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

Example 56 with Coordinate

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

the class CurveRenderer method updateOriginAndScaling2D.

/**
 * Insert the method's description here.
 * Creation date: (10/16/00 6:45:56 PM)
 */
private void updateOriginAndScaling2D() {
    // 
    if (getWorldDelta() == null) {
        setScaling2D(null);
    } else {
        Coordinate wd = getWorldDelta();
        double wd_x = Coordinate.convertAxisFromStandardXYZToNormal(wd.getX(), wd.getY(), wd.getZ(), Coordinate.X_AXIS, getNormalAxis());
        double wd_y = Coordinate.convertAxisFromStandardXYZToNormal(wd.getX(), wd.getY(), wd.getZ(), Coordinate.Y_AXIS, getNormalAxis());
        setScaling2D(new Point2D.Double(1 / wd_x, 1 / wd_y));
    }
    // 
    if (getWorldOrigin() == null || getWorldDelta() == null) {
        setOrigin2D(null);
    } else {
        Point2D.Double origin2DScaled = CurveRendererCurveInfo.projectAndScale3DPoint(getWorldOrigin(), getNormalAxis(), getScaling2D());
        setOrigin2D(origin2DScaled);
    }
}

Example 57 with Coordinate

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

the class CurveRenderer method setWorldOrigin.

/**
 * Sets the worldDelta property (cbit.vcell.geometry.Coordinate) value.
 * @param worldDelta The new value for the property.
 * @see #getWorldDelta
 */
public void setWorldOrigin(org.vcell.util.Coordinate wo) {
    if (wo == null && fieldWorldOrigin == null) {
        return;
    }
    Coordinate oldValue = fieldWorldOrigin;
    fieldWorldOrigin = wo;
    updateOriginAndScaling2D();
    firePropertyChange("worldOrigin", oldValue, wo);
}

Example 58 with Coordinate

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

the class XmlReader method getCoordinate.

/**
 * This method returns a Coordinate object from a XML Element.
 * Creation date: (5/22/2001 5:53:05 PM)
 * @return cbit.vcell.geometry.Coordinate
 * @param param org.jdom.Element
 */
public Coordinate getCoordinate(Element param) {
    // get attributes
    double x = Double.parseDouble(param.getAttributeValue(XMLTags.XAttrTag));
    double y = Double.parseDouble(param.getAttributeValue(XMLTags.YAttrTag));
    double z = Double.parseDouble(param.getAttributeValue(XMLTags.ZAttrTag));
    // **** create coordinate ***
    Coordinate coord = new Coordinate(x, y, z);
    return coord;
}

Example 59 with Coordinate

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

the class MathTestingUtilities method resample3DSpatial.

/**
 * Insert the method's description here.
 * Creation date: (10/27/2003 5:07:42 PM)
 * @return double[]
 * @param data double[]
 * @param sourceMesh cbit.vcell.solvers.CartesianMesh
 * @param targetMesh cbit.vcell.solvers.CartesianMesh
 */
public static double[] resample3DSpatial(double[] sourceData, CartesianMesh sourceMesh, CartesianMesh refMesh) {
    if (sourceData.length != sourceMesh.getNumVolumeElements()) {
        throw new RuntimeException("must be volume data, data length doesn't match number of volume elements");
    }
    // for volume samples:
    // 
    // loop through volumeIndexes from refMesh
    // Coordinate refCoordinate = refMesh.getCoordinate(volumeIndex);
    // Coordinate fractionalIndex = sourceMesh.getFractionCoordinateIndex(Coordinate refCoordinate);
    // ....interpolate in z
    // start with integer portion of fractionIndex
    double[] resampledData = new double[refMesh.getSizeX() * refMesh.getSizeY() * refMesh.getSizeZ()];
    for (int i = 0; i < resampledData.length; i++) {
        Coordinate refCoordinate = refMesh.getCoordinateFromVolumeIndex(i);
        Coordinate fractionalIndex = sourceMesh.getFractionalCoordinateIndex(refCoordinate);
        int ceil_x;
        int floor_x;
        int ceil_y;
        int floor_y;
        int ceil_z;
        int floor_z;
        if (fractionalIndex.getX() < 0) {
            floor_x = 0;
            ceil_x = 1;
        } else if (fractionalIndex.getX() > sourceMesh.getSizeX() - 1) {
            floor_x = sourceMesh.getSizeX() - 2;
            ceil_x = sourceMesh.getSizeX() - 1;
        } else {
            ceil_x = (int) Math.ceil(fractionalIndex.getX());
            floor_x = (int) Math.floor(fractionalIndex.getX());
        }
        if (fractionalIndex.getY() < 0) {
            floor_y = 0;
            ceil_y = 1;
        } else if (fractionalIndex.getY() > sourceMesh.getSizeY() - 1) {
            floor_y = sourceMesh.getSizeY() - 2;
            ceil_y = sourceMesh.getSizeY() - 1;
        } else {
            ceil_y = (int) Math.ceil(fractionalIndex.getY());
            floor_y = (int) Math.floor(fractionalIndex.getY());
        }
        if (fractionalIndex.getZ() < 0) {
            floor_z = 0;
            ceil_z = 1;
        } else if (fractionalIndex.getZ() > sourceMesh.getSizeZ() - 1) {
            floor_z = sourceMesh.getSizeZ() - 2;
            ceil_z = sourceMesh.getSizeZ() - 1;
        } else {
            ceil_z = (int) Math.ceil(fractionalIndex.getZ());
            floor_z = (int) Math.floor(fractionalIndex.getZ());
        }
        double fract_x = fractionalIndex.getX() - floor_x;
        double fract_y = fractionalIndex.getY() - floor_y;
        double fract_z = fractionalIndex.getZ() - floor_z;
        CoordinateIndex coord_1 = new CoordinateIndex(floor_x, floor_y, floor_z);
        CoordinateIndex coord_2 = new CoordinateIndex(ceil_x, floor_y, floor_z);
        CoordinateIndex coord_3 = new CoordinateIndex(floor_x, floor_y, ceil_z);
        CoordinateIndex coord_4 = new CoordinateIndex(ceil_x, floor_y, ceil_z);
        CoordinateIndex coord_5 = new CoordinateIndex(floor_x, ceil_y, ceil_z);
        CoordinateIndex coord_6 = new CoordinateIndex(ceil_x, ceil_y, ceil_z);
        CoordinateIndex coord_7 = new CoordinateIndex(floor_x, ceil_y, floor_z);
        CoordinateIndex coord_8 = new CoordinateIndex(ceil_x, ceil_y, floor_z);
        int volIndx1 = sourceMesh.getVolumeIndex(coord_1);
        int volIndx2 = sourceMesh.getVolumeIndex(coord_2);
        int volIndx3 = sourceMesh.getVolumeIndex(coord_3);
        int volIndx4 = sourceMesh.getVolumeIndex(coord_4);
        int volIndx5 = sourceMesh.getVolumeIndex(coord_5);
        int volIndx6 = sourceMesh.getVolumeIndex(coord_6);
        int volIndx7 = sourceMesh.getVolumeIndex(coord_7);
        int volIndx8 = sourceMesh.getVolumeIndex(coord_8);
        // use it to compute a, b, c, d, then e & f	 ** Interpolation in X **
        if (sourceMesh.getSubVolumeFromVolumeIndex(volIndx1) == refMesh.getSubVolumeFromVolumeIndex(i) && sourceMesh.getSubVolumeFromVolumeIndex(volIndx2) != refMesh.getSubVolumeFromVolumeIndex(i)) {
            volIndx2 = volIndx1;
        } else if (sourceMesh.getSubVolumeFromVolumeIndex(volIndx1) != refMesh.getSubVolumeFromVolumeIndex(i) && sourceMesh.getSubVolumeFromVolumeIndex(volIndx2) == refMesh.getSubVolumeFromVolumeIndex(i)) {
            volIndx1 = volIndx2;
        } else if (sourceMesh.getSubVolumeFromVolumeIndex(volIndx1) != refMesh.getSubVolumeFromVolumeIndex(i) && sourceMesh.getSubVolumeFromVolumeIndex(volIndx2) != refMesh.getSubVolumeFromVolumeIndex(i)) {
            throw new RuntimeException("Either subvolume in sourceMesh not equal to refMesh subVol cannot be handled at this time!");
        }
        if (sourceMesh.getSubVolumeFromVolumeIndex(volIndx3) == refMesh.getSubVolumeFromVolumeIndex(i) && sourceMesh.getSubVolumeFromVolumeIndex(volIndx4) != refMesh.getSubVolumeFromVolumeIndex(i)) {
            volIndx4 = volIndx3;
        } else if (sourceMesh.getSubVolumeFromVolumeIndex(volIndx3) != refMesh.getSubVolumeFromVolumeIndex(i) && sourceMesh.getSubVolumeFromVolumeIndex(volIndx4) == refMesh.getSubVolumeFromVolumeIndex(i)) {
            volIndx3 = volIndx4;
        } else if (sourceMesh.getSubVolumeFromVolumeIndex(volIndx3) != refMesh.getSubVolumeFromVolumeIndex(i) && sourceMesh.getSubVolumeFromVolumeIndex(volIndx4) != refMesh.getSubVolumeFromVolumeIndex(i)) {
            throw new RuntimeException("Either subvolume in sourceMesh not equal to refMesh subVol cannot be handled at this time!");
        }
        if (sourceMesh.getSubVolumeFromVolumeIndex(volIndx5) == refMesh.getSubVolumeFromVolumeIndex(i) && sourceMesh.getSubVolumeFromVolumeIndex(volIndx6) != refMesh.getSubVolumeFromVolumeIndex(i)) {
            volIndx6 = volIndx5;
        } else if (sourceMesh.getSubVolumeFromVolumeIndex(volIndx5) != refMesh.getSubVolumeFromVolumeIndex(i) && sourceMesh.getSubVolumeFromVolumeIndex(volIndx6) == refMesh.getSubVolumeFromVolumeIndex(i)) {
            volIndx5 = volIndx6;
        } else if (sourceMesh.getSubVolumeFromVolumeIndex(volIndx5) != refMesh.getSubVolumeFromVolumeIndex(i) && sourceMesh.getSubVolumeFromVolumeIndex(volIndx6) != refMesh.getSubVolumeFromVolumeIndex(i)) {
            throw new RuntimeException("Either subvolume in sourceMesh not equal to refMesh subVol cannot be handled at this time!");
        }
        if (sourceMesh.getSubVolumeFromVolumeIndex(volIndx7) == refMesh.getSubVolumeFromVolumeIndex(i) && sourceMesh.getSubVolumeFromVolumeIndex(volIndx8) != refMesh.getSubVolumeFromVolumeIndex(i)) {
            volIndx8 = volIndx7;
        } else if (sourceMesh.getSubVolumeFromVolumeIndex(volIndx7) != refMesh.getSubVolumeFromVolumeIndex(i) && sourceMesh.getSubVolumeFromVolumeIndex(volIndx8) == refMesh.getSubVolumeFromVolumeIndex(i)) {
            volIndx7 = volIndx8;
        } else if (sourceMesh.getSubVolumeFromVolumeIndex(volIndx7) != refMesh.getSubVolumeFromVolumeIndex(i) && sourceMesh.getSubVolumeFromVolumeIndex(volIndx8) != refMesh.getSubVolumeFromVolumeIndex(i)) {
            throw new RuntimeException("Either subvolume in sourceMesh not equal to refMesh subVol cannot be handled at this time!");
        }
        double val_a = sourceData[volIndx1] + fract_x * (sourceData[volIndx2] - sourceData[volIndx1]);
        double val_b = sourceData[volIndx3] + fract_x * (sourceData[volIndx4] - sourceData[volIndx3]);
        double val_c = sourceData[volIndx5] + fract_x * (sourceData[volIndx6] - sourceData[volIndx5]);
        double val_d = sourceData[volIndx7] + fract_x * (sourceData[volIndx8] - sourceData[volIndx7]);
        // Interpolate in Y
        double val_e = val_a + fract_y * (val_d - val_a);
        double val_f = val_b + fract_y * (val_c - val_b);
        // Interpolate in Z - final resampledSourceData value
        resampledData[i] = val_e + fract_z * (val_f - val_e);
    }
    return resampledData;
}

Example 60 with Coordinate

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

the class CartesianMesh method getCoordinateFromContourIndex.

/**
 * This method was created in VisualAge.
 * @return cbit.vcell.geometry.Coordinate
 * @param coordIndex cbit.vcell.math.CoordinateIndex
 */
public Coordinate getCoordinateFromContourIndex(int contourIndex) {
    ContourElement ce = getContourElements()[contourIndex];
    Coordinate begCoord = ce.getBeginCoordinate();
    Coordinate endCoord = ce.getEndCoordinate();
    return (new Coordinate(0.5 * (begCoord.getX() + endCoord.getX()), 0.5 * (begCoord.getY() + endCoord.getY()), 0.5 * (begCoord.getZ() + endCoord.getZ())));
}