Examples with Coordinate org.vcell.util.Coordinate used on opensource projects

Example 61 with Coordinate

use of org.vcell.util.Coordinate in project vcell by virtualcell.

the class CartesianMesh method getVolumeSliceIndices.

/**
 * This method was created in VisualAge.
 * @return java.lang.String
 * @param variable java.lang.String
 * @param time double
 */
public int[] getVolumeSliceIndices(int normalAxis, int sliceNumber) {
    Coordinate normalAxisDimension = Coordinate.convertAxisFromStandardXYZToNormal(getSizeX(), getSizeY(), getSizeZ(), normalAxis);
    int[] indices = new int[(int) normalAxisDimension.getX() * (int) normalAxisDimension.getY()];
    int counter = 0;
    CoordinateIndex coordIndex = new CoordinateIndex();
    for (int y = 0; y < normalAxisDimension.getY(); y += 1) {
        for (int x = 0; x < normalAxisDimension.getX(); x += 1) {
            // 
            // indexing through "normal" slice, converting each X,Y pair into equivalent
            // (X,Y,Z) in mesh coordinates.
            // 
            coordIndex.x = x;
            coordIndex.y = y;
            coordIndex.z = sliceNumber;
            Coordinate.convertCoordinateIndexFromNormalToStandardXYZ(coordIndex, normalAxis);
            // 
            // store mesh coordinates in "normal" slice sample array.
            // 
            indices[counter] = getVolumeIndex(coordIndex.x, coordIndex.y, coordIndex.z);
            counter += 1;
        }
    }
    return indices;
}

Example 62 with Coordinate

use of org.vcell.util.Coordinate in project vcell by virtualcell.

the class CartesianMesh method getCoordinate.

/**
 * This method was created in VisualAge.
 * @return cbit.vcell.geometry.Coordinate
 * @param coordIndex cbit.vcell.math.CoordinateIndex
 */
public Coordinate getCoordinate(CoordinateIndex coordIndex) {
    // 
    // 
    // calculate coordinates based on element coordinates
    // 
    // 1--------2--------3-------4--------N
    // 
    // so spacing is divided into (N-1) regions.
    // 
    // 
    // if N is 1, then take middle of that dimension
    // 
    // 
    // extent.getX()/2.0 + origin.getX();
    double x = Coordinate.coordComponentFromSinglePlanePolicy(origin, extent, Coordinate.X_AXIS);
    if (getSizeX() > 1) {
        x = (((double) coordIndex.x) / (getSizeX() - 1)) * extent.getX() + origin.getX();
    }
    // extent.getY()/2.0 + origin.getY();
    double y = Coordinate.coordComponentFromSinglePlanePolicy(origin, extent, Coordinate.Y_AXIS);
    if (getSizeY() > 1) {
        y = (((double) coordIndex.y) / (getSizeY() - 1)) * extent.getY() + origin.getY();
    }
    // extent.getZ()/2.0 + origin.getZ();
    double z = Coordinate.coordComponentFromSinglePlanePolicy(origin, extent, Coordinate.Z_AXIS);
    if (getSizeZ() > 1) {
        z = (((double) coordIndex.z) / (getSizeZ() - 1)) * extent.getZ() + origin.getZ();
    }
    return (new Coordinate(x, y, z));
}

Example 63 with Coordinate

use of org.vcell.util.Coordinate in project vcell by virtualcell.

the class CartesianMeshChombo method collectVertices.

private static void collectVertices(CartesianMeshChombo chomboMesh, Vector vectValues) {
    int c = -1;
    double[] x = (double[]) vectValues.get(++c);
    double[] y = (double[]) vectValues.get(++c);
    double[] z = null;
    if (chomboMesh.dimension == 3) {
        z = (double[]) vectValues.get(++c);
    }
    chomboMesh.vertices = new Coordinate[x.length];
    for (int i = 0; i < x.length; ++i) {
        chomboMesh.vertices[i] = new Coordinate(x[i], y[i], z == null ? 0 : z[i]);
    }
}

Example 64 with Coordinate

use of org.vcell.util.Coordinate in project vcell by virtualcell.

the class CartesianMeshChombo method collect3dSurfaceTriangles.

private static void collect3dSurfaceTriangles(CartesianMeshChombo chomboMesh, Vector vectValues) {
    int c = 0;
    int[] index = (int[]) vectValues.get(c);
    int[] faceIndex = (int[]) vectValues.get(++c);
    int[] neighbor = (int[]) vectValues.get(++c);
    double[] x0 = (double[]) vectValues.get(++c);
    double[] y0 = (double[]) vectValues.get(++c);
    double[] z0 = null;
    if (chomboMesh.dimension == 3) {
        z0 = (double[]) vectValues.get(++c);
    }
    double[] x1 = (double[]) vectValues.get(++c);
    double[] y1 = (double[]) vectValues.get(++c);
    double[] z1 = null;
    if (chomboMesh.dimension == 3) {
        z1 = (double[]) vectValues.get(++c);
    }
    double[] x2 = (double[]) vectValues.get(++c);
    double[] y2 = (double[]) vectValues.get(++c);
    double[] z2 = null;
    if (chomboMesh.dimension == 3) {
        z2 = (double[]) vectValues.get(++c);
    }
    for (int n = 0; n < index.length; ++n) {
        int memIndex = index[n];
        List<SurfaceTriangleEntry3D> edgeList = chomboMesh.surfaceTriangleMap.get(memIndex);
        if (edgeList == null) {
            edgeList = new ArrayList<SurfaceTriangleEntry3D>();
            chomboMesh.surfaceTriangleMap.put(index[n], edgeList);
        }
        SurfaceTriangleEntry3D mp = new SurfaceTriangleEntry3D();
        mp.memIndex = index[n];
        mp.faceIndex = faceIndex[n];
        mp.p0 = new Coordinate(x0[n], y0[n], z0 == null ? 0 : z0[n]);
        mp.p1 = new Coordinate(x1[n], y1[n], z1 == null ? 0 : z1[n]);
        mp.p2 = new Coordinate(x2[n], y2[n], z2 == null ? 0 : z2[n]);
        edgeList.add(mp);
    }
}

Example 65 with Coordinate

use of org.vcell.util.Coordinate in project vcell by virtualcell.

the class MeshDisplayAdapter method getProjectedSegment.

/**
 * Insert the method's description here.
 * Creation date: (8/30/00 6:25:14 PM)
 * @return cbit.vcell.geometry.Line
 */
private Line getProjectedSegment(MembraneElement membraneElement, int normalAxis) {
    // Find midpoint between the 2 volume elements for this MembraneElement
    Coordinate c0 = getMesh().getCoordinateFromMembraneIndex(membraneElement.getMembraneIndex());
    double x0 = c0.getX(), y0 = c0.getY(), z0 = c0.getZ();
    double x1 = c0.getX(), y1 = c0.getY(), z1 = c0.getZ();
    // Stretch endpoints for the line segment based on membranePlane and size of volumeElement
    int membranePlane = getParalellAxis(membraneElement, normalAxis);
    if (membranePlane == Coordinate.Z_AXIS) {
        double elementZSize = (1.0 / (double) (mesh.getSizeZ() - 1)) * mesh.getExtent().getZ();
        z0 -= (elementZSize / 2.0);
        z1 += (elementZSize / 2.0);
    } else if (membranePlane == Coordinate.Y_AXIS) {
        double elementYSize = (1.0 / (double) (mesh.getSizeY() - 1)) * mesh.getExtent().getY();
        y0 -= (elementYSize / 2.0);
        y1 += (elementYSize / 2.0);
    } else if (membranePlane == Coordinate.X_AXIS) {
        double elementXSize = (1.0 / (double) (mesh.getSizeX() - 1)) * mesh.getExtent().getX();
        x0 -= (elementXSize / 2.0);
        x1 += (elementXSize / 2.0);
    }
    // Clip to edge of world
    x0 = (x0 < mesh.getOrigin().getX() ? mesh.getOrigin().getX() : x0);
    y0 = (y0 < mesh.getOrigin().getY() ? mesh.getOrigin().getY() : y0);
    z0 = (z0 < mesh.getOrigin().getZ() ? mesh.getOrigin().getZ() : z0);
    x1 = (x1 > (mesh.getOrigin().getX() + mesh.getExtent().getX()) ? mesh.getOrigin().getX() + mesh.getExtent().getX() : x1);
    y1 = (y1 > (mesh.getOrigin().getY() + mesh.getExtent().getY()) ? mesh.getOrigin().getY() + mesh.getExtent().getY() : y1);
    z1 = (z1 > (mesh.getOrigin().getZ() + mesh.getExtent().getZ()) ? mesh.getOrigin().getZ() + mesh.getExtent().getZ() : z1);
    // 
    return new Line(new Coordinate(x0, y0, z0), new Coordinate(x1, y1, z1));
}