/**
* decode triangle data found within <jvxlTriangleData> element as created with
* jvxlEncodeTriangleData (see above)
*
* @param tdata tag and contents
* @param edgeData
* @param colorData
* @throws Exception
*/
void jvxlDecodeTriangleData(String tdata, String edgeData, String colorData) throws Exception {
int nTriangles = parseIntStr(XmlReader.getXmlAttrib(tdata, "count"));
if (nTriangles < 0) return;
int[] nextc = new int[1];
int nColors = (colorData == null ? -1 : PT.parseIntNext(colorData, nextc));
int color = 0;
Logger.info("Reading " + nTriangles + " triangles");
String encoding = getEncoding(tdata);
tdata = getData(tdata, "jvxlTriangleData");
String edata = getData(edgeData, "jvxlTriangleEdgeData");
int[] vertex = new int[3];
int[] nextp = new int[1];
int[] nexte = null;
int edgeMask = 7;
boolean haveEdgeInfo;
boolean haveEncoding = !"none".equals(encoding);
if (haveEncoding) {
tdata = JvxlCoder.jvxlDecompressString(tdata);
edata = JvxlCoder.jvxlDecompressString(edata).trim();
haveEdgeInfo = (edata.length() == nTriangles);
} else {
int n = PT.parseIntNext(tdata, nextp);
haveEdgeInfo = (edata.length() > 0);
if (haveEdgeInfo) {
nexte = new int[1];
PT.parseIntNext(edata, nexte); // throw away count
} else if (n > 0) {
Logger.info("JvxlXmlReader: jvxlTriangleEdgeData count=" + n + "; expected " + nTriangles);
}
}
for (int i = 0, v = 0, p = 0, pt = -1; i < nTriangles; ) {
if (haveEncoding) {
char ch = tdata.charAt(++pt);
int diff;
switch (ch) {
case '!':
diff = 0;
break;
case '+':
case '.':
case ' ':
case '\n':
case '\r':
case '\t':
case ',':
continue;
case '-':
case '0':
case '1':
case '2':
case '3':
case '4':
case '5':
case '6':
case '7':
case '8':
case '9':
nextp[0] = pt;
diff = PT.parseIntNext(tdata, nextp);
pt = nextp[0] - 1;
break;
default:
diff = ch - 92; // '\' character
}
v += diff;
} else {
v = PT.parseIntNext(tdata, nextp) - 1;
}
vertex[p] = v;
if (++p == 3) {
p = 0;
if (haveEdgeInfo) {
edgeMask =
(nexte == null ? edata.charAt(i) - '0' : javajs.util.PT.parseIntNext(edata, nexte));
if (edgeMask < 0 || edgeMask > 7) edgeMask = 7;
}
if (nColors > 0) {
int c = PT.parseIntNext(colorData, nextc);
if (c == Integer.MIN_VALUE) nColors = 0;
else color = c;
nColors--;
}
addTriangleCheck(vertex[0], vertex[1], vertex[2], edgeMask, 0, false, color);
i++;
}
}
}
@Override
protected String readColorData() {
if (!jvxlDataIsColorMapped) return "";
// overloads SurfaceReader
// standard jvxl file read for color
int vertexCount = jvxlData.vertexCount = meshData.vertexCount;
// the problem is that the new way to read data in Marching Cubes
// is to ignore all points that are NaN. But then we also have to
// remove those points from the color string.
short[] colixes = meshData.vertexColixes;
float[] vertexValues = meshData.vertexValues;
/*
* haveReadColorData?
= (isJvxl ? jvxlColorDataRead : "");
if (isJvxl && strValueTemp.length() == 0) {
Logger
.error("You cannot use JVXL data to map onto OTHER data, because it only contains the data for one surface. Use ISOSURFACE \"file.jvxl\" not ISOSURFACE .... MAP \"file.jvxl\".");
return "";
}
*/
if ("none".equals(jvxlColorEncodingRead)) {
jvxlData.vertexColors = new int[vertexCount];
int[] nextc = new int[1];
int n = PT.parseIntNext(jvxlColorDataRead, nextc);
n = Math.min(n, vertexCount);
String[] tokens = PT.getTokens(jvxlColorDataRead.substring(nextc[0]));
boolean haveTranslucent = false;
float trans = jvxlData.translucency;
int lastColor = 0;
for (int i = 0; i < n; i++)
// colix will be one of 8 shades of translucent if A in ARGB is not FF.
try {
int c = getColor(tokens[i]);
if (c == 0) c = lastColor;
else lastColor = c;
colixes[i] = C.getColixTranslucent(jvxlData.vertexColors[i] = c);
if (C.isColixTranslucent(colixes[i])) haveTranslucent = true;
else if (trans != 0) colixes[i] = C.getColixTranslucent3(colixes[i], true, trans);
} catch (Exception e) {
Logger.info("JvxlXmlReader: Cannot interpret color code: " + tokens[i]);
// ignore this color if parsing error
}
if (haveTranslucent && trans == 0) {
// set to show in pass2
jvxlData.translucency = 0.5f;
}
return "-";
}
if (params.colorEncoder == null) params.colorEncoder = new ColorEncoder(null);
params.colorEncoder.setColorScheme(null, false);
params.colorEncoder.setRange(
params.valueMappedToRed, params.valueMappedToBlue, params.isColorReversed);
Logger.info(
"JVXL reading color data mapped min/max: "
+ params.mappedDataMin
+ "/"
+ params.mappedDataMax
+ " for "
+ vertexCount
+ " vertices."
+ " using encoding keys "
+ colorFractionBase
+ " "
+ colorFractionRange);
Logger.info(
"mapping red-->blue for "
+ params.valueMappedToRed
+ " to "
+ params.valueMappedToBlue
+ " colorPrecision:"
+ jvxlData.isJvxlPrecisionColor);
boolean getValues = (Float.isNaN(valueMin));
if (getValues) setValueMinMax();
float contourPlaneMinimumValue = Float.MAX_VALUE;
float contourPlaneMaximumValue = -Float.MAX_VALUE;
if (colixes == null || colixes.length < vertexCount)
meshData.vertexColixes = colixes = new short[vertexCount];
// hasColorData = true;
short colixNeg = 0, colixPos = 0;
if (params.colorBySign) {
colixPos = C.getColix(params.isColorReversed ? params.colorNeg : params.colorPos);
colixNeg = C.getColix(params.isColorReversed ? params.colorPos : params.colorNeg);
}
int vertexIncrement = meshData.vertexIncrement;
// here's the problem: we are assuming here that vertexCount == nPointsRead
boolean needContourMinMax = (params.mappedDataMin == Float.MAX_VALUE);
for (int i = 0; i < vertexCount; i += vertexIncrement) {
float value;
if (getValues) value = vertexValues[i] = getNextValue();
else value = vertexValues[i];
if (needContourMinMax) {
if (value < contourPlaneMinimumValue) contourPlaneMinimumValue = value;
if (value > contourPlaneMaximumValue) contourPlaneMaximumValue = value;
}
}
if (needContourMinMax) {
params.mappedDataMin = contourPlaneMinimumValue;
params.mappedDataMax = contourPlaneMaximumValue;
}
if (jvxlData.colorScheme != null)
for (int i = 0; i < vertexCount; i += vertexIncrement) {
float value = vertexValues[i];
// note: these are just default colorings
// orbital color had a bug through 11.2.6/11.3.6
if (marchingSquares != null && params.isContoured) {
marchingSquares.setContourData(i, value);
continue;
}
short colix =
(!params.colorBySign
? params.colorEncoder.getColorIndex(value)
: (params.isColorReversed ? value > 0 : value <= 0) ? colixNeg : colixPos);
colixes[i] = C.getColixTranslucent3(colix, true, jvxlData.translucency);
}
return jvxlColorDataRead + "\n";
}