protected void initPlanes() {
yzCount = nPointsY * nPointsZ;
if (!isQuiet) Logger.info("reading data progressively -- yzCount = " + yzCount);
yzPlanes = new float[2][];
yzPlanes[0] = new float[yzCount];
yzPlanes[1] = new float[yzCount];
}
protected boolean gotoAndReadVoxelData(boolean isMapData) {
// overloaded in jvxlReader
initializeVolumetricData();
if (nPointsX > 0 && nPointsY > 0 && nPointsZ > 0)
try {
gotoData(params.fileIndex - 1, nPointsX * nPointsY * nPointsZ);
readSurfaceData(isMapData);
} catch (Exception e) {
Logger.error(e.toString());
return false;
}
return true;
}
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();
}
boolean createIsosurface(boolean justForPlane) {
resetIsosurface();
jvxlData.cutoff = Float.NaN;
if (!readAndSetVolumeParameters(justForPlane)) return false;
if (!justForPlane && !Float.isNaN(params.sigma) && !allowSigma) {
if (params.sigma > 0)
Logger.error("Reader does not support SIGMA option -- using cutoff 1.6");
params.cutoff = 1.6f;
}
// negative sigma just ignores the error message
// and means it was inserted by Jmol as a default option
if (params.sigma < 0) params.sigma = -params.sigma;
nPointsX = voxelCounts[0];
nPointsY = voxelCounts[1];
nPointsZ = voxelCounts[2];
jvxlData.isSlabbable = ((params.dataType & Parameters.IS_SLABBABLE) != 0);
jvxlData.insideOut = params.insideOut;
jvxlData.dataXYReversed = params.dataXYReversed;
jvxlData.isBicolorMap = params.isBicolorMap;
jvxlData.nPointsX = nPointsX;
jvxlData.nPointsY = nPointsY;
jvxlData.nPointsZ = nPointsZ;
jvxlData.jvxlVolumeDataXml = volumeData.xmlData;
jvxlData.voxelVolume = volumeData.voxelVolume;
if (justForPlane) {
// float[][][] voxelDataTemp = volumeData.voxelData;
volumeData.setMappingPlane(params.thePlane);
// volumeData.setDataDistanceToPlane(params.thePlane);
if (meshDataServer != null)
meshDataServer.fillMeshData(meshData, MeshData.MODE_GET_VERTICES, null);
params.setMapRanges(this, false);
generateSurfaceData();
volumeData.setMappingPlane(null);
// if (volumeData != null)
// volumeData.voxelData = voxelDataTemp;
} else {
if (!readVolumeData(false)) return false;
generateSurfaceData();
}
if (jvxlFileHeaderBuffer != null) {
String s = jvxlFileHeaderBuffer.toString();
int i = s.indexOf('\n', s.indexOf('\n', s.indexOf('\n') + 1) + 1) + 1;
jvxlData.jvxlFileTitle = s.substring(0, i);
}
if (params.contactPair == null) setBoundingBox();
if (!params.isSilent)
Logger.info("boundbox corners " + Escape.escape(xyzMin) + " " + Escape.escape(xyzMax));
jvxlData.boundingBox = new Point3f[] {xyzMin, xyzMax};
jvxlData.dataMin = dataMin;
jvxlData.dataMax = dataMax;
jvxlData.cutoff = (isJvxl ? jvxlCutoff : params.cutoff);
jvxlData.isCutoffAbsolute = params.isCutoffAbsolute;
jvxlData.pointsPerAngstrom = 1f / volumeData.volumetricVectorLengths[0];
jvxlData.jvxlColorData = "";
jvxlData.jvxlPlane = params.thePlane;
jvxlData.jvxlEdgeData = edgeData;
jvxlData.isBicolorMap = params.isBicolorMap;
jvxlData.isContoured = params.isContoured;
jvxlData.colorDensity = params.colorDensity;
if (jvxlData.vContours != null) params.nContours = jvxlData.vContours.length;
jvxlData.nContours = (params.contourFromZero ? params.nContours : -1 - params.nContours);
jvxlData.nEdges = edgeCount;
jvxlData.edgeFractionBase = edgeFractionBase;
jvxlData.edgeFractionRange = edgeFractionRange;
jvxlData.colorFractionBase = colorFractionBase;
jvxlData.colorFractionRange = colorFractionRange;
jvxlData.jvxlDataIs2dContour = jvxlDataIs2dContour;
jvxlData.jvxlDataIsColorMapped = jvxlDataIsColorMapped;
jvxlData.jvxlDataIsColorDensity = jvxlDataIsColorDensity;
jvxlData.isXLowToHigh = isXLowToHigh;
jvxlData.vertexDataOnly = vertexDataOnly;
jvxlData.saveVertexCount = 0;
if (jvxlDataIsColorMapped || jvxlData.nVertexColors > 0) {
if (meshDataServer != null) {
meshDataServer.fillMeshData(meshData, MeshData.MODE_GET_VERTICES, null);
meshDataServer.fillMeshData(meshData, MeshData.MODE_GET_COLOR_INDEXES, null);
}
jvxlData.jvxlColorData = readColorData();
updateSurfaceData();
if (meshDataServer != null) meshDataServer.notifySurfaceMappingCompleted();
}
return true;
}