@Override
protected BS getVoxelBitSet(int nPoints) throws Exception {
if (bsVoxelBitSet != null) return bsVoxelBitSet;
BS bs = new BS();
int bsVoxelPtr = 0;
if (surfaceDataCount <= 0) return bs; // unnecessary -- probably a plane or color density
int nThisValue = 0;
while (bsVoxelPtr < nPoints) {
nThisValue = parseInt();
if (nThisValue == Integer.MIN_VALUE) {
readLine();
// note -- does not allow for empty lines;
// must be a continuous block of numbers.
if (line == null || (nThisValue = parseIntStr(line)) == Integer.MIN_VALUE) {
if (!endOfData) Logger.error("end of file in JvxlReader?" + " line=" + line);
endOfData = true;
nThisValue = 10000;
// throw new NullPointerException();
}
}
thisInside = !thisInside;
++jvxlNSurfaceInts;
if (thisInside) bs.setBits(bsVoxelPtr, bsVoxelPtr + nThisValue);
bsVoxelPtr += nThisValue;
}
return bs;
}
public boolean slabPolygons(Object[] slabObject, boolean allowCap) {
if (polygonCount0 < 0) return false; // disabled for some surface types
int slabType = ((Integer) slabObject[0]).intValue();
if (slabType == T.none || slabType == T.brillouin) {
if (bsSlabDisplay != null && (polygonCount0 != 0 || vertexCount0 != 0)) {
pc = polygonCount0;
vc = vertexCount0;
polygonCount0 = vertexCount0 = 0;
normixCount = (isTriangleSet ? pc : vc);
bsSlabDisplay.setBits(0, (pc == 0 ? vc : pc));
slabOptions = new SB().append(meshType + " slab none");
bsSlabGhost = null;
slabMeshType = T.none;
}
if (slabType == T.none) return false;
}
Object slabbingObject = slabObject[1];
boolean andCap = ((Boolean) slabObject[2]).booleanValue() && !(slabType == T.brillouin);
if (andCap && !allowCap) return false;
Object[] colorData = (Object[]) slabObject[3];
boolean isGhost = (colorData != null);
if (bsSlabDisplay == null || polygonCount0 == 0 && vertexCount0 == 0) {
polygonCount0 = pc;
vertexCount0 = vc;
bsSlabDisplay = BSUtil.setAll(pc == 0 ? vc : pc);
bsSlabGhost = null;
if (pc == 0 && vc == 0) return false;
} else if (isMerged) {
if (pc == 0) bsSlabDisplay.setBits(mergeVertexCount0, vc);
else bsSlabDisplay.setBits(mergePolygonCount0, pc);
}
if (isGhost) {
if (bsSlabGhost == null) bsSlabGhost = new BS();
slabMeshType = ((Integer) colorData[0]).intValue();
slabColix = ((Short) colorData[1]).shortValue();
// if (C.isColixColorInherited(slabColix))
// slabColix = C.copyColixTranslucency(slabColix, colix);
andCap = false;
colix = C.getColixTranslucent3(colix, false, 0);
}
SB sb = new SB();
sb.append(andCap ? " cap " : " slab ");
if (isGhost) {
sb.append("translucent ").appendF(C.getColixTranslucencyFractional(slabColix)).append(" ");
String s = C.getHexCode(slabColix);
if (s != null) sb.append(s).append(" ");
if (slabMeshType == T.mesh) sb.append("mesh ");
}
switch (slabType) {
case T.brillouin:
sb.append("brillouin");
slabBrillouin((P3[]) slabbingObject);
break;
case T.decimal:
getIntersection(
0,
null,
null,
null,
null,
(BS) slabbingObject,
null,
andCap,
false,
T.decimal,
isGhost);
break;
case T.plane:
P4 plane = (P4) slabbingObject;
sb.append(Escape.eP4(plane));
getIntersection(0, plane, null, null, null, null, null, andCap, false, T.plane, isGhost);
break;
case T.unitcell:
case T.boundbox:
P3[] box = (P3[]) slabbingObject;
sb.append("within ").append(Escape.eAP(box));
P4[] faces = BoxInfo.getFacesFromCriticalPoints(box);
for (int i = 0; i < faces.length; i++) {
getIntersection(
0, faces[i], null, null, null, null, null, andCap, false, T.plane, isGhost);
}
break;
case T.data:
getIntersection(
0,
null,
null,
null,
(float[]) slabbingObject,
null,
null,
false,
false,
T.min,
isGhost);
break;
case T.within:
case T.range:
case T.mesh:
Object[] o = (Object[]) slabbingObject;
float distance = ((Float) o[0]).floatValue();
switch (slabType) {
case T.within:
P3[] points = (P3[]) o[1];
BS bs = (BS) o[2];
sb.append("within ")
.appendF(distance)
.append(bs == null ? Escape.e(points) : Escape.e(bs));
getIntersection(
distance,
null,
points,
null,
null,
null,
null,
andCap,
false,
(distance > 0 ? T.distance : T.sphere),
isGhost);
break;
case T.range:
// isosurface slab within range x.x y.y
// if y.y < x.x then this effectively means "NOT within range y.y x.x"
if (vvs == null) return false;
float distanceMax = ((Float) o[1]).floatValue();
sb.append("within range ").appendF(distance).append(" ").appendF(distanceMax);
bs = (distanceMax < distance ? BSUtil.copy(bsSlabDisplay) : null);
getIntersection(
distance, null, null, null, null, null, null, andCap, false, T.min, isGhost);
BS bsA = (bs == null ? null : BSUtil.copy(bsSlabDisplay));
BSUtil.copy2(bs, bsSlabDisplay);
getIntersection(
distanceMax, null, null, null, null, null, null, andCap, false, T.max, isGhost);
if (bsA != null) bsSlabDisplay.or(bsA);
break;
case T.mesh:
// NOT IMPLEMENTED
MeshSurface mesh = (MeshSurface) o[1];
// distance = -1;
getIntersection(
0,
null,
null,
null,
null,
null,
mesh,
andCap,
false,
distance < 0 ? T.min : T.max,
isGhost);
// TODO: unresolved how exactly to store this in the state
// -- must indicate exact set of triangles to slab and how!
break;
}
break;
}
String newOptions = sb.toString();
if (slabOptions == null) slabOptions = new SB();
if (slabOptions.indexOf(newOptions) < 0)
slabOptions.append(slabOptions.length() > 0 ? "; " : "").append(meshType).append(newOptions);
return true;
}