/* $RCSfile$
 * $Author: hansonr $
 * $Date: 2007-03-30 11:40:16 -0500 (Fri, 30 Mar 2007) $
 * $Revision: 7273 $
 *
 * Copyright (C) 2007 Miguel, Bob, Jmol Development
 *
 * Contact: hansonr@stolaf.edu
 *
 *  This library is free software; you can redistribute it and/or
 *  modify it under the terms of the GNU Lesser General Public
 *  License as published by the Free Software Foundation; either
 *  version 2.1 of the License, or (at your option) any later version.
 *
 *  This library is distributed in the hope that it will be useful,
 *  but WITHOUT ANY WARRANTY; without even the implied warranty of
 *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 *  Lesser General License for more details.
 *
 *  You should have received a copy of the GNU Lesser General Public
 *  License along with this library; if not, write to the Free Software
 *  Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
 */
package org.jmol.jvxl.calc;



import javajs.util.BS;
import org.jmol.jvxl.api.VertexDataServer;
import org.jmol.jvxl.data.JvxlCoder;
import org.jmol.jvxl.data.VolumeData;
import org.jmol.jvxl.readers.Parameters;

import javajs.util.SB;
import javajs.util.P3;
import javajs.util.P3i;
import javajs.util.P4;
import org.jmol.util.TriangleData;
import javajs.util.V3;

public class MarchingCubes extends TriangleData {

  /*
   * An adaptation of Marching Cubes that includes data slicing. 
   * Associated SurfaceReader and VoxelData structures are required 
   * to store the sequential values in the case of a plane
   * and to deliver the sequential vertex numbers in any case.
   * 
   * Author: Bob Hanson, hansonr@stolaf.edu
   *  
   * inputs: surfaceReader: interface to other methods
   *         volumeData, containing all information relating to origin, axes, etc.
   *         
   *         MODE_PLANE volume data will be read progressively, by yz planes, starting from x = 0.
   *            This is a very efficient way to read the data -- only two active planes, 
   *            which are swapped.
   *         MODE_CUBE volumeData.voxelData possibly with 3D voxel data
   *         MODE_JVXL bsVoxels -- optional alternative, JVXL-type BitSet indicating 
   *            which vertices are inside and which outside
   *            in the order for(x 0 to nX){for(y 0 to nY){for(z 0 to nZ){}}}
   * 
   * surfaceReader.getSurfacePointIndex gets the actual Point3f vertex points and
   * returns the fraction information. It is exported here, because the JVXL reader may use this
   * as an opportunity to deliver the fractional information, thus providing the
   * actual position of the vertex point on the isosurface. 
   *      
   * outputs: Point3f positions of isosurface intersections with grid via SurfaceReader.addVertex()
   *          Point4f triangle data via surfaceReader.addTriangleCheck()
   *          bsVoxels -- returned same (JVXL file data) or filled (otherwise)
   *          edgeData -- encoded fraction data as a string
   *          
   *          bsExcludedVertices -- an option to exclude vertices based on having NaN values
   *          bsExcludedTriangles -- an option to exclude triangles based on position in space
   *  
   */

  protected VertexDataServer surfaceReader;
  protected VolumeData volumeData;
  protected int contourType;
  protected boolean isContoured;
  protected float cutoff;
  protected boolean isCutoffAbsolute;
  protected boolean isSquared;
  protected boolean isXLowToHigh;

  protected int cubeCountX, cubeCountY, cubeCountZ;
  protected int nY, nZ;
  protected int yzCount;
  
  protected boolean colorDensity;
  protected boolean integrateSquared = true;
  public BS bsVoxels;
  protected BS bsExcludedVertices;
  protected BS bsExcludedTriangles;
  protected BS bsExcludedPlanes;

  protected SB edgeData = new SB();
  
  private boolean excludePartialCubes = true; // original way
  
  public MarchingCubes() {
    // as triangleServer  
  }
  
  public MarchingCubes(VertexDataServer surfaceReader, VolumeData volumeData,
      Parameters params, BS bsVoxels) {

    // If just creating a JVXL file, see org.openscience.jmol.jvxl.simplewriter.SimpleMarchingCubes.java
    //
  
    // setting this false could upset reading 
    // older Jmol version files -- will need a flag IN the file for this if we do it
    excludePartialCubes = true; 
    
    this.surfaceReader = surfaceReader;
    this.bsVoxels = bsVoxels;
    BS[] bsExcluded = params.bsExcluded;
    bsExcludedVertices =  (bsExcluded[0] == null ? bsExcluded[0] = new BS() : bsExcluded[0]);
    bsExcludedPlanes =    (bsExcluded[2] == null ? bsExcluded[2] = new BS() : bsExcluded[2]);
    bsExcludedTriangles = (bsExcluded[3] == null ? bsExcluded[3] = new BS() : bsExcluded[3]);
    // TODO -- need not be setting up planes for simple value-readers
    
    mode = (volumeData.getVoxelData() != null || volumeData.mappingPlane != null ? MODE_CUBE 
        : bsVoxels != null ? MODE_JVXL : MODE_PLANES);
    setParameters(volumeData, params);
  }

  protected void setParameters(VolumeData volumeData, Parameters params) {
    this.volumeData = volumeData;
    colorDensity = params.colorDensity;
    isContoured = params.thePlane == null && params.isContoured && !colorDensity;
    cutoff = params.cutoff;
    isCutoffAbsolute = params.isCutoffAbsolute;
    contourType = params.contourType;
    isSquared = params.isSquared;
    isXLowToHigh = params.isXLowToHigh;

    cubeCountX = volumeData.voxelCounts[0] - 1;
    cubeCountY = volumeData.voxelCounts[1] - 1;
    cubeCountZ = volumeData.voxelCounts[2] - 1;
    volumeData.getYzCount();
    if (params.mapLattice != null) {
      // extend plane out to full lattice, if specified
      cubeCountX *= Math.abs(params.mapLattice.x);
      cubeCountY *= Math.abs(params.mapLattice.y);
      cubeCountZ *= Math.abs(params.mapLattice.z);
    }
    nY = cubeCountY + 1;
    nZ = cubeCountZ + 1;
    yzCount = nY * nZ;
    if (bsVoxels == null)
      bsVoxels = new BS();
    edgeVertexPointers = (isXLowToHigh ? edgeVertexPointersLowToHigh : edgeVertexPointersHighToLow);
    edgeVertexPlanes =  (isXLowToHigh ? edgeVertexPlanesLowToHigh : edgeVertexPlanesHighToLow);
    isoPointIndexPlanes = new int[2][yzCount][3];
    yzPlanes = (mode == MODE_PLANES ? new float[2][yzCount] : null);
    setLinearOffsets();
    calcVoxelVertexVectors();
  }

  protected int mode;
  protected final static int MODE_CUBE = 1;
  protected final static int MODE_JVXL = 2;
  protected final static int MODE_PLANES = 3;

  protected final float[] vertexValues = new float[8];

  protected int edgeCount;

  protected final V3[] voxelVertexVectors = new V3[8];
  protected final V3[] edgeVectors = new V3[12];
  {
    for (int i = 12; --i >= 0;)
      edgeVectors[i] = new V3();
  }

  protected void calcVoxelVertexVectors() {
    for (int i = 8; --i >= 0;)
      volumeData.transform(cubeVertexVectors[i],
          voxelVertexVectors[i] = new V3());
    for (int i = 12; --i >= 0;)
      edgeVectors[i].sub2(voxelVertexVectors[edgeVertexes[i + i + 1]],
          voxelVertexVectors[edgeVertexes[i + i]]);
  }

  /* see also org.openscience.jmol.jvxl.simplewriter.SimpleMarchingCubes.java
   * for a streamlined version of this method that does simple writing
   * of JVXL files from cube data. 
   * 
   */

  protected static int[] yzPlanePts = new int[] { 
      0, 1, 1, 0, 
      0, 1, 1, 0 
  };
  protected final int[] edgePointIndexes = new int[12];
  protected int[][][] isoPointIndexPlanes;
  protected float[][] yzPlanes;

  protected int[][] resetIndexPlane(int[][] plane) {
    for (int i = 0; i < yzCount; i++)
      for (int j = 0; j < 3; j++)
        plane[i][j] = Integer.MIN_VALUE;
    return plane;
  }

  private P4 mappingPlane;
  private boolean allInside;
  private boolean isInside;
  private P3i offset;
  private float[][][] voxelData;
  
  public String getEdgeData() {

    if (cubeCountX < 0 || cubeCountY < 0 || cubeCountZ < 0)
      return "";
    mappingPlane = volumeData.mappingPlane;

    // Logger.startTimer();

    /*
     * The (new, Jmol 11.7.26) Marching Cubes code creates the
     * isoPointIndexes[2][nY * nZ][3] array that holds two slices of edge data.
     * Each edge is assigned a specific vertex, such that each vertex may have
     * up to 3 associated edges.
     * 
     * Feb 10, 2009 -- Bob Hanson
     */

    //int insideCount = 0, outsideCount = 0, surfaceCount = 0;
    edgeCount = 0;

    int x0, x1, xStep, ptStep, pt, ptX;
    if (isXLowToHigh) {
      // used for progressive plane readers
      // we are starting at the top corner, in the next to last
      // cell on the next to last row of the first plane
      x0 = 0;
      x1 = cubeCountX + (colorDensity ? 1 : 0);
      if (colorDensity) {
        x1 = cubeCountX + 1;
        ptX = yzCount - 1;
      } else {
        x1 = cubeCountX;
        ptX = (yzCount - 1) - nZ - 1;        
      }
      xStep = 1;
      ptStep = yzCount;
    } else {
      // NOTE: isXLowToHigh FALSE is not compatible with progressive plane reading.
      //       One should never need to do that anyway, because one can always
      //       define the cube axes such that they go "from low to high in X"
      // we are starting at the top corner, in the next to last
      // cell on the next to last row of the next to last plane(!)
      if (colorDensity) {
        x0 = cubeCountX;
        ptX = (cubeCountX + 1) * yzCount - 1;
      } else {
        x0 = cubeCountX - 1;
        ptX = (cubeCountX * yzCount - 1) - nZ - 1;
      }
      x1 = -1;
      xStep = -1;
      ptStep = -yzCount;
    }
    pt = ptX;
    resetIndexPlane(isoPointIndexPlanes[1]);
    voxelData = null;
    int y1 = cubeCountY + (colorDensity ? 1 : 0);
    int z1 = cubeCountZ + (colorDensity ? 1 : 0);
    switch (mode) {
    case MODE_PLANES:
      getPlane(x0, false);
      break;
    case MODE_CUBE:
      voxelData = volumeData.getVoxelData();
      break;
    }
    allInside = (colorDensity && (cutoff == 0 
        || mode == MODE_JVXL && bsVoxels.nextSetBit(0) < 0));
    boolean colorDensityAll = (colorDensity && cutoff == 0);
    float v = 0;
    for (int x = x0; x != x1; x += xStep, ptX += ptStep, pt = ptX) {

      // we swap planes of grid data when
      // obtaining the grid data point by point

      if (mode == MODE_PLANES) {
        // for a progressive reader, we read the next two planes
        // for x = 0, 2, 4, 6...
        // say we have 50 points; then we have 49 cubes
        // we definely what planes 0-49, but we will be processing those
        // [0 1] [1 2] [2 3] ... [48 49]
        // so our last x is 48, and there is no problem with (x + xStep) being == x1.
        // fixed in Jmol 12.1.51 -- was "x + xStep != x1"
        if (x + xStep <= x1)
          getPlane(x + xStep, true);
      }

      // now scan the plane of cubicals

      if (bsExcludedPlanes.get(x) && bsExcludedPlanes.get(x + xStep))
        continue;
      
      if (colorDensity) {
        // MODE_JVXL not allowed here
        for (int y = y1; --y >= 0;)
          for (int z = z1; --z >= 0; pt--) {
            // 0 cutoff read as "show grid points only"
            v = getValue(x, y, z, pt, 0);
            if (colorDensityAll || isInside) {
              // xyz corner is inside, so add this point
              // TODO - we are missing the outside edges of these 
              // in the Y and Z direction 
              addVertex(x, y, z, pt, v);
            }
          }
        continue;
      }

      // we swap the edge vertex index planes

      int[][] indexPlane = isoPointIndexPlanes[0];
      isoPointIndexPlanes[0] = isoPointIndexPlanes[1];
      isoPointIndexPlanes[1] = resetIndexPlane(indexPlane);

      boolean noValues = true;
      for (int y = y1; --y >= 0; pt--) {
        for (int z = z1; --z >= 0; pt--) {
          int insideMask = 0;
          // create the bitset mask indicating which vertices are inside.
          // 0xFF here means "all inside"; 0x00 means "all outside"
          for (int i = 8; --i >= 0;) {
            v = getValue(x, y, z, pt, i);
            if (isInside)
              insideMask |= Pwr2[i];
          }
          // last value for i is 0, the x,y,z point itself
          // so we need only check it for noValues -- on THIS plane
          if (noValues && !Float.isNaN(v))
            noValues = false;
          if (insideMask == 0) {
            //++outsideCount;
            continue;
          }
          if (insideMask == 0xFF) {
            //++insideCount;
            continue;
          }
          //++surfaceCount;

          // This cube is straddling the cutoff. We must check all edges
          // Note that we do not process it if it has an NaN values
          if (processOneCubical(insideMask, x, y, z, pt) && !isContoured
              && !colorDensity) {
            processTriangles(insideMask);
          }
        }
      }
      if (noValues) {
        bsExcludedPlanes.set(x);
      }
    }

    return edgeData.toString();
  }

  private float getValue(int x, int y, int z, int pt, int i) {
    float v;

    // cubeVertexOffsets just gets us 
    // the specific grid point relative
    // to our base x,y,z cube position

    offset = cubeVertexOffsets[i];
    int pti = pt + linearOffsets[i];
    switch (mode) {
    case MODE_PLANES:
      v = vertexValues[i] = getValueArray(x + offset.x, y + offset.y, z
          + offset.z, pti, yzPlanes[yzPlanePts[i]]);
      isInside = (allInside || bsVoxels.get(pti));
      break;
    case MODE_JVXL:
      isInside = (allInside || bsVoxels.get(pti));
      v = vertexValues[i] = (bsExcludedVertices.get(pti) ? Float.NaN
          : isInside ? 1 : 0);
      break;
    default:
    case MODE_CUBE:
      //if (i == 0 && y == 0 && z == 0)
        //dumpPlane(x, null);
      if (mappingPlane == null) {
        v = vertexValues[i] = voxelData[x + offset.x][y
          + offset.y][z + offset.z];
      } else {
        volumeData.voxelPtToXYZ(x + offset.x, y + offset.y, z
            + offset.z, pt0);
        v = vertexValues[i] = volumeData.distanceToMappingPlane(pt0);
      }
      if (isSquared)
        vertexValues[i] *= vertexValues[i];
      isInside = (allInside ? true : isInside(vertexValues[i], cutoff, isCutoffAbsolute));
      if (isInside)
        bsVoxels.set(pti);
    }
    return v;
  }

  private void getPlane(int i, boolean andSwap) {
    if (i < 0 || i > cubeCountX)
      return;
    /*float[] p = */surfaceReader.getPlane(i);
    //dumpPlane(i, p);
    if (andSwap) {
      float[] plane = yzPlanes[0];
      yzPlanes[0] = yzPlanes[1];
      yzPlanes[1] = plane;
    }
  }
//  private void dumpPlane(int n, float[] plane) {
//    float test = 0;
//    if (plane == null)
//      for (int y = 0; y <= cubeCountY; y++)
//        for (int z = 0; z <= cubeCountZ; z++)
//          test += volumeData.voxelData[n][y][z];
//    else
//      for (int i = 0; i < yzCount; i++)
//        test += plane[i];
//    System.out.println(isXLowToHigh + " test " + n + "=" + test);
//  }
  
  protected void processTriangles(int insideMask) {

    // the inside mask serves to define the triangles necessary
    // if just creating JVXL files, this step is unnecessary

    byte[] triangles = triangleTable2[insideMask];
    for (int i = triangles.length; (i -= 4) >= 0;)
      addTriangle(triangles[i], triangles[i + 1], triangles[i + 2],
          triangles[i + 3]);   
  }

  protected void addVertex(int x, int y, int z, int pti, float value) {
    volumeData.voxelPtToXYZ(x, y, z, pt0);
    if (surfaceReader.addVertexCopy(pt0, value, -4, true) < 0)
      bsExcludedVertices.set(pti);
  }

  protected int nTriangles;
  protected void addTriangle(int ia, int ib, int ic, int edgeType) {
    if (!bsExcludedTriangles.get(nTriangles) &&
        surfaceReader.addTriangleCheck(edgePointIndexes[ia], 
        edgePointIndexes[ib], edgePointIndexes[ic], 
        edgeType, 0, isCutoffAbsolute, 0) < 0) {
      bsExcludedTriangles.set(nTriangles);
    }
    nTriangles++;
  }

  protected BS bsValues = new BS();

  protected float getValueArray(int x, int y, int z, int pt, float[] tempValues) {
    int ptyz = pt % yzCount;
    //if (bsValues.get(pt))
      //return tempValues[ptyz];
    bsValues.set(pt);
    float value = surfaceReader.getValue(x, y, z, ptyz);
    if (isSquared)
      value *= value;
    tempValues[ptyz] = value;
    if (isInside(value, cutoff, isCutoffAbsolute))
      bsVoxels.set(pt);
    return value;
  }

  public static boolean isInside(float voxelValue, float max, boolean isAbsolute) {
    return ((max > 0 && (isAbsolute ? Math.abs(voxelValue) : voxelValue) >= max) || (max <= 0 && voxelValue <= max));
  }

  protected final P3 pt0 = new P3();
  protected final P3 pointA = new P3();

  protected final static int[] edgeVertexPointersLowToHigh = new int[] {
      1, 1, 2, 0, 
      5, 5, 6, 4,
      0, 1, 2, 3
  };
  
  protected final static int[] edgeVertexPointersHighToLow = new int[] {
      0, 1, 3, 0, 
      4, 5, 7, 4,
      0, 1, 2, 3
  };

  protected int[] edgeVertexPointers;

  protected final static int[] edgeVertexPlanesLowToHigh = new int[] {
      1, 1, 1, 0, 
      1, 1, 1, 0, 
      0, 1, 1, 0
  };  // from high to low, only edges 3, 7, 8, and 11 are from plane 0

  protected final static int[] edgeVertexPlanesHighToLow = new int[] {
      1, 0, 1, 1,
      1, 0, 1, 1,
      1, 0, 0, 1
  }; //from high to low, only edges 1, 5, 9, and 10 are from plane 0

  protected int[] edgeVertexPlanes;
  
  protected boolean processOneCubical(int insideMask, int x, int y, int z, int pt) {

    /*
     * The key to the algorithm is that we have a catalog that
     * maps the inside-vertex mask to an edge mask, and then
     * each edge is associated with a specific vertex. 
     * 
     * Each cube vertex may be associated with from 0 to 3 edges,
     * depending upon where it lies in the overall cube of data.
     * 
     * When scanning X from low to high, the "leading vertex" is
     * vertex 1 and edgeVertexPlanes[1]. Edges 0, 1, and 9 are 
     * associated with vertex 1, and others are associated similarly.
     * 
     * When scanning X from high to low, the "leading vertex" is
     * vertex 0 and edgeVertexPlanes[1]. Edges 0, 3, and 8 are 
     * associated with vertex 0, and others are associated similarly.
     * 
     * edgePointIndexes[iEdge] tracks the vertex index for this
     * specific cubical so that triangles can be created properly.
     *  
     * 
     *                      Y 
     *                      4 --------4--------- 5  
     *                     /|                   /|
     *                    / |                  / |
     *                   /  |                 /  |
     *                  7   8                5   |
     *                 /    |               /    9
     *                /     |              /     |
     *               7 --------6--------- 6      |
     *               |      |             |      |
     *               |      0 ---------0--|----- 1    X
     *               |     /              |     /
     *              11    /               10   /
     *               |   3                |   1
     *               |  /                 |  /
     *               | /                  | /
     *               3 ---------2-------- 2
     *              Z 
     *              /                    /              
     *  edgeVertexPlanes[0]            [1] (scanning x low to high)
     *  edgeVertexPlanes[1]            [0] (scanning x high to low)
     *           
     */
    


    int edgeMask = insideMaskTable[insideMask];
    boolean isNaN = false;
    for (int iEdge = 12; --iEdge >= 0;) {

      // bit set to one means it's a relevant edge

      int xEdge = Pwr2[iEdge];
      if ((edgeMask & xEdge) == 0)
        continue;

      // if we have a point already, we don't need to check this edge.
      // for triangles, this will be an index into an array;
      // for just creating JVXL files, this can just be 0

      int iPlane = edgeVertexPlanes[iEdge];
      int iPt = (pt + linearOffsets[edgeVertexPointers[iEdge]]) % yzCount;
      int iType = edgeTypeTable[iEdge];
      int index = edgePointIndexes[iEdge] = isoPointIndexPlanes[iPlane][iPt][iType];
      if (index != Integer.MIN_VALUE) {
        if (index == -1)
          isNaN = excludePartialCubes; // -- problem with older Jmol files? 
          // this says, "If any point on the cube is NaN, then 
          //don't process the cube. 
        continue; // propagated from neighbor
      }
      // here's an edge that has to be checked.

      // get the vertex numbers 0 - 7

      int vertexA = edgeVertexes[iEdge << 1];
      int vertexB = edgeVertexes[(iEdge << 1) + 1];

      // pick up the actual value at each vertex
      // this array of 8 values is updated as we go.

      float valueA = vertexValues[vertexA];
      float valueB = vertexValues[vertexB];

      // we allow for NaN values -- missing triangles


      // the exact point position -- not important for just
      // creating the JVXL file. In that case, all you 
      // need are the two values valueA and valueB and the cutoff.
      // from those you can define the fractional offset

      // here is where we get the value and assign the point for that edge
      // it is where the JVXL surface data line is appended

      calcVertexPoint(x, y, z, vertexA, pointA);

      edgeCount++;

      int i = edgePointIndexes[iEdge] = isoPointIndexPlanes[iPlane][iPt][iType] = surfaceReader
          .getSurfacePointIndexAndFraction(cutoff, isCutoffAbsolute, x, y, z,
              cubeVertexOffsets[vertexA], vertexA, vertexB, valueA, valueB,
              pointA, edgeVectors[iEdge], iType == contourType, fReturn);

      addEdgeData(i < 0 ? Float.NaN : fReturn[0]);

      // If the fraction returns NaN, this is because one of the end points
      // is NaN; if the point index returns -1, then the point has been 
      // excluded by the meshDataServer (Isosurface) for some other reason,
      // for example because it is outside the limits of the box.
      
      if (Float.isNaN(fReturn[0]) || i < 0)
        isNaN = excludePartialCubes;
    }
    return !isNaN;
  }

  protected void addEdgeData(float f) {
    char ch = JvxlCoder.jvxlFractionAsCharacter(f);
    edgeData.appendC(ch);
  }

  protected float[] fReturn = new float[1];
  
  public void calcVertexPoint(int x, int y, int z, int vertex, P3 pt) {
    volumeData.voxelPtToXYZ(x, y, z, pt0);
    pt.add2(pt0, voxelVertexVectors[vertex]);
  }

  protected final static V3[] cubeVertexVectors = { 
    V3.new3(0, 0, 0),
    V3.new3(1, 0, 0), 
    V3.new3(1, 0, 1), 
    V3.new3(0, 0, 1),
    V3.new3(0, 1, 0), 
    V3.new3(1, 1, 0), 
    V3.new3(1, 1, 1),
    V3.new3(0, 1, 1) };


  /*                     Y 
   *                      4 --------4--------- 5                     +z --------4--------- +yz+z                  
   *                     /|                   /|                     /|                   /|
   *                    / |                  / |                    / |                  / |
   *                   /  |                 /  |                   /  |                 /  |
   *                  7   8                5   |                  7   8                5   |
   *                 /    |               /    9                 /    |               /    9
   *                /     |              /     |                /     |              /     |
   *               7 --------6--------- 6      |            +z+1 --------6--------- +yz+z+1|
   *               |      |             |      |               |      |             |      |
   *               |      0 ---------0--|----- 1    X          |      0 ---------0--|----- +yz    X(outer)    
   *               |     /              |     /                |     /              |     /
   *              11    /               10   /                11    /               10   /
   *               |   3                |   1                  |   3                |   1
   *               |  /                 |  /                   |  /                 |  /
   *               | /                  | /                    | /                  | /
   *               3 ---------2-------- 2                     +1 ---------2-------- +yz+1
   *              Z                                           Z (inner)
   * 
   *                                                              streaming data offsets
   * type 0: x-edges: 0 2 4 6
   * type 1: y-edges: 8 9 10 11
   * type 2: z-edges: 1 3 5 7
   * 
   * Data stream offsets for vertices, relative to point 0, based on reading 
   * loops {for x {for y {for z}}} 0-->n-1
   * y and z are numbers of grid points in those directions:
   * 
   *            0    1      2      3      4      5      6        7
   *            0   +yz   +yz+1   +1     +z    +yz+z  +yz+z+1  +z+1     
   * 
   * These are just looked up in a table. After the first set of cubes, 
   * we are only adding points 1, 2, 5 or 6. This means that initially
   * we need two data slices, but after that only one (slice 1):
   * 
   *            base
   *           offset 0    1      2      3      4      5      6     7
   *  slice[0]        0                 +1     +z                 +z+1     
   *  slice[1]  +yz        0     +1                   +z    +z+1      
   * 
   *  slice:          0    1      1      0      0      1      1     0
   *  
   *  We can request reading of two slices (2*nY*nZ data points) first, then
   *  from then on, just nY*nZ points. "Reading" is really just being handed a 
   *  pointer into an array. Perhaps that array is already filled completely;
   *  perhaps it is being read incrementally. 
   *  
   *  As it is now, the JVXL data are read into a BitSet 
   *  so we can continue to do that with NON progressive files.
   *  
   *   
   */

  protected final static int edgeTypeTable[] = { 
    0, 2, 0, 2, 
    0, 2, 0, 2, 
    1, 1, 1, 1 };
  // 0=along X, 1=along Y, 2=along Z

  protected final int[] linearOffsets = new int[8];

  /* 
   * set the linear offsets for generating a unique cell ID,
   * for pointing into the inside/outside BitSet,
   * and for finding the associated vertex for an edge.
   * 
   */
  
  protected void setLinearOffsets() {
    linearOffsets[0] = 0;
    linearOffsets[1] = yzCount;
    linearOffsets[2] = yzCount + 1;
    linearOffsets[3] = 1;
    linearOffsets[4] = nZ;
    linearOffsets[5] = yzCount + nZ;
    linearOffsets[6] = yzCount + nZ + 1;
    linearOffsets[7] = nZ + 1;
  }

  public int getLinearOffset(int x, int y, int z, int offset) {
    return x * yzCount + y * nZ + z + linearOffsets[offset];
  }

  protected final static short insideMaskTable[] = { 0x0000, 0x0109, 0x0203,
      0x030A, 0x0406, 0x050F, 0x0605, 0x070C, 0x080C, 0x0905, 0x0A0F, 0x0B06,
      0x0C0A, 0x0D03, 0x0E09, 0x0F00, 0x0190, 0x0099, 0x0393, 0x029A, 0x0596,
      0x049F, 0x0795, 0x069C, 0x099C, 0x0895, 0x0B9F, 0x0A96, 0x0D9A, 0x0C93,
      0x0F99, 0x0E90, 0x0230, 0x0339, 0x0033, 0x013A, 0x0636, 0x073F, 0x0435,
      0x053C, 0x0A3C, 0x0B35, 0x083F, 0x0936, 0x0E3A, 0x0F33, 0x0C39, 0x0D30,
      0x03A0, 0x02A9, 0x01A3, 0x00AA, 0x07A6, 0x06AF, 0x05A5, 0x04AC, 0x0BAC,
      0x0AA5, 0x09AF, 0x08A6, 0x0FAA, 0x0EA3, 0x0DA9, 0x0CA0, 0x0460, 0x0569,
      0x0663, 0x076A, 0x0066, 0x016F, 0x0265, 0x036C, 0x0C6C, 0x0D65, 0x0E6F,
      0x0F66, 0x086A, 0x0963, 0x0A69, 0x0B60, 0x05F0, 0x04F9, 0x07F3, 0x06FA,
      0x01F6, 0x00FF, 0x03F5, 0x02FC, 0x0DFC, 0x0CF5, 0x0FFF, 0x0EF6, 0x09FA,
      0x08F3, 0x0BF9, 0x0AF0, 0x0650, 0x0759, 0x0453, 0x055A, 0x0256, 0x035F,
      0x0055, 0x015C, 0x0E5C, 0x0F55, 0x0C5F, 0x0D56, 0x0A5A, 0x0B53, 0x0859,
      0x0950, 0x07C0, 0x06C9, 0x05C3, 0x04CA, 0x03C6, 0x02CF, 0x01C5, 0x00CC,
      0x0FCC, 0x0EC5, 0x0DCF, 0x0CC6, 0x0BCA, 0x0AC3, 0x09C9, 0x08C0, 0x08C0,
      0x09C9, 0x0AC3, 0x0BCA, 0x0CC6, 0x0DCF, 0x0EC5, 0x0FCC, 0x00CC, 0x01C5,
      0x02CF, 0x03C6, 0x04CA, 0x05C3, 0x06C9, 0x07C0, 0x0950, 0x0859, 0x0B53,
      0x0A5A, 0x0D56, 0x0C5F, 0x0F55, 0x0E5C, 0x015C, 0x0055, 0x035F, 0x0256,
      0x055A, 0x0453, 0x0759, 0x0650, 0x0AF0, 0x0BF9, 0x08F3, 0x09FA, 0x0EF6,
      0x0FFF, 0x0CF5, 0x0DFC, 0x02FC, 0x03F5, 0x00FF, 0x01F6, 0x06FA, 0x07F3,
      0x04F9, 0x05F0, 0x0B60, 0x0A69, 0x0963, 0x086A, 0x0F66, 0x0E6F, 0x0D65,
      0x0C6C, 0x036C, 0x0265, 0x016F, 0x0066, 0x076A, 0x0663, 0x0569, 0x0460,
      0x0CA0, 0x0DA9, 0x0EA3, 0x0FAA, 0x08A6, 0x09AF, 0x0AA5, 0x0BAC, 0x04AC,
      0x05A5, 0x06AF, 0x07A6, 0x00AA, 0x01A3, 0x02A9, 0x03A0, 0x0D30, 0x0C39,
      0x0F33, 0x0E3A, 0x0936, 0x083F, 0x0B35, 0x0A3C, 0x053C, 0x0435, 0x073F,
      0x0636, 0x013A, 0x0033, 0x0339, 0x0230, 0x0E90, 0x0F99, 0x0C93, 0x0D9A,
      0x0A96, 0x0B9F, 0x0895, 0x099C, 0x069C, 0x0795, 0x049F, 0x0596, 0x029A,
      0x0393, 0x0099, 0x0190, 0x0F00, 0x0E09, 0x0D03, 0x0C0A, 0x0B06, 0x0A0F,
      0x0905, 0x080C, 0x070C, 0x0605, 0x050F, 0x0406, 0x030A, 0x0203, 0x0109,
      0x0000 };


}
