Package gov.nih.mipav.view.renderer.J3D.model.structures

Class ModelQuadMesh

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

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