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(RandomAccessFile kIn, ViewJProgressBar progress, int added, int total)
    Load the quad mesh from a binary file.
    protected void
    print(PrintWriter kOut)
    Internal support for 'void print (String)' and 'void print (String, ModelTriangleMesh[])'.
    void
    print(String kName)
    Save the quad mesh to a text file.
    static void
    print(String kName, ModelTriangleMesh[] akComponent)
    Save an array of quad meshes to a text file.
    protected void
    save(RandomAccessFile kOut, ViewJProgressBar progress, int added, int total)
    Internal support for 'void save (String)' and 'void save (String, ModelQuadMesh[])'.
    static void
    save(String kName, ModelQuadMesh[] akComponent, ViewJProgressBar progress)
    Save an array of quad meshes to a binary file.
    void
    save(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 Details

    • 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 Details

    • 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 Details

    • loadQMesh

      public static ModelQuadMesh loadQMesh(RandomAccessFile kIn, ViewJProgressBar progress, int added, int total) throws 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:
      IOException - if there is an error reading from the file

    • print

      public static void print(String kName, ModelTriangleMesh[] akComponent) throws 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:
      IOException - if the specified file could not be opened for writing.

    • save

      public static void save(String kName, ModelQuadMesh[] akComponent, ViewJProgressBar progress) throws 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:
      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(String kName) throws 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:
      IOException - If the specified file could not be opened for writing.

    • save

      public void save(String kName, ViewJProgressBar progress, int added, int total) throws 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:
      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(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.

    • save

      protected void save(RandomAccessFile kOut, ViewJProgressBar progress, int added, int total) throws 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:
      IOException - if there is an error writing to the file