void colorIsosurface() {
if (params.isSquared && volumeData != null) volumeData.filterData(true, Float.NaN);
/* if (params.isContoured && marchingSquares == null) {
// if (params.isContoured && !(jvxlDataIs2dContour || params.thePlane != null)) {
Logger.error("Isosurface error: Cannot contour this type of data.");
return;
}
*/
if (meshDataServer != null) {
meshDataServer.fillMeshData(meshData, MeshData.MODE_GET_VERTICES, null);
}
jvxlData.saveVertexCount = 0;
if (params.isContoured && marchingSquares != null) {
initializeMapping();
params.setMapRanges(this, false);
marchingSquares.setMinMax(params.valueMappedToRed, params.valueMappedToBlue);
jvxlData.saveVertexCount = marchingSquares.contourVertexCount;
contourVertexCount =
marchingSquares.generateContourData(
jvxlDataIs2dContour, (params.isSquared ? 1e-8f : 1e-4f));
jvxlData.contourValuesUsed = marchingSquares.getContourValues();
minMax = marchingSquares.getMinMax();
if (meshDataServer != null) meshDataServer.notifySurfaceGenerationCompleted();
finalizeMapping();
}
applyColorScale();
jvxlData.nContours = (params.contourFromZero ? params.nContours : -1 - params.nContours);
jvxlData.jvxlFileMessage =
"mapped: min = " + params.valueMappedToRed + "; max = " + params.valueMappedToBlue;
}
public int getSurfacePointIndexAndFraction(
float cutoff,
boolean isCutoffAbsolute,
int x,
int y,
int z,
Point3i offset,
int vA,
int vB,
float valueA,
float valueB,
Point3f pointA,
Vector3f edgeVector,
boolean isContourType,
float[] fReturn) {
float thisValue =
getSurfacePointAndFraction(
cutoff,
isCutoffAbsolute,
valueA,
valueB,
pointA,
edgeVector,
x,
y,
z,
vA,
vB,
fReturn,
ptTemp);
/*
* from MarchingCubes
*
* In the case of a setup for a Marching Squares calculation,
* we are collecting just the desired type of intersection for the 2D marching
* square contouring -- x, y, or z. In the case of a contoured f(x,y) surface,
* we take every point.
*
*/
if (marchingSquares != null && params.isContoured)
return marchingSquares.addContourVertex(ptTemp, cutoff);
int assocVertex =
(assocCutoff > 0
? (fReturn[0] < assocCutoff
? vA
: fReturn[0] > 1 - assocCutoff ? vB : MarchingSquares.CONTOUR_POINT)
: MarchingSquares.CONTOUR_POINT);
if (assocVertex >= 0) assocVertex = marchingCubes.getLinearOffset(x, y, z, assocVertex);
int n = addVertexCopy(ptTemp, thisValue, assocVertex);
if (n >= 0 && params.iAddGridPoints) {
marchingCubes.calcVertexPoint(x, y, z, vB, ptTemp);
addVertexCopy(valueA < valueB ? pointA : ptTemp, Float.NaN, MarchingSquares.EDGE_POINT);
addVertexCopy(valueA < valueB ? ptTemp : pointA, Float.NaN, MarchingSquares.EDGE_POINT);
}
return n;
}
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));
}
private void generateSurfaceData() {
edgeData = "";
if (vertexDataOnly) {
try {
readSurfaceData(false);
} catch (Exception e) {
e.printStackTrace();
Logger.error("Exception in SurfaceReader::readSurfaceData: " + e.getMessage());
}
return;
}
contourVertexCount = 0;
int contourType = -1;
marchingSquares = null;
if (params.thePlane != null || params.isContoured) {
marchingSquares =
new MarchingSquares(
this,
volumeData,
params.thePlane,
params.contoursDiscrete,
params.nContours,
params.thisContour,
params.contourFromZero);
contourType = marchingSquares.getContourType();
marchingSquares.setMinMax(params.valueMappedToRed, params.valueMappedToBlue);
}
params.contourType = contourType;
params.isXLowToHigh = isXLowToHigh;
marchingCubes = new MarchingCubes(this, volumeData, params, jvxlVoxelBitSet);
String data = marchingCubes.getEdgeData();
if (params.thePlane == null) edgeData = data;
jvxlData.setSurfaceInfoFromBitSet(marchingCubes.getBsVoxels(), params.thePlane);
jvxlData.jvxlExcluded = params.bsExcluded;
if (isJvxl) edgeData = jvxlEdgeDataRead;
postProcessVertices();
}