java.lang.Object
- javax.media.j3d.SceneGraphObject
- - javax.media.j3d.NodeComponent
  - - javax.media.j3d.Geometry
    - - javax.media.j3d.GeometryArray
      - javax.media.j3d.IndexedGeometryArray
        
        javax.media.j3d.IndexedTriangleArray
        
        gov.nih.mipav.view.renderer.J3D.model.structures.ModelTriangleMesh

```
public class ModelTriangleMesh
extends javax.media.j3d.IndexedTriangleArray
```
A simple triangle mesh that represents a level surface. The mesh only stores vertex positions and vertex normals. The surface viewer creates a Shape3D object whose geometry is an object from ModelTriangleMesh. The surface color is provided by attaching to the Shape3D object an appearance that contains a material. The vertex normals in ModelTriangleMesh are used by the lighting system in conjunction with the surface material to produce the surface color.

Nested Class Summary

Nested Classes
Modifier and Type	Class	Description
`protected class`	`ModelTriangleMesh.Edge`	A representation of an edge for the vertex-edge-triangle table.
`class`	`ModelTriangleMesh.UnorderedSetInt`	DOCUMENT ME!

Field Summary

Fields
Modifier and Type	Field	Description
`private static float[]`	`box`	DOCUMENT ME!
`protected double[][]`	`cellData`	support for vtk
`private java.util.HashSet[]`	`connections`	used in smoothing.
`private static int[]`	`direction`	DOCUMENT ME!
`(package private) java.lang.Integer`	`kInvalid`	DOCUMENT ME!
`(package private) float[]`	`m_afCurvature`	DOCUMENT ME!
`(package private) ModelTriangleMesh.UnorderedSetInt[]`	`m_akAdjacent`	DOCUMENT ME!
`(package private) javax.vecmath.Vector3f[]`	`m_akSNormal`	DOCUMENT ME!
`(package private) javax.vecmath.Vector3f[]`	`m_akSTangent`	DOCUMENT ME!
`(package private) javax.vecmath.Vector3f[]`	`m_akVMean`	DOCUMENT ME!
`(package private) javax.vecmath.Vector3f[]`	`m_akVNormal`	DOCUMENT ME!
`(package private) float`	`m_fEParam`	DOCUMENT ME!
`(package private) float`	`m_fFParam`	DOCUMENT ME!
`(package private) float`	`m_fMeanEdgeLength`	DOCUMENT ME!
`(package private) float`	`m_fStiffness`	DOCUMENT ME!
`private float`	`m_fTransparency`	store the mesh transparency:
`private javax.vecmath.Color4f[]`	`m_kColors`	Store the mesh colors:
`private javax.vecmath.Vector3f`	`m_kE0`	DOCUMENT ME!
`private javax.vecmath.Vector3f`	`m_kE1`	DOCUMENT ME!
`(package private) java.util.HashMap`	`m_kEMap`	DOCUMENT ME!
`private java.lang.Object`	`m_kGenerator`	The ModelClodMesh object that generated the ModelTriangleMesh object, null otherwise.
`private javax.media.j3d.Material`	`m_kMaterial`	store the Material properties of the mesh:
`private javax.vecmath.Vector3f`	`m_kN`	DOCUMENT ME!
`private javax.vecmath.Point3f`	`m_kV0`	temporary variables to avoid 'new' calls.
`private javax.vecmath.Point3f`	`m_kV1`	temporary variables to avoid 'new' calls.
`private javax.vecmath.Point3f`	`m_kV2`	temporary variables to avoid 'new' calls.
`private javax.vecmath.Point3f`	`m_kV3`	temporary variables to avoid 'new' calls.
`private javax.vecmath.Color4f[]`	`perVertexColor`	Per vertex color array, which store the color data saved in .sur file.
`private static float[]`	`startLocation`	DOCUMENT ME!
`protected double[][]`	`vertexData`	support for vtk

Fields inherited from class javax.media.j3d.IndexedGeometryArray
ALLOW_COLOR_INDEX_READ, ALLOW_COLOR_INDEX_WRITE, ALLOW_COORDINATE_INDEX_READ, ALLOW_COORDINATE_INDEX_WRITE, ALLOW_NORMAL_INDEX_READ, ALLOW_NORMAL_INDEX_WRITE, ALLOW_TEXCOORD_INDEX_READ, ALLOW_TEXCOORD_INDEX_WRITE, ALLOW_VERTEX_ATTR_INDEX_READ, ALLOW_VERTEX_ATTR_INDEX_WRITE

Fields inherited from class javax.media.j3d.GeometryArray
ALLOW_COLOR_READ, ALLOW_COLOR_WRITE, ALLOW_COORDINATE_READ, ALLOW_COORDINATE_WRITE, ALLOW_COUNT_READ, ALLOW_COUNT_WRITE, ALLOW_FORMAT_READ, ALLOW_NORMAL_READ, ALLOW_NORMAL_WRITE, ALLOW_REF_DATA_READ, ALLOW_REF_DATA_WRITE, ALLOW_TEXCOORD_READ, ALLOW_TEXCOORD_WRITE, ALLOW_VERTEX_ATTR_READ, ALLOW_VERTEX_ATTR_WRITE, BY_REFERENCE, BY_REFERENCE_INDICES, COLOR_3, COLOR_4, COORDINATES, INTERLEAVED, NORMALS, TEXTURE_COORDINATE_2, TEXTURE_COORDINATE_3, TEXTURE_COORDINATE_4, USE_COORD_INDEX_ONLY, USE_NIO_BUFFER, VERTEX_ATTRIBUTES

Fields inherited from class javax.media.j3d.Geometry
ALLOW_INTERSECT

Constructor Summary

Constructors
Constructor	Description
`ModelTriangleMesh(ModelTriangleMesh kMesh)`	Copies a ModelTriangleMesh by copying it's components.
`ModelTriangleMesh(javax.vecmath.Point3f[] akVertex, int[] aiConnect)`	A triangle mesh whose vertex normal vectors are computed from the geometry of the mesh itself.
`ModelTriangleMesh(javax.vecmath.Point3f[] akVertex, javax.vecmath.Vector3f[] akNormal, int[] aiConnect)`	A triangle mesh whose vertex normal vectors have been precomputed.
`ModelTriangleMesh(javax.vecmath.Point3f[] akVertex, javax.vecmath.Vector3f[] akNormal, int[] aiConnect, javax.vecmath.Color4f[] vertexColor)`	A triangle mesh whose vertex normal vectors have been precomputed.
`ModelTriangleMesh(javax.vecmath.Point3f[] akVertex, javax.vecmath.Vector3f[] akNormal, javax.vecmath.Color4f[] akColor, int[] aiConnect)`	A triangle mesh whose vertex normal vectors have been precomputed.
`ModelTriangleMesh(javax.vecmath.Point3f[] akVertex, javax.vecmath.Vector3f[] akNormal, javax.vecmath.Color4f[] akColor, javax.vecmath.TexCoord3f[] akTexCoord, int[] aiConnect)`	A triangle mesh whose vertex normal vectors have been precomputed.
`ModelTriangleMesh(javax.vecmath.Point3f[] akVertex, javax.vecmath.Vector3f[] akNormal, javax.vecmath.TexCoord3f[] akTexCoord, int[] aiConnect)`	A triangle mesh whose vertex normal vectors have been precomputed.
`ModelTriangleMesh(WildMagic.LibFoundation.Mathematics.Vector3f[] akVertex, int[] aiConnect)`	A triangle mesh whose vertex normal vectors are computed from the geometry of the mesh itself.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`affineTransform(double[][] aafH)`	The input 4x4 homogeneous matrix H is assumed to multiply vectors V as H*V where V = (x,y,z,1).
`void`	`affineTransform(float[][] afRot, float[] afTrn, float[] afScale)`	Rotation R is 3x3, translation T is 3x1, and scale S is 3x1.
`float`	`area()`	Calculate the surface mesh area.
`private void`	`buildConnections()`	Builds a list of cross-references, so that connections[i] contains all the verticies that are connected to vertex at i.
`javax.vecmath.Point3f`	`center()`	Calculates and returns the center point of the Mesh:
`private void`	`computeMeanEdgeLength()`	Compute the average length of all the edges in the triangle mesh.
`void`	`computeNormals()`	A normal vector at a vertex is computed by averaging the triangle normals for all triangles sharing the vertex.
`private void`	`computeVertexInformation()`	Let V[i] be a vertex in the triangle mesh.
`private void`	`computeVertexNormals()`	Compute the vertex normals of the triangle mesh.
`double[][]`	`getCellData()`
`javax.vecmath.Color4f[]`	`getColorCopy()`	Make a copy of the colors of a triangle mesh.
`void`	`getColorLocal(int index, javax.vecmath.Color4f kColor)`	Gets the stored local color.
`ModelTriangleMesh[]`	`getComponents()`	Construct the connected components of the triangle mesh.
`void`	`getConsistentComponents()`	Construct the connected components of the triangle mesh.
`void`	`getCopies(javax.vecmath.Point3f[] akVertex, javax.vecmath.Vector3f[] akNormal, javax.vecmath.Color4f[] akColor, javax.vecmath.TexCoord3f[] akTexCoord)`	Copies the components of a ModelTriangleMesh into the parameters.
`static int[]`	`getDirection()`	DOCUMENT ME!
`java.lang.Object`	`getGenerator()`	Support for regenerating an ModelTriangleMesh from an ModelClodMesh whenever the level of detail is changed for the ModelClodMesh.
`int[]`	`getIndexCopy()`	Make a copy of the connectivity array of a triangle mesh.
`javax.media.j3d.Material`	`getMaterial()`	Gets the material properties of the mesh:
`javax.vecmath.Vector3f[]`	`getNormalCopy()`	Make a copy of the normals of a triangle mesh.
`javax.vecmath.Color4f[]`	`getPerVertexColor()`
`static float[]`	`getStartLocation()`	DOCUMENT ME!
`javax.vecmath.TexCoord3f[]`	`getTexCoordCopy()`	Make a copy of the texture coordinates of a triangle mesh.
`float`	`getTransparency()`	Gets the mesh transparency.
`javax.vecmath.Point3f[]`	`getVertexCopy()`	Make a copy of the vertices of a triangle mesh.
`WildMagic.LibFoundation.Mathematics.Vector3f[]`	`getVertexCopyAsVector3f()`	Make a copy of the vertices of a triangle mesh.
`double[][]`	`getVertexData()`
`double[]`	`getVertexData(int i)`
`private void`	`init()`	Initializes capabilities and temporary variables.
`void`	`invertMesh()`	Invert the mesh z-coord, reorder the triangles, and recompute the normals:
`static ModelTriangleMesh`	`loadTMesh(java.io.RandomAccessFile kIn, ViewJProgressBar progress, int added, int total, boolean isVisible)`	Load the triangle mesh from a binary file.
`static ModelTriangleMesh`	`loadTMesh(java.io.RandomAccessFile kIn, javax.swing.JProgressBar pBar, int added, int total)`	Load the triangle mesh from a binary file.
`static ModelTriangleMesh`	`loadVRMLMesh(java.io.RandomAccessFile kIn, ViewJProgressBar progress, int added, int total, boolean flag)`	Load the triangle mesh from a VRML file specifically written by MIPAV!.
`static ModelTriangleMesh`	`loadVTKLegacyMesh(java.io.RandomAccessFile kIn, ViewJProgressBar progress, int added, int total, boolean flag, java.lang.String fileName)`
`static ModelTriangleMesh`	`loadVTKXMLMesh(java.lang.String absPath, ViewJProgressBar progress, int added, int total, boolean flag, java.lang.String fileName, java.lang.String dir)`
`static int`	`parseVRMLMesh(java.io.RandomAccessFile kIn)`	Parses the VRML to see how many surfaces there are.
`protected void`	`print(java.io.PrintWriter kOut)`	Internal support for 'void print (String)' and 'void print (String, ModelTriangleMesh[])'.
`protected void`	`printSMFAscii(java.io.PrintWriter kOut)`
`protected void`	`printSTLAscii(java.io.PrintWriter kOut)`	Print the STL file format in ASCII.
`protected void`	`printSTLBinary(java.io.RandomAccessFile kOut)`	Print the STL file format in binary ( little endian ).
`protected void`	`save(java.io.RandomAccessFile kOut, boolean flip, int[] direction, float[] startLocation, float[] box, TransMatrix inverseDicomMatrix, javax.vecmath.Color4f[] perVertexColorArray)`	Internal support for 'void save (String)' and 'void save (String, ModelTriangleMesh[])'.
`void`	`save(java.lang.String kName, boolean flip, int[] direction, float[] startLocation, float[] box, TransMatrix inverseDicomMatrix)`	Save the triangle mesh to a binary file.
`static void`	`save(java.lang.String kName, ModelTriangleMesh[] akComponent, boolean flip, int[] direction, float[] startLocation, float[] box, TransMatrix inverseDicomMatrix, javax.vecmath.Color4f[][] perVertexColorArray)`	Save an array of triangle meshes to a binary file.
`void`	`saveAsPlyFile(java.lang.String kName)`
`protected void`	`saveAsPortableVRML(java.io.PrintWriter kOut, boolean flip, int[] direction, float[] startLocation, float[] box, javax.vecmath.Color3f color)`	Saves the triangle mesh in VRML97 (VRML 2.0) format.
`void`	`saveAsPortableVRML(java.io.PrintWriter kOut, boolean flip, int numberOfShapes, int[] direction, float[] startLocation, float[] box, javax.vecmath.Color3f color)`	Saves the triangle mesh in VRML97 (VRML 2.0) format (text format).
`static void`	`saveAsPortableVRML(java.io.PrintWriter kOut, ModelTriangleMesh[] akComponent, boolean flip, int[] direction, float[] startLocation, float[] box, javax.vecmath.Color3f color)`	Saves the triangle mesh in VRML97 (VRML 2.0) format (text format).
`void`	`saveAsSMFAsciiFile(java.lang.String kName)`	Sate the SMF ACII file format.
`void`	`saveAsSTLAsciiFile(java.lang.String kName)`	Sate the STIL ACII file format.
`void`	`saveAsSTLBinaryFile(java.lang.String kName)`	Sate the STIL Binary file format.
`void`	`saveAsTextFile(java.lang.String kName)`	Save the triangle mesh to a text file.
`static void`	`saveAsTextFile(java.lang.String kName, ModelTriangleMesh[] akComponent)`	Save an array of triangle meshes to a text file.
`protected void`	`saveAsVRML(java.io.PrintWriter kOut, boolean flip, int[] direction, float[] startLocation, float[] box, javax.vecmath.Color3f color)`	Saves the triangle mesh in VRML97 (VRML 2.0) format.
`void`	`saveAsVRML(java.lang.String kName, boolean flip, int numberOfShapes, int[] direction, float[] startLocation, float[] box, javax.vecmath.Color3f color)`	Saves the triangle mesh in VRML97 (VRML 2.0) format (text format).
`static void`	`saveAsVRML(java.lang.String kName, ModelTriangleMesh[] akComponent, boolean flip, int[] direction, float[] startLocation, float[] box, javax.vecmath.Color3f color)`	Saves the triangle mesh in VRML97 (VRML 2.0) format (text format).
`void`	`saveAsVTKLegacy(java.lang.String kName)`	Saves the triangle mesh to VTK Legacy format
`void`	`saveAsVTKXML(java.lang.String fileName)`	saves thr triangle mesh to VTK XML format
`protected void`	`saveAsXML(java.lang.String fileName, int[] direction, float[] startLocation, float[] box)`	Internal support for 'void save (String)' and 'void save (String, ModelTriangleMesh[])'.
`void`	`saveXMLHeader(java.lang.String kName)`
`void`	`setCellData(double[][] cellData)`
`void`	`setColor(int index, javax.vecmath.Color4f kColor)`	Sets the color and stores the color update information in a local copy.
`void`	`setColorDelay(int index, javax.vecmath.Color4f kColor)`	Used for fast color update while painting the triangle mesh, stores the color update information for later loading into the surface.
`void`	`setColorUpdate()`	Used for fast color update while painting.
`void`	`setGenerator(java.lang.Object kGenerator)`	Support for regenerating an ModelTriangleMesh from an ModelClodMesh whenever the level of detail is changed for the ModelClodMesh.
`void`	`setMaterial(javax.media.j3d.Material kMaterial)`	Sets the material properties of the mesh.
`void`	`setTransparency(float transparency)`	Sets the mesh transparency.
`void`	`setVertexData(double[][] data)`
`void`	`setVertexData(int i, double val)`
`void`	`setVertexData(int i, double[] array)`
`void`	`setVertexData(int i, int j, double val)`
`void`	`setVerticies(javax.vecmath.Point3f[] akVertex)`	Replace the verticies with a new set.
`void`	`smoothMesh(int iteration, float alpha, boolean volumeLimit, float volumePercent, boolean pVisible)`	Smooth mesh.
`void`	`smoothThree(int iteration, float lambda, float mu, boolean pVisible)`	Smooth mesh.
`void`	`smoothTwo(int iterations, float m_fStiffness, boolean volumeLimit, float volumePercent, boolean pVisible)`	Derived from the first 2 of the 3 components of AlgorithmBrainExtraction Note that m_fStiffness does not increase and then decrease as in AlgorithmBrainExtraction but instead remains constant.
`private float`	`update2(int i)`	Compute the coefficient of the surface normal for the update of the mesh vertex V[i] in the SNormal[i] direction.
`private void`	`updateMesh()`	The heart of the segmentation.
`float`	`volume()`	Calculates volume of triangle mesh.

Methods inherited from class javax.media.j3d.IndexedTriangleArray
cloneNodeComponent

Methods inherited from class javax.media.j3d.IndexedGeometryArray
getColorIndex, getColorIndices, getCoordinateIndex, getCoordinateIndices, getCoordIndicesRef, getIndexCount, getInitialIndexIndex, getNormalIndex, getNormalIndices, getTextureCoordinateIndex, getTextureCoordinateIndex, getTextureCoordinateIndices, getTextureCoordinateIndices, getValidIndexCount, getVertexAttrIndex, getVertexAttrIndices, setColorIndex, setColorIndices, setCoordinateIndex, setCoordinateIndices, setCoordIndicesRef, setInitialColorIndex, setInitialCoordIndex, setInitialIndexIndex, setInitialNormalIndex, setInitialTexCoordIndex, setInitialVertexAttrIndex, setInitialVertexIndex, setNormalIndex, setNormalIndices, setTextureCoordinateIndex, setTextureCoordinateIndex, setTextureCoordinateIndices, setTextureCoordinateIndices, setValidIndexCount, setValidVertexCount, setVertexAttrIndex, setVertexAttrIndices

Methods inherited from class javax.media.j3d.GeometryArray
getColor, getColor, getColor, getColor, getColor, getColor, getColorRef3b, getColorRef3f, getColorRef4b, getColorRef4f, getColorRefBuffer, getColorRefByte, getColorRefFloat, getColors, getColors, getColors, getColors, getColors, getColors, getCoordinate, getCoordinate, getCoordinate, getCoordinate, getCoordinates, getCoordinates, getCoordinates, getCoordinates, getCoordRef3d, getCoordRef3f, getCoordRefBuffer, getCoordRefDouble, getCoordRefFloat, getInitialColorIndex, getInitialCoordIndex, getInitialNormalIndex, getInitialTexCoordIndex, getInitialVertexAttrIndex, getInitialVertexIndex, getInterleavedVertexBuffer, getInterleavedVertices, getNormal, getNormal, getNormalRef3f, getNormalRefBuffer, getNormalRefFloat, getNormals, getNormals, getTexCoordRef2f, getTexCoordRef3f, getTexCoordRefBuffer, getTexCoordRefFloat, getTexCoordSetCount, getTexCoordSetMap, getTexCoordSetMapLength, getTextureCoordinate, getTextureCoordinate, getTextureCoordinate, getTextureCoordinate, getTextureCoordinate, getTextureCoordinate, getTextureCoordinate, getTextureCoordinates, getTextureCoordinates, getTextureCoordinates, getTextureCoordinates, getTextureCoordinates, getTextureCoordinates, getTextureCoordinates, getValidVertexCount, getVertexAttr, getVertexAttr, getVertexAttr, getVertexAttr, getVertexAttrCount, getVertexAttrRefBuffer, getVertexAttrRefFloat, getVertexAttrs, getVertexAttrs, getVertexAttrs, getVertexAttrs, getVertexAttrSizes, getVertexCount, getVertexFormat, setColor, setColor, setColor, setColor, setColor, setColorRef3b, setColorRef3f, setColorRef4b, setColorRef4f, setColorRefBuffer, setColorRefByte, setColorRefFloat, setColors, setColors, setColors, setColors, setColors, setColors, setColors, setColors, setColors, setColors, setColors, setColors, setCoordinate, setCoordinate, setCoordinate, setCoordinate, setCoordinates, setCoordinates, setCoordinates, setCoordinates, setCoordinates, setCoordinates, setCoordinates, setCoordinates, setCoordRef3d, setCoordRef3f, setCoordRefBuffer, setCoordRefDouble, setCoordRefFloat, setInterleavedVertexBuffer, setInterleavedVertices, setNormal, setNormal, setNormalRef3f, setNormalRefBuffer, setNormalRefFloat, setNormals, setNormals, setNormals, setNormals, setTexCoordRef2f, setTexCoordRef3f, setTexCoordRefBuffer, setTexCoordRefFloat, setTextureCoordinate, setTextureCoordinate, setTextureCoordinate, setTextureCoordinate, setTextureCoordinate, setTextureCoordinate, setTextureCoordinate, setTextureCoordinates, setTextureCoordinates, setTextureCoordinates, setTextureCoordinates, setTextureCoordinates, setTextureCoordinates, setTextureCoordinates, setTextureCoordinates, setTextureCoordinates, setTextureCoordinates, setTextureCoordinates, setTextureCoordinates, setTextureCoordinates, setTextureCoordinates, setVertexAttr, setVertexAttr, setVertexAttr, setVertexAttr, setVertexAttrRefBuffer, setVertexAttrRefFloat, setVertexAttrs, setVertexAttrs, setVertexAttrs, setVertexAttrs, setVertexAttrs, setVertexAttrs, setVertexAttrs, setVertexAttrs, updateData

Methods inherited from class javax.media.j3d.NodeComponent
cloneNodeComponent, duplicateNodeComponent, duplicateNodeComponent, getDuplicateOnCloneTree, setDuplicateOnCloneTree

Methods inherited from class javax.media.j3d.SceneGraphObject
clearCapability, clearCapabilityIsFrequent, duplicateSceneGraphObject, getCapability, getCapabilityIsFrequent, getName, getUserData, isCompiled, isLive, setCapability, setCapabilityIsFrequent, setName, setUserData, toString, updateNodeReferences

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

- Field Detail
  - direction
```
private static int[] direction
```
    DOCUMENT ME!
  - startLocation
```
private static float[] startLocation
```
    DOCUMENT ME!
  - box
```
private static float[] box
```
    DOCUMENT ME!
  - kInvalid
```
java.lang.Integer kInvalid
```
    DOCUMENT ME!
  - m_afCurvature
```
float[] m_afCurvature
```
    DOCUMENT ME!
  - m_akAdjacent
```
ModelTriangleMesh.UnorderedSetInt[] m_akAdjacent
```
    DOCUMENT ME!
  - m_akSNormal
```
javax.vecmath.Vector3f[] m_akSNormal
```
    DOCUMENT ME!
  - m_akSTangent
```
javax.vecmath.Vector3f[] m_akSTangent
```
    DOCUMENT ME!
  - m_akVMean
```
javax.vecmath.Vector3f[] m_akVMean
```
    DOCUMENT ME!
  - m_akVNormal
```
javax.vecmath.Vector3f[] m_akVNormal
```
    DOCUMENT ME!
  - m_fEParam
```
float m_fEParam
```
    DOCUMENT ME!
  - m_fFParam
```
float m_fFParam
```
    DOCUMENT ME!
  - m_fMeanEdgeLength
```
float m_fMeanEdgeLength
```
    DOCUMENT ME!
  - m_fStiffness
```
float m_fStiffness
```
    DOCUMENT ME!
  - m_kEMap
```
java.util.HashMap m_kEMap
```
    DOCUMENT ME!
  - connections
```
private java.util.HashSet[] connections
```
    used in smoothing.
  - m_kE0
```
private javax.vecmath.Vector3f m_kE0
```
    DOCUMENT ME!
  - m_kE1
```
private javax.vecmath.Vector3f m_kE1
```
    DOCUMENT ME!
  - m_kN
```
private javax.vecmath.Vector3f m_kN
```
    DOCUMENT ME!
  - m_kGenerator
```
private java.lang.Object m_kGenerator
```
    The ModelClodMesh object that generated the ModelTriangleMesh object, null otherwise.
  - m_kV0
```
private javax.vecmath.Point3f m_kV0
```
    temporary variables to avoid 'new' calls.
  - m_kV1
```
private javax.vecmath.Point3f m_kV1
```
    temporary variables to avoid 'new' calls.
  - m_kV2
```
private javax.vecmath.Point3f m_kV2
```
    temporary variables to avoid 'new' calls.
  - m_kV3
```
private javax.vecmath.Point3f m_kV3
```
    temporary variables to avoid 'new' calls.
  - m_kMaterial
```
private javax.media.j3d.Material m_kMaterial
```
    store the Material properties of the mesh:
  - m_fTransparency
```
private float m_fTransparency
```
    store the mesh transparency:
  - m_kColors
```
private javax.vecmath.Color4f[] m_kColors
```
    Store the mesh colors:
  - perVertexColor
```
private javax.vecmath.Color4f[] perVertexColor
```
    Per vertex color array, which store the color data saved in .sur file.
  - vertexData
```
protected double[][] vertexData
```
    support for vtk
  - cellData
```
protected double[][] cellData
```
    support for vtk
- Constructor Detail
  - ModelTriangleMesh
```
public ModelTriangleMesh(javax.vecmath.Point3f[] akVertex,
                         int[] aiConnect)
```
    A triangle mesh whose vertex normal vectors are computed from the geometry of the mesh itself. The normal at a vertex is the normalized average of normals of the triangles that share the vertex.
    
    Parameters:
    
    akVertex - array of vertices in the mesh
    
    aiConnect - Connectivity array for the triangles. Each triple of indices represents one triangle. The triangle is counterclockwise ordered as viewed by an observer outside the mesh.
  - ModelTriangleMesh
```
public ModelTriangleMesh(javax.vecmath.Point3f[] akVertex,
                         javax.vecmath.Vector3f[] akNormal,
                         int[] aiConnect)
```
    A triangle mesh whose vertex normal vectors have been precomputed.
    
    Parameters:
    
    akVertex - array of vertices in the mesh
    
    akNormal - array of vertex normals for the mesh
    
    aiConnect - Connectivity array for the triangles. Each triple of indices represents one triangle. The triangle is counterclockwise ordered as viewed by an observer outside the mesh.
  - ModelTriangleMesh
```
public ModelTriangleMesh(javax.vecmath.Point3f[] akVertex,
                         javax.vecmath.Vector3f[] akNormal,
                         int[] aiConnect,
                         javax.vecmath.Color4f[] vertexColor)
```
    A triangle mesh whose vertex normal vectors have been precomputed.
    
    Parameters:
    
    akVertex - array of vertices in the mesh
    
    akNormal - array of vertex normals for the mesh
    
    aiConnect - Connectivity array for the triangles. Each triple of indices represents one triangle. The triangle is counterclockwise ordered as viewed by an observer outside the mesh.
  - ModelTriangleMesh
```
public ModelTriangleMesh(javax.vecmath.Point3f[] akVertex,
                         javax.vecmath.Vector3f[] akNormal,
                         javax.vecmath.Color4f[] akColor,
                         int[] aiConnect)
```
    A triangle mesh whose vertex normal vectors have been precomputed.
    
    Parameters:
    
    akVertex - array of vertices in the mesh
    
    akNormal - array of vertex normals for the mesh
    
    akColor - array of vertex colors
    
    aiConnect - Connectivity array for the triangles. Each triple of indices represents one triangle. The triangle is counterclockwise ordered as viewed by an observer outside the mesh.
  - ModelTriangleMesh
```
public ModelTriangleMesh(javax.vecmath.Point3f[] akVertex,
                         javax.vecmath.Vector3f[] akNormal,
                         javax.vecmath.TexCoord3f[] akTexCoord,
                         int[] aiConnect)
```
    A triangle mesh whose vertex normal vectors have been precomputed.
    
    Parameters:
    
    akVertex - array of vertices in the mesh
    
    akNormal - array of vertex normals for the mesh
    
    akColor - array of vertex colors
    
    akTexCoord - array of Texture Coordinates
    
    aiConnect - Connectivity array for the triangles. Each triple of indices represents one triangle. The triangle is counterclockwise ordered as viewed by an observer outside the mesh.
  - ModelTriangleMesh
```
public ModelTriangleMesh(javax.vecmath.Point3f[] akVertex,
                         javax.vecmath.Vector3f[] akNormal,
                         javax.vecmath.Color4f[] akColor,
                         javax.vecmath.TexCoord3f[] akTexCoord,
                         int[] aiConnect)
```
    A triangle mesh whose vertex normal vectors have been precomputed.
    
    Parameters:
    
    akVertex - array of vertices in the mesh
    
    akNormal - array of vertex normals for the mesh
    
    akColor - array of vertex colors
    
    akTexCoord - array of Texture Coordinates
    
    aiConnect - Connectivity array for the triangles. Each triple of indices represents one triangle. The triangle is counterclockwise ordered as viewed by an observer outside the mesh.
  - ModelTriangleMesh
```
public ModelTriangleMesh(ModelTriangleMesh kMesh)
```
    Copies a ModelTriangleMesh by copying it's components.
    
    Parameters:
    
    ModelTriangleMesh - ModelTriangleMesh to copy
  - ModelTriangleMesh
```
public ModelTriangleMesh(WildMagic.LibFoundation.Mathematics.Vector3f[] akVertex,
                         int[] aiConnect)
```
    A triangle mesh whose vertex normal vectors are computed from the geometry of the mesh itself. The normal at a vertex is the normalized average of normals of the triangles that share the vertex.
    
    Parameters:
    
    akVertex - array of vertices in the mesh
    
    aiConnect - Connectivity array for the triangles. Each triple of indices represents one triangle. The triangle is counterclockwise ordered as viewed by an observer outside the mesh.
- Method Detail
  - init
```
private void init()
```
    Initializes capabilities and temporary variables.
  - getPerVertexColor
```
public javax.vecmath.Color4f[] getPerVertexColor()
```
  - getVertexData
```
public double[][] getVertexData()
```
  - getVertexData
```
public double[] getVertexData(int i)
```
  - setVertexData
```
public void setVertexData(double[][] data)
```
  - setVertexData
```
public void setVertexData(int i,
                          double val)
```
  - setVertexData
```
public void setVertexData(int i,
                          int j,
                          double val)
```
  - setVertexData
```
public void setVertexData(int i,
                          double[] array)
```
  - setCellData
```
public void setCellData(double[][] cellData)
```
  - getCellData
```
public double[][] getCellData()
```
  - getDirection
```
public static int[] getDirection()
```
    DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - getStartLocation
```
public static float[] getStartLocation()
```
    DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - loadTMesh
```
public static ModelTriangleMesh loadTMesh(java.io.RandomAccessFile kIn,
                                          javax.swing.JProgressBar pBar,
                                          int added,
                                          int total)
                                   throws java.io.IOException
```
    Load the triangle mesh from a binary file. The caller must have already opened the file and read the mesh type (0 = ModelTriangleMesh, 1 = ModelClodMesh) and the number of meshes in the file. The caller then calls this function for each mesh. The format for a mesh is
    int vCount; // number of vertices Point3f vertices[vCount]; Point3f normals[vCount]; int iCount; // number of indices in the connectivity array int indices[iCount];
    with 4-byte quantities stored in Big Endian format.
    Parameters:
    
    kIn - the file from which the triangle mesh is loaded
    
    pBar - DOCUMENT ME!
    
    added - DOCUMENT ME!
    
    total - DOCUMENT ME!
    
    Returns:
    
    the loaded triangle mesh
    
    Throws:
    
    java.io.IOException - if there is an error reading from the file
  - loadTMesh
```
public static ModelTriangleMesh loadTMesh(java.io.RandomAccessFile kIn,
                                          ViewJProgressBar progress,
                                          int added,
                                          int total,
                                          boolean isVisible)
                                   throws java.io.IOException
```
    Load the triangle mesh from a binary file. The caller must have already opened the file and read the mesh type (0 = ModelTriangleMesh, 1 = ModelClodMesh) and the number of meshes in the file. The caller then calls this function for each mesh. The format for a mesh is
    int vCount; // number of vertices Point3f vertices[vCount]; Point3f normals[vCount]; int iCount; // number of indices in the connectivity array int indices[iCount];
    with 4-byte quantities stored in Big Endian format.
    Parameters:
    
    kIn - the file from which the triangle mesh is loaded
    
    progress - DOCUMENT ME!
    
    added - DOCUMENT ME!
    
    total - DOCUMENT ME!
    
    isVisible - DOCUMENT ME!
    
    Returns:
    
    the loaded triangle mesh
    
    Throws:
    
    java.io.IOException - if there is an error reading from the file
  - save
```
public static void save(java.lang.String kName,
                        ModelTriangleMesh[] akComponent,
                        boolean flip,
                        int[] direction,
                        float[] startLocation,
                        float[] box,
                        TransMatrix inverseDicomMatrix,
                        javax.vecmath.Color4f[][] perVertexColorArray)
                 throws java.io.IOException
```
    Save an array of triangle meshes to a binary file. The format for the file is
    int type; // 0 = ModelTriangleMesh, 1 = ModelClodMesh int aCount; // number of array elements array of 'aCount' meshes, each of the form: int vCount; // number of vertices Point3f vertices[vCount]; Point3f normals[vCount]; int iCount; // number of indices in the connectivity array int indices[iCount];
    with 4-byte quantities stored in Big Endian format.
    Parameters:
    
    kName - the name of the file to which the components are saved
    
    akComponent - the array of mesh components to be saved
    
    flip - if the y and z axes should be flipped - true in extract and in save of JDialogSurface To have proper orientations in surface file if flip is true flip y and z on reading.
    
    direction - either 1 or -1 for each axis
    
    startLocation - DOCUMENT ME!
    
    box - (dim-1)*res
    
    inverseDicomMatrix - dicom transform
    
    perVertexColorArray - color per vertex array.
    
    Throws:
    
    java.io.IOException - if there is an error writing to the file
  - loadVRMLMesh
```
public static ModelTriangleMesh loadVRMLMesh(java.io.RandomAccessFile kIn,
                                             ViewJProgressBar progress,
                                             int added,
                                             int total,
                                             boolean flag)
                                      throws java.io.IOException
```
    Load the triangle mesh from a VRML file specifically written by MIPAV!. The caller must have already opened the file. Must be made more robust to better parse the file. It only reads VRML 2.0 that MIPAV has written.
    
    Parameters:
    
    kIn - the file from which the triangle mesh is loaded
    
    progress - DOCUMENT ME!
    
    added - DOCUMENT ME!
    
    total - DOCUMENT ME!
    
    flag - DOCUMENT ME!
    
    Returns:
    
    the loaded triangle mesh
    
    Throws:
    
    java.io.IOException - if there is an error reading from the file
  - loadVTKLegacyMesh
```
public static ModelTriangleMesh loadVTKLegacyMesh(java.io.RandomAccessFile kIn,
                                                  ViewJProgressBar progress,
                                                  int added,
                                                  int total,
                                                  boolean flag,
                                                  java.lang.String fileName)
                                           throws java.io.IOException
```
    Parameters:
    
    kIn -
    
    progress -
    
    added -
    
    total -
    
    flag -
    
    Returns:
    
    Throws:
    
    java.io.IOException
  - loadVTKXMLMesh
```
public static ModelTriangleMesh loadVTKXMLMesh(java.lang.String absPath,
                                               ViewJProgressBar progress,
                                               int added,
                                               int total,
                                               boolean flag,
                                               java.lang.String fileName,
                                               java.lang.String dir)
                                        throws java.io.IOException
```
    Parameters:
    
    kIn -
    
    progress -
    
    added -
    
    total -
    
    flag -
    
    fileName -
    
    Returns:
    
    Throws:
    
    java.io.IOException
  - parseVRMLMesh
```
public static int parseVRMLMesh(java.io.RandomAccessFile kIn)
                         throws java.io.IOException,
                                java.util.NoSuchElementException
```
    Parses the VRML to see how many surfaces there are.
    
    Parameters:
    
    kIn - the file to parse
    
    Returns:
    
    DOCUMENT ME!
    
    Throws:
    
    java.io.IOException - DOCUMENT ME!
    
    java.util.NoSuchElementException - DOCUMENT ME!
  - saveAsPortableVRML
```
public static void saveAsPortableVRML(java.io.PrintWriter kOut,
                                      ModelTriangleMesh[] akComponent,
                                      boolean flip,
                                      int[] direction,
                                      float[] startLocation,
                                      float[] box,
                                      javax.vecmath.Color3f color)
                               throws java.io.IOException
```
    Saves the triangle mesh in VRML97 (VRML 2.0) format (text format).
    
    Parameters:
    
    kOut - the name of file to which the triangle mesh is saved
    
    akComponent - DOCUMENT ME!
    
    flip - if the y and z axes should be flipped - true in extract and in save of JDialogSurface To have proper orientations in surface file if flip is true flip y and z on reading.
    
    direction - 1 or -1 for each axis
    
    startLocation - DOCUMENT ME!
    
    box - (dim-1)*resolution
    
    color - DOCUMENT ME!
    
    Throws:
    
    java.io.IOException - if the specified file could not be opened for writing
  - saveAsTextFile
```
public static void saveAsTextFile(java.lang.String kName,
                                  ModelTriangleMesh[] akComponent)
                           throws java.io.IOException
```
    Save an array of triangle meshes to a text file. The format for the file is
    int type; // 0 = ModelTriangleMesh, 1 = ModelClodMesh int aCount; // number of array elements array of 'aCount' meshes, each of the form: int vCount; // number of vertices vertex[0].x vertex[0].y vertex[0].z; : normal[0].x normal[0].y normal[0].z; : int tCount; // number of triangles index[0] index[1] index[2] : index[3*(tCount-1)] index[3*(tCount-1)+1] index[3*(tCount-1)+2]
    Parameters:
    
    kName - the name of the file to which the components are saved
    
    akComponent - the array of mesh components to save
    
    Throws:
    
    java.io.IOException - if the specified file could not be opened for writing
  - saveAsVRML
```
public static void saveAsVRML(java.lang.String kName,
                              ModelTriangleMesh[] akComponent,
                              boolean flip,
                              int[] direction,
                              float[] startLocation,
                              float[] box,
                              javax.vecmath.Color3f color)
                       throws java.io.IOException
```
    Saves the triangle mesh in VRML97 (VRML 2.0) format (text format).
    
    Parameters:
    
    kName - the name of file to which the triangle mesh is saved
    
    akComponent - DOCUMENT ME!
    
    flip - if the y and z axes should be flipped - true in extract and in save of JDialogSurface To have proper orientations in surface file if flip is true flip y and z on reading. param direction 1 or -1 for each axis param startLocation param box (dim-1)*resolution
    
    direction - DOCUMENT ME!
    
    startLocation - DOCUMENT ME!
    
    box - DOCUMENT ME!
    
    color - DOCUMENT ME!
    
    Throws:
    
    java.io.IOException - if the specified file could not be opened for writing
  - affineTransform
```
public void affineTransform(double[][] aafH)
```
    The input 4x4 homogeneous matrix H is assumed to multiply vectors V as H*V where V = (x,y,z,1). Let the upper left 3x3 block of H be A. Let the upper right 3x1 block of H be B. The last row is [0 0 0 1]. Let the upper 3x1 block of V be X. The lower 1x1 block is 1. The product H*V = A*X + B.
    
    Parameters:
    
    aafH - Affine transformation matrix.
  - affineTransform
```
public void affineTransform(float[][] afRot,
                            float[] afTrn,
                            float[] afScale)
```
    Rotation R is 3x3, translation T is 3x1, and scale S is 3x1. The product with 3x1 vector X is Diag(S)*R*X + T where Diag(S) is the diagonal matrix whose diagonal entries are the values of S. As a homogeneous matrix (see notation above), A = diag(S)*R and B = T.
    
    Parameters:
    
    afRot - Affine rotation matrix.
    
    afTrn - Affine translation matrix.
    
    afScale - Affine scale matrix.
  - area
```
public float area()
```
    Calculate the surface mesh area. Each surface mesh is composed of triangles. Calculate the surface area from the summation of the each triangle area. Based on the Area by Stokes' Theorem. Area(S) = 1/2 * Normal dot ( Sum from i = 0 to n-1 of ( V1 cross V2) ) ==> Area(S) = 1/2 * ( Sum from i = 0 to n-1 of ( Normal dot ( V1 cross V2) ) )
    
    Returns:
    
    float
  - center
```
public javax.vecmath.Point3f center()
```
    Calculates and returns the center point of the Mesh:
    
    Returns:
    
    DOCUMENT ME!
  - computeNormals
```
public void computeNormals()
```
    A normal vector at a vertex is computed by averaging the triangle normals for all triangles sharing the vertex. This routine computes all vertex normals.
  - getComponents
```
public ModelTriangleMesh[] getComponents()
```
    Construct the connected components of the triangle mesh.
    
    Returns:
    
    An array of connected components of the triangle mesh. Each component has its own vertex and connectivity index arrays.
  - getConsistentComponents
```
public void getConsistentComponents()
```
    Construct the connected components of the triangle mesh.
  - getGenerator
```
public java.lang.Object getGenerator()
```
    Support for regenerating an ModelTriangleMesh from an ModelClodMesh whenever the level of detail is changed for the ModelClodMesh. If the mesh was generated from an ModelClodMesh, the generator member refers to that ModelClodMesh object. If the mesh was not generated from an ModelClodMesh, the generator member is null.
    
    Returns:
    
    the generator of this mesh
  - getIndexCopy
```
public int[] getIndexCopy()
```
    Make a copy of the connectivity array of a triangle mesh.
    
    Returns:
    
    A copy of the array of connectivity indices of the triangle mesh.
  - getNormalCopy
```
public javax.vecmath.Vector3f[] getNormalCopy()
```
    Make a copy of the normals of a triangle mesh.
    
    Returns:
    
    A copy of the array of normals of the triangle mesh.
  - getVertexCopy
```
public javax.vecmath.Point3f[] getVertexCopy()
```
    Make a copy of the vertices of a triangle mesh.
    
    Returns:
    
    A copy of the array of vertices of the triangle mesh.
  - getVertexCopyAsVector3f
```
public WildMagic.LibFoundation.Mathematics.Vector3f[] getVertexCopyAsVector3f()
```
    Make a copy of the vertices of a triangle mesh.
    
    Returns:
    
    A copy of the array of vertices of the triangle mesh.
  - getColorCopy
```
public javax.vecmath.Color4f[] getColorCopy()
```
    Make a copy of the colors of a triangle mesh.
    
    Returns:
    
    A copy of the array of colors of the triangle mesh.
  - getCopies
```
public void getCopies(javax.vecmath.Point3f[] akVertex,
                      javax.vecmath.Vector3f[] akNormal,
                      javax.vecmath.Color4f[] akColor,
                      javax.vecmath.TexCoord3f[] akTexCoord)
```
    Copies the components of a ModelTriangleMesh into the parameters. More efficient than copying the components individually.
    
    Parameters:
    
    akVertex - the array of coordinates to copy into.
    
    akNormal - the array of normals to copy into.
    
    akColor - the array of colors to copy into.
    
    akTexCoord - the array of texture coordinates to copy into.
  - getTexCoordCopy
```
public javax.vecmath.TexCoord3f[] getTexCoordCopy()
```
    Make a copy of the texture coordinates of a triangle mesh.
    
    Returns:
    
    A copy of the array of texture coordinates of the triangle mesh.
  - setColorDelay
```
public void setColorDelay(int index,
                          javax.vecmath.Color4f kColor)
```
    Used for fast color update while painting the triangle mesh, stores the color update information for later loading into the surface.
    
    Parameters:
    
    index - the vertex index to set the color for
    
    kColor - the new color
  - setColor
```
public void setColor(int index,
                     javax.vecmath.Color4f kColor)
```
    Sets the color and stores the color update information in a local copy.
    
    Overrides:
    
    setColor in class javax.media.j3d.GeometryArray
    
    Parameters:
    
    index - the vertex index to set the color for
    
    kColor - the new color
  - getColorLocal
```
public void getColorLocal(int index,
                          javax.vecmath.Color4f kColor)
```
    Gets the stored local color.
    
    Parameters:
    
    index - the vertex index to get the color for.
    
    kColor - the stored local color.
  - setColorUpdate
```
public void setColorUpdate()
```
    Used for fast color update while painting. After paint operations, set the color of the triangle mesh with the stored colors.
  - save
```
public void save(java.lang.String kName,
                 boolean flip,
                 int[] direction,
                 float[] startLocation,
                 float[] box,
                 TransMatrix inverseDicomMatrix)
          throws java.io.IOException
```
    Save the triangle mesh to a binary file. The format for the file is
    int type; // 0 = ModelTriangleMesh, 1 = ModelClodMesh int aCount; // 1, write the entire mesh as a single component int vCount; // number of vertices Point3f vertices[vCount]; Point3f normals[vCount]; int iCount; // number of indices in the connectivity array int indices[iCount];
    with 4-byte quantities stored in Big Endian format.
    Parameters:
    
    kName - the name of the file to which the triangle mesh is saved
    
    flip - if the y and z axes should be flipped - true in extract and in save of JDialogSurface To have proper orientations in surface file if flip is true flip y and z on reading.
    
    direction - equal 1 or -1 for each axis
    
    startLocation - DOCUMENT ME!
    
    box - (dim-1)*res
    
    inverseDicomMatrix - DOCUMENT ME!
    
    Throws:
    
    java.io.IOException - if the specified file could not be opened for writing
  - saveXMLHeader
```
public void saveXMLHeader(java.lang.String kName)
```
  - saveAsPortableVRML
```
public void saveAsPortableVRML(java.io.PrintWriter kOut,
                               boolean flip,
                               int numberOfShapes,
                               int[] direction,
                               float[] startLocation,
                               float[] box,
                               javax.vecmath.Color3f color)
                        throws java.io.IOException
```
    Saves the triangle mesh in VRML97 (VRML 2.0) format (text format).
    
    Parameters:
    
    kOut - the name of file to which the triangle mesh is saved
    
    flip - if the y and z axes should be flipped - true in extract and in save of JDialogSurface To have proper orientations in surface file if flip is true flip y and z on reading.
    
    numberOfShapes - DOCUMENT ME!
    
    direction - 1 or -1 for each axis
    
    startLocation - DOCUMENT ME!
    
    box - (dimension-1)*resolution
    
    color - DOCUMENT ME!
    
    Throws:
    
    java.io.IOException - if the specified file could not be opened for writing
  - saveAsVTKLegacy
```
public void saveAsVTKLegacy(java.lang.String kName)
                     throws java.io.IOException
```
    Saves the triangle mesh to VTK Legacy format
    
    Parameters:
    
    kName -
    
    Throws:
    
    java.io.IOException
  - saveAsVTKXML
```
public void saveAsVTKXML(java.lang.String fileName)
                  throws java.io.IOException
```
    saves thr triangle mesh to VTK XML format
    
    Parameters:
    
    kName -
    
    Throws:
    
    java.io.IOException
  - saveAsTextFile
```
public void saveAsTextFile(java.lang.String kName)
                    throws java.io.IOException
```
    Save the triangle mesh to a text file. The format for the file is
    int type; // 0 = ModelTriangleMesh, 1 = ModelClodMesh, 2 = ModelQuadMesh int aCount; // 1, write the entire mesh as a single component int vCount; // number of vertices vertex[0].x vertex[0].y vertex[0].z; : normal[0].x normal[0].y normal[0].z; : int tCount; // number of triangles index[0] index[1] index[2] : index[3*(tCount-1)] index[3*(tCount-1)+1] index[3*(tCount-1)+2]
    Parameters:
    
    kName - the name of file to which the triangle mesh is saved
    
    Throws:
    
    java.io.IOException - if the specified file could not be opened for writing
  - saveAsPlyFile
```
public void saveAsPlyFile(java.lang.String kName)
                   throws java.io.IOException
```
    Throws:
    
    java.io.IOException
  - saveAsSMFAsciiFile
```
public void saveAsSMFAsciiFile(java.lang.String kName)
                        throws java.io.IOException
```
    Sate the SMF ACII file format.
    
    Parameters:
    
    kName - file name
    
    Throws:
    
    java.io.IOException
  - saveAsSTLAsciiFile
```
public void saveAsSTLAsciiFile(java.lang.String kName)
                        throws java.io.IOException
```
    Sate the STIL ACII file format.
    
    Parameters:
    
    kName - file name
    
    Throws:
    
    java.io.IOException
  - saveAsSTLBinaryFile
```
public void saveAsSTLBinaryFile(java.lang.String kName)
                         throws java.io.IOException
```
    Sate the STIL Binary file format.
    
    Parameters:
    
    kName - file name
    
    Throws:
    
    java.io.IOException
  - saveAsVRML
```
public void saveAsVRML(java.lang.String kName,
                       boolean flip,
                       int numberOfShapes,
                       int[] direction,
                       float[] startLocation,
                       float[] box,
                       javax.vecmath.Color3f color)
                throws java.io.IOException
```
    Saves the triangle mesh in VRML97 (VRML 2.0) format (text format).
    
    Parameters:
    
    kName - the name of file to which the triangle mesh is saved
    
    flip - if the y and z axes should be flipped - true in extract and in save of JDialogSurface To have proper orientations in surface file if flip is true flip y and z on reading.
    
    numberOfShapes - DOCUMENT ME!
    
    direction - 1 or -1 for each axis
    
    startLocation - DOCUMENT ME!
    
    box - (dimension-1)*resolution
    
    color - DOCUMENT ME!
    
    Throws:
    
    java.io.IOException - if the specified file could not be opened for writing
  - setGenerator
```
public void setGenerator(java.lang.Object kGenerator)
```
    Support for regenerating an ModelTriangleMesh from an ModelClodMesh whenever the level of detail is changed for the ModelClodMesh. If the mesh was generated from an ModelClodMesh, the generator member refers to that ModelClodMesh object. If the mesh was not generated from an ModelClodMesh, the generator member is null.
    
    Parameters:
    
    kGenerator - the generator of this mesh
  - setVerticies
```
public void setVerticies(javax.vecmath.Point3f[] akVertex)
```
    Replace the verticies with a new set.
    
    Parameters:
    
    akVertex - DOCUMENT ME!
  - smoothMesh
```
public void smoothMesh(int iteration,
                       float alpha,
                       boolean volumeLimit,
                       float volumePercent,
                       boolean pVisible)
```
    Smooth mesh. The formula can be found in "The Visualization Toolkit" by Will Schoeder, Ken Martin, and Bill Lorensen, p. 389. Mesh smoothing moves the verticies of the mesh closer to an average of the points. Each point is moved so that it is the average of the points around it. The formula is:
    xi+1 = xi + (alpha * (Sum from j=0 to n of {xj - xi}))
    where xi+1 is the new point, xi is the orginal point, and the xjs are points that are connected to xi. Alpha is some smoothing factor between .01 and .10. This formula is run for a number of iterations to obtain a smooth mesh. Usually the iterations will be between 50 and 100.
    Parameters:
    
    iteration - Number of times to run smoothing formula on data set.
    
    alpha - Smoothing factor.
    
    volumeLimit - if true stop iterations when the present volume is volumePercent or more different from the initial
    
    volumePercent - percentage from initial volume for stopping iterations
    
    pVisible - if true display progress bar
  - smoothThree
```
public void smoothThree(int iteration,
                        float lambda,
                        float mu,
                        boolean pVisible)
```
    Smooth mesh. This method smoothes without shrinking by 2 Gaussian smoothing steps. First, a Gaussian smoothing is performed with a positive scale factor lambda. Second, a Gaussian smoothing is performed with a negative scale factor mu, which is greater in magnitude than lambda. To produce a significant smoothing, these steps must be repeated a number of times. 3 references for this smoothing: 1.) Curve and Surface Smoothing Without Shrinkage by Gabriel Taubin, Technical Report RC-19536, IBM Research, April, 1994. (also in Proceedings, Fifth International Conference on Computer Vision, pages 852-857, June, 1995). 2.) A Signal Processing Approach to Fair Surface Design by Gabriel Taubin, Computer Graphics, pages 351-358, August, 1995 (Proceedings SIGGRAPH '95). 3.) Optimal Surface Smoothing as Filter Design by Gabriel Taubin, Tong Zhang, and Gene Golub, IBM Research Report RC-20404 (#90237). Usually the iterations will be between 30 and 100.
    
    Parameters:
    
    iteration - Number of times to run smoothing formula on data set.
    
    lambda - positive scale factor
    
    mu - negative scale factor
    
    pVisible - if true display progress bar Require: 0 < lambda < -mu (1/lambda) + (1/mu) < 2
  - smoothTwo
```
public void smoothTwo(int iterations,
                      float m_fStiffness,
                      boolean volumeLimit,
                      float volumePercent,
                      boolean pVisible)
```
    Derived from the first 2 of the 3 components of AlgorithmBrainExtraction Note that m_fStiffness does not increase and then decrease as in AlgorithmBrainExtraction but instead remains constant. This is because the change in m_fStiffness only applies to the third component of AlgorithmBrainExtraction which uses image intensities.
    
    Parameters:
    
    iterations - DOCUMENT ME!
    
    m_fStiffness - DOCUMENT ME!
    
    volumeLimit - if true stop iterations when the present volume is volumePercent or more different from the initial
    
    volumePercent - percentage from initial volume for stopping iterations
    
    pVisible - if true display progress bar
  - volume
```
public float volume()
```
    Calculates volume of triangle mesh. The mesh consists of triangle faces and encloses a bounded region. Face j, 0 <= j <= n-1 has verticies P0, P1, and P2. The order of the verticies is counterclockwise as you view the face from outside the bounded region. The mesh is closed and manifold in the sense that each edge is shared by exactly two triangles. The volume of the bounded region is:
    
    V = 1/6 (Sum from j=0 to n-1 of {P0 dot P1 cross P2})
    The terms of the summation can be positive, negative, or zero. The term is positive if the face is counterclockwise when viewed from the zero vector, or zero if the face appears to be a line segment when viewed from the zero vector. NOTICE THAT THERE ARE 2 DIFFERENT DEFINITIONS OF COUNTERCLOCKWISE, COUNTERCLOCKWISE AS VIEWED FROM OUTSIDE THE BOUNDED REGION AND COUNTERCLOCKWISE AS VIEWED FROM THE ZERO VECTOR.
    A 3D image on a rectangular lattice contains points (i0, i1, i2) where 0 <= ik < Bk for specified dimension bounds Bk. These are just indicies. The actual physical measurements are provided by scaling factors Dk > 0. For example, a 256x256x256 MRI has B0 = B1 = B2 = 256. If each voxel is 1 mm in x, 1 mm in y, and 5 mm in z, then D0 = D1 = 1 and D2 = 5. The 3D image encloses a rectangular region [0,C0] x [0,C1] x [0,C2] in physical space where Ck = Dk*Bk. In the example, C0 = D0*B0 = 256 mm in x, C1 = D1*B1 = 256 mm in y, and C2 = D2*B2 = 1280 mm in z. Volume calculations are required to use physical measurements. In the example, volume will be in cubic millimeters.
    
    The surface extraction is performed by mapping [0,C0] x [0,C1] x [0,C2] into [-1,1] x [-1,1] x [-1,1] using uniform scaling. This is done to keep the floating point values within order 1 to avoid the floating point errors that occur if you were to use the index values themselves. The topology of a level surface is invariant under any scaling (not just uniform), but the continuous level of detail algorithm for triangle decimation does edge collapses based on various geometric measurements of the mesh representing the level surface. The geometric measurements are not invariant under nonuniform scaling. Map the image into a cube using uniform scaling so that the triangle collapse order is invariant. The uniform scaling is done so that the largest image dimension [0,M] is mapped to [-1,1]. The other ranges are mapped to intervals of the form [-L,L) where L < 1. If (i0,i1,i2) is in [0,B0) x [0,B1) x [0,B2), the corresponding (x0,x1,x2) in [-1,1) is:
    
    2*Dk*ik - Ck xk = ------------ max{C0,C1,C2}
    
    However, we want to map from [0,Bk) to an inclusive interval [-Rk,Rk], where 0 < Rk < 1 and Rk = 1 - Dk/max{C0,C1,C2}. This ensures that surfaces begin in the center of a voxel rather than at the (0,0,0) corner of the voxel. The problem is easiest to see in the Z direction: a surface that should cover the full Z range will end before the last slice. Therefore, the formula should be:
    
    2*Dk*ik - Ck + Dk xk = ----------------- max{C0,C1,C2}
    
    Once a closed manifold triangle mesh is extracted, the problem is now to compute its volume in physical space. Note that ik are indicies in the original image, but the true physical length that is measured (relative to other index locations) is yk = Dk*ik. Any triangle mesh (x0,x1,x2) must be mapped to (y0,y1,y2) before the volume calculation. The mapping is:
    
    max{C0,C1,C2}*xk + Ck - Dk yk = -------------------------- 2
    
    The volume calculations use the previously mentioned formula where the P points are the (y0,y1,y2) values.
    Returns:
    
    The volume of the surface.
  - print
```
protected void print(java.io.PrintWriter kOut)
              throws java.io.IOException
```
    Internal support for 'void print (String)' and 'void print (String, ModelTriangleMesh[])'. ModelTriangleMesh uses this function to print vertices, normals, and connectivity indices to the file. ModelClodMesh overrides this to additionally print collapse records to the file
    
    Parameters:
    
    kOut - the file to which the triangle mesh is saved
    
    Throws:
    
    java.io.IOException - if there is an error writing to the file
  - printSMFAscii
```
protected void printSMFAscii(java.io.PrintWriter kOut)
                      throws java.io.IOException
```
    Throws:
    
    java.io.IOException
  - printSTLAscii
```
protected void printSTLAscii(java.io.PrintWriter kOut)
                      throws java.io.IOException
```
    Print the STL file format in ASCII. STLA Examples: solid MYSOLID facet normal 0.4 0.4 0.2 outerloop vertex 1.0 2.1 3.2 vertex 2.1 3.7 4.5 vertex 3.1 4.5 6.7 endloop endfacet ... facet normal 0.2 0.2 0.4 outerloop vertex 2.0 2.3 3.4 vertex 3.1 3.2 6.5 vertex 4.1 5.5 9.0 endloop endfacet endsolid MYSOLID
    
    Parameters:
    
    kOut -
    
    Throws:
    
    java.io.IOException
  - printSTLBinary
```
protected void printSTLBinary(java.io.RandomAccessFile kOut)
                       throws java.io.IOException
```
    Print the STL file format in binary ( little endian ). STLB Example: 80 byte string = header containing nothing in particular 4 byte int = number of faces For each face: 3 4-byte floats = components of normal vector to face; 3 4-byte floats = coordinates of first node; 3 4-byte floats = coordinates of second node; 3 4-byte floats = coordinates of third and final node; 2-byte int = attribute, whose value is 0.
    
    Parameters:
    
    kOut - binary file output
    
    Throws:
    
    java.io.IOException
  - saveAsXML
```
protected void saveAsXML(java.lang.String fileName,
                         int[] direction,
                         float[] startLocation,
                         float[] box)
```
    Internal support for 'void save (String)' and 'void save (String, ModelTriangleMesh[])'. ModelTriangleMesh uses this function to write vertices, normals, and connectivity indices to the XML file. ModelClodMesh overrides this to additionally write collapse records to the file
    
    Parameters:
    
    fileName - the file to which the triangle mesh is saved
    
    direction - either 1 or -1 for each axis
    
    startLocation - image origin coordinate
    
    box - (dim-1)*res
    
    Throws:
    
    java.io.IOException - if there is an error writing to the file
  - save
```
protected void save(java.io.RandomAccessFile kOut,
                    boolean flip,
                    int[] direction,
                    float[] startLocation,
                    float[] box,
                    TransMatrix inverseDicomMatrix,
                    javax.vecmath.Color4f[] perVertexColorArray)
             throws java.io.IOException
```
    Internal support for 'void save (String)' and 'void save (String, ModelTriangleMesh[])'. ModelTriangleMesh uses this function to write vertices, normals, and connectivity indices to the file. ModelClodMesh overrides this to additionally write collapse records to the file
    
    Parameters:
    
    kOut - the file to which the triangle mesh is saved
    
    flip - if the y and z axes should be flipped - true in extraction algorithms and in JDialogSurface. To have proper orientations in surface file if flip is true flip y and z on reading.
    
    direction - either 1 or -1 for each axis
    
    startLocation - DOCUMENT ME!
    
    box - (dim-1)*res
    
    inverseDicomArray - DOCUMENT ME!
    
    perVertexColorArray - color per vertex array.
    
    Throws:
    
    java.io.IOException - if there is an error writing to the file
  - saveAsPortableVRML
```
protected void saveAsPortableVRML(java.io.PrintWriter kOut,
                                  boolean flip,
                                  int[] direction,
                                  float[] startLocation,
                                  float[] box,
                                  javax.vecmath.Color3f color)
                           throws java.io.IOException
```
    Saves the triangle mesh in VRML97 (VRML 2.0) format. File name should end with ".wrl"
    
    Parameters:
    
    kOut - the file to which the triangle mesh is saved
    
    flip - if the y and z axes should be flipped - true in extract and in save of JDialogSurface To have proper orientations in surface file if flip is true flip y and z on reading.
    
    direction - 1 or -1 for each axis
    
    startLocation - DOCUMENT ME!
    
    box - (dimension-1)*resolution
    
    color - DOCUMENT ME!
    
    Throws:
    
    java.io.IOException - if there is an error writing to the file
  - saveAsVRML
```
protected void saveAsVRML(java.io.PrintWriter kOut,
                          boolean flip,
                          int[] direction,
                          float[] startLocation,
                          float[] box,
                          javax.vecmath.Color3f color)
                   throws java.io.IOException
```
    Saves the triangle mesh in VRML97 (VRML 2.0) format. File name should end with ".wrl"
    
    Parameters:
    
    kOut - the file to which the triangle mesh is saved
    
    flip - if the y and z axes should be flipped - true in extract and in save of JDialogSurface To have proper orientations in surface file if flip is true flip y and z on reading.
    
    direction - 1 or -1 for each axis
    
    startLocation - DOCUMENT ME!
    
    box - (dimension-1)*resolution
    
    color - DOCUMENT ME!
    
    Throws:
    
    java.io.IOException - if there is an error writing to the file
  - buildConnections
```
private void buildConnections()
```
    Builds a list of cross-references, so that connections[i] contains all the verticies that are connected to vertex at i.
  - computeMeanEdgeLength
```
private void computeMeanEdgeLength()
```
    Compute the average length of all the edges in the triangle mesh.
  - computeVertexInformation
```
private void computeVertexInformation()
```
    Let V[i] be a vertex in the triangle mesh. This function computes VMean[i], the average of the immediate neighbors of V[i]. Define S[i] = VMean[i] - V[i]. The function also computes a surface normal SNormal[i], the component of S[i] in the vertex normal direction. STangent[i] = S[i] - SNormal[i] is computed as an approximation to a tangent to the surface. Finally, Curvature[i] is an approximation of the surface curvature at V[i].
  - computeVertexNormals
```
private void computeVertexNormals()
```
    Compute the vertex normals of the triangle mesh. Each vertex normal is the unitized average of the non-unit triangle normals for those triangles sharing the vertex.
  - update2
```
private float update2(int i)
```
    Compute the coefficient of the surface normal for the update of the mesh vertex V[i] in the SNormal[i] direction. See BrainExtraction.pdf for a description of the update.
    
    Parameters:
    
    i - the index of the vertex to update
    
    Returns:
    
    the coefficient of SNormal[i] for the update
  - updateMesh
```
private void updateMesh()
```
    The heart of the segmentation. This function is responsible for the evolution of the triangle mesh that approximates the brain surface. The update has a tangential component, a surface normal component, and a vertex normal component for each vertex in the mesh. The first two components control the geometry of the mesh. The last component is based on the MRI data itself. See BrainExtraction.pdf for a detailed description of the update terms.
  - invertMesh
```
public void invertMesh()
```
    Invert the mesh z-coord, reorder the triangles, and recompute the normals:
  - setMaterial
```
public void setMaterial(javax.media.j3d.Material kMaterial)
```
    Sets the material properties of the mesh.
    
    Parameters:
    
    kMaterial - new material properties.
  - getMaterial
```
public javax.media.j3d.Material getMaterial()
```
    Gets the material properties of the mesh:
    
    Returns:
    
    material properties.
  - setTransparency
```
public void setTransparency(float transparency)
```
    Sets the mesh transparency.
    
    Parameters:
    
    transparency - mesh transparency
  - getTransparency
```
public float getTransparency()
```
    Gets the mesh transparency.
    
    Returns:
    
    mesh transparency.

Class ModelTriangleMesh

Nested Class Summary

Field Summary

Fields inherited from class javax.media.j3d.IndexedGeometryArray

Fields inherited from class javax.media.j3d.GeometryArray

Fields inherited from class javax.media.j3d.Geometry

Constructor Summary

Method Summary

Methods inherited from class javax.media.j3d.IndexedTriangleArray

Methods inherited from class javax.media.j3d.IndexedGeometryArray

Methods inherited from class javax.media.j3d.GeometryArray

Methods inherited from class javax.media.j3d.NodeComponent

Methods inherited from class javax.media.j3d.SceneGraphObject

Methods inherited from class java.lang.Object

Field Detail

direction

startLocation

box

kInvalid

m_afCurvature

m_akAdjacent

m_akSNormal

m_akSTangent

m_akVMean

m_akVNormal

m_fEParam

m_fFParam

m_fMeanEdgeLength

m_fStiffness

m_kEMap

connections

m_kE0

m_kE1

m_kN

m_kGenerator

m_kV0

m_kV1

m_kV2

m_kV3

m_kMaterial

m_fTransparency

m_kColors

perVertexColor

vertexData

cellData

Constructor Detail

ModelTriangleMesh

ModelTriangleMesh

ModelTriangleMesh

ModelTriangleMesh

ModelTriangleMesh

ModelTriangleMesh

ModelTriangleMesh

ModelTriangleMesh

Method Detail

init

getPerVertexColor

getVertexData

getVertexData

setVertexData

setVertexData

setVertexData

setVertexData

setCellData

getCellData

getDirection

getStartLocation

loadTMesh

loadTMesh

save

loadVRMLMesh

loadVTKLegacyMesh

loadVTKXMLMesh

parseVRMLMesh

saveAsPortableVRML

saveAsTextFile

saveAsVRML

affineTransform

affineTransform

area