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);
}
}
void applyColorScale() {
colorFractionBase = jvxlData.colorFractionBase = JvxlCoder.defaultColorFractionBase;
colorFractionRange = jvxlData.colorFractionRange = JvxlCoder.defaultColorFractionRange;
if (params.colorPhase == 0) params.colorPhase = 1;
if (meshDataServer == null) {
meshData.vertexColixes = new short[meshData.vertexCount];
} else {
meshDataServer.fillMeshData(meshData, MeshData.MODE_GET_VERTICES, null);
if (params.contactPair == null)
meshDataServer.fillMeshData(meshData, MeshData.MODE_GET_COLOR_INDEXES, null);
}
// colorBySign is true when colorByPhase is true, but not vice-versa
// old: boolean saveColorData = !(params.colorByPhase && !params.isBicolorMap &&
// !params.colorBySign); //sorry!
boolean saveColorData =
(params.colorDensity || params.isBicolorMap || params.colorBySign || !params.colorByPhase);
if (params.contactPair != null) saveColorData = false;
// colors mappable always now
jvxlData.isJvxlPrecisionColor = true;
jvxlData.vertexCount = (contourVertexCount > 0 ? contourVertexCount : meshData.vertexCount);
jvxlData.minColorIndex = -1;
jvxlData.maxColorIndex = 0;
jvxlData.contourValues = params.contoursDiscrete;
jvxlData.isColorReversed = params.isColorReversed;
if (!params.colorDensity)
if (params.isBicolorMap && !params.isContoured || params.colorBySign) {
jvxlData.minColorIndex =
Graphics3D.getColixTranslucent(
Graphics3D.getColix(params.isColorReversed ? params.colorPos : params.colorNeg),
jvxlData.translucency != 0,
jvxlData.translucency);
jvxlData.maxColorIndex =
Graphics3D.getColixTranslucent(
Graphics3D.getColix(params.isColorReversed ? params.colorNeg : params.colorPos),
jvxlData.translucency != 0,
jvxlData.translucency);
}
jvxlData.isTruncated = (jvxlData.minColorIndex >= 0 && !params.isContoured);
boolean useMeshDataValues =
jvxlDataIs2dContour
||
// !jvxlDataIs2dContour && (params.isContoured && jvxlData.jvxlPlane != null ||
hasColorData
|| vertexDataOnly
|| params.colorDensity
|| params.isBicolorMap && !params.isContoured;
if (!useMeshDataValues) {
if (haveSurfaceAtoms && meshData.vertexSource == null)
meshData.vertexSource = new int[meshData.vertexCount];
float min = Float.MAX_VALUE;
float max = -Float.MAX_VALUE;
float value;
initializeMapping();
for (int i = meshData.vertexCount; --i >= meshData.mergeVertexCount0; ) {
/* right, so what we are doing here is setting a range within the
* data for which we want red-->blue, but returning the actual
* number so it can be encoded more precisely. This turned out to be
* the key to making the JVXL contours work.
*
*/
if (params.colorBySets) {
value = meshData.vertexSets[i];
} else if (params.colorByPhase) {
value = getPhase(meshData.vertices[i]);
// else if (jvxlDataIs2dContour)
// marchingSquares
// .getInterpolatedPixelValue(meshData.vertices[i]);
} else {
value = volumeData.lookupInterpolatedVoxelValue(meshData.vertices[i]);
if (haveSurfaceAtoms) meshData.vertexSource[i] = getSurfaceAtomIndex();
}
if (value < min) min = value;
if (value > max && value != Float.MAX_VALUE) max = value;
meshData.vertexValues[i] = value;
}
if (params.rangeSelected && minMax == null) minMax = new float[] {min, max};
finalizeMapping();
}
params.setMapRanges(this, true);
jvxlData.mappedDataMin = params.mappedDataMin;
jvxlData.mappedDataMax = params.mappedDataMax;
jvxlData.valueMappedToRed = params.valueMappedToRed;
jvxlData.valueMappedToBlue = params.valueMappedToBlue;
if (params.contactPair == null) colorData();
JvxlCoder.jvxlCreateColorData(jvxlData, (saveColorData ? meshData.vertexValues : null));
if (haveSurfaceAtoms && meshDataServer != null)
meshDataServer.fillMeshData(meshData, MeshData.MODE_PUT_VERTICES, null);
if (meshDataServer != null && params.colorBySets)
meshDataServer.fillMeshData(meshData, MeshData.MODE_PUT_SETS, null);
}
