@Override
public String getShapeState() {
Map<String, BitSet> temp = new Hashtable<String, BitSet>();
if (atomFormats != null)
for (int i = viewer.getAtomCount(); --i >= 0; )
if (atomFormats[i] != null)
setStateInfo(temp, i, "set hoverLabel " + Escape.escapeStr(atomFormats[i]));
return "\n hover "
+ Escape.escapeStr((labelFormat == null ? "" : labelFormat))
+ ";\n"
+ getShapeCommands(temp, null);
}
private String getMoState(int modelIndex) {
strID = getId(modelIndex);
if (!getSettings(strID)) return "";
SB s = new SB();
int modelCount = vwr.getModelCount();
if (modelCount > 1) appendCmd(s, "frame " + vwr.getModelNumberDotted(modelIndex));
if (moCutoff != null)
appendCmd(s, "mo cutoff " + (sg.getIsPositiveOnly() ? "+" : "") + moCutoff);
if (moScale != null) appendCmd(s, "mo scale " + moScale);
if (moMonteCarloCount != null)
appendCmd(s, "mo points " + moMonteCarloCount + " " + moRandomSeed);
if (moResolution != null) appendCmd(s, "mo resolution " + moResolution);
if (moPlane != null)
appendCmd(
s, "mo plane {" + moPlane.x + " " + moPlane.y + " " + moPlane.z + " " + moPlane.w + "}");
if (moTitleFormat != null) appendCmd(s, "mo titleFormat " + PT.esc(moTitleFormat));
// the following is a correct object==object test
if (moColorNeg != null)
appendCmd(
s,
"mo color "
+ Escape.escapeColor(moColorNeg.intValue())
+ (moColorNeg.equals(moColorPos)
? ""
: " " + Escape.escapeColor(moColorPos.intValue())));
if (moSlab != null) {
if (thisMesh.slabOptions != null) appendCmd(s, thisMesh.slabOptions.toString());
if (thisMesh.jvxlData.slabValue != Integer.MIN_VALUE)
appendCmd(s, "mo slab " + thisMesh.jvxlData.slabValue);
}
if (moLinearCombination == null) {
appendCmd(s, "mo " + (moSquareData == Boolean.TRUE ? "squared " : "") + moNumber);
} else {
appendCmd(
s,
"mo "
+ QS.getMOString(moLinearCombination)
+ (moSquareLinear == Boolean.TRUE ? " squared" : ""));
}
if (moTranslucency != null) appendCmd(s, "mo translucent " + moTranslucentLevel);
appendCmd(s, ((IsosurfaceMesh) thisModel.get("mesh")).getState("mo"));
return s.toString();
}
@Override
public String getShapeState() {
StringBuffer sb = new StringBuffer();
sb.append(" axes scale ").append(viewer.getAxesScale()).append(";\n");
if (fixedOrigin != null)
sb.append(" axes center ").append(Escape.escape(fixedOrigin)).append(";\n");
if (axisXY.z != 0)
sb.append(" axes position [")
.append((int) axisXY.x)
.append(" ")
.append((int) axisXY.y)
.append(" ")
.append(axisXY.z < 0 ? " %" : "")
.append("];\n");
if (labels != null) {
sb.append(" axes labels ");
for (int i = 0; i < labels.length; i++) sb.append(Escape.escape(labels[i])).append(" ");
sb.append(";\n");
}
return super.getShapeState() + sb;
}
private void loadFiles(List<File> fileList) {
StringBuffer sb = new StringBuffer();
for (int i = 0; i < fileList.size(); ++i) {
File f = fileList.get(i);
String fname = f.getAbsolutePath();
fname = fname.replace('\\', '/').trim();
fname = (fname.startsWith("/") ? "file://" : "file:///") + fname;
sb.append("load ").append(i == 0 ? "" : "APPEND ").append(Escape.escape(fname)).append(";\n");
}
sb.append("frame *;reset;");
viewer.script(sb.toString());
}
/**
* legacy -- for some scripts with early isosurface slabbing
*
* @param s
* @param isCap
* @return slabInfo object
*/
public static Object[] getCapSlabObject(String s, boolean isCap) {
try {
if (s.indexOf("array") == 0) {
String[] pts = PT.split(s.substring(6, s.length() - 1), ",");
return TempArray.getSlabObjectType(
T.boundbox,
new P3[] {
(P3) Escape.uP(pts[0]),
(P3) Escape.uP(pts[1]),
(P3) Escape.uP(pts[2]),
(P3) Escape.uP(pts[3])
},
isCap,
null);
}
Object plane = Escape.uP(s);
if (plane instanceof P4) return TempArray.getSlabObjectType(T.plane, plane, isCap, null);
} catch (Exception e) {
//
}
return null;
}
private void getStateID(SB sb) {
V3 v1 = new V3();
for (Ellipsoid ellipsoid : simpleEllipsoids.values()) {
Tensor t = ellipsoid.tensor;
if (!ellipsoid.isValid || t == null) continue;
sb.append(" Ellipsoid ID ")
.append(ellipsoid.id)
.append(" modelIndex ")
.appendI(t.modelIndex)
.append(" center ")
.append(Escape.eP(ellipsoid.center))
.append(" axes");
for (int i = 0; i < 3; i++) {
v1.setT(t.eigenVectors[i]);
v1.scale(ellipsoid.lengths[i]);
sb.append(" ").append(Escape.eP(v1));
}
sb.append(" " + getColorCommandUnk("", ellipsoid.colix, translucentAllowed));
if (ellipsoid.options != null) sb.append(" options ").append(PT.esc(ellipsoid.options));
if (!ellipsoid.isOn) sb.append(" off");
sb.append(";\n");
}
}
public String getShapeState() {
if (!isValid) return "";
StringBuffer s = new StringBuffer();
s.append("dipole ID ").append(thisID);
if (haveAtoms)
s.append(" ({")
.append(atoms[0].getAtomIndex())
.append(" ")
.append(atoms[1].getAtomIndex())
.append("})");
else if (coords[0] == null) return "";
else
s.append(" ").append(Escape.escape(coords[0])).append(" ").append(Escape.escape(coords[1]));
if (isUserValue) s.append(" value ").append(dipoleValue);
if (mad != Dipoles.DEFAULT_MAD) s.append(" width ").append(mad / 1000f);
if (offsetAngstroms != 0) s.append(" offset ").append(offsetAngstroms);
else if (offsetPercent != 0) s.append(" offset ").append(offsetPercent);
if (offsetSide != Dipoles.DEFAULT_OFFSETSIDE) s.append(" offsetSide ").append(offsetSide);
if (noCross) s.append(" nocross");
if (!visible) s.append(" off");
s.append(";\n");
return s.toString();
}
public static void main(String[] args) {
// note that -o-x are implied, but -n is not.
// in this case -n means "no GRAPHICS" for speed
JmolApp jmolApp = new JmolApp();
jmolApp.isDataOnly = true;
jmolApp.haveConsole = false;
// jmolApp.haveDisplay = false;
jmolApp.info.put("exit", Boolean.TRUE);
jmolApp.parseCommandLine(args);
if (!jmolApp.isSilent) {
System.out.println("JmolData using command options " + Escape.escape(args));
if (!jmolApp.info.containsKey("noGraphics"))
System.out.println(
"Add -n (NOGRAPHICS) for faster performance if you are not creating images.");
}
new JmolData(jmolApp);
}
protected void jvxlDecodeContourData(JvxlData jvxlData, String data) throws Exception {
List<List<Object>> vs = new List<List<Object>>();
SB values = new SB();
SB colors = new SB();
int pt = -1;
jvxlData.vContours = null;
if (data == null) return;
while ((pt = data.indexOf("<jvxlContour", pt + 1)) >= 0) {
List<Object> v = new List<Object>();
String s = xr.getXmlData("jvxlContour", data.substring(pt), true, false);
float value = parseFloatStr(XmlReader.getXmlAttrib(s, "value"));
values.append(" ").appendF(value);
int color = getColor(XmlReader.getXmlAttrib(s, "color"));
short colix = C.getColix(color);
colors.append(" ").append(Escape.escapeColor(color));
String fData = JvxlCoder.jvxlDecompressString(XmlReader.getXmlAttrib(s, "data"));
BS bs = JvxlCoder.jvxlDecodeBitSet(xr.getXmlData("jvxlContour", s, false, false));
int n = bs.length();
IsosurfaceMesh.setContourVector(v, n, bs, value, colix, color, SB.newS(fData));
vs.addLast(v);
}
int n = vs.size();
if (n > 0) {
jvxlData.vContours = AU.createArrayOfArrayList(n);
// 3D contour values and colors
jvxlData.contourColixes = params.contourColixes = new short[n];
jvxlData.contourValues = params.contoursDiscrete = new float[n];
for (int i = 0; i < n; i++) {
jvxlData.vContours[i] = vs.get(i);
jvxlData.contourValues[i] = ((Float) jvxlData.vContours[i].get(2)).floatValue();
jvxlData.contourColixes[i] = ((short[]) jvxlData.vContours[i].get(3))[0];
}
jvxlData.contourColors = C.getHexCodes(jvxlData.contourColixes);
Logger.info("JVXL read: " + n + " discrete contours");
Logger.info("JVXL read: contour values: " + values);
Logger.info("JVXL read: contour colors: " + colors);
}
}
protected void jvxlReadSurfaceInfo() throws Exception {
String s;
String data = xr.getXmlData("jvxlSurfaceInfo", null, true, true);
isXLowToHigh = XmlReader.getXmlAttrib(data, "isXLowToHigh").equals("true");
jvxlCutoff = parseFloatStr(XmlReader.getXmlAttrib(data, "cutoff"));
if (!Float.isNaN(jvxlCutoff)) Logger.info("JVXL read: cutoff " + jvxlCutoff);
int nContourData = parseIntStr(XmlReader.getXmlAttrib(data, "nContourData"));
haveContourData = (nContourData > 0);
params.isContoured = XmlReader.getXmlAttrib(data, "contoured").equals("true");
if (params.isContoured) {
int nContoursRead = parseIntStr(XmlReader.getXmlAttrib(data, "nContours"));
if (nContoursRead <= 0) {
nContoursRead = 0;
} else {
s = XmlReader.getXmlAttrib(data, "contourValues");
if (s.length() > 0) {
jvxlData.contourValues = params.contoursDiscrete = parseFloatArrayStr(s);
Logger.info("JVXL read: contourValues " + Escape.eAF(jvxlData.contourValues));
}
s = XmlReader.getXmlAttrib(data, "contourColors");
if (s.length() > 0) {
jvxlData.contourColixes = params.contourColixes = C.getColixArray(s);
jvxlData.contourColors = C.getHexCodes(jvxlData.contourColixes);
Logger.info("JVXL read: contourColixes " + C.getHexCodes(jvxlData.contourColixes));
}
params.contourFromZero = XmlReader.getXmlAttrib(data, "contourFromZero").equals("true");
}
params.nContours = (haveContourData ? nContourData : nContoursRead);
// TODO ? params.contourFromZero = false; // MEP data to complete the plane
}
jvxlData.nVertexColors = parseIntStr(XmlReader.getXmlAttrib(data, "nVertexColors"));
params.isBicolorMap = XmlReader.getXmlAttrib(data, "bicolorMap").equals("true");
if (params.isBicolorMap) {
// TODO -- not quite right, because
s = XmlReader.getXmlAttrib(data, "colorPositive");
if (s.length() > 0
&& params.colorRgb == Integer.MIN_VALUE
&& params.colorPos == Parameters.defaultColorPositive)
params.colorPos = CU.getArgbFromString(s);
s = XmlReader.getXmlAttrib(data, "colorNegative");
if (s.length() > 0
&& params.colorRgb == Integer.MIN_VALUE
&& params.colorNeg == Parameters.defaultColorNegative)
params.colorNeg = CU.getArgbFromString(s);
}
if (params.isBicolorMap || params.colorBySign) jvxlCutoff = 0;
jvxlDataIsColorMapped =
((params.colorRgb == Integer.MIN_VALUE || params.colorRgb == Integer.MAX_VALUE)
&& (params.isBicolorMap || XmlReader.getXmlAttrib(data, "colorMapped").equals("true")));
// isJvxlPrecisionColor is for information only -- will be superceded by encoding attribute of
// jvxlColorData
jvxlData.isJvxlPrecisionColor = XmlReader.getXmlAttrib(data, "precisionColor").equals("true");
jvxlData.jvxlDataIsColorDensity =
params.colorDensity =
(params.colorRgb == Integer.MIN_VALUE
&& XmlReader.getXmlAttrib(data, "colorDensity").equals("true"));
if (jvxlData.jvxlDataIsColorDensity && Float.isNaN(params.pointSize)) {
s = XmlReader.getXmlAttrib(data, "pointSize");
if (s.length() > 0) jvxlData.pointSize = params.pointSize = parseFloatStr(s);
}
s = XmlReader.getXmlAttrib(data, "allowVolumeRender");
jvxlData.allowVolumeRender =
params.allowVolumeRender = (s.length() == 0 || s.equalsIgnoreCase("true"));
s = XmlReader.getXmlAttrib(data, "plane");
if (s.indexOf("{") >= 0) {
params.thePlane = null;
params.mapLattice = null;
try {
params.thePlane = (P4) Escape.uP(s);
s = XmlReader.getXmlAttrib(data, "maplattice");
Logger.info("JVXL read: plane " + params.thePlane);
if (s.indexOf("{") >= 0) {
params.mapLattice = (P3) Escape.uP(s);
Logger.info("JVXL read: mapLattice " + params.mapLattice);
}
if (params.scale3d == 0)
params.scale3d = parseFloatStr(XmlReader.getXmlAttrib(data, "scale3d"));
if (Float.isNaN(params.scale3d)) params.scale3d = 0;
} catch (Exception e) {
if (params.thePlane == null) {
Logger.error("JVXL Error reading plane definition -- setting to 0 0 1 0 (z=0)");
params.thePlane = P4.new4(0, 0, 1, 0);
} else {
Logger.error("JVXL Error reading mapLattice definition -- ignored");
}
}
surfaceDataCount = 0;
edgeDataCount = 0;
} else {
params.thePlane = null;
surfaceDataCount = parseIntStr(XmlReader.getXmlAttrib(data, "nSurfaceInts"));
edgeDataCount = parseIntStr(XmlReader.getXmlAttrib(data, "nBytesUncompressedEdgeData"));
}
excludedVertexCount = parseIntStr(XmlReader.getXmlAttrib(data, "nExcludedVertexes"));
excludedTriangleCount = parseIntStr(XmlReader.getXmlAttrib(data, "nExcludedTriangles"));
invalidatedVertexCount = parseIntStr(XmlReader.getXmlAttrib(data, "nInvalidatedVertexes"));
s = XmlReader.getXmlAttrib(data, "slabInfo");
if (s.length() > 0) jvxlData.slabInfo = s;
colorDataCount =
Math.max(0, parseIntStr(XmlReader.getXmlAttrib(data, "nBytesUncompressedColorData")));
jvxlDataIs2dContour = (params.thePlane != null && jvxlDataIsColorMapped);
// new Jmol 12.1.50
jvxlData.color = XmlReader.getXmlAttrib(data, "color");
if (jvxlData.color.length() == 0 || jvxlData.color.indexOf("null") >= 0)
jvxlData.color = "orange";
jvxlData.translucency = parseFloatStr(XmlReader.getXmlAttrib(data, "translucency"));
if (Float.isNaN(jvxlData.translucency)) jvxlData.translucency = 0;
s = XmlReader.getXmlAttrib(data, "meshColor");
if (s.length() > 0) jvxlData.meshColor = s;
s = XmlReader.getXmlAttrib(data, "rendering");
if (s.length() > 0) jvxlData.rendering = s;
jvxlData.colorScheme = XmlReader.getXmlAttrib(data, "colorScheme");
if (jvxlData.colorScheme.length() == 0) jvxlData.colorScheme = null;
if (jvxlData.thisSet < 0) {
int n = parseIntStr(XmlReader.getXmlAttrib(data, "set"));
if (n > 0) jvxlData.thisSet = n - 1;
}
jvxlData.slabValue = parseIntStr(XmlReader.getXmlAttrib(data, "slabValue"));
jvxlData.isSlabbable = (XmlReader.getXmlAttrib(data, "slabbable").equalsIgnoreCase("true"));
jvxlData.diameter = parseIntStr(XmlReader.getXmlAttrib(data, "diameter"));
if (jvxlData.diameter == Integer.MIN_VALUE) jvxlData.diameter = 0;
if (jvxlDataIs2dContour) params.isContoured = true;
if (params.colorBySign) params.isBicolorMap = true;
boolean insideOut = XmlReader.getXmlAttrib(data, "insideOut").equals("true");
float dataMin = Float.NaN;
float dataMax = Float.NaN;
float red = Float.NaN;
float blue = Float.NaN;
if (jvxlDataIsColorMapped) {
dataMin = parseFloatStr(XmlReader.getXmlAttrib(data, "dataMinimum"));
dataMax = parseFloatStr(XmlReader.getXmlAttrib(data, "dataMaximum"));
red = parseFloatStr(XmlReader.getXmlAttrib(data, "valueMappedToRed"));
blue = parseFloatStr(XmlReader.getXmlAttrib(data, "valueMappedToBlue"));
if (Float.isNaN(dataMin)) {
dataMin = red = -1f;
dataMax = blue = 1f;
}
}
jvxlSetColorRanges(dataMin, dataMax, red, blue, insideOut);
}
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;
}
boolean createIsosurface(boolean justForPlane) {
resetIsosurface();
jvxlData.cutoff = Float.NaN;
if (!readAndSetVolumeParameters(justForPlane)) return false;
if (!justForPlane && !Float.isNaN(params.sigma) && !allowSigma) {
if (params.sigma > 0)
Logger.error("Reader does not support SIGMA option -- using cutoff 1.6");
params.cutoff = 1.6f;
}
// negative sigma just ignores the error message
// and means it was inserted by Jmol as a default option
if (params.sigma < 0) params.sigma = -params.sigma;
nPointsX = voxelCounts[0];
nPointsY = voxelCounts[1];
nPointsZ = voxelCounts[2];
jvxlData.isSlabbable = ((params.dataType & Parameters.IS_SLABBABLE) != 0);
jvxlData.insideOut = params.insideOut;
jvxlData.dataXYReversed = params.dataXYReversed;
jvxlData.isBicolorMap = params.isBicolorMap;
jvxlData.nPointsX = nPointsX;
jvxlData.nPointsY = nPointsY;
jvxlData.nPointsZ = nPointsZ;
jvxlData.jvxlVolumeDataXml = volumeData.xmlData;
jvxlData.voxelVolume = volumeData.voxelVolume;
if (justForPlane) {
// float[][][] voxelDataTemp = volumeData.voxelData;
volumeData.setMappingPlane(params.thePlane);
// volumeData.setDataDistanceToPlane(params.thePlane);
if (meshDataServer != null)
meshDataServer.fillMeshData(meshData, MeshData.MODE_GET_VERTICES, null);
params.setMapRanges(this, false);
generateSurfaceData();
volumeData.setMappingPlane(null);
// if (volumeData != null)
// volumeData.voxelData = voxelDataTemp;
} else {
if (!readVolumeData(false)) return false;
generateSurfaceData();
}
if (jvxlFileHeaderBuffer != null) {
String s = jvxlFileHeaderBuffer.toString();
int i = s.indexOf('\n', s.indexOf('\n', s.indexOf('\n') + 1) + 1) + 1;
jvxlData.jvxlFileTitle = s.substring(0, i);
}
if (params.contactPair == null) setBoundingBox();
if (!params.isSilent)
Logger.info("boundbox corners " + Escape.escape(xyzMin) + " " + Escape.escape(xyzMax));
jvxlData.boundingBox = new Point3f[] {xyzMin, xyzMax};
jvxlData.dataMin = dataMin;
jvxlData.dataMax = dataMax;
jvxlData.cutoff = (isJvxl ? jvxlCutoff : params.cutoff);
jvxlData.isCutoffAbsolute = params.isCutoffAbsolute;
jvxlData.pointsPerAngstrom = 1f / volumeData.volumetricVectorLengths[0];
jvxlData.jvxlColorData = "";
jvxlData.jvxlPlane = params.thePlane;
jvxlData.jvxlEdgeData = edgeData;
jvxlData.isBicolorMap = params.isBicolorMap;
jvxlData.isContoured = params.isContoured;
jvxlData.colorDensity = params.colorDensity;
if (jvxlData.vContours != null) params.nContours = jvxlData.vContours.length;
jvxlData.nContours = (params.contourFromZero ? params.nContours : -1 - params.nContours);
jvxlData.nEdges = edgeCount;
jvxlData.edgeFractionBase = edgeFractionBase;
jvxlData.edgeFractionRange = edgeFractionRange;
jvxlData.colorFractionBase = colorFractionBase;
jvxlData.colorFractionRange = colorFractionRange;
jvxlData.jvxlDataIs2dContour = jvxlDataIs2dContour;
jvxlData.jvxlDataIsColorMapped = jvxlDataIsColorMapped;
jvxlData.jvxlDataIsColorDensity = jvxlDataIsColorDensity;
jvxlData.isXLowToHigh = isXLowToHigh;
jvxlData.vertexDataOnly = vertexDataOnly;
jvxlData.saveVertexCount = 0;
if (jvxlDataIsColorMapped || jvxlData.nVertexColors > 0) {
if (meshDataServer != null) {
meshDataServer.fillMeshData(meshData, MeshData.MODE_GET_VERTICES, null);
meshDataServer.fillMeshData(meshData, MeshData.MODE_GET_COLOR_INDEXES, null);
}
jvxlData.jvxlColorData = readColorData();
updateSurfaceData();
if (meshDataServer != null) meshDataServer.notifySurfaceMappingCompleted();
}
return true;
}