/* $RCSfile$
* $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.openscience.jvxl.simplewriter;
import java.util.ArrayList;
import java.util.List;
import javax.vecmath.Point3f;
import javax.vecmath.Vector3f;
import org.jmol.jvxl.calc.MarchingCubes;
import org.jmol.jvxl.data.JvxlData;
import org.jmol.jvxl.data.VolumeData;
import org.jmol.jvxl.readers.Parameters;
//import org.jmol.util.Logger;
public class SimpleMarchingCubes extends MarchingCubes {
/*
* An adaptation of Marching Cubes to include data slicing and the option
* for progressive reading of the data. 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
*
* The "Simple" version does not create triangle data,
* just the JVXL edgeData string
*
*/
private boolean doCalcArea;
private boolean doSaveSurfacePoints;
private float calculatedArea = Float.NaN;
private float calculatedVolume = Float.NaN;
private List surfacePoints;
private VoxelDataCreator vdc;
public SimpleMarchingCubes(VoxelDataCreator vdc, VolumeData volumeData,
Parameters params, JvxlData jvxlData,
List surfacePointsReturn, float[] areaVolumeReturn) {
// when just creating a JVXL file all you really need are:
//
// volumeData.voxelData[x][y][z]
// cutoff
//
// also includes the option to return a List of surfacePoints
// and/or calculate the area of the surface.
//
/* these next two bitsets encode vertices excluded because they are NaN
* (which will exclude the entire cell)
* and triangles because, perhaps, they are out of range.
*
*/
this.vdc = vdc;
mode = (vdc == null ? MODE_CUBE : MODE_GETXYZ);
setParameters(volumeData, params);
doCalcArea = (areaVolumeReturn != null);
surfacePoints = surfacePointsReturn;
if (surfacePoints == null && doCalcArea)
surfacePoints = new ArrayList();
doSaveSurfacePoints = (surfacePoints != null);
jvxlData.jvxlEdgeData = getEdgeData();
jvxlData.nPointsX = volumeData.voxelCounts[0];
jvxlData.nPointsY = volumeData.voxelCounts[1];
jvxlData.nPointsZ = volumeData.voxelCounts[2];
jvxlData.setSurfaceInfoFromBitSet(bsVoxels, null);
if (doCalcArea) {
areaVolumeReturn[0] = calculatedArea;
areaVolumeReturn[1] = calculatedVolume;
}
}
protected float getValue(int i, int x, int y, int z, int pt, float[] tempValues) {
if (bsValues.get(pt))
return tempValues[pt % yzCount];
bsValues.set(pt);
float value = vdc.getValue(x, y, z);
tempValues[pt % yzCount] = value;
if (isInside(value, cutoff, isCutoffAbsolute))
bsVoxels.set(pt);
return value;
}
protected int newVertex(Point3f pointA, Vector3f edgeVector, float f) {
// you could do something with this point if you wanted to
// here we save it for the surface area/volume calculation
if (doSaveSurfacePoints) {
Point3f pt = new Point3f();
pt.scaleAdd(f, edgeVector, pointA);
surfacePoints.add(pt);
}
return edgeCount++;
}
protected void processTriangles(int insideMask) {
if (doCalcArea)
super.processTriangles(insideMask);
}
private Vector3f vTemp = new Vector3f();
private Vector3f vAC = new Vector3f();
private Vector3f vAB = new Vector3f();
protected void addTriangle(int ia, int ib, int ic, int edgeType) {
// If you were doing something with the triangle vertices
// you would do it here.
// In this example we are just computing the area and volume
Point3f pta = (Point3f) surfacePoints.get(edgePointIndexes[ia]);
Point3f ptb = (Point3f) surfacePoints.get(edgePointIndexes[ib]);
Point3f ptc = (Point3f) surfacePoints.get(edgePointIndexes[ic]);
vAB.sub(ptb, pta);
vAC.sub(ptc, pta);
vTemp.cross(vAB, vAC);
float area = vTemp.length() / 2;
calculatedArea += area;
vAB.set(ptb);
vAC.set(ptc);
vTemp.cross(vAB, vAC);
vAC.set(pta);
calculatedVolume += vAC.dot(vTemp) / 6;
}
}