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

Example 21 with Coordinate

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

the class CurveRenderer method setWorldDelta.

/**
 * Sets the worldDelta property (cbit.vcell.geometry.Coordinate) value.
 * @param worldDelta The new value for the property.
 * @see #getWorldDelta
 */
public void setWorldDelta(org.vcell.util.Coordinate wd) {
    if (wd == null && fieldWorldDelta == null) {
        return;
    }
    Coordinate oldValue = fieldWorldDelta;
    fieldWorldDelta = wd;
    // Calc smallest 1 Pixel distance of the 3 axes
    // unitDistance[Coordinate.X_AXIS] = Math.sqrt((wd.getZ() * wd.getZ()) + (wd.getY() * wd.getY()));
    // unitDistance[Coordinate.Y_AXIS] = Math.sqrt((wd.getX() * wd.getX()) + (wd.getZ() * wd.getZ()));
    // unitDistance[Coordinate.Z_AXIS] = Math.sqrt((wd.getX() * wd.getX()) + (wd.getY() * wd.getY()));
    // 
    updateOriginAndScaling2D();
    firePropertyChange("worldDelta", oldValue, wd);
}

Example 22 with Coordinate

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

the class MathTestingUtilities method comparePDEResultsWithExact.

/**
 * Insert the method's description here.
 * Creation date: (8/20/2003 12:58:10 PM)
 */
public static SimulationComparisonSummary comparePDEResultsWithExact(SimulationSymbolTable simSymbolTable, PDEDataManager dataManager, String type, double absErrorThreshold, double relErrorThreshold) throws DataAccessException, ExpressionException {
    java.util.Hashtable<String, DataErrorSummary> tempVarHash = new java.util.Hashtable<String, DataErrorSummary>();
    double[] timeArray = dataManager.getDataSetTimes();
    Variable[] vars = simSymbolTable.getVariables();
    CartesianMesh mesh = dataManager.getMesh();
    MathDescription mathDesc = simSymbolTable.getSimulation().getMathDescription();
    // Get volumeSubdomains from mathDesc/mesh and store in lookupTable
    int numVol = mesh.getSizeX() * mesh.getSizeY() * mesh.getSizeZ();
    CompartmentSubDomain[] volSubDomainLookup = new CompartmentSubDomain[numVol];
    for (int i = 0; i < numVol; i++) {
        int subVolumeIndex = mesh.getSubVolumeFromVolumeIndex(i);
        SubVolume subVolume = mathDesc.getGeometry().getGeometrySpec().getSubVolume(subVolumeIndex);
        CompartmentSubDomain compSubDomain = mathDesc.getCompartmentSubDomain(subVolume.getName());
        volSubDomainLookup[i] = compSubDomain;
    }
    // Get membraneSubdomains from mathDesc/mesh and store in lookupTable
    int numMem = mesh.getMembraneElements().length;
    MembraneSubDomain[] memSubDomainLookup = new MembraneSubDomain[numMem];
    for (int i = 0; i < numMem; i++) {
        int insideVolIndex = mesh.getMembraneElements()[i].getInsideVolumeIndex();
        int outsideVolIndex = mesh.getMembraneElements()[i].getOutsideVolumeIndex();
        MembraneSubDomain memSubDomain = mathDesc.getMembraneSubDomain(volSubDomainLookup[insideVolIndex], volSubDomainLookup[outsideVolIndex]);
        memSubDomainLookup[i] = memSubDomain;
    }
    double[] valueArray = new double[4];
    SimpleSymbolTable symbolTable = new SimpleSymbolTable(new String[] { "t", "x", "y", "z" });
    int tIndex = symbolTable.getEntry("t").getIndex();
    int xIndex = symbolTable.getEntry("x").getIndex();
    int yIndex = symbolTable.getEntry("y").getIndex();
    int zIndex = symbolTable.getEntry("z").getIndex();
    SimulationComparisonSummary simComparisonSummary = new SimulationComparisonSummary();
    String hashKey = new String("");
    long dataLength = 0;
    // for each var, do the following :
    for (int i = 0; i < vars.length; i++) {
        if (vars[i] instanceof VolVariable || vars[i] instanceof MemVariable || vars[i] instanceof FilamentVariable || vars[i] instanceof VolumeRegionVariable || vars[i] instanceof MembraneRegionVariable || vars[i] instanceof FilamentRegionVariable) {
            // for each time in timeArray,
            for (int j = 0; j < timeArray.length; j++) {
                if (type.equals(TestCaseNew.EXACT_STEADY)) {
                    if (j != (timeArray.length - 1)) {
                        continue;
                    }
                }
                // get data block from varName, data from datablock
                SimDataBlock simDataBlock = dataManager.getSimDataBlock(vars[i].getName(), timeArray[j]);
                double[] data = simDataBlock.getData();
                dataLength = data.length;
                SubDomain subDomain = null;
                Coordinate subDomainCoord = null;
                // for each point in data block ...
                for (int k = 0; k < dataLength; k++) {
                    // Get subdomain from mesh (from the lookupTable), get coordinates (x,y,z) from mesh, evaluate EXACT SOLN at that coord
                    if (vars[i] instanceof VolVariable) {
                        subDomain = volSubDomainLookup[k];
                        subDomainCoord = mesh.getCoordinateFromVolumeIndex(k);
                    } else if (vars[i] instanceof MemVariable) {
                        subDomain = memSubDomainLookup[k];
                        subDomainCoord = mesh.getCoordinateFromMembraneIndex(k);
                    } else {
                        throw new RuntimeException("Var " + vars[i].getName() + " not supported yet!");
                    }
                    hashKey = vars[i].getName() + ":" + subDomain.getName();
                    DataErrorSummary tempVar = (DataErrorSummary) tempVarHash.get(hashKey);
                    if (tempVar == null) {
                        Expression exp = new Expression(subDomain.getEquation(vars[i]).getExactSolution());
                        exp.bindExpression(simSymbolTable);
                        exp = MathUtilities.substituteFunctions(exp, simSymbolTable);
                        exp = exp.flatten();
                        exp.bindExpression(symbolTable);
                        tempVar = new DataErrorSummary(exp);
                        tempVarHash.put(hashKey, tempVar);
                    }
                    // time
                    valueArray[tIndex] = timeArray[j];
                    // x
                    valueArray[xIndex] = subDomainCoord.getX();
                    // y
                    valueArray[yIndex] = subDomainCoord.getY();
                    // z
                    valueArray[zIndex] = subDomainCoord.getZ();
                    // EXACT soln at coord subDomainCoord
                    double value = tempVar.getExactExp().evaluateVector(valueArray);
                    tempVar.addDataValues(value, data[k], timeArray[j], k, absErrorThreshold, relErrorThreshold);
                }
            // end for (k)
            }
        // end for (j)
        }
    // end - if (var)
    }
    // end for (i)
    Enumeration<String> enumKeys = tempVarHash.keys();
    while (enumKeys.hasMoreElements()) {
        String key = enumKeys.nextElement();
        DataErrorSummary tempVarSummary = tempVarHash.get(key);
        simComparisonSummary.addVariableComparisonSummary(new VariableComparisonSummary(key, tempVarSummary.getMinRef(), tempVarSummary.getMaxRef(), tempVarSummary.getMaxAbsoluteError(), tempVarSummary.getMaxRelativeError(), tempVarSummary.getL2Norm(), tempVarSummary.getTimeAtMaxAbsoluteError(), tempVarSummary.getIndexAtMaxAbsoluteError(), tempVarSummary.getTimeAtMaxRelativeError(), tempVarSummary.getIndexAtMaxRelativeError()));
    }
    return simComparisonSummary;
}

Example 23 with Coordinate

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

the class MathTestingUtilities method resample3DSpatialSimple.

/**
 * 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[] resample3DSpatialSimple(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);
        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 24 with Coordinate

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

the class MathTestingUtilities method resample1DSpatialSimple.

/**
 * 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[] resample1DSpatialSimple(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);
        // Interpolate in X - final resampledSourceData value
        resampledData[i] = sourceData[volIndx1] + fract_x * (sourceData[volIndx2] - sourceData[volIndx1]);
    }
    return resampledData;
}

Example 25 with Coordinate

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

the class CartesianMesh method getCoordinateFromMembraneIndex.

/**
 * This method was created in VisualAge.
 * @return cbit.vcell.geometry.Coordinate
 * @param coordIndex cbit.vcell.math.CoordinateIndex
 */
public Coordinate getCoordinateFromMembraneIndex(int membraneIndex) {
    MembraneElement me = getMembraneElements()[membraneIndex];
    Coordinate inCoord = getCoordinateFromVolumeIndex(me.getInsideVolumeIndex());
    Coordinate outCoord = getCoordinateFromVolumeIndex(me.getOutsideVolumeIndex());
    return (new Coordinate(0.5 * (inCoord.getX() + outCoord.getX()), 0.5 * (inCoord.getY() + outCoord.getY()), 0.5 * (inCoord.getZ() + outCoord.getZ())));
}