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; }
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); }
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; }