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

Example 11 with VisPoint

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

the class MovingBoundaryMeshMapping method fromReader.

public VisMesh fromReader(MovingBoundaryReader reader, DomainType domainType, int timeIndex) {
    MeshInfo meshInfo = reader.getMeshInfo();
    ISize size = new ISize(meshInfo.xinfo.number(), meshInfo.yinfo.number(), 1);
    Plane plane = reader.getPlane(timeIndex);
    int numX = size.getX();
    int numY = size.getY();
    int dimension = 2;
    Vect3D origin = new Vect3D(meshInfo.xinfo.start, meshInfo.yinfo.start, 0.0);
    Vect3D extent = new Vect3D(meshInfo.xinfo.end - meshInfo.xinfo.start, meshInfo.yinfo.end - meshInfo.yinfo.start, 1.0);
    // invoke VisMesh() constructor
    VisMesh visMesh = new VisMesh(dimension, origin, extent);
    int currPointIndex = 0;
    HashMap<String, Integer> pointDict = new HashMap<String, Integer>();
    PointIndex pointIndex = reader.getPointIndex();
    if (domainType == DomainType.INSIDE || domainType == DomainType.OUTSIDE) {
        int volumeIndex = 0;
        for (int j = 0; j < numY; j++) {
            for (int i = 0; i < numX; i++) {
                Element mbElement = plane.get(i, j);
                if ((domainType == DomainType.INSIDE && (mbElement.position == Position.INSIDE || mbElement.position == Position.BOUNDARY)) || (domainType == DomainType.OUTSIDE && mbElement.position == Position.OUTSIDE)) {
                    ArrayList<Integer> elementVisIndices = new ArrayList<Integer>();
                    int[] elementPointIndices = mbElement.boundary();
                    // first and last index is same
                    int numUniqueElementIndices = elementPointIndices.length - 1;
                    for (int p = 0; p < numUniqueElementIndices; p++) {
                        Vect3Didx point = pointIndex.lookup(elementPointIndices[p]);
                        VisPoint visPoint = new VisPoint(point.x, point.y, point.z);
                        String visPointKey = toStringKey(visPoint);
                        Integer visPointIndex = pointDict.get(visPointKey);
                        if (visPointIndex == null) {
                            visPointIndex = currPointIndex++;
                            pointDict.put(visPointKey, visPointIndex);
                            visMesh.addToPoints(visPoint);
                        }
                        elementVisIndices.add(visPointIndex);
                    }
                    VisPolygon polygon = new VisPolygon(elementVisIndices);
                    polygon.setMovingBoundaryVolumeIndex(new MovingBoundaryVolumeIndex(volumeIndex));
                    visMesh.addToPolygons(polygon);
                    volumeIndex++;
                }
            // end if
            }
        // end i
        }
    // end j
    } else if (domainType == DomainType.MEMBRANE) {
        throw new RuntimeException("DomainType MEMBRANE not yet implemented for moving boundary vtk processing");
    }
    return visMesh;
}

Example 12 with VisPoint

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

the class DebugWriteProblem method main.

/**
 * @param args
 */
public static void main(String[] args) {
    try {
        VisMesh visMesh = new VisMesh(3, new Vect3D(0, 0, 0), new Vect3D(3, 1, 1));
        VisPoint[] points0 = new VisPoint[] { new VisPoint(0, 0, 0), new VisPoint(1, 0, 0), new VisPoint(0, 1, 0), new VisPoint(0, 0, 1) };
        visMesh.addToPoints(points0[0]);
        visMesh.addToPoints(points0[1]);
        visMesh.addToPoints(points0[2]);
        visMesh.addToPoints(points0[3]);
        List<PolyhedronFace> faces0 = Arrays.asList(new PolyhedronFace(Arrays.asList(0, 1, 3)), new PolyhedronFace(Arrays.asList(0, 3, 2)), new PolyhedronFace(Arrays.asList(0, 2, 1)), new PolyhedronFace(Arrays.asList(1, 3, 2)));
        int level = 0;
        int boxNumber = 0;
        int boxIndex = 0;
        int fraction = 0;
        VisIrregularPolyhedron genPolyhedra0 = new VisIrregularPolyhedron(faces0);
        genPolyhedra0.setChomboVolumeIndex(new ChomboVolumeIndex(level, boxNumber, boxIndex, fraction));
        visMesh.addToIrregularPolyhedra(genPolyhedra0);
    // VisPoint[] points1 = new VisPoint[] {
    // new VisPoint(2+0, 0, 0),
    // new VisPoint(2+1, 0, 0),
    // new VisPoint(2+0, 1, 0),
    // new VisPoint(2+0, 0, 1)
    // };
    // 
    // visMesh.addPoint(points1[0]);
    // visMesh.addPoint(points1[1]);
    // visMesh.addPoint(points1[2]);
    // visMesh.addPoint(points1[3]);
    // 
    // vtkUnstructuredGrid vtkgrid = VtkGridUtils.getVolumeVtkGrid(visMesh);
    // String filenameASCII = "testASCII.vtk";
    // String filenameBinary = "testBinary.vtk";
    // VtkGridUtils.writeXML(vtkgrid, filenameASCII, true);
    // VtkGridUtils.writeXML(vtkgrid, filenameBinary, false);
    // vtkgrid = VtkGridUtils.read(filenameBinary);
    // vtkgrid.BuildLinks();
    // SimpleVTKViewer simpleViewer = new SimpleVTKViewer();
    // String[] varNames = visDomain.getVisMeshData().getVarNames();
    // simpleViewer.showGrid(vtkgrid, varNames[0], varNames[1]);
    } catch (Exception e) {
        e.printStackTrace(System.out);
    }
}