Examples with Face org.vcell.vis.vismesh.thrift.Face used on opensource projects

Example 1 with Face

use of org.vcell.vis.vismesh.thrift.Face in project vcell by virtualcell.

the class ChomboMeshMapping method fromMeshData3D.

private VisMesh fromMeshData3D(ChomboMeshData chomboMeshData, ChomboCombinedVolumeMembraneDomain chomboCombinedVolumeMembraneDomain) {
    int dimension = chomboMeshData.getMesh().getDimension();
    if (dimension != 3) {
        throw new RuntimeException("expecting a 3D mesh");
    }
    ChomboMesh chomboMesh = chomboMeshData.getMesh();
    ChomboLevel finestLevel = chomboMesh.getLevel(chomboMesh.getNumLevels() - 1);
    int finestAbsRefinement = finestLevel.getAbsoluteRefinement();
    ISize size = finestLevel.getSize();
    int numX = size.getX();
    int numY = size.getY();
    int numZ = size.getZ();
    Vect3D origin = new Vect3D(chomboMesh.getOrigin().x, chomboMesh.getOrigin().y, chomboMesh.getOrigin().z);
    Vect3D extent = new Vect3D(chomboMesh.getExtent().x, chomboMesh.getExtent().y, chomboMesh.getExtent().z);
    // invoke VisMesh() constructor
    VisMesh visMesh = new VisMesh(chomboMesh.getDimension(), origin, extent);
    int currPointIndex = 0;
    HashMap<String, Integer> pointDict = new HashMap<String, Integer>();
    double originX = chomboMesh.getOrigin().x;
    double originY = chomboMesh.getOrigin().y;
    double originZ = chomboMesh.getOrigin().z;
    double extentX = chomboMesh.getExtent().x;
    double extentY = chomboMesh.getExtent().y;
    double extentZ = chomboMesh.getExtent().z;
    ChomboBoundaries chomboBoundaries = chomboMesh.getBoundaries();
    for (ChomboBoundaries.Point chomboPoint : chomboBoundaries.getPoints()) {
        double px = chomboPoint.x;
        double py = chomboPoint.y;
        double pz = chomboPoint.z;
        px = (px - originX) * (numX) / extentX * 2 - 1;
        py = (py - originY) * (numY) / extentY * 2 - 1;
        pz = (pz - originZ) * (numZ) / extentZ * 2 - 1;
        VisPoint newVisPoint = new VisPoint(px, py, pz);
        String coordKey = toStringKey(newVisPoint);
        pointDict.put(coordKey, currPointIndex);
        visMesh.addToPoints(newVisPoint);
        visMesh.addToSurfacePoints(newVisPoint);
        currPointIndex += 1;
    }
    for (ChomboBoundaries.SurfaceTriangle surfaceTriangle : chomboBoundaries.getSurfaceTriangles()) {
        List<Integer> vertices = Arrays.asList(new Integer[] { surfaceTriangle.getP1(), surfaceTriangle.getP2(), surfaceTriangle.getP3() });
        org.vcell.vis.vismesh.thrift.Face face = org.vcell.vis.vismesh.thrift.Face.valueOf(surfaceTriangle.getFace().name());
        VisSurfaceTriangle newVisSurfaceTriangle = new VisSurfaceTriangle(vertices, face);
        newVisSurfaceTriangle.setChomboSurfaceIndex(new ChomboSurfaceIndex(surfaceTriangle.getChomboIndex()));
        visMesh.addToSurfaceTriangles(newVisSurfaceTriangle);
    }
    for (int levelIndex = 0; levelIndex < chomboMesh.getNumLevels(); levelIndex++) {
        ChomboLevelData chomboLevelData = chomboMeshData.getLevelData(levelIndex);
        ChomboLevel currLevel = chomboMesh.getLevel(levelIndex);
        int currAbsRefinement = currLevel.getAbsoluteRefinement();
        Covering covering = currLevel.getCovering();
        int[] levelMap = covering.getLevelMap();
        int[] boxNumberMap = covering.getBoxNumberMap();
        int[] boxIndexMap = covering.getBoxIndexMap();
        int levelNumX = currLevel.getSize().getX();
        int levelNumY = currLevel.getSize().getY();
        int levelNumZ = currLevel.getSize().getZ();
        for (int x = 0; x < levelNumX; x++) {
            for (int y = 0; y < levelNumY; y++) {
                for (int z = 0; z < levelNumZ; z++) {
                    int mapIndex = x + y * levelNumX + z * levelNumX * levelNumY;
                    if (levelMap[mapIndex] == levelIndex) {
                        // 
                        // if fraction (volume fraction of element in box) is 0 ... then skip this element
                        // 
                        int boxNumber = boxNumberMap[mapIndex];
                        int boxIndex = boxIndexMap[mapIndex];
                        double fraction = chomboLevelData.getCellFraction(currLevel, boxNumber, boxIndex);
                        if (fraction > 0) {
                            // 
                            // add cell
                            // 
                            ChomboBox chomboBox = new ChomboBox(currLevel, x, x, y, y, z, z, dimension).getProjectedBox(currAbsRefinement, finestAbsRefinement);
                            double minX = 2 * chomboBox.getMinX() - 1;
                            double maxX = 2 * chomboBox.getMaxX() + 1;
                            double minY = 2 * chomboBox.getMinY() - 1;
                            double maxY = 2 * chomboBox.getMaxY() + 1;
                            double minZ = 2 * chomboBox.getMinZ() - 1;
                            double maxZ = 2 * chomboBox.getMaxZ() + 1;
                            // 
                            // points for a VisPolyhedra ... initially a hex ... then may be clipped
                            // 
                            // p6-------------------p7
                            // /|                   /|
                            // / |                  / |
                            // p4-------------------p5  |
                            // |  |                 |  |
                            // |  |                 |  |
                            // |  |                 |  |         z   y
                            // |  p2................|..p3        |  /
                            // | /                  | /          | /
                            // |/                   |/           |/
                            // p0-------------------p1            O----- x
                            // 
                            // p0 = (X-,Y-,Z-)
                            // p1 = (X+,Y-,Z-)
                            // p2 = (X-,Y+,Z-)
                            // p3 = (X+,Y+,Z-)
                            // p4 = (X-,Y-,Z+)
                            // p5 = (X+,Y-,Z+)
                            // p6 = (X-,Y+,Z+)
                            // p7 = (X+,Y+,Z+)
                            // 
                            VisPoint[] visPoints = { // p0
                            new VisPoint(minX, minY, minZ), // p1
                            new VisPoint(maxX, minY, minZ), // p2
                            new VisPoint(minX, maxY, minZ), // p3
                            new VisPoint(maxX, maxY, minZ), // p4
                            new VisPoint(minX, minY, maxZ), // p5
                            new VisPoint(maxX, minY, maxZ), // p6
                            new VisPoint(minX, maxY, maxZ), // p7
                            new VisPoint(maxX, maxY, maxZ) };
                            Integer[] indices = new Integer[8];
                            for (int v = 0; v < 8; v++) {
                                VisPoint visPoint = visPoints[v];
                                String key = toStringKey(visPoint);
                                Integer i = pointDict.get(key);
                                if (i == null) {
                                    pointDict.put(key, currPointIndex);
                                    i = currPointIndex;
                                    visMesh.addToPoints(visPoint);
                                    currPointIndex++;
                                }
                                indices[v] = i;
                            }
                            VisVoxel voxel = new VisVoxel(Arrays.asList(indices));
                            voxel.setChomboVolumeIndex(new ChomboVolumeIndex(levelIndex, boxNumber, boxIndex, fraction));
                            // print('adding a cell at level '+str(currLevel.getLevel())+" from "+str(p1Coord)+" to "+str(p3Coord))
                            visMesh.addToVisVoxels(voxel);
                        }
                    }
                }
            }
        }
    }
    cropVoxels(visMesh, chomboBoundaries, chomboCombinedVolumeMembraneDomain);
    return visMesh;
}