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

Example 66 with Coordinate

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

the class MathTestingUtilities method resample1DSpatial.

/**
 * 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[] resample1DSpatial(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()];
    for (int i = 0; i < resampledData.length; i++) {
        Coordinate refCoordinate = refMesh.getCoordinateFromVolumeIndex(i);
        Coordinate fractionalIndex = sourceMesh.getFractionalCoordinateIndex(refCoordinate);
        int ceil_x;
        int floor_x;
        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());
        }
        double fract_x = fractionalIndex.getX() - floor_x;
        // ***** SHOULD Y,Z BE 0 OR 1 ???? *****
        CoordinateIndex coord_1 = new CoordinateIndex(floor_x, 0, 0);
        CoordinateIndex coord_2 = new CoordinateIndex(ceil_x, 0, 0);
        int volIndx1 = sourceMesh.getVolumeIndex(coord_1);
        int volIndx2 = sourceMesh.getVolumeIndex(coord_2);
        boolean bBoth1_2 = false;
        boolean bNoneOf1_2 = false;
        boolean bOne = false;
        boolean bTwo = false;
        boolean bOneOf1_2 = false;
        // use it to compute a, b, 	 ** Interpolation in X **
        if (sourceMesh.getSubVolumeFromVolumeIndex(volIndx1) == refMesh.getSubVolumeFromVolumeIndex(i) && sourceMesh.getSubVolumeFromVolumeIndex(volIndx2) != refMesh.getSubVolumeFromVolumeIndex(i)) {
            bOneOf1_2 = true;
            bOne = true;
            volIndx2 = volIndx1;
        } else if (sourceMesh.getSubVolumeFromVolumeIndex(volIndx1) != refMesh.getSubVolumeFromVolumeIndex(i) && sourceMesh.getSubVolumeFromVolumeIndex(volIndx2) == refMesh.getSubVolumeFromVolumeIndex(i)) {
            bOneOf1_2 = true;
            bTwo = true;
            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!");
            bNoneOf1_2 = true;
        } else {
            bBoth1_2 = true;
        }
        // Interpolate in X - final resampledSourceData value
        if (bBoth1_2) {
            resampledData[i] = sourceData[volIndx1] + fract_x * (sourceData[volIndx2] - sourceData[volIndx1]);
        }
        if (bOneOf1_2) {
            if (bOne) {
                resampledData[i] = sourceData[volIndx1];
            } else if (bTwo) {
                resampledData[i] = sourceData[volIndx2];
            }
        }
        // 
        if (bNoneOf1_2) {
            // resampledData[i] = BLAH_BLAH;
            throw new RuntimeException("Cannot handle the case where both points are not in ref subvolume");
        }
    }
    return resampledData;
}

Example 67 with Coordinate

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

the class MathTestingUtilities method resample2DSpatialSimple.

/**
 * 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[] resample2DSpatialSimple(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 y
    // 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;
        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());
        }
        double fract_x = fractionalIndex.getX() - floor_x;
        double fract_y = fractionalIndex.getY() - floor_y;
        // ***** SHOULD THIS BE 0 OR 1 ???? *****
        CoordinateIndex coord_1 = new CoordinateIndex(floor_x, floor_y, 0);
        CoordinateIndex coord_2 = new CoordinateIndex(ceil_x, floor_y, 0);
        CoordinateIndex coord_3 = new CoordinateIndex(floor_x, ceil_y, 0);
        CoordinateIndex coord_4 = new CoordinateIndex(ceil_x, ceil_y, 0);
        int volIndx1 = sourceMesh.getVolumeIndex(coord_1);
        int volIndx2 = sourceMesh.getVolumeIndex(coord_2);
        int volIndx3 = sourceMesh.getVolumeIndex(coord_3);
        int volIndx4 = sourceMesh.getVolumeIndex(coord_4);
        // Interpolate in X (first order)
        double val_a = sourceData[volIndx1] + fract_x * (sourceData[volIndx2] - sourceData[volIndx1]);
        double val_b = sourceData[volIndx3] + fract_x * (sourceData[volIndx4] - sourceData[volIndx3]);
        // Interpolate in Y - final resampledSourceData value
        resampledData[i] = val_a + fract_y * (val_b - val_a);
    }
    return resampledData;
}

Example 68 with Coordinate

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

the class MathTestingUtilities method resample2DSpatial.

/**
 * 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[] resample2DSpatial(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 y
    // 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;
        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());
        }
        double fract_x = fractionalIndex.getX() - floor_x;
        double fract_y = fractionalIndex.getY() - floor_y;
        // ***** SHOULD THIS BE 0 OR 1 ???? *****
        CoordinateIndex coord_1 = new CoordinateIndex(floor_x, floor_y, 0);
        CoordinateIndex coord_2 = new CoordinateIndex(ceil_x, floor_y, 0);
        CoordinateIndex coord_3 = new CoordinateIndex(floor_x, ceil_y, 0);
        CoordinateIndex coord_4 = new CoordinateIndex(ceil_x, ceil_y, 0);
        int volIndx1 = sourceMesh.getVolumeIndex(coord_1);
        int volIndx2 = sourceMesh.getVolumeIndex(coord_2);
        int volIndx3 = sourceMesh.getVolumeIndex(coord_3);
        int volIndx4 = sourceMesh.getVolumeIndex(coord_4);
        boolean bBoth1_2 = false;
        boolean bNoneOf1_2 = false;
        boolean bOne = false;
        boolean bTwo = false;
        boolean bOneOf1_2 = false;
        boolean bBoth3_4 = false;
        boolean bNoneOf3_4 = false;
        boolean bThree = false;
        boolean bFour = false;
        boolean bOneOf3_4 = false;
        // use it to compute a, b, 	 ** Interpolation in X **
        if (sourceMesh.getSubVolumeFromVolumeIndex(volIndx1) == refMesh.getSubVolumeFromVolumeIndex(i) && sourceMesh.getSubVolumeFromVolumeIndex(volIndx2) != refMesh.getSubVolumeFromVolumeIndex(i)) {
            bOneOf1_2 = true;
            bOne = true;
            volIndx2 = volIndx1;
        } else if (sourceMesh.getSubVolumeFromVolumeIndex(volIndx1) != refMesh.getSubVolumeFromVolumeIndex(i) && sourceMesh.getSubVolumeFromVolumeIndex(volIndx2) == refMesh.getSubVolumeFromVolumeIndex(i)) {
            bOneOf1_2 = true;
            bTwo = true;
            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!");
            bNoneOf1_2 = true;
        } else {
            bBoth1_2 = true;
        }
        if (sourceMesh.getSubVolumeFromVolumeIndex(volIndx3) == refMesh.getSubVolumeFromVolumeIndex(i) && sourceMesh.getSubVolumeFromVolumeIndex(volIndx4) != refMesh.getSubVolumeFromVolumeIndex(i)) {
            bOneOf3_4 = true;
            bThree = true;
            volIndx4 = volIndx3;
        } else if (sourceMesh.getSubVolumeFromVolumeIndex(volIndx3) != refMesh.getSubVolumeFromVolumeIndex(i) && sourceMesh.getSubVolumeFromVolumeIndex(volIndx4) == refMesh.getSubVolumeFromVolumeIndex(i)) {
            bOneOf3_4 = true;
            bFour = true;
            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!");
            bNoneOf3_4 = true;
        } else {
            bBoth3_4 = true;
        }
        // First order interpolation if 4, 3, 2 points are within the ref subVolume.
        if ((bBoth1_2 && bBoth3_4) || (bBoth1_2 && bOneOf3_4) || (bOneOf1_2 && bBoth3_4) || (bOneOf1_2 && bOneOf3_4)) {
            // Interpolate in X (first order)
            double val_a = sourceData[volIndx1] + fract_x * (sourceData[volIndx2] - sourceData[volIndx1]);
            double val_b = sourceData[volIndx3] + fract_x * (sourceData[volIndx4] - sourceData[volIndx3]);
            // Interpolate in Y - final resampledSourceData value
            resampledData[i] = val_a + fract_y * (val_b - val_a);
        }
        // 0th order interpolation if only one point is in ref subVol.
        if ((bBoth1_2 && bNoneOf3_4)) {
            resampledData[i] = sourceData[volIndx1] + fract_x * (sourceData[volIndx2] - sourceData[volIndx1]);
        }
        if ((bNoneOf1_2 && bBoth3_4)) {
            resampledData[i] = sourceData[volIndx3] + fract_x * (sourceData[volIndx4] - sourceData[volIndx3]);
        }
        if ((bOneOf1_2 && bNoneOf3_4)) {
            if (bOne) {
                resampledData[i] = sourceData[volIndx1];
            } else if (bTwo) {
                resampledData[i] = sourceData[volIndx2];
            }
        }
        if ((bNoneOf1_2 && bOneOf3_4)) {
            if (bThree) {
                resampledData[i] = sourceData[volIndx3];
            } else if (bFour) {
                resampledData[i] = sourceData[volIndx4];
            }
        }
        // 
        if (bNoneOf1_2 && bNoneOf3_4) {
            // resampledData[i] = BLAH_BLAH;
            throw new RuntimeException("Cannot handle the case where all 4 points are not in ref subvolume1");
        }
    }
    return resampledData;
}

Example 69 with Coordinate

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

the class XmlReader method getElectrode.

/**
 * This method returns an Electrode object from a XML representation.
 * Creation date: (6/6/2002 4:22:55 PM)
 * @return cbit.vcell.mapping.Electrode
 */
private Electrode getElectrode(org.jdom.Element elem, SimulationContext currentSimulationContext) {
    // retrieve feature
    String featureName = unMangle(elem.getAttributeValue(XMLTags.FeatureAttrTag));
    Feature feature = (Feature) currentSimulationContext.getModel().getStructure(featureName);
    // retrieve position
    Coordinate position = getCoordinate(elem.getChild(XMLTags.CoordinateTag, vcNamespace));
    Electrode newElect = new Electrode(feature, position);
    return newElect;
}

Example 70 with Coordinate

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

the class GeometrySubVolumePanel method createAnalyticSubVolume.

public static AnalyticSubVolume createAnalyticSubVolume(Component requester, int dimensions, Coordinate center, String newSubVolName) throws UserCancelException {
    // Geometry g = getGeometry();
    // final int dim = g.getDimension();
    AddShapeJPanel addShapeJPanel = new AddShapeJPanel(dimensions);
    addShapeJPanel.setBorder(BorderFactory.createEtchedBorder(EtchedBorder.RAISED));
    addShapeJPanel.setDefaultCenter(center.getX(), center.getY(), center.getZ());
    // (getGeometry().getDimension() > 2?getGeometry().getOrigin().getZ()+getGeometry().getExtent().getZ()/2:null));
    while (true) {
        try {
            final boolean[] acceptFlag = new boolean[] { false };
            LWContainerHandle lwParent = LWNamespace.findLWOwner(requester);
            final JDialog d = new LWTitledDialog(lwParent, "Define New Subdomain Shape");
            // BeanUtils.centerOnComponent(d, GeometrySubVolumePanel.this);
            JPanel main = new JPanel();
            BoxLayout mainBoxLayout = new BoxLayout(main, BoxLayout.Y_AXIS);
            main.setLayout(mainBoxLayout);
            JPanel menuPanel = new JPanel(new FlowLayout(FlowLayout.RIGHT));
            menuPanel.add(LWNamespace.createRightSideIconMenuBar());
            main.add(menuPanel);
            JPanel addCancelJPanel = new JPanel();
            addCancelJPanel.setBorder(new EmptyBorder(10, 10, 10, 10));
            BoxLayout addCancelBoxLayout = new BoxLayout(addCancelJPanel, BoxLayout.X_AXIS);
            addCancelJPanel.setLayout(addCancelBoxLayout);
            {
                JButton helpButton = new JButton("Help");
                helpButton.addActionListener(ae -> {
                    VcellHelpViewer.showStandaloneViewer();
                });
                addCancelJPanel.add(helpButton);
            }
            JButton addJButton = new JButton("New Subdomain");
            addJButton.addActionListener(new ActionListener() {

                public void actionPerformed(ActionEvent e) {
                    d.dispose();
                    acceptFlag[0] = true;
                }
            });
            addCancelJPanel.add(addJButton);
            JButton cancelJButton = new JButton("Cancel");
            cancelJButton.addActionListener(new ActionListener() {

                public void actionPerformed(ActionEvent e) {
                    d.dispose();
                }
            });
            addCancelJPanel.add(cancelJButton);
            main.add(addShapeJPanel);
            main.add(Box.createVerticalStrut(10));
            main.add(addCancelJPanel);
            main.add(Box.createVerticalStrut(10));
            addShapeJPanel.addPropertyChangeListener(new PropertyChangeListener() {

                public void propertyChange(PropertyChangeEvent evt) {
                    if (evt.getPropertyName().equals(AddShapeJPanel.PROPCHANGE_VALID_ANALYTIC)) {
                        addJButton.setEnabled(((Boolean) evt.getNewValue()));
                    }
                }
            });
            d.setModalityType(ModalityType.DOCUMENT_MODAL);
            // d.setModal(true);
            d.getContentPane().add(main);
            d.pack();
            d.setSize(new Dimension(400, 400));
            d.setVisible(true);
            if (acceptFlag[0]) {
                // new Expression(addShapeJPanel.getCurrentAnalyticExpression()), -1));
                return new AnalyticSubVolume(null, newSubVolName, new Expression(addShapeJPanel.getCurrentAnalyticExpression()), -1);
            } else {
                throw UserCancelException.CANCEL_GENERIC;
            }
        } catch (UserCancelException uce) {
            throw uce;
        } catch (Exception e1) {
            e1.printStackTrace();
            DialogUtils.showErrorDialog(requester, "Error adding shape:\n" + e1.getMessage(), e1);
        }
    }
}