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.IndexedQuadArray
        
        gov.nih.mipav.view.renderer.J3D.model.structures.ModelQuadMesh

All Implemented Interfaces:

javax.media.j3d.GeometryUpdater
```
public class ModelQuadMesh
extends javax.media.j3d.IndexedQuadArray
implements javax.media.j3d.GeometryUpdater
```
A simple quadrilateral 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 ModelQuadMesh. The surface color is provided through the LUT. To save memory, everything is done by reference - the connection array, the vertex array, the normal array, and the color array are all stored here and modified directly.

Author:

Matthew J. McAuliffe, Ph.D., David Eberley, Neva Cherniavsky

Field Summary

Fields
Modifier and Type	Field	Description
`private javax.vecmath.Color3f[]`	`colors3f`	Holds colors for vertices.
`private int[]`	`connect`	Holds how vertices are connected.
`private float`	`heightRange`	Scale the height of the vertice - typically relative the image size.
`private float[][]`	`LUT`	Holds current LUT which dictates colors for vertices.
`private int[]`	`lutBufferRemapped`	DOCUMENT ME!
`private javax.vecmath.Vector3f`	`m_kE0`	Temporary variables to avoid 'new' calls.
`private javax.vecmath.Vector3f`	`m_kE1`	Temporary variables to avoid 'new' calls.
`private javax.vecmath.Vector3f`	`m_kN1`	Temporary variables to avoid 'new' calls.
`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.Vector3f[]`	`normal`	Holds normals in the mesh.
`private javax.vecmath.Point3f[]`	`vertex`	Holds vertices in the mesh.

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
`ModelQuadMesh(javax.vecmath.Point3f[] akVertex, int[] aiConnect, int length1, int length2, float[][] LUT, float hgtRange)`	A quad mesh whose vertex normal vectors are computed from the geometry of the mesh itself.
`ModelQuadMesh(javax.vecmath.Point3f[] akVertex, javax.vecmath.Vector3f[] akNormal, int[] aiConnect)`	A quad mesh whose vertex normal vectors have been precomputed.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`computeNormals()`	A normal vector at a vertex is computed by averaging the triangle normals for all triangles sharing the vertex.
`void`	`dispose()`	Sets all variables to null.
`static ModelQuadMesh`	`loadQMesh(java.io.RandomAccessFile kIn, ViewJProgressBar progress, int added, int total)`	Load the quad mesh from a binary file.
`protected void`	`print(java.io.PrintWriter kOut)`	Internal support for 'void print (String)' and 'void print (String, ModelTriangleMesh[])'.
`void`	`print(java.lang.String kName)`	Save the quad mesh to a text file.
`static void`	`print(java.lang.String kName, ModelTriangleMesh[] akComponent)`	Save an array of quad meshes to a text file.
`protected void`	`save(java.io.RandomAccessFile kOut, ViewJProgressBar progress, int added, int total)`	Internal support for 'void save (String)' and 'void save (String, ModelQuadMesh[])'.
`static void`	`save(java.lang.String kName, ModelQuadMesh[] akComponent, ViewJProgressBar progress)`	Save an array of quad meshes to a binary file.
`void`	`save(java.lang.String kName, ViewJProgressBar progress, int added, int total)`	Save the quad mesh to a binary file.
`void`	`setLUT(float[][] LUT)`	I don't think both are needed in the new Model LUT design. /** Accessor that sets the LUT for the colors of the indices.
`void`	`setLUTBufferRemapped(int[] lutBufferRemapped)`	Set.
`void`	`updateData(javax.media.j3d.Geometry geometry)`	This method is required for an implementor of the GeometryUpdater interface.

Methods inherited from class javax.media.j3d.IndexedQuadArray
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, 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
  - colors3f
```
private javax.vecmath.Color3f[] colors3f
```
    Holds colors for vertices.
  - connect
```
private int[] connect
```
    Holds how vertices are connected.
  - heightRange
```
private float heightRange
```
    Scale the height of the vertice - typically relative the image size.
  - LUT
```
private float[][] LUT
```
    Holds current LUT which dictates colors for vertices.
  - lutBufferRemapped
```
private int[] lutBufferRemapped
```
    DOCUMENT ME!
  - m_kE0
```
private javax.vecmath.Vector3f m_kE0
```
    Temporary variables to avoid 'new' calls.
  - m_kE1
```
private javax.vecmath.Vector3f m_kE1
```
    Temporary variables to avoid 'new' calls.
  - m_kN1
```
private javax.vecmath.Vector3f m_kN1
```
    Temporary variables to avoid 'new' calls.
  - 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.
  - normal
```
private javax.vecmath.Vector3f[] normal
```
    Holds normals in the mesh.
  - vertex
```
private javax.vecmath.Point3f[] vertex
```
    Holds vertices in the mesh.
- Constructor Detail
  - ModelQuadMesh
```
public ModelQuadMesh(javax.vecmath.Point3f[] akVertex,
                     javax.vecmath.Vector3f[] akNormal,
                     int[] aiConnect)
```
    A quad 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.
  - ModelQuadMesh
```
public ModelQuadMesh(javax.vecmath.Point3f[] akVertex,
                     int[] aiConnect,
                     int length1,
                     int length2,
                     float[][] LUT,
                     float hgtRange)
```
    A quad 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. This constructor makes a quad mesh whose vertices and colors are set by reference.
    
    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.
    
    length1 - True length of vertex array.
    
    length2 - True length of connection array.
    
    LUT - LUT for colors.
    
    hgtRange - Used to scale the height of the vertices
- Method Detail
  - loadQMesh
```
public static ModelQuadMesh loadQMesh(java.io.RandomAccessFile kIn,
                                      ViewJProgressBar progress,
                                      int added,
                                      int total)
                               throws java.io.IOException
```
    Load the quad mesh from a binary 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!
    
    Returns:
    
    The loaded quad mesh.
    
    Throws:
    
    java.io.IOException - if there is an error reading from the file
  - print
```
public static void print(java.lang.String kName,
                         ModelTriangleMesh[] akComponent)
                  throws java.io.IOException
```
    Save an array of quad meshes to a text file. The format for the file is
    int type; // 2 = ModelQuadMesh 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 quadrilaterals index[0] index[1] index[2] index[3] : index[4*(tCount-1)] index[4*(tCount-1)+1] index[4*(tCount-1)+2] index[4*(tCount-1)+3]
    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.
  - save
```
public static void save(java.lang.String kName,
                        ModelQuadMesh[] akComponent,
                        ViewJProgressBar progress)
                 throws java.io.IOException
```
    Save an array of quad meshes to a binary file. The format for the file is
    int type; // 2 = ModelQuadMesh 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.
    
    progress - DOCUMENT ME!
    
    Throws:
    
    java.io.IOException - if there is an error writing to the file.
  - 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.
  - dispose
```
public void dispose()
```
    Sets all variables to null.
  - print
```
public void print(java.lang.String kName)
           throws java.io.IOException
```
    Save the quad mesh to a text file. The format for the file is
    int type; // 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 quadrilaterals index[0] index[1] index[2] index[3] : index[4*(tCount-1)] index[4*(tCount-1)+1] index[4*(tCount-1)+2] index[4*(tCount-1)+3]
    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.
  - save
```
public void save(java.lang.String kName,
                 ViewJProgressBar progress,
                 int added,
                 int total)
          throws java.io.IOException
```
    Save the quad mesh to a binary file. The format for the file is
    int type; // 2 = ModelQuadMesh 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.
    
    progress - DOCUMENT ME!
    
    added - DOCUMENT ME!
    
    total - DOCUMENT ME!
    
    Throws:
    
    java.io.IOException - if the specified file could not be opened for writing.
  - setLUT
```
public void setLUT(float[][] LUT)
```
    I don't think both are needed in the new Model LUT design. /** Accessor that sets the LUT for the colors of the indices.
    
    Parameters:
    
    LUT - New LUT to use when setting vertex colors.
  - setLUTBufferRemapped
```
public void setLUTBufferRemapped(int[] lutBufferRemapped)
```
    Set.
    
    Parameters:
    
    lutBufferRemapped - int[]
  - updateData
```
public void updateData(javax.media.j3d.Geometry geometry)
```
    This method is required for an implementor of the GeometryUpdater interface. It is not called directly by the application. It sets the colors of the vertices based on the LUT. The System.gc() call is necessary because otherwise the application eats up memory.
    
    Specified by:
    
    updateData in interface javax.media.j3d.GeometryUpdater
    
    Parameters:
    
    geometry - Geometry object to update (ignored).
  - 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.
  - save
```
protected void save(java.io.RandomAccessFile kOut,
                    ViewJProgressBar progress,
                    int added,
                    int total)
             throws java.io.IOException
```
    Internal support for 'void save (String)' and 'void save (String, ModelQuadMesh[])'. ModelQuadMesh uses this function to write vertices, normals, and connectivity indices to the file.
    
    Parameters:
    
    kOut - The file to which the quad mesh is saved.
    
    progress - DOCUMENT ME!
    
    added - DOCUMENT ME!
    
    total - DOCUMENT ME!
    
    Throws:
    
    java.io.IOException - if there is an error writing to the file

Class ModelQuadMesh

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.IndexedQuadArray

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

colors3f

connect

heightRange

LUT

lutBufferRemapped

m_kE0

m_kE1

m_kN1

m_kV0

m_kV1

m_kV2

normal

vertex

Constructor Detail

ModelQuadMesh

ModelQuadMesh

Method Detail

loadQMesh

print

save

computeNormals

dispose

print

save

setLUT

setLUTBufferRemapped

updateData

print

save