private Geometry Triangle3DGeometry(
Iterator<il.ac.idc.jdt.Triangle> triangles_iter, int num_of_triangles) {
_triangle_arr =
new TriangleArray(3 * num_of_triangles, TriangleArray.COORDINATES | TriangleArray.COLOR_3);
int i = 0;
while ((i < num_of_triangles) && (triangles_iter.hasNext())) {
il.ac.idc.jdt.Triangle curr_triangle = triangles_iter.next();
if ((curr_triangle.getA() != null)
&& (curr_triangle.getB() != null)
&& (curr_triangle.getC() != null)) {
_triangle_arr.setCoordinate(
3 * i,
new Point3d(
curr_triangle.getA().getX(),
curr_triangle.getA().getY(),
curr_triangle.getA().getZ()));
_triangle_arr.setCoordinate(
3 * i + 1,
new Point3d(
curr_triangle.getB().getX(),
curr_triangle.getB().getY(),
curr_triangle.getB().getZ()));
_triangle_arr.setCoordinate(
3 * i + 2,
new Point3d(
curr_triangle.getC().getX(),
curr_triangle.getC().getY(),
curr_triangle.getC().getZ()));
_triangle_arr.setColor(3 * i, get_col_by_height((int) curr_triangle.getA().getZ()));
_triangle_arr.setColor(3 * i + 1, get_col_by_height((int) curr_triangle.getB().getZ()));
_triangle_arr.setColor(3 * i + 2, get_col_by_height((int) curr_triangle.getC().getZ()));
i++;
}
}
System.out.println("DEBUG INFO successfuly displayed " + i + " Triangles");
return _triangle_arr;
}
/**
* Build the 3D scene on a Java3D enabled draw.
*
* @param objRot the transform object
*/
@Override
public void buildJava3DScene(TransformGroup objRot) {
if (objRot == null) return;
AtomInfo ai = AtomInfo.getInstance();
double xMin = gridProperty.getBoundingBox().getUpperLeft().getX(),
yMin = gridProperty.getBoundingBox().getUpperLeft().getY(),
zMin = gridProperty.getBoundingBox().getUpperLeft().getZ();
double f1, f2, f3;
double[] functionValues = gridProperty.getFunctionValues();
double incInX = gridProperty.getXIncrement(),
incInY = gridProperty.getYIncrement(),
incInZ = gridProperty.getZIncrement();
int pointsAlongX = gridProperty.getNoOfPointsAlongX(),
pointsAlongY = gridProperty.getNoOfPointsAlongY(),
pointsAlongZ = gridProperty.getNoOfPointsAlongZ();
int i, j, k;
Atom atom;
String symbol;
SphereTriSetGenerator stsg;
Point3DI point1, point2, point3;
int noOfAtoms = molecule.getNumberOfAtoms();
int pointsAlongSlice = pointsAlongY * pointsAlongZ;
HashMap<String, SphereTriSetGenerator> triSetTableTmp =
new HashMap<String, SphereTriSetGenerator>(5);
if (noOfAtoms > largeMoleculeSize) triSetTableTmp = triSetTable;
Matrix3D tmat = new Matrix3D();
tmat.unit();
TransformGroup surfaceScene = new TransformGroup();
for (int atomIndex = 0; atomIndex < noOfAtoms; atomIndex++) {
atom = molecule.getAtom(atomIndex);
// check to see if we are with in the bounding box?
if (!gridProperty.getBoundingBox().contains(atom.getAtomCenter())) continue;
symbol = atom.getSymbol();
if ((stsg = triSetTableTmp.get(symbol)) == null) {
stsg =
new SphereTriSetGenerator(
atom.getAtomCenter(), ai.getVdwRadius(symbol), numberOfSphereDivisions);
triSetTableTmp.put(symbol, stsg);
} // end if
// setup color
Color3f eColor = new Color3f(0.0f, 0.0f, 0.0f);
Color3f sColor = new Color3f(1.0f, 1.0f, 1.0f);
Color3f objColor = new Color3f(colorMap.getInterpolatedColor(currentFunctionValue));
Appearance app = new Appearance();
Material mm = new Material(objColor, eColor, objColor, sColor, 100.0f);
mm.setLightingEnable(true);
app.setMaterial(mm);
if (fillTransperency > 0) {
app.setTransparencyAttributes(
new TransparencyAttributes(
TransparencyAttributes.NICEST, (float) (fillTransperency / 255.0)));
} // end if
int idx = 0;
stsg.setTransform(tmat);
stsg.setCenter(atom.getAtomCenter());
ArrayList<Point3d> validPoints = new ArrayList<Point3d>();
ArrayList<Color3f> validColors = new ArrayList<Color3f>();
while (true) {
Triangle t = stsg.nextVisibleTriSet();
if (t == null) break;
// first point
point1 = t.getPoint1();
i = (int) Math.round(Math.abs((point1.getX() - xMin) / incInX));
j = (int) Math.round(Math.abs((point1.getY() - yMin) / incInY));
k = (int) Math.round(Math.abs((point1.getZ() - zMin) / incInZ));
if (i > pointsAlongX - 1) i = pointsAlongX - 1;
if (j > pointsAlongY - 1) j = pointsAlongY - 1;
if (k > pointsAlongZ - 1) k = pointsAlongZ - 1;
f1 = functionValues[(i * pointsAlongSlice) + (j * pointsAlongZ) + k];
// second point
point2 = t.getPoint2();
i = (int) Math.round(Math.abs((point2.getX() - xMin) / incInX));
j = (int) Math.round(Math.abs((point2.getY() - yMin) / incInY));
k = (int) Math.round(Math.abs((point2.getZ() - zMin) / incInZ));
if (i > pointsAlongX - 1) i = pointsAlongX - 1;
if (j > pointsAlongY - 1) j = pointsAlongY - 1;
if (k > pointsAlongZ - 1) k = pointsAlongZ - 1;
f2 = functionValues[(i * pointsAlongSlice) + (j * pointsAlongZ) + k];
// third point
point3 = t.getPoint3();
i = (int) Math.round(Math.abs((point3.getX() - xMin) / incInX));
j = (int) Math.round(Math.abs((point3.getY() - yMin) / incInY));
k = (int) Math.round(Math.abs((point3.getZ() - zMin) / incInZ));
if (i > pointsAlongX - 1) i = pointsAlongX - 1;
if (j > pointsAlongY - 1) j = pointsAlongY - 1;
if (k > pointsAlongZ - 1) k = pointsAlongZ - 1;
f3 = functionValues[(i * pointsAlongSlice) + (j * pointsAlongZ) + k];
validPoints.add(new Point3d(point1.getX(), point1.getY(), point1.getZ()));
validColors.add(new Color3f(colorMap.getInterpolatedColor(f1)));
validPoints.add(new Point3d(point2.getX(), point2.getY(), point2.getZ()));
validColors.add(new Color3f(colorMap.getInterpolatedColor(f2)));
validPoints.add(new Point3d(point3.getX(), point3.getY(), point3.getZ()));
validColors.add(new Color3f(colorMap.getInterpolatedColor(f3)));
} // end while
TriangleArray ta =
new TriangleArray(validPoints.size(), GeometryArray.COORDINATES | GeometryArray.COLOR_3);
for (idx = 0; idx < validPoints.size(); idx++) {
ta.setCoordinate(idx, validPoints.get(idx));
ta.setColor(idx, validColors.get(idx));
}
validColors = null;
validPoints = null;
GeometryInfo gi = new GeometryInfo(ta);
gi.compact();
gi.recomputeIndices();
// generate normals
NormalGenerator ng = new NormalGenerator();
ng.generateNormals(gi);
// stripify
Stripifier st = new Stripifier();
st.stripify(gi);
surfaceScene.addChild(new Shape3D(gi.getGeometryArray(), app));
} // end for
if (showBoundingBox) {
boundingBox.setTransform(transform);
boundingBox.applyTransforms();
(new ScreenCuboidJ3D(boundingBox)).buildJava3DScene(surfaceScene);
} // end if
objRot.addChild(surfaceScene);
}