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 HashSet[]

connections

used in smoothing.

private static int[]

direction

DOCUMENT ME!

(package private) 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) HashMap

m_kEMap

DOCUMENT ME!

private 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

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!

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(RandomAccessFile kIn, ViewJProgressBar progress, int added, int total, boolean isVisible)

Load the triangle mesh from a binary file.

static ModelTriangleMesh

loadTMesh(RandomAccessFile kIn, JProgressBar pBar, int added, int total)

Load the triangle mesh from a binary file.

static ModelTriangleMesh

loadVRMLMesh(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(RandomAccessFile kIn, ViewJProgressBar progress, int added, int total, boolean flag, String fileName)

static ModelTriangleMesh

loadVTKXMLMesh(String absPath, ViewJProgressBar progress, int added, int total, boolean flag, String fileName, String dir)

static int

parseVRMLMesh(RandomAccessFile kIn)

Parses the VRML to see how many surfaces there are.

protected void

print(PrintWriter kOut)

Internal support for 'void print (String)' and 'void print (String, ModelTriangleMesh[])'.

protected void

printSMFAscii(PrintWriter kOut)

protected void

printSTLAscii(PrintWriter kOut)

Print the STL file format in ASCII.

protected void

printSTLBinary(RandomAccessFile kOut)

Print the STL file format in binary ( little endian ).

protected void

save(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(String kName, boolean flip, int[] direction, float[] startLocation, float[] box, TransMatrix inverseDicomMatrix)

Save the triangle mesh to a binary file.

static void

save(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(String kName)

protected void

saveAsPortableVRML(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(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(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(String kName)

Sate the SMF ACII file format.

void

saveAsSTLAsciiFile(String kName)

Sate the STIL ACII file format.

void

saveAsSTLBinaryFile(String kName)

Sate the STIL Binary file format.

void

saveAsTextFile(String kName)

Save the triangle mesh to a text file.

static void

saveAsTextFile(String kName, ModelTriangleMesh[] akComponent)

Save an array of triangle meshes to a text file.

protected void

saveAsVRML(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(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(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(String kName)

Saves the triangle mesh to VTK Legacy format

void

saveAsVTKXML(String fileName)

saves thr triangle mesh to VTK XML format

protected void

saveAsXML(String fileName, int[] direction, float[] startLocation, float[] box)

Internal support for 'void save (String)' and 'void save (String, ModelTriangleMesh[])'.

void

saveXMLHeader(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(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 Details
- direction
  
  private static int[] direction
  
  DOCUMENT ME!
- startLocation
  
  private static float[] startLocation
  
  DOCUMENT ME!
- box
  
  private static float[] box
  
  DOCUMENT ME!
- kInvalid
  
  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
  
  HashMap m_kEMap
  
  DOCUMENT ME!
- connections
  
  private 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 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 Details
- 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
  
  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.
  
  akColor - array of vertex colors
- 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 Details
- 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(RandomAccessFile kIn, JProgressBar pBar, int added, int total) throws 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:
  
  IOException - if there is an error reading from the file
- loadTMesh
  
  public static ModelTriangleMesh loadTMesh(RandomAccessFile kIn, ViewJProgressBar progress, int added, int total, boolean isVisible) throws 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:
  
  IOException - if there is an error reading from the file
- save
  
  public static void save(String kName, ModelTriangleMesh[] akComponent, boolean flip, int[] direction, float[] startLocation, float[] box, TransMatrix inverseDicomMatrix, javax.vecmath.Color4f[][] perVertexColorArray) throws 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:
  
  IOException - if there is an error writing to the file
- loadVRMLMesh
  
  public static ModelTriangleMesh loadVRMLMesh(RandomAccessFile kIn, ViewJProgressBar progress, int added, int total, boolean flag) throws 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:
  
  IOException - if there is an error reading from the file
- loadVTKLegacyMesh
  
  public static ModelTriangleMesh loadVTKLegacyMesh(RandomAccessFile kIn, ViewJProgressBar progress, int added, int total, boolean flag, String fileName) throws IOException
  
  Parameters:
  
  kIn -
  
  progress -
  
  added -
  
  total -
  
  flag -
  
  Returns:
  
  Throws:
  
  IOException
- loadVTKXMLMesh
  
  public static ModelTriangleMesh loadVTKXMLMesh(String absPath, ViewJProgressBar progress, int added, int total, boolean flag, String fileName, String dir) throws IOException
  
  Parameters:
  
  progress -
  
  added -
  
  total -
  
  flag -
  
  fileName -
  
  kIn -
  
  Returns:
  
  Throws:
  
  IOException
- parseVRMLMesh
  
  public static int parseVRMLMesh(RandomAccessFile kIn) throws IOException, NoSuchElementException
  
  Parses the VRML to see how many surfaces there are.
  
  Parameters:
  
  kIn - the file to parse
  
  Returns:
  
  DOCUMENT ME!
  
  Throws:
  
  IOException - DOCUMENT ME!
  
  NoSuchElementException - DOCUMENT ME!
- saveAsPortableVRML
  
  public static void saveAsPortableVRML(PrintWriter kOut, ModelTriangleMesh[] akComponent, boolean flip, int[] direction, float[] startLocation, float[] box, javax.vecmath.Color3f color) throws 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:
  
  IOException - if the specified file could not be opened for writing
- saveAsTextFile
  
  public static void saveAsTextFile(String kName, ModelTriangleMesh[] akComponent) throws 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:
  
  IOException - if the specified file could not be opened for writing
- saveAsVRML
  
  public static void saveAsVRML(String kName, ModelTriangleMesh[] akComponent, boolean flip, int[] direction, float[] startLocation, float[] box, javax.vecmath.Color3f color) throws 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:
  
  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 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(String kName, boolean flip, int[] direction, float[] startLocation, float[] box, TransMatrix inverseDicomMatrix) throws 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:
  
  IOException - if the specified file could not be opened for writing
- saveXMLHeader
  
  public void saveXMLHeader(String kName)
- saveAsPortableVRML
  
  public void saveAsPortableVRML(PrintWriter kOut, boolean flip, int numberOfShapes, int[] direction, float[] startLocation, float[] box, javax.vecmath.Color3f color) throws 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:
  
  IOException - if the specified file could not be opened for writing
- saveAsVTKLegacy
  
  public void saveAsVTKLegacy(String kName) throws IOException
  
  Saves the triangle mesh to VTK Legacy format
  
  Parameters:
  
  kName -
  
  Throws:
  
  IOException
- saveAsVTKXML
  
  public void saveAsVTKXML(String fileName) throws IOException
  
  saves thr triangle mesh to VTK XML format
  
  Parameters:
  
  kName -
  
  Throws:
  
  IOException
- saveAsTextFile
  
  public void saveAsTextFile(String kName) throws 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:
  
  IOException - if the specified file could not be opened for writing
- saveAsPlyFile
  
  public void saveAsPlyFile(String kName) throws IOException
  
  Throws:
  
  IOException
- saveAsSMFAsciiFile
  
  public void saveAsSMFAsciiFile(String kName) throws IOException
  
  Sate the SMF ACII file format.
  
  Parameters:
  
  kName - file name
  
  Throws:
  
  IOException
- saveAsSTLAsciiFile
  
  public void saveAsSTLAsciiFile(String kName) throws IOException
  
  Sate the STIL ACII file format.
  
  Parameters:
  
  kName - file name
  
  Throws:
  
  IOException
- saveAsSTLBinaryFile
  
  public void saveAsSTLBinaryFile(String kName) throws IOException
  
  Sate the STIL Binary file format.
  
  Parameters:
  
  kName - file name
  
  Throws:
  
  IOException
- saveAsVRML
  
  public void saveAsVRML(String kName, boolean flip, int numberOfShapes, int[] direction, float[] startLocation, float[] box, javax.vecmath.Color3f color) throws 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:
  
  IOException - if the specified file could not be opened for writing
- setGenerator
  
  public void setGenerator(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 invalid input: '<' lambda invalid input: '<' -mu (1/lambda) + (1/mu) invalid input: '<' 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 invalid input: '<'= j invalid input: '<'= 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 invalid input: '<'= ik invalid input: '<' 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 invalid input: '<' 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 invalid input: '<' Rk invalid input: '<' 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(PrintWriter kOut) throws 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:
  
  IOException - if there is an error writing to the file
- printSMFAscii
  
  protected void printSMFAscii(PrintWriter kOut) throws IOException
  
  Throws:
  
  IOException
- printSTLAscii
  
  protected void printSTLAscii(PrintWriter kOut) throws 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:
  
  IOException
- printSTLBinary
  
  protected void printSTLBinary(RandomAccessFile kOut) throws 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:
  
  IOException
- saveAsXML
  
  protected void saveAsXML(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:
  
  IOException - if there is an error writing to the file
- save
  
  protected void save(RandomAccessFile kOut, boolean flip, int[] direction, float[] startLocation, float[] box, TransMatrix inverseDicomMatrix, javax.vecmath.Color4f[] perVertexColorArray) throws 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
  
  perVertexColorArray - color per vertex array.
  
  inverseDicomArray - DOCUMENT ME!
  
  Throws:
  
  IOException - if there is an error writing to the file
- saveAsPortableVRML
  
  protected void saveAsPortableVRML(PrintWriter kOut, boolean flip, int[] direction, float[] startLocation, float[] box, javax.vecmath.Color3f color) throws 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:
  
  IOException - if there is an error writing to the file
- saveAsVRML
  
  protected void saveAsVRML(PrintWriter kOut, boolean flip, int[] direction, float[] startLocation, float[] box, javax.vecmath.Color3f color) throws 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:
  
  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 Details

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 Details

ModelTriangleMesh

ModelTriangleMesh

ModelTriangleMesh

ModelTriangleMesh

ModelTriangleMesh

ModelTriangleMesh

ModelTriangleMesh

ModelTriangleMesh

Method Details

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