Example #1
0
 void resetIsosurface() {
   meshData = new MeshData();
   xyzMin = xyzMax = null;
   jvxlData.isBicolorMap = params.isBicolorMap;
   if (meshDataServer != null) meshDataServer.fillMeshData(null, 0, null);
   contourVertexCount = 0;
   if (params.cutoff == Float.MAX_VALUE) params.cutoff = defaultCutoff;
   jvxlData.jvxlSurfaceData = "";
   jvxlData.jvxlEdgeData = "";
   jvxlData.jvxlColorData = "";
   // TODO: more resets of jvxlData?
   edgeCount = 0;
   edgeFractionBase = JvxlCoder.defaultEdgeFractionBase;
   edgeFractionRange = JvxlCoder.defaultEdgeFractionRange;
   colorFractionBase = JvxlCoder.defaultColorFractionBase;
   colorFractionRange = JvxlCoder.defaultColorFractionRange;
   params.mappedDataMin = Float.MAX_VALUE;
 }
Example #2
0
  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;
  }