@Override
public SB getAllDataFiles(String binaryFileList, String firstFile) {
if (firstFile != null) {
for (int i = 0; i < directory.size(); i++) {
CompoundDocDirEntry thisEntry = directory.get(i);
if (thisEntry.entryName.equals(firstFile)) {
directory.remove(i);
directory.add(1, thisEntry); // after ROOT_ENTRY
break;
}
}
}
data = new SB();
data.append("Compound Document File Directory: ");
data.append(getDirectoryListing("|"));
data.append("\n");
binaryFileList = "|" + binaryFileList + "|";
for (int i = 0; i < directory.size(); i++) {
CompoundDocDirEntry thisEntry = directory.get(i);
Logger.info("reading " + thisEntry.entryName);
if (!thisEntry.isEmpty && thisEntry.entryType != 5) {
String name = thisEntry.entryName;
if (name.endsWith(".gz")) name = name.substring(0, name.length() - 3);
data.append("BEGIN Directory Entry ").append(name).append("\n");
data.appendSB(
getEntryAsString(
thisEntry, binaryFileList.indexOf("|" + thisEntry.entryName + "|") >= 0));
data.append("\n");
data.append("END Directory Entry ").append(thisEntry.entryName).append("\n");
}
}
close();
return data;
}
/**
* Sets all local file references in a script file to point to files within dataPath. If a file
* reference contains dataPath, then the file reference is left with that RELATIVE path.
* Otherwise, it is changed to a relative file name within that dataPath.
*
* <p>Only file references starting with "file://" are changed.
*
* @param script
* @param dataPath
* @param isLocal
* @return revised script
*/
private static String setScriptFileRefs(String script, String dataPath, boolean isLocal) {
if (dataPath == null) return script;
boolean noPath = (dataPath.length() == 0);
List<String> fileNames = new List<String>();
JmolBinary.getFileReferences(script, fileNames);
List<String> oldFileNames = new List<String>();
List<String> newFileNames = new List<String>();
int nFiles = fileNames.size();
for (int iFile = 0; iFile < nFiles; iFile++) {
String name0 = fileNames.get(iFile);
String name = name0;
if (isLocal == isLocal(name)) {
int pt = (noPath ? -1 : name.indexOf("/" + dataPath + "/"));
if (pt >= 0) {
name = name.substring(pt + 1);
} else {
pt = name.lastIndexOf("/");
if (pt < 0 && !noPath) name = "/" + name;
if (pt < 0 || noPath) pt++;
name = dataPath + name.substring(pt);
}
}
Logger.info("FileManager substituting " + name0 + " --> " + name);
oldFileNames.addLast("\"" + name0 + "\"");
newFileNames.addLast("\1\"" + name + "\"");
}
return Txt.replaceStrings(script, oldFileNames, newFileNames);
}
public SB getFileAsString(String entryName) {
for (int i = 0; i < directory.size(); i++) {
CompoundDocDirEntry thisEntry = directory.get(i);
if (thisEntry.entryName.equals(entryName)) return getEntryAsString(thisEntry, false);
}
return new SB();
}
Object createAtomSeCollectionFromArrayData(
List<Object> arrayData, Map<String, Object> htParams, boolean isAppend) {
// NO STATE SCRIPT -- HERE WE ARE TRYING TO CONSERVE SPACE
Logger.info("FileManager.getAtomSetCollectionFromArrayData(Vector)");
int nModels = arrayData.size();
String[] fullPathNames = new String[nModels];
DataReader[] readers = new DataReader[nModels];
for (int i = 0; i < nModels; i++) {
fullPathNames[i] = "String[" + i + "]";
readers[i] = newDataReader(arrayData.get(i));
}
JmolFilesReaderInterface filesReader =
newFilesReader(fullPathNames, fullPathNames, null, readers, htParams, isAppend);
filesReader.run();
return filesReader.getAtomSetCollection();
}
public String getDirectoryListing(String separator) {
String str = "";
for (int i = 0; i < directory.size(); i++) {
CompoundDocDirEntry thisEntry = directory.get(i);
if (!thisEntry.isEmpty)
str +=
separator
+ thisEntry.entryName
+ "\tlen="
+ thisEntry.lenStream
+ "\tSID="
+ thisEntry.SIDfirstSector
+ (thisEntry.isStandard
? "\tfileOffset=" + getOffset(thisEntry.SIDfirstSector)
: "");
}
return str;
}
/**
* reads a compound document directory and saves all data in a Hashtable so that the files may be
* organized later in a different order. Also adds a #Directory_Listing entry.
*
* <p>Files are bracketed by BEGIN Directory Entry and END Directory Entry lines, similar to
* ZipUtil.getAllData.
*
* @param prefix
* @param binaryFileList |-separated list of files that should be saved as xx xx xx hex byte
* strings. The directory listing is appended with ":asBinaryString"
* @param fileData
*/
@Override
public void getAllDataMapped(String prefix, String binaryFileList, Map<String, String> fileData) {
fileData.put("#Directory_Listing", getDirectoryListing("|"));
binaryFileList = "|" + binaryFileList + "|";
for (int i = 0; i < directory.size(); i++) {
CompoundDocDirEntry thisEntry = directory.get(i);
if (!thisEntry.isEmpty && thisEntry.entryType != 5) {
String name = thisEntry.entryName;
Logger.info("CompoundDocument file " + name);
boolean isBinary = (binaryFileList.indexOf("|" + name + "|") >= 0);
if (isBinary) name += ":asBinaryString";
SB data = new SB();
data.append("BEGIN Directory Entry ").append(name).append("\n");
data.appendSB(getEntryAsString(thisEntry, isBinary));
data.append("\nEND Directory Entry ").append(name).append("\n");
fileData.put(prefix + "/" + name, data.toString());
}
}
close();
}
/**
* after the vectors intinfo and floatinfo are completed, we
*
* @param doScale
* @param doSort TODO
*/
protected final void setSlaters(boolean doScale, boolean doSort) {
if (slaterArray == null) {
int nSlaters = slaters.size();
slaterArray = new SlaterData[nSlaters];
for (int i = 0; i < slaterArray.length; i++) slaterArray[i] = slaters.get(i);
}
if (doScale)
for (int i = 0; i < slaterArray.length; i++) {
SlaterData sd = slaterArray[i];
sd.coef *= scaleSlater(sd.x, sd.y, sd.z, sd.r, sd.zeta);
if (Logger.debugging) {
Logger.debug(
"SlaterReader "
+ i
+ ": "
+ sd.iAtom
+ " "
+ sd.x
+ " "
+ sd.y
+ " "
+ sd.z
+ " "
+ sd.r
+ " "
+ sd.zeta
+ " "
+ sd.coef);
}
}
if (doSort) {
Arrays.sort(slaterArray, new SlaterSorter());
int[] pointers = new int[slaterArray.length];
for (int i = 0; i < slaterArray.length; i++) pointers[i] = slaterArray[i].index;
sortOrbitalCoefficients(pointers);
}
moData.put("slaters", slaterArray);
atomSetCollection.setAtomSetAuxiliaryInfo("moData", moData);
}
@Override
protected void outputSurface(
P3[] vertices,
V3[] normals,
short[] colixes,
int[][] indices,
short[] polygonColixes,
int nVertices,
int nPolygons,
int nFaces,
BS bsPolygons,
int faceVertexMax,
short colix,
List<Short> colorList,
Map<Short, Integer> htColixes,
P3 offset) {
if (polygonColixes != null) {
boolean isAll = (bsPolygons == null);
int i0 = (isAll ? nPolygons - 1 : bsPolygons.nextSetBit(0));
for (int i = i0; i >= 0; i = (isAll ? i - 1 : bsPolygons.nextSetBit(i + 1))) {
// if ((p++) % 10 == 0)
// output("\n");
output("polygon { 4\n");
for (int j = 0; j <= 3; j++) outputVertex(vertices[indices[i][j % 3]], offset);
output("\n");
output("pigment{rgbt<" + color4(colix = polygonColixes[i]) + ">}\n");
output(" translucentFinish(" + translucencyFractionalFromColix(colix) + ")\n");
output(" check_shadow()\n");
output(" clip()\n");
output("}\n");
}
return;
}
output("mesh2 {\n");
output("vertex_vectors { " + nVertices);
for (int i = 0; i < nVertices; i++) outputVertex(vertices[i], offset);
output("\n}\n");
boolean haveNormals = (normals != null);
if (haveNormals) {
output("normal_vectors { " + nVertices);
for (int i = 0; i < nVertices; i++) {
setTempVertex(vertices[i], offset, tempP2);
output(getScreenNormal(tempP2, normals[i], 1));
output("\n");
}
output("\n}\n");
}
if (colixes != null) {
int nColix = colorList.size();
output("texture_list { " + nColix);
// just using the transparency of the first colix there...
String finish =
">}" + " translucentFinish(" + translucencyFractionalFromColix(colixes[0]) + ")}";
for (int i = 0; i < nColix; i++)
output("\n, texture{pigment{rgbt<" + color4(colorList.get(i).shortValue()) + finish);
output("\n}\n");
}
output("face_indices { " + nFaces);
boolean isAll = (bsPolygons == null);
int i0 = (isAll ? nPolygons - 1 : bsPolygons.nextSetBit(0));
for (int i = i0; i >= 0; i = (isAll ? i - 1 : bsPolygons.nextSetBit(i + 1))) {
output(", <" + getTriad(indices[i]) + ">");
if (colixes != null) {
output("," + htColixes.get(Short.valueOf(colixes[indices[i][0]])));
output("," + htColixes.get(Short.valueOf(colixes[indices[i][1]])));
output("," + htColixes.get(Short.valueOf(colixes[indices[i][2]])));
}
if (faceVertexMax == 4 && indices[i].length == 4) {
output(", <" + indices[i][0] + "," + indices[i][2] + "," + indices[i][3] + ">");
if (colixes != null) {
output("," + htColixes.get(Short.valueOf(colixes[indices[i][0]])));
output("," + htColixes.get(Short.valueOf(colixes[indices[i][2]])));
output("," + htColixes.get(Short.valueOf(colixes[indices[i][3]])));
}
}
output("\n");
}
output("\n}\n");
if (colixes == null) {
output("pigment{rgbt<" + color4(colix) + ">}\n");
output(" translucentFinish(" + translucencyFractionalFromColix(colix) + ")\n");
}
output(" check_shadow()\n");
output(" clip()\n");
output("}\n");
/*
mesh2 {
vertex_vectors {
9,
<0,0,0>, <0.5,0,0>, <0.5,0.5,0>,
<1,0,0>, <1,0.5,0>, <1,1,0>
<0.5,1,0>, <0,1,0>, <0,0.5,0>
}
normal_vectors {
9,
<-1,-1,0>, <0,-1,0>, <0,0,1>,
<1,-1,0>, <1,0,0>, <1,1,0>,
<0,1,0>, <-1,1,0>, <-1,0,0>
}
texture_list {
3,
texture{pigment{rgb <0,0,1>}},
texture{pigment{rgb 1}},
texture{pigment{rgb <1,0,0>}}
}
face_indices {
8,
<0,1,2>,0,1,2, <1,3,2>,1,0,2,
<3,4,2>,0,1,2, <4,5,2>,1,0,2,
<5,6,2>,0,1,2, <6,7,2>,1,0,2,
<7,8,2>,0,1,2, <8,0,2>,1,0,2
}
}
*/
}
/**
* @param distance a distance from a plane or point
* @param plane a slabbing plane
* @param ptCenters a set of atoms to measure distance from
* @param vData when not null, this is a query, not an actual slabbing
* @param fData vertex values or other data to overlay
* @param bsSource TODO
* @param meshSurface second surface; not implemented -- still some problems there
* @param andCap to cap this off, crudely only
* @param doClean compact set - draw only
* @param tokType type of slab
* @param isGhost translucent slab, so we mark slabbed triangles
*/
public void getIntersection(
float distance,
P4 plane,
P3[] ptCenters,
List<P3[]> vData,
float[] fData,
BS bsSource,
MeshSurface meshSurface,
boolean andCap,
boolean doClean,
int tokType,
boolean isGhost) {
boolean isSlab = (vData == null);
P3[] pts = null;
if (fData == null) {
if (tokType == T.decimal && bsSource != null) {
fData = new float[vertexCount];
for (int i = 0; i < vertexCount; i++)
if ((fData[i] = vertexSource[i]) == -1) System.out.println("meshsurface hmm");
} else {
fData = vertexValues;
}
}
Map<String, Integer> mapEdge = new Hashtable<String, Integer>();
/*
Vector3f vNorm = null;
Vector3f vBC = null;
Vector3f vAC = null;
Point3f[] pts2 = null;
Vector3f vTemp3 = null;
Point4f planeTemp = null;
boolean isMeshIntersect = (meshSurface != null);
if (isMeshIntersect) {
// NOT IMPLEMENTED
vBC = new Vector3f();
vAC = new Vector3f();
vNorm = new Vector3f();
plane = new Point4f();
planeTemp = new Point4f();
vTemp3 = new Vector3f();
pts2 = new Point3f[] { null, new Point3f(), new Point3f() };
}
*/
if (ptCenters != null || isGhost)
andCap = false; // can only cap faces, and no capping of ghosts
float[] values = new float[2];
float[] fracs = new float[2];
double absD = Math.abs(distance);
float d1, d2, d3, valA, valB, valC;
int sourceA = 0, sourceB = 0, sourceC = 0, setA = 0;
List<int[]> iPts = (andCap ? new List<int[]>() : null);
if (polygonCount == 0) {
for (int i = mergeVertexCount0; i < vertexCount; i++) {
if (Float.isNaN(fData[i])
|| checkSlab(tokType, vertices[i], fData[i], distance, plane, ptCenters, bsSource) > 0)
bsSlabDisplay.clear(i);
}
return;
}
int iLast = polygonCount;
for (int i = mergePolygonCount0; i < iLast; i++) {
if (!setABC(i)) continue;
BS bsSlab = (bsSlabGhost != null && bsSlabGhost.get(i) ? bsSlabGhost : bsSlabDisplay);
int check1 = polygonIndexes[i][3];
int check2 = (checkCount == 2 ? polygonIndexes[i][4] : 0);
P3 vA = vertices[iA];
P3 vB = vertices[iB];
P3 vC = vertices[iC];
valA = fData[iA];
valB = fData[iB];
valC = fData[iC];
if (vertexSource != null) {
sourceA = vertexSource[iA];
sourceB = vertexSource[iB];
sourceC = vertexSource[iC];
}
if (vertexSets != null) setA = vertexSets[iA];
d1 =
checkSlab(
tokType,
vA,
valA,
(bsSource == null ? distance : sourceA),
plane,
ptCenters,
bsSource);
d2 =
checkSlab(
tokType,
vB,
valB,
(bsSource == null ? distance : sourceB),
plane,
ptCenters,
bsSource);
d3 =
checkSlab(
tokType,
vC,
valC,
(bsSource == null ? distance : sourceC),
plane,
ptCenters,
bsSource);
int test1 =
(d1 != 0 && d1 < 0 ? 1 : 0) + (d2 != 0 && d2 < 0 ? 2 : 0) + (d3 != 0 && d3 < 0 ? 4 : 0);
/*
if (iA == 955 || iB == 955 || iC == 955) {
System.out.println(i + " " + iA + " " + iB + " " + iC + " "+ d1 + " " + d2 + " " + d3 + " " + test1);
System.out.println("testing messhsurf ");
}
*/
/*
if (isMeshIntersect && test1 != 7 && test1 != 0) {
// NOT IMPLEMENTED
boolean isOK = (d1 == 0 && d2 * d3 >= 0 || d2 == 0 && (d1 * d3) >= 0 || d3 == 0
&& d1 * d2 >= 0);
if (isOK)
continue;
// We have a potential crossing. Now to find the exact point of crossing
// the other isosurface.
if (checkIntersection(vA, vB, vC, meshSurface, pts2, vNorm, vBC, vAC,
plane, planeTemp, vTemp3)) {
iD = addIntersectionVertex(pts2[0], 0, sourceA, mapEdge, -1, -1); // have to choose some source
addPolygon(iA, iB, iD, check1 & 1, check2, 0, bsSlabDisplay);
addPolygon(iD, iB, iC, check1 & 2, check2, 0, bsSlabDisplay);
addPolygon(iA, iD, iC, check1 & 4, check2, 0, bsSlabDisplay);
test1 = 0; // toss original
iLast = polygonCount;
} else {
// process normally for now
// not fully implemented -- need to check other way as well.
}
}
*/
switch (test1) {
default:
case 7:
case 0:
// all on the same side
break;
case 1:
case 6:
// BC on same side
if (ptCenters == null)
pts =
new P3[] {
interpolatePoint(vA, vB, -d1, d2, valA, valB, values, fracs, 0),
interpolatePoint(vA, vC, -d1, d3, valA, valC, values, fracs, 1)
};
else
pts =
new P3[] {
interpolateSphere(vA, vB, -d1, -d2, absD, valA, valB, values, fracs, 0),
interpolateSphere(vA, vC, -d1, -d3, absD, valA, valC, values, fracs, 1)
};
break;
case 2:
case 5:
// AC on same side
if (ptCenters == null)
pts =
new P3[] {
interpolatePoint(vB, vA, -d2, d1, valB, valA, values, fracs, 1),
interpolatePoint(vB, vC, -d2, d3, valB, valC, values, fracs, 0)
};
else
pts =
new P3[] {
interpolateSphere(vB, vA, -d2, -d1, absD, valB, valA, values, fracs, 1),
interpolateSphere(vB, vC, -d2, -d3, absD, valB, valC, values, fracs, 0)
};
break;
case 3:
case 4:
// AB on same side need A-C, B-C
if (ptCenters == null)
pts =
new P3[] {
interpolatePoint(vC, vA, -d3, d1, valC, valA, values, fracs, 0),
interpolatePoint(vC, vB, -d3, d2, valC, valB, values, fracs, 1)
};
else
pts =
new P3[] {
interpolateSphere(vC, vA, -d3, -d1, absD, valC, valA, values, fracs, 0),
interpolateSphere(vC, vB, -d3, -d2, absD, valC, valB, values, fracs, 1)
};
break;
}
doClear = true;
doGhost = isGhost;
doCap = andCap;
BS bs;
// adjust for minor discrepencies
// for (int j = 0; j < 2; j++)
// if (fracs[j] == 0)
// fracs[1 - j] = (fracs[1 - j] < 0.5 ? 0 : 1);
if (isSlab) {
// iD = iE = -1;
switch (test1) {
// A
// / \
// B---C
case 0:
// all on the same side -- toss
doCap = false;
break;
case 7:
// all on the same side -- keep
continue;
case 1:
case 6:
// 0 A 0
// / \
// 0 -------- 1
// / \
// 1 B-------C 1
boolean tossBC = (test1 == 1);
if (tossBC || isGhost) {
// 1: BC on side to toss -- +tossBC+isGhost -tossBC+isGhost
if (!getDE(fracs, 0, iA, iB, iC, tossBC)) break;
if (iD < 0)
iD = addIntersectionVertex(pts[0], values[0], sourceA, setA, mapEdge, iA, iB);
if (iE < 0)
iE = addIntersectionVertex(pts[1], values[1], sourceA, setA, mapEdge, iA, iC);
bs = (tossBC ? bsSlab : bsSlabGhost);
addPolygonV3(iA, iD, iE, check1 & 5 | 2, check2, 0, bs);
if (!isGhost) break;
}
// BC on side to keep -- -tossBC+isGhost, +tossBC+isGhost
if (!getDE(fracs, 1, iA, iC, iB, tossBC)) break;
bs = (tossBC ? bsSlabGhost : bsSlab);
if (iE < 0) {
iE = addIntersectionVertex(pts[0], values[0], sourceB, setA, mapEdge, iA, iB);
addPolygonV3(iE, iB, iC, check1 & 3, check2, 0, bs);
}
if (iD < 0) {
iD = addIntersectionVertex(pts[1], values[1], sourceC, setA, mapEdge, iA, iC);
addPolygonV3(iD, iE, iC, check1 & 4 | 1, check2, 0, bs);
}
break;
case 5:
case 2:
// A
// \/ \
// /\ \
// B--\--C
// \
//
boolean tossAC = (test1 == 2);
if (tossAC || isGhost) {
// AC on side to toss
if (!getDE(fracs, 0, iB, iC, iA, tossAC)) break;
bs = (tossAC ? bsSlab : bsSlabGhost);
if (iE < 0)
iE = addIntersectionVertex(pts[0], values[0], sourceB, setA, mapEdge, iB, iA);
if (iD < 0)
iD = addIntersectionVertex(pts[1], values[1], sourceB, setA, mapEdge, iB, iC);
addPolygonV3(iE, iB, iD, check1 & 3 | 4, check2, 0, bs);
if (!isGhost) break;
}
// AC on side to keep
if (!getDE(fracs, 1, iB, iA, iC, tossAC)) break;
bs = (tossAC ? bsSlabGhost : bsSlab);
if (iD < 0) {
iD = addIntersectionVertex(pts[0], values[0], sourceA, setA, mapEdge, iB, iA);
addPolygonV3(iA, iD, iC, check1 & 5, check2, 0, bs);
}
if (iE < 0) {
iE = addIntersectionVertex(pts[1], values[1], sourceC, setA, mapEdge, iB, iC);
addPolygonV3(iD, iE, iC, check1 & 2 | 1, check2, 0, bs);
}
break;
case 4:
case 3:
// A
// / \/
// / /\
// B--/--C
// /
//
boolean tossAB = (test1 == 4);
if (tossAB || isGhost) {
if (!getDE(fracs, 0, iC, iA, iB, tossAB)) break;
if (iD < 0)
iD = addIntersectionVertex(pts[0], values[0], sourceC, setA, mapEdge, iA, iC); // CA
if (iE < 0)
iE = addIntersectionVertex(pts[1], values[1], sourceC, setA, mapEdge, iB, iC); // CB
bs = (tossAB ? bsSlab : bsSlabGhost);
addPolygonV3(iD, iE, iC, check1 & 6 | 1, check2, 0, bs);
if (!isGhost) break;
}
// AB on side to keep
if (!getDE(fracs, 1, iC, iB, iA, tossAB)) break;
bs = (tossAB ? bsSlabGhost : bsSlab);
if (iE < 0) {
iE = addIntersectionVertex(pts[0], values[0], sourceA, setA, mapEdge, iA, iC); // CA
addPolygonV3(iA, iB, iE, check1 & 5, check2, 0, bs);
}
if (iD < 0) {
iD = addIntersectionVertex(pts[1], values[1], sourceB, setA, mapEdge, iB, iC); // CB
addPolygonV3(iE, iB, iD, check1 & 2 | 4, check2, 0, bs);
}
break;
}
if (doClear) {
bsSlab.clear(i);
if (doGhost) bsSlabGhost.set(i);
}
if (doCap) {
iPts.addLast(new int[] {iD, iE});
}
} else if (pts != null) {
vData.addLast(pts);
}
}
if (andCap && iPts.size() > 0) {
P3 center = new P3();
for (int i = iPts.size(); --i >= 0; ) {
int[] ipts = iPts.get(i);
center.add(vertices[ipts[0]]);
center.add(vertices[ipts[1]]);
}
center.scale(0.5f / iPts.size());
int v0 = addIntersectionVertex(center, 0, -1, setA, mapEdge, -1, -1);
for (int i = iPts.size(); --i >= 0; ) {
int[] ipts = iPts.get(i);
// int p =
addPolygonV3(ipts[0], v0, ipts[1], 0, 0, 0, bsSlabDisplay);
}
}
if (!doClean) return;
BS bsv = new BS();
BS bsp = new BS();
for (int i = 0; i < polygonCount; i++) {
if (polygonIndexes[i] == null) continue;
bsp.set(i);
for (int j = 0; j < 3; j++) bsv.set(polygonIndexes[i][j]);
}
int n = 0;
int nPoly = bsp.cardinality();
if (nPoly != polygonCount) {
int[] map = new int[vertexCount];
for (int i = 0; i < vertexCount; i++) if (bsv.get(i)) map[i] = n++;
P3[] vTemp = new P3[n];
n = 0;
for (int i = 0; i < vertexCount; i++) if (bsv.get(i)) vTemp[n++] = vertices[i];
int[][] pTemp = AU.newInt2(nPoly);
nPoly = 0;
for (int i = 0; i < polygonCount; i++)
if (polygonIndexes[i] != null) {
for (int j = 0; j < 3; j++) polygonIndexes[i][j] = map[polygonIndexes[i][j]];
pTemp[nPoly++] = polygonIndexes[i];
}
vertices = vTemp;
vertexCount = n;
polygonIndexes = pTemp;
polygonCount = nPoly;
}
}
public void slabPolygonsList(List<Object[]> slabInfo, boolean allowCap) {
for (int i = 0; i < slabInfo.size(); i++) if (!slabPolygons(slabInfo.get(i), allowCap)) break;
}