@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); } }