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); }