java.lang.Object
- gov.nih.mipav.view.renderer.WildMagic.brainflattenerview_WM.MjCorticalMesh_WM

public class MjCorticalMesh_WM
extends java.lang.Object

Nested Class Summary

Nested Classes
Modifier and Type Class Description

static class MjCorticalMesh_WM.Polylines
DOCUMENT ME!

Field Summary

Fields
Modifier and Type	Field	Description
`private float[]`	`m_afAvrConvexity`	DOCUMENT ME!
`private float[]`	`m_afMeanCurvature`	DOCUMENT ME!
`private WildMagic.LibFoundation.Mathematics.Vector3f[]`	`m_akCylinder`	projection of sphere onto cylinder.
`private WildMagic.LibFoundation.Meshes.BasicMesh.Edge[]`	`m_akEdge`	DOCUMENT ME!
`private WildMagic.LibFoundation.Mathematics.Vector2f[]`	`m_akPlane`	Conformal mapping to a plane.
`private WildMagic.LibFoundation.Mathematics.Vector3f[]`	`m_akPoint`
`private WildMagic.LibFoundation.Mathematics.Vector3f[]`	`m_akSphere`	Conformal mapping to a sphere. rho is the radius of the stereographic sphere.
`private WildMagic.LibFoundation.Meshes.BasicMesh.Triangle[]`	`m_akTriangle`	DOCUMENT ME!
`private WildMagic.LibFoundation.Meshes.BasicMesh.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 WildMagic.LibFoundation.Meshes.BasicMesh`	`m_kBasicMesh`
`private WildMagic.LibGraphics.SceneGraph.TriMesh`	`m_kCylinderMesh`
`private java.util.HashMap<WildMagic.LibFoundation.Meshes.EdgeKey,java.lang.Float>`	`m_kDistance`	vertex-vertex distances measured along edge paths.
`private java.util.HashMap<WildMagic.LibFoundation.Meshes.EdgeKey,java.lang.Float>`	`m_kInitDistance`	surface inflation.
`private WildMagic.LibGraphics.SceneGraph.TriMesh`	`m_kMesh`
`private WildMagic.LibGraphics.SceneGraph.TriMesh`	`m_kSphereMesh`

Constructor Summary

Constructors
Constructor	Description
`MjCorticalMesh_WM(WildMagic.LibGraphics.SceneGraph.TriMesh kMesh, WildMagic.LibFoundation.Mathematics.Vector3f kCenter)`	Creates a new MjCorticalMesh object.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`boolean`	`CheckManifold()`
`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.
`void`	`computeSurfaceArea()`	surface area of the mesh (input mesh is closed, manifold).
`private static boolean`	`contains(WildMagic.LibFoundation.Mathematics.Vector2f[] akVertex, WildMagic.LibFoundation.Mathematics.Vector2f 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 WildMagic.LibFoundation.Mathematics.Vector3f`	`getBarycentric(WildMagic.LibFoundation.Mathematics.Vector2f kP, int i)`	Support for conformal mapping to planar triangle mesh.
`private int`	`getContainingTriangle(WildMagic.LibFoundation.Mathematics.Vector2f kP, int iStart)`	Support for conformal mapping to planar triangle mesh.
`WildMagic.LibGraphics.SceneGraph.TriMesh`	`getCylinder()`	DOCUMENT ME!
`WildMagic.LibFoundation.Mathematics.Vector3f[]`	`getCylinderCoordinates()`	DOCUMENT ME!
`float`	`getDistance(int iV0, int iV1)`	Vertex-vertex distance measured along the shortest edge-path connecting the two vertices.
`MjCorticalMesh_WM.Polylines`	`getLatitude(float fZNormal, float fMBias, float fSBias, float fPBias)`	Produce polylines that are superimposed on the input cortical mesh, sphere, and plane.
`MjCorticalMesh_WM.Polylines`	`getLongitude(float fAngle, float fMBias, float fSBias, float fPBias)`	DOCUMENT ME!
`float`	`getMaxMeanCurvature()`	DOCUMENT ME!
`float[]`	`getMeanCurvature()`	DOCUMENT ME!
`WildMagic.LibGraphics.SceneGraph.TriMesh`	`getMesh()`
`float`	`getMinMeanCurvature()`	DOCUMENT ME!
`WildMagic.LibGraphics.SceneGraph.TriMesh`	`getSphere()`	DOCUMENT ME!
`private float`	`getStereographicRadius()`	support for unfolding.
`float`	`getSurfaceArea()`	DOCUMENT ME!
`int`	`getVQuantity()`
`void`	`setColor(int i, float fRed, float fGreen, float fBlue)`
`void`	`setPunctureTriangle(int[] aiIndex)`	Set the index of the triangle used to "puncture" the mesh before the conformal mapping is computed.
`void`	`updateMesh(boolean bUpdateNormals)`

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_akCylinder
```
private WildMagic.LibFoundation.Mathematics.Vector3f[] m_akCylinder
```
    projection of sphere onto cylinder.
  - m_akEdge
```
private WildMagic.LibFoundation.Meshes.BasicMesh.Edge[] m_akEdge
```
    DOCUMENT ME!
  - m_akPlane
```
private WildMagic.LibFoundation.Mathematics.Vector2f[] m_akPlane
```
    Conformal mapping to a plane. The (u,v) points correspond to the (x,y,z) mesh points.
  - m_akSphere
```
private WildMagic.LibFoundation.Mathematics.Vector3f[] m_akSphere
```
    Conformal mapping to a sphere. rho is the radius of the stereographic sphere.
  - m_akTriangle
```
private WildMagic.LibFoundation.Meshes.BasicMesh.Triangle[] m_akTriangle
```
    DOCUMENT ME!
  - m_akVertex
```
private WildMagic.LibFoundation.Meshes.BasicMesh.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_kDistance
```
private java.util.HashMap<WildMagic.LibFoundation.Meshes.EdgeKey,java.lang.Float> m_kDistance
```
    vertex-vertex distances measured along edge paths.
  - m_kInitDistance
```
private java.util.HashMap<WildMagic.LibFoundation.Meshes.EdgeKey,java.lang.Float> m_kInitDistance
```
    surface inflation.
  - m_kMesh
```
private WildMagic.LibGraphics.SceneGraph.TriMesh m_kMesh
```
  - m_kBasicMesh
```
private WildMagic.LibFoundation.Meshes.BasicMesh m_kBasicMesh
```
  - m_akPoint
```
private WildMagic.LibFoundation.Mathematics.Vector3f[] m_akPoint
```
  - m_kSphereMesh
```
private WildMagic.LibGraphics.SceneGraph.TriMesh m_kSphereMesh
```
  - m_kCylinderMesh
```
private WildMagic.LibGraphics.SceneGraph.TriMesh m_kCylinderMesh
```
- Constructor Detail
  - MjCorticalMesh_WM
```
public MjCorticalMesh_WM(WildMagic.LibGraphics.SceneGraph.TriMesh kMesh,
                         WildMagic.LibFoundation.Mathematics.Vector3f kCenter)
```
    Creates a new MjCorticalMesh object.
- Method Detail
  - contains
```
private static boolean contains(WildMagic.LibFoundation.Mathematics.Vector2f[] akVertex,
                                WildMagic.LibFoundation.Mathematics.Vector2f kP)
```
    support for point-in-triangle tests; The akVertex array must have length 3.
    
    Parameters:
    
    akVertex - DOCUMENT ME!
    
    kP - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - CheckManifold
```
public boolean CheckManifold()
```
  - 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!
  - getCylinder
```
public WildMagic.LibGraphics.SceneGraph.TriMesh getCylinder()
```
    DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - getCylinderCoordinates
```
public WildMagic.LibFoundation.Mathematics.Vector3f[] 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!
  - getLatitude
```
public MjCorticalMesh_WM.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_WM.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!
  - getMaxMeanCurvature
```
public float getMaxMeanCurvature()
```
    DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - getMeanCurvature
```
public float[] getMeanCurvature()
```
    DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - getMesh
```
public WildMagic.LibGraphics.SceneGraph.TriMesh getMesh()
```
  - getMinMeanCurvature
```
public float getMinMeanCurvature()
```
    DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - getSphere
```
public WildMagic.LibGraphics.SceneGraph.TriMesh getSphere()
```
    DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - getSurfaceArea
```
public float getSurfaceArea()
```
    DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - getVQuantity
```
public int getVQuantity()
```
  - setColor
```
public void setColor(int i,
                     float fRed,
                     float fGreen,
                     float fBlue)
```
  - 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!
  - updateMesh
```
public void updateMesh(boolean bUpdateNormals)
```
  - 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!
  - doInflationStep
```
private float doInflationStep()
```
    surface inflation.
    
    Returns:
    
    DOCUMENT ME!
  - getBarycentric
```
private WildMagic.LibFoundation.Mathematics.Vector3f getBarycentric(WildMagic.LibFoundation.Mathematics.Vector2f 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(WildMagic.LibFoundation.Mathematics.Vector2f 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!
  - finalize
```
protected void finalize()
                 throws java.lang.Throwable
```
    DOCUMENT ME!
    
    Overrides:
    
    finalize in class java.lang.Object
    
    Throws:
    
    java.lang.Throwable - DOCUMENT ME!

Class MjCorticalMesh_WM

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

m_afAvrConvexity

m_afMeanCurvature

m_akCylinder

m_akEdge

m_akPlane

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_kDistance

m_kInitDistance

m_kMesh

m_kBasicMesh

m_akPoint

m_kSphereMesh

m_kCylinderMesh

Constructor Detail

MjCorticalMesh_WM

Method Detail

contains

CheckManifold

computeConformalMapping

computeDistances

computeMeanCurvature

computeNormals

computeSurfaceArea

disposeLocal

doInflation

getAvrConvexity

getCylinder

getCylinderCoordinates

getDistance

getLatitude

getLongitude

getMaxMeanCurvature

getMeanCurvature

getMesh

getMinMeanCurvature

getSphere

getSurfaceArea

getVQuantity

setColor

setPunctureTriangle

updateMesh

computeDistance

computeExtremes

doInflationStep

getBarycentric

getContainingTriangle

getStereographicRadius

finalize