@Override
protected void readParameters() throws Exception {
String s = xr.getXmlData("jvxlFileTitle", null, false, false);
jvxlFileHeaderBuffer = SB.newS(s);
xr.toTag("jvxlVolumeData");
String data = tempDataXml = xr.getXmlData("jvxlVolumeData", null, true, false);
volumetricOrigin.setT(xr.getXmlPoint(data, "origin"));
isAngstroms = true;
readVector(0);
readVector(1);
readVector(2);
line = xr.toTag("jvxlSurfaceSet");
nSurfaces = parseIntStr(XmlReader.getXmlAttrib(line, "count"));
Logger.info("jvxl file surfaces: " + nSurfaces);
Logger.info("using default edge fraction base and range");
Logger.info("using default color fraction base and range");
cJvxlEdgeNaN = (char) (edgeFractionBase + edgeFractionRange);
}
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);
}
}
