/**
* 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;
}
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);
}