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

Example 16 with CoordinateIndex

use of org.vcell.util.CoordinateIndex 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 17 with CoordinateIndex

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

the class CartesianMesh method calculateMeshElementVolumeFromVolumeIndex.

/**
 * Insert the method's description here.
 * Creation date: (2/23/2006 12:52:44 PM)
 */
public double calculateMeshElementVolumeFromVolumeIndex(int volumeIndex) {
    CoordinateIndex ci = getCoordinateIndexFromVolumeIndex(volumeIndex);
    double fxMESize = (ci.x == 0 || ci.x == (getSizeX() - 1) ? .5 : 1);
    double fyMESize = (getGeometryDimension() >= 2 ? (ci.y == 0 || ci.y == (getSizeY() - 1) ? .5 : 1) : 0);
    double fzMESize = (getGeometryDimension() == 3 ? (ci.z == 0 || ci.z == (getSizeZ() - 1) ? .5 : 1) : 0);
    return (fxMESize != 0 ? fxMESize * (getExtent().getX() / (getSizeX() - 1)) : 1) * (fyMESize != 0 ? fyMESize * (getExtent().getY() / (getSizeY() - 1)) : 1) * (fzMESize != 0 ? fzMESize * (getExtent().getZ() / (getSizeZ() - 1)) : 1);
}

Example 18 with CoordinateIndex

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

the class CartesianMeshChombo method findMembraneIndexFromVolumeCoordinate.

public int findMembraneIndexFromVolumeCoordinate(Coordinate wc) {
    if (dx == null) {
        dx = new double[3];
        dx[0] = getExtent().getX() / getSizeX();
        dx[1] = getExtent().getY() / getSizeY();
        dx[2] = getExtent().getZ() / getSizeZ();
    }
    int i = (int) ((wc.getX() - getOrigin().getX()) / dx[0]);
    int j = (int) ((wc.getY() - getOrigin().getY()) / dx[1]);
    int k = dimension < 3 ? 0 : (int) ((wc.getZ() - getOrigin().getZ()) / dx[2]);
    return findMembraneIndexFromVolumeIndex(new CoordinateIndex(i, j, k));
}

Example 19 with CoordinateIndex

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

the class CartesianMeshChombo method findMembraneIndexFromVolumeIndex.

public int findMembraneIndexFromVolumeIndex(CoordinateIndex ci) {
    for (MembraneElementMetricsEntry me : membraneElementMetrics) {
        CoordinateIndex ci0 = new CoordinateIndex(me.i, me.j, me.k);
        CoordinateIndex ci1 = ci;
        if (me.level < viewLevel) {
            ci1 = convertDownToLevel(ci1, me.level, viewLevel);
        } else if (me.level > viewLevel) {
            // we will worry about this later.
            return -1;
        }
        if (ci0.x == ci1.x && ci0.y == ci1.y && (dimension == 2 || ci0.z == ci1.z)) {
            return me.index;
        }
    }
    return -1;
}

Example 20 with CoordinateIndex

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

the class MeshDisplayAdapter method isMembraneElementVisible.

/**
 * Insert the method's description here.
 * Creation date: (8/30/00 6:25:14 PM)
 * @return cbit.vcell.geometry.Line
 */
private boolean isMembraneElementVisible(MembraneElement membraneElement, int normalAxis, int slice) {
    int membranePlane = getNormalAxis(membraneElement);
    if (membranePlane == normalAxis) {
        // MembraneElement perpendicular to our view
        return false;
    }
    CoordinateIndex insideCI = mesh.getCoordinateIndexFromVolumeIndex(membraneElement.getInsideVolumeIndex());
    // MembraneElement not visible in slice
    if (normalAxis == Coordinate.Z_AXIS && insideCI.z != slice) {
        return false;
    } else if (normalAxis == Coordinate.Y_AXIS && insideCI.y != slice) {
        return false;
    } else if (normalAxis == Coordinate.X_AXIS && insideCI.x != slice) {
        return false;
    }
    return true;
}