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - getPointCopy
```
public javax.vecmath.Point3f[] getPointCopy()
```
    DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - getPoints
```
public javax.vecmath.Point3f[] getPoints()
```
    attribute member access.
    
    Returns:
    
    DOCUMENT ME!
  - getSphereCoordinates
```
public javax.vecmath.Point3f[] getSphereCoordinates()
```
    DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - getSurfaceArea
```
public float getSurfaceArea()
```
    DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - getTQuantity
```
public int getTQuantity()
```
    DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - getTriangles
```
public MjCorticalMesh.Triangle[] getTriangles()
```
    DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - getVertices
```
public MjCorticalMesh.Vertex[] getVertices()
```
    DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - getVQuantity
```
public int getVQuantity()
```
    topology member access.
    
    Returns:
    
    DOCUMENT ME!
  - 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:
    
    DOCUMENT ME!
  - 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 java.lang.Throwable
```
    DOCUMENT ME!
    
    Overrides:
    
    finalize in class java.lang.Object
    
    Throws:
    
    java.lang.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:
    
    DOCUMENT ME!
  - 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()
```
    DOCUMENT ME!
  - computeRadius
```
private float computeRadius(MjVector2f kV0,
                            MjVector2f kV1,
                            MjVector2f kV2,
                            float fAreaFraction)
```
    DOCUMENT ME!
    
    Parameters:
    
    kV0 - DOCUMENT ME!
    
    kV1 - DOCUMENT ME!
    
    kV2 - DOCUMENT ME!
    
    fAreaFraction - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - doInflationStep
```
private float doInflationStep()
```
    surface inflation.
    
    Returns:
    
    DOCUMENT ME!
  - 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:
    
    DOCUMENT ME!
  - 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:
    
    DOCUMENT ME!
  - getStereographicRadius
```
private float getStereographicRadius()
```
    support for unfolding.
    
    Returns:
    
    DOCUMENT ME!

Class MjCorticalMesh

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

m_afAvrConvexity

m_afMeanCurvature

m_aiConnect

m_akColor

m_akCylinder

m_akEdge

m_akNormal

m_akPlane

m_akPoint

m_akSphere

m_akTriangle

m_akVertex

m_fMaxAvrConvexity

m_fMaxDistance

m_fMaxMeanCurvature

m_fMinAvrConvexity

m_fMinDistance

m_fMinMeanCurvature

m_fRho

m_fSurfaceArea

m_iEQuantity

m_iPunctureTri

m_iTQuantity

m_iVQuantity

m_kDistance

m_kInitDistance

m_kPlaneMax

m_kPlaneMin

Constructor Detail

MjCorticalMesh

Method Detail

computeConformalMapping

computeDistances

computeMeanCurvature

computeNormals

computeSurfaceArea

disposeLocal

doInflation

getAvrConvexity

getColorCopy

getColors

getConnectivity

getConnectivityCopy

getCylinderCoordinates

getDistance

getDistanceMap

getEdges

getEQuantity

getLatitude

getLongitude

getMaxAvrConvexity

getMaxDistance

getMaxMeanCurvature

getMeanCurvature

getMinAvrConvexity

getMinDistance

getMinMeanCurvature

getNormalCopy

getNormals

getPlaneCoordinates

getPlaneMax

getPlaneMin

getPointCopy

getPoints

getSphereCoordinates

getSurfaceArea

getTQuantity

getTriangles

getVertices

getVQuantity

scaleToCube

setPunctureTriangle

finalize