void excludeMaximumSet() {
if (meshDataServer != null)
meshDataServer.fillMeshData(meshData, MeshData.MODE_GET_VERTICES, null);
meshData.getSurfaceSet();
BitSet bs;
for (int i = meshData.nSets; --i >= 0; )
if ((bs = meshData.surfaceSet[i]) != null && bs.cardinality() > params.maxSet)
meshData.invalidateSurfaceSet(i);
updateSurfaceData();
if (meshDataServer != null) meshDataServer.fillMeshData(meshData, MeshData.MODE_PUT_SETS, null);
}
public int addTriangleCheck(
int iA, int iB, int iC, int check, int check2, boolean isAbsolute, int color) {
if (marchingSquares != null && params.isContoured) {
if (color == 0) // from marching cubes
return marchingSquares.addTriangle(iA, iB, iC, check, check2);
color = 0; // from marchingSquares
}
return (meshDataServer != null
? meshDataServer.addTriangleCheck(iA, iB, iC, check, check2, isAbsolute, color)
: isAbsolute && !MeshData.checkCutoff(iA, iB, iC, meshData.vertexValues)
? -1
: meshData.addTriangleCheck(iA, iB, iC, check, check2, color));
}
public void slabIsosurface(List<Object[]> slabInfo) {
if (meshDataServer != null)
meshDataServer.fillMeshData(meshData, MeshData.MODE_GET_VERTICES, null);
meshData.slabPolygons(slabInfo, true);
if (meshDataServer != null)
meshDataServer.fillMeshData(meshData, MeshData.MODE_PUT_VERTICES, null);
}
void updateTriangles() {
if (meshDataServer == null) {
meshData.invalidatePolygons();
} else {
meshDataServer.invalidateTriangles();
}
}
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);
}
}
void updateSurfaceData() {
meshData.setVertexSets(true);
updateTriangles();
if (params.bsExcluded[1] == null) params.bsExcluded[1] = new BitSet();
meshData.updateInvalidatedVertices(params.bsExcluded[1]);
}
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);
}
public int addVertexCopy(Point3f vertexXYZ, float value, int assocVertex) {
if (Float.isNaN(value) && assocVertex != MarchingSquares.EDGE_POINT) return -1;
if (meshDataServer == null) return meshData.addVertexCopy(vertexXYZ, value, assocVertex);
return meshDataServer.addVertexCopy(vertexXYZ, value, assocVertex);
}