Examples with Vect3Didx cbit.vcell.solvers.mb.Vect3Didx used on opensource projects

Example 1 with Vect3Didx

use of cbit.vcell.solvers.mb.Vect3Didx in project vcell by virtualcell.

the class ValidateMesh method indexPoint.

private int indexPoint(String[] parts, int start) {
    combiner.setLength(0);
    for (int i = 0; i < 3; i++) {
        String s = parts[start + i];
        vertices[i] = Double.parseDouble(s);
        combiner.append(s);
    }
    Vect3Didx vi = theIndex.index(vertices[0], vertices[1], vertices[2]);
    final int idx = vi.getIndex();
    String prev = sameStrings.get(idx);
    if (prev == null) {
        sameStrings.put(idx, combiner.toString());
    } else {
        VCAssert.assertTrue(prev.equals(combiner.toString()), "not exact same string");
    }
    return idx;
}

Example 2 with Vect3Didx

use of cbit.vcell.solvers.mb.Vect3Didx 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;
}