private void colorData() {
float[] vertexValues = meshData.vertexValues;
short[] vertexColixes = meshData.vertexColixes;
meshData.polygonColixes = null;
float valueBlue = jvxlData.valueMappedToBlue;
float valueRed = jvxlData.valueMappedToRed;
short minColorIndex = jvxlData.minColorIndex;
short maxColorIndex = jvxlData.maxColorIndex;
if (params.colorEncoder == null) params.colorEncoder = new ColorEncoder(null);
params.colorEncoder.setRange(
params.valueMappedToRed, params.valueMappedToBlue, params.isColorReversed);
for (int i = meshData.vertexCount; --i >= 0; ) {
float value = vertexValues[i];
if (minColorIndex >= 0) {
if (value <= 0) vertexColixes[i] = minColorIndex;
else if (value > 0) vertexColixes[i] = maxColorIndex;
} else {
if (value <= valueRed) value = valueRed;
if (value >= valueBlue) value = valueBlue;
vertexColixes[i] = params.colorEncoder.getColorIndex(value);
}
}
if ((params.nContours > 0 || jvxlData.contourValues != null)
&& jvxlData.contourColixes == null) {
int n = (jvxlData.contourValues == null ? params.nContours : jvxlData.contourValues.length);
short[] colors = jvxlData.contourColixes = new short[n];
float[] values = jvxlData.contourValues;
if (values == null) values = jvxlData.contourValuesUsed;
if (jvxlData.contourValuesUsed == null)
jvxlData.contourValuesUsed = (values == null ? new float[n] : values);
float dv = (valueBlue - valueRed) / (n + 1);
// n + 1 because we want n lines between n + 1 slices
params.colorEncoder.setRange(
params.valueMappedToRed, params.valueMappedToBlue, params.isColorReversed);
for (int i = 0; i < n; i++) {
float v = (values == null ? valueRed + (i + 1) * dv : values[i]);
jvxlData.contourValuesUsed[i] = v;
colors[i] = Graphics3D.getColixTranslucent(params.colorEncoder.getArgb(v));
}
// TODO -- this strips translucency
jvxlData.contourColors = Graphics3D.getHexCodes(colors);
}
}
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);
}
}
