Examples with Expression cbit.vcell.parser.Expression used on opensource projects

Example 36 with Expression

use of cbit.vcell.parser.Expression in project vcell by virtualcell.

the class XmlReader method getElectricalStimulus.

/**
 * This method process Electrical Stimulus, also called Clamps.
 * Creation date: (6/6/2002 4:46:18 PM)
 * @return cbit.vcell.mapping.ElectricalStimulus
 * @param param org.jdom.Element
 */
private ElectricalStimulus getElectricalStimulus(Element param, SimulationContext currentSimulationContext) throws XmlParseException {
    ElectricalStimulus clampStimulus = null;
    // get name
    // String name = unMangle( param.getAttributeValue(XMLTags.NameAttrTag) );
    // get Electrode
    Electrode electrode = getElectrode(param.getChild(XMLTags.ElectrodeTag, vcNamespace), currentSimulationContext);
    if (param.getAttributeValue(XMLTags.TypeAttrTag).equalsIgnoreCase(XMLTags.VoltageClampTag)) {
        // is a voltage clamp
        clampStimulus = new VoltageClampStimulus(electrode, "voltClampElectrode", new Expression(0.0), currentSimulationContext);
    } else if (param.getAttributeValue(XMLTags.TypeAttrTag).equalsIgnoreCase(XMLTags.CurrentDensityClampTag) || param.getAttributeValue(XMLTags.TypeAttrTag).equalsIgnoreCase(XMLTags.CurrentDensityClampTag_oldName)) {
        // is a current density clamp
        clampStimulus = new CurrentDensityClampStimulus(electrode, "currDensityClampElectrode", new Expression(0.0), currentSimulationContext);
    } else if (param.getAttributeValue(XMLTags.TypeAttrTag).equalsIgnoreCase(XMLTags.TotalCurrentClampTag)) {
        // is a "total" current clamp
        clampStimulus = new TotalCurrentClampStimulus(electrode, "totalCurrClampElectrode", new Expression(0.0), currentSimulationContext);
    }
    try {
        // transaction begin flag ... yeah, this is a hack
        clampStimulus.reading(true);
        // Read all of the parameters
        List<Element> list = param.getChildren(XMLTags.ParameterTag, vcNamespace);
        // add constants that may be used in the electrical stimulus.
        VariableHash varHash = new VariableHash();
        Model model = currentSimulationContext.getModel();
        addResevedSymbols(varHash, model);
        // 
        for (Element xmlParam : list) {
            String paramName = unMangle(xmlParam.getAttributeValue(XMLTags.NameAttrTag));
            String role = xmlParam.getAttributeValue(XMLTags.ParamRoleAttrTag);
            String paramExpStr = xmlParam.getText();
            Expression paramExp = unMangleExpression(paramExpStr);
            try {
                if (varHash.getVariable(paramName) == null) {
                    Domain domain = null;
                    varHash.addVariable(new Function(paramName, paramExp, domain));
                } else {
                    if (model.getReservedSymbolByName(paramName) != null) {
                        varHash.removeVariable(paramName);
                        Domain domain = null;
                        varHash.addVariable(new Function(paramName, paramExp, domain));
                    }
                }
            } catch (MathException e) {
                e.printStackTrace(System.out);
                throw new XmlParseException("error reordering parameters according to dependencies:", e);
            }
            LocalParameter tempParam = null;
            if (!role.equals(XMLTags.ParamRoleUserDefinedTag)) {
                if (role.equals(XMLTags.ParamRoleTotalCurrentTag)) {
                    if (clampStimulus instanceof TotalCurrentClampStimulus) {
                        tempParam = ((TotalCurrentClampStimulus) clampStimulus).getCurrentParameter();
                    } else {
                        varHash.removeVariable(paramName);
                        continue;
                    }
                } else if (role.equals(XMLTags.ParamRoleTotalCurrentDensityTag) || role.equals(XMLTags.ParamRoleTotalCurrentDensityOldNameTag)) {
                    if (clampStimulus instanceof CurrentDensityClampStimulus) {
                        tempParam = ((CurrentDensityClampStimulus) clampStimulus).getCurrentDensityParameter();
                    } else {
                        varHash.removeVariable(paramName);
                        continue;
                    }
                } else if (role.equals(XMLTags.ParamRolePotentialDifferenceTag)) {
                    if (clampStimulus instanceof VoltageClampStimulus) {
                        tempParam = ((VoltageClampStimulus) clampStimulus).getVoltageParameter();
                    } else {
                        varHash.removeVariable(paramName);
                        continue;
                    }
                }
            } else {
                continue;
            }
            if (tempParam == null) {
                throw new XmlParseException("parameter with role '" + role + "' not found in electricalstimulus");
            }
            // 
            if (!tempParam.getName().equals(paramName)) {
                LocalParameter multNameParam = clampStimulus.getLocalParameter(paramName);
                int n = 0;
                while (multNameParam != null) {
                    String tempName = paramName + "_" + n++;
                    clampStimulus.renameParameter(paramName, tempName);
                    multNameParam = clampStimulus.getLocalParameter(tempName);
                }
                clampStimulus.renameParameter(tempParam.getName(), paramName);
            }
        }
        // 
        // create unresolved parameters for all unresolved symbols
        // 
        String unresolvedSymbol = varHash.getFirstUnresolvedSymbol();
        while (unresolvedSymbol != null) {
            try {
                Domain domain = null;
                // will turn into an UnresolvedParameter.
                varHash.addVariable(new Function(unresolvedSymbol, new Expression(0.0), domain));
            } catch (MathException e) {
                e.printStackTrace(System.out);
                throw new XmlParseException(e.getMessage());
            }
            clampStimulus.addUnresolvedParameter(unresolvedSymbol);
            unresolvedSymbol = varHash.getFirstUnresolvedSymbol();
        }
        Variable[] sortedVariables = varHash.getTopologicallyReorderedVariables();
        ModelUnitSystem modelUnitSystem = model.getUnitSystem();
        for (int i = sortedVariables.length - 1; i >= 0; i--) {
            if (sortedVariables[i] instanceof Function) {
                Function paramFunction = (Function) sortedVariables[i];
                Element xmlParam = null;
                for (int j = 0; j < list.size(); j++) {
                    Element tempParam = (Element) list.get(j);
                    if (paramFunction.getName().equals(unMangle(tempParam.getAttributeValue(XMLTags.NameAttrTag)))) {
                        xmlParam = tempParam;
                        break;
                    }
                }
                if (xmlParam == null) {
                    // must have been an unresolved parameter
                    continue;
                }
                String symbol = xmlParam.getAttributeValue(XMLTags.VCUnitDefinitionAttrTag);
                VCUnitDefinition unit = null;
                if (symbol != null) {
                    unit = modelUnitSystem.getInstance(symbol);
                }
                LocalParameter tempParam = clampStimulus.getLocalParameter(paramFunction.getName());
                if (tempParam == null) {
                    clampStimulus.addUserDefinedParameter(paramFunction.getName(), paramFunction.getExpression(), unit);
                } else {
                    if (tempParam.getExpression() != null) {
                        // if the expression is null, it should remain null.
                        clampStimulus.setParameterValue(tempParam, paramFunction.getExpression());
                    }
                    tempParam.setUnitDefinition(unit);
                }
            }
        }
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace(System.out);
        throw new XmlParseException("Exception while setting parameters for simContext : " + currentSimulationContext.getName(), e);
    } catch (ExpressionException e) {
        e.printStackTrace(System.out);
        throw new XmlParseException("Exception while settings parameters for simContext : " + currentSimulationContext.getName(), e);
    } finally {
        clampStimulus.reading(false);
    }
    return clampStimulus;
}

Example 37 with Expression

use of cbit.vcell.parser.Expression in project vcell by virtualcell.

the class XmlReader method getConvolutionDataGenerator.

private ConvolutionDataGenerator getConvolutionDataGenerator(Element element) {
    String name = unMangle(element.getAttributeValue(XMLTags.NameAttrTag));
    Expression volumeFunction = null;
    Element volumeFunctionElement = element.getChild(XMLTags.FunctionTag, vcNamespace);
    if (volumeFunctionElement == null) {
        volumeFunctionElement = element.getChild(XMLTags.VolumeFunctionTag, vcNamespace);
    }
    if (volumeFunctionElement != null) {
        String s = volumeFunctionElement.getText();
        volumeFunction = unMangleExpression(s);
    }
    Expression membraneFunction = null;
    Element membraneFunctionElement = element.getChild(XMLTags.MembraneFunctionTag, vcNamespace);
    if (membraneFunctionElement != null) {
        String s = membraneFunctionElement.getText();
        membraneFunction = unMangleExpression(s);
    }
    ConvolutionDataGeneratorKernel kernel = null;
    Element kernelElement = element.getChild(XMLTags.Kernel, vcNamespace);
    String kernelType = kernelElement.getAttributeValue(XMLTags.TypeAttrTag);
    if (kernelType.equals(XMLTags.KernelType_Gaussian)) {
        Element e0 = kernelElement.getChild(XMLTags.KernelGaussianSigmaXY, vcNamespace);
        String s = e0.getText();
        Expression sigmaXY = unMangleExpression(s);
        e0 = kernelElement.getChild(XMLTags.KernelGaussianSigmaZ, vcNamespace);
        s = e0.getText();
        Expression sigmaZ = unMangleExpression(s);
        kernel = new GaussianConvolutionDataGeneratorKernel(sigmaXY, sigmaZ);
    }
    ConvolutionDataGenerator cdg = new ConvolutionDataGenerator(name, kernel, volumeFunction, membraneFunction);
    return cdg;
}

Example 38 with Expression

use of cbit.vcell.parser.Expression in project vcell by virtualcell.

the class XmlReader method getAnalyticSubVolume.

/**
 * This method returns an AnalyticSubVolume object from a XML representation.
 * Creation date: (5/1/2001 5:26:17 PM)
 * @return cbit.vcell.geometry.AnalyticSubVolume
 * @param param org.jdom.Element
 */
private AnalyticSubVolume getAnalyticSubVolume(Element param) throws XmlParseException {
    // retrieve the attributes
    String name = param.getAttributeValue(XMLTags.NameAttrTag);
    int handle = Integer.parseInt(param.getAttributeValue(XMLTags.HandleAttrTag));
    // process the key
    KeyValue key = null;
    String temp = param.getAttributeValue(XMLTags.KeyValueAttrTag);
    if (temp != null && temp.length() > 0 && this.readKeysFlag) {
        key = new KeyValue(temp);
    }
    // Retrieve the expression
    temp = param.getChildText(XMLTags.AnalyticExpressionTag, vcNamespace);
    if (temp == null) {
        throw new XmlParseException("A Problem occured while retrieving the analytic expression of the AnalyticSubvolume " + name);
    }
    Expression newexpression = unMangleExpression(temp);
    // Create the AnalyticCompartment
    AnalyticSubVolume newsubvolume = null;
    try {
        newsubvolume = new AnalyticSubVolume(key, name, newexpression, handle);
    } catch (ExpressionException e) {
        e.printStackTrace();
        throw new XmlParseException("An ExpressionException occured when creating the new AnalyticSubvolume " + name, e);
    }
    return newsubvolume;
}

Example 39 with Expression

use of cbit.vcell.parser.Expression in project vcell by virtualcell.

the class Xmlproducer method getXML.

/**
 * This method returns a XML representation of a SpeciesContextSpec object.
 * Creation date: (3/1/2001 9:13:56 PM)
 * @return Element
 * @param param cbit.vcell.mapping.SpeciesContextSpec
 */
private Element getXML(SpeciesContextSpec param) {
    Element speciesContextSpecElement = new Element(XMLTags.SpeciesContextSpecTag);
    // Add Attributes
    speciesContextSpecElement.setAttribute(XMLTags.SpeciesContextRefAttrTag, mangle(param.getSpeciesContext().getName()));
    speciesContextSpecElement.setAttribute(XMLTags.ForceConstantAttrTag, String.valueOf(param.isConstant()));
    // speciesContextSpecElement.setAttribute(XMLTags.EnableDiffusionAttrTag, String.valueOf(param.isEnableDiffusing()));
    if (param.isWellMixed() != null) {
        speciesContextSpecElement.setAttribute(XMLTags.WellMixedAttrTag, String.valueOf(param.isWellMixed()));
    }
    if (param.isForceContinuous() != null) {
        speciesContextSpecElement.setAttribute(XMLTags.ForceContinuousAttrTag, String.valueOf(param.isForceContinuous()));
    }
    // Add initial
    Expression initCon = param.getInitialConcentrationParameter().getExpression();
    Expression initAmt = param.getInitialCountParameter().getExpression();
    if (initCon != null) {
        Element initial = new Element(XMLTags.InitialConcentrationTag);
        initial.addContent(mangleExpression(initCon));
        speciesContextSpecElement.addContent(initial);
    } else if (initAmt != null) {
        Element initial = new Element(XMLTags.InitialAmountTag);
        initial.addContent(mangleExpression(initAmt));
        speciesContextSpecElement.addContent(initial);
    }
    // Add diffusion
    cbit.vcell.parser.Expression diffRate = param.getDiffusionParameter().getExpression();
    if (diffRate != null) {
        Element diffusion = new Element(XMLTags.DiffusionTag);
        diffusion.addContent(mangleExpression(diffRate));
        speciesContextSpecElement.addContent(diffusion);
    }
    // write BoundaryConditions
    cbit.vcell.parser.Expression exp;
    Element boundaries = new Element(XMLTags.BoundariesTag);
    // XM
    exp = param.getBoundaryXmParameter().getExpression();
    if (exp != null) {
        boundaries.setAttribute(XMLTags.BoundaryAttrValueXm, mangleExpression(exp));
    }
    // XP
    exp = param.getBoundaryXpParameter().getExpression();
    if (exp != null) {
        boundaries.setAttribute(XMLTags.BoundaryAttrValueXp, mangleExpression(exp));
    }
    // YM
    exp = param.getBoundaryYmParameter().getExpression();
    if (exp != null) {
        boundaries.setAttribute(XMLTags.BoundaryAttrValueYm, mangleExpression(exp));
    }
    // YP
    exp = param.getBoundaryYpParameter().getExpression();
    if (exp != null) {
        boundaries.setAttribute(XMLTags.BoundaryAttrValueYp, mangleExpression(exp));
    }
    // ZM
    exp = param.getBoundaryZmParameter().getExpression();
    if (exp != null) {
        boundaries.setAttribute(XMLTags.BoundaryAttrValueZm, mangleExpression(exp));
    }
    // ZP
    exp = param.getBoundaryZpParameter().getExpression();
    if (exp != null) {
        boundaries.setAttribute(XMLTags.BoundaryAttrValueZp, mangleExpression(exp));
    }
    if (boundaries.getAttributes().size() > 0) {
        speciesContextSpecElement.addContent(boundaries);
    }
    // Add Velocities Vx, Vy, Vz
    Element velocityElement = null;
    Expression velX = param.getVelocityXParameter().getExpression();
    if (velX != null) {
        velocityElement = new Element(XMLTags.VelocityTag);
        velocityElement.setAttribute(XMLTags.XAttrTag, mangleExpression(velX));
    }
    Expression velY = param.getVelocityYParameter().getExpression();
    if (velY != null) {
        if (velocityElement == null) {
            velocityElement = new Element(XMLTags.VelocityTag);
        }
        velocityElement.setAttribute(XMLTags.YAttrTag, mangleExpression(velY));
    }
    Expression velZ = param.getVelocityZParameter().getExpression();
    if (velZ != null) {
        if (velocityElement == null) {
            velocityElement = new Element(XMLTags.VelocityTag);
        }
        velocityElement.setAttribute(XMLTags.ZAttrTag, mangleExpression(velZ));
    }
    if (velocityElement != null) {
        speciesContextSpecElement.addContent(velocityElement);
    }
    return speciesContextSpecElement;
}

Example 40 with Expression

use of cbit.vcell.parser.Expression in project vcell by virtualcell.

the class MathModel_SBMLExporter method addGeometry.

private static void addGeometry(Model sbmlModel, MathModel vcMathModel) {
    SpatialModelPlugin mplugin = (SpatialModelPlugin) sbmlModel.getPlugin(SBMLUtils.SBML_SPATIAL_NS_PREFIX);
    // Creates a geometry object via SpatialModelPlugin object.
    org.sbml.jsbml.ext.spatial.Geometry sbmlGeometry = mplugin.getGeometry();
    sbmlGeometry.setCoordinateSystem(GeometryKind.cartesian);
    Geometry vcGeometry = vcMathModel.getGeometry();
    // 
    // list of CoordinateComponents : 1 if geometry is 1-d, 2 if geometry is 2-d, 3 if geometry is 3-d
    // 
    int dimension = vcGeometry.getDimension();
    Extent vcExtent = vcGeometry.getExtent();
    Origin vcOrigin = vcGeometry.getOrigin();
    // add x coordinate component
    CoordinateComponent coordCompX = sbmlGeometry.createCoordinateComponent();
    coordCompX.setSpatialId("CoordCompX");
    coordCompX.setType(CoordinateKind.cartesianX);
    Boundary minX = coordCompX.getBoundaryMaximum();
    minX.setSpatialId("Xmin");
    minX.setValue(vcOrigin.getX());
    Boundary maxX = coordCompX.getBoundaryMaximum();
    maxX.setSpatialId("Xmax");
    maxX.setValue(vcOrigin.getX() + (vcExtent.getX()));
    Parameter parameterX = sbmlModel.createParameter();
    // note for exporting BioModels rather than MathModels, get ReservedSymbol from Model with Role of ReservedSymbolRole.X
    parameterX.setId(ReservedVariable.X.getName());
    SpatialSymbolReference coordXSpatialRef = new SpatialSymbolReference();
    coordXSpatialRef.setSpatialRef(coordCompX.getSpatialId());
    SpatialParameterPlugin parameterXSpatialPlugin = (SpatialParameterPlugin) parameterX.getPlugin(SBMLUtils.SBML_SPATIAL_NS_PREFIX);
    parameterXSpatialPlugin.setParamType(coordXSpatialRef);
    // add y coordinate component
    if (dimension == 2 || dimension == 3) {
        CoordinateComponent coordCompY = sbmlGeometry.createCoordinateComponent();
        coordCompY.setSpatialId("CoordCompY");
        coordCompY.setType(CoordinateKind.cartesianY);
        Boundary minY = coordCompY.getBoundaryMinimum();
        minY.setId("Ymin");
        minY.setValue(vcOrigin.getY());
        Boundary maxY = coordCompY.getBoundaryMaximum();
        maxY.setId("Ymax");
        maxY.setValue(vcOrigin.getY() + (vcExtent.getY()));
        Parameter parameterY = sbmlModel.createParameter();
        // note for exporting BioModels rather than MathModels, get ReservedSymbol from Model with Role of ReservedSymbolRole.Y
        parameterY.setId(ReservedVariable.Y.getName());
        SpatialSymbolReference coordYSpatialRef = new SpatialSymbolReference();
        coordYSpatialRef.setSpatialRef(coordCompY.getSpatialId());
        SpatialParameterPlugin parameterYSpatialPlugin = (SpatialParameterPlugin) parameterY.getPlugin(SBMLUtils.SBML_SPATIAL_NS_PREFIX);
        parameterYSpatialPlugin.setParamType(coordYSpatialRef);
    }
    // add z coordinate component
    if (dimension == 3) {
        CoordinateComponent coordCompZ = sbmlGeometry.createCoordinateComponent();
        coordCompZ.setSpatialId("CoordCompZ");
        coordCompZ.setType(CoordinateKind.cartesianZ);
        Boundary minZ = coordCompZ.getBoundaryMinimum();
        minZ.setId("Zmin");
        minZ.setValue(vcOrigin.getZ());
        Boundary maxZ = coordCompZ.getBoundaryMaximum();
        maxZ.setId("Zmax");
        maxZ.setValue(vcOrigin.getZ() + (vcExtent.getZ()));
        Parameter parameterZ = sbmlModel.createParameter();
        // note for exporting BioModels rather than MathModels, get ReservedSymbol from Model with Role of ReservedSymbolRole.Y
        parameterZ.setId(ReservedVariable.Z.getName());
        SpatialSymbolReference coordZSpatialRef = new SpatialSymbolReference();
        coordZSpatialRef.setSpatialRef(coordCompZ.getSpatialId());
        SpatialParameterPlugin parameterZSpatialPlugin = (SpatialParameterPlugin) parameterZ.getPlugin(SBMLUtils.SBML_SPATIAL_NS_PREFIX);
        parameterZSpatialPlugin.setParamType(coordZSpatialRef);
    }
    // 
    // list of domain types : subvolumes and surface classes from VC
    // Also create compartments - one compartment for each geometryClass. set id and spatialDimension based on type of geometryClass.
    // 
    boolean bAnalyticGeom = false;
    boolean bImageGeom = false;
    GeometryClass[] vcGeomClasses = vcGeometry.getGeometryClasses();
    int numVCGeomClasses = vcGeomClasses.length;
    for (int i = 0; i < numVCGeomClasses; i++) {
        DomainType domainType = sbmlGeometry.createDomainType();
        domainType.setId(vcGeomClasses[i].getName());
        if (vcGeomClasses[i] instanceof SubVolume) {
            if (((SubVolume) vcGeomClasses[i]) instanceof AnalyticSubVolume) {
                bAnalyticGeom = true;
            } else if (((SubVolume) vcGeomClasses[i]) instanceof ImageSubVolume) {
                bImageGeom = true;
            }
            domainType.setSpatialDimensions(3);
        } else if (vcGeomClasses[i] instanceof SurfaceClass) {
            domainType.setSpatialDimensions(2);
        }
    }
    // 
    // list of domains, adjacent domains : from VC geometricRegions
    // 
    GeometrySurfaceDescription vcGSD = vcGeometry.getGeometrySurfaceDescription();
    if (vcGSD.getRegionImage() == null) {
        try {
            vcGSD.updateAll();
        } catch (Exception e) {
            e.printStackTrace(System.out);
            throw new RuntimeException("Unable to generate region images for geometry");
        }
    }
    GeometricRegion[] vcGeometricRegions = vcGSD.getGeometricRegions();
    ISize sampleSize = vcGSD.getVolumeSampleSize();
    int numX = sampleSize.getX();
    int numY = sampleSize.getY();
    int numZ = sampleSize.getZ();
    double ox = vcOrigin.getX();
    double oy = vcOrigin.getY();
    double oz = vcOrigin.getZ();
    RegionInfo[] regionInfos = vcGSD.getRegionImage().getRegionInfos();
    Compartment compartment = null;
    for (int i = 0; i < vcGeometricRegions.length; i++) {
        // domains
        Domain domain = sbmlGeometry.createDomain();
        domain.setId(vcGeometricRegions[i].getName());
        compartment = sbmlModel.createCompartment();
        compartment.setId("compartment" + i);
        if (vcGeometricRegions[i] instanceof VolumeGeometricRegion) {
            domain.setDomainType(((VolumeGeometricRegion) vcGeometricRegions[i]).getSubVolume().getName());
            // domain.setImplicit(false);
            compartment.setSpatialDimensions(3);
            InteriorPoint interiorPt = domain.createInteriorPoint();
            int regionID = ((VolumeGeometricRegion) vcGeometricRegions[i]).getRegionID();
            boolean bFound = false;
            int regInfoIndx = 0;
            for (int j = 0; j < regionInfos.length; j++) {
                regInfoIndx = j;
                if (regionInfos[j].getRegionIndex() == regionID) {
                    int volIndx = 0;
                    for (int z = 0; z < numZ && !bFound; z++) {
                        for (int y = 0; y < numY && !bFound; y++) {
                            for (int x = 0; x < numX && !bFound; x++) {
                                if (regionInfos[j].isIndexInRegion(volIndx)) {
                                    bFound = true;
                                    double unit_z = (numZ > 1) ? ((double) z) / (numZ - 1) : 0.5;
                                    double coordZ = oz + vcExtent.getZ() * unit_z;
                                    double unit_y = (numY > 1) ? ((double) y) / (numY - 1) : 0.5;
                                    double coordY = oy + vcExtent.getY() * unit_y;
                                    double unit_x = (numX > 1) ? ((double) x) / (numX - 1) : 0.5;
                                    double coordX = ox + vcExtent.getX() * unit_x;
                                    interiorPt.setCoord1(coordX);
                                    interiorPt.setCoord2(coordY);
                                    interiorPt.setCoord3(coordZ);
                                }
                                volIndx++;
                            }
                        // end - for x
                        }
                    // end - for y
                    }
                // end - for z
                }
            // end if
            }
            // end for regionInfos
            if (!bFound) {
                throw new RuntimeException("Unable to find interior point for region '" + regionInfos[regInfoIndx].toString());
            }
        } else if (vcGeometricRegions[i] instanceof SurfaceGeometricRegion) {
            SurfaceGeometricRegion vcSurfaceGeomReg = (SurfaceGeometricRegion) vcGeometricRegions[i];
            GeometricRegion geomRegion0 = vcSurfaceGeomReg.getAdjacentGeometricRegions()[0];
            GeometricRegion geomRegion1 = vcSurfaceGeomReg.getAdjacentGeometricRegions()[1];
            SurfaceClass surfaceClass = vcGSD.getSurfaceClass(((VolumeGeometricRegion) geomRegion0).getSubVolume(), ((VolumeGeometricRegion) geomRegion1).getSubVolume());
            domain.setDomainType(surfaceClass.getName());
            // domain.setImplicit(true);
            compartment.setSpatialDimensions(2);
            // adjacent domains : 2 adjacent domain objects for each surfaceClass in VC.
            // adjacent domain 1
            AdjacentDomains adjDomain = sbmlGeometry.createAdjacentDomain();
            adjDomain.setId(TokenMangler.mangleToSName(vcSurfaceGeomReg.getName() + "_" + geomRegion0.getName()));
            adjDomain.setDomain1(vcSurfaceGeomReg.getName());
            adjDomain.setDomain2(geomRegion0.getName());
            // adjacent domain 2
            adjDomain = sbmlGeometry.createAdjacentDomain();
            adjDomain.setId(TokenMangler.mangleToSName(vcSurfaceGeomReg.getName() + "_" + geomRegion1.getName()));
            adjDomain.setDomain1(vcSurfaceGeomReg.getName());
            adjDomain.setDomain2(geomRegion1.getName());
        }
        // 
        // Mathmodel does not have structureMapping, hence creating compartmentMapping while creating domains.
        // @TODO : how to assign unitSize for compartmentMapping?
        // 
        SpatialCompartmentPlugin cplugin = (SpatialCompartmentPlugin) compartment.getPlugin(SBMLUtils.SBML_SPATIAL_NS_PREFIX);
        CompartmentMapping compMapping = cplugin.getCompartmentMapping();
        String compMappingId = TokenMangler.mangleToSName(domain.getDomainType() + "_" + compartment.getId());
        compMapping.setId(compMappingId);
        compMapping.setDomainType(TokenMangler.mangleToSName(domain.getDomainType()));
    // try {
    // compMapping.setUnitSize(1.0);
    // } catch (ExpressionException e) {
    // e.printStackTrace(System.out);
    // throw new RuntimeException("Unable to create compartment mapping for structureMapping '" + compMapping.getId() +"' : " + e.getMessage());
    // }
    }
    AnalyticGeometry sbmlAnalyticGeom = null;
    SampledFieldGeometry sbmlSFGeom = null;
    // both image and analytic subvolumes?? == not handled in SBML at this time.
    if (bAnalyticGeom && !bImageGeom) {
        sbmlAnalyticGeom = sbmlGeometry.createAnalyticGeometry();
        sbmlAnalyticGeom.setId(TokenMangler.mangleToSName(vcGeometry.getName()));
    } else if (bImageGeom && !bAnalyticGeom) {
        // assuming image based geometry if not analytic geometry
        sbmlSFGeom = sbmlGeometry.createSampledFieldGeometry();
        sbmlSFGeom.setId(TokenMangler.mangleToSName(vcGeometry.getName()));
    } else if (bAnalyticGeom && bImageGeom) {
        throw new RuntimeException("Export to SBML of a combination of Image-based and Analytic geometries is not supported yet.");
    } else if (!bAnalyticGeom && !bImageGeom) {
        throw new RuntimeException("Unknown geometry type.");
    }
    // 
    for (int i = 0; i < vcGeomClasses.length; i++) {
        if (vcGeomClasses[i] instanceof AnalyticSubVolume) {
            // add analytiVols to sbmlAnalyticGeometry
            if (sbmlAnalyticGeom != null) {
                AnalyticVolume analyticVol = sbmlAnalyticGeom.createAnalyticVolume();
                analyticVol.setId(vcGeomClasses[i].getName());
                analyticVol.setDomainType(vcGeomClasses[i].getName());
                analyticVol.setFunctionType(FunctionKind.layered);
                analyticVol.setOrdinal(i);
                Expression expr = ((AnalyticSubVolume) vcGeomClasses[i]).getExpression();
                try {
                    String mathMLStr = ExpressionMathMLPrinter.getMathML(expr, true);
                    ASTNode mathMLNode = ASTNode.readMathMLFromString(mathMLStr);
                    analyticVol.setMath(mathMLNode);
                } catch (Exception e) {
                    e.printStackTrace(System.out);
                    throw new RuntimeException("Error converting VC subvolume expression to mathML" + e.getMessage());
                }
            } else {
                throw new RuntimeException("SBML AnalyticGeometry is null.");
            }
        } else if (vcGeomClasses[i] instanceof ImageSubVolume) {
            // add sampledVols to sbmlSFGeometry
            if (sbmlSFGeom != null) {
                SampledVolume sampledVol = sbmlSFGeom.createSampledVolume();
                sampledVol.setId(vcGeomClasses[i].getName());
                sampledVol.setDomainType(vcGeomClasses[i].getName());
                sampledVol.setSampledValue(((ImageSubVolume) vcGeomClasses[i]).getPixelValue());
            } else {
                throw new RuntimeException("SBML SampledFieldGeometry is null.");
            }
        }
    }
    if (sbmlSFGeom != null) {
        // add sampledField to sampledFieldGeometry
        SampledField sampledField = sbmlGeometry.createSampledField();
        VCImage vcImage = vcGeometry.getGeometrySpec().getImage();
        sampledField.setId(vcImage.getName());
        sampledField.setNumSamples1(vcImage.getNumX());
        if (vcImage.getNumY() > 1) {
            sampledField.setNumSamples2(vcImage.getNumY());
        }
        if (vcImage.getNumZ() > 1) {
            sampledField.setNumSamples3(vcImage.getNumZ());
        }
        sampledField.setInterpolationType(InterpolationKind.nearestneighbor);
        sampledField.setDataType(DataKind.UINT8);
        // add image from vcGeometrySpec to sampledField.
        try {
            StringBuffer sb = new StringBuffer();
            byte[] imagePixelsBytes = vcImage.getPixelsCompressed();
            for (int i = 0; i < imagePixelsBytes.length; i++) {
                int uint8_sample = ((int) imagePixelsBytes[i]) & 0xff;
                sb.append(uint8_sample + " ");
            }
            sampledField.setSamplesLength(vcImage.getNumXYZ());
            sampledField.setSamples(sb.toString().trim());
        } catch (ImageException e) {
            e.printStackTrace(System.out);
            throw new RuntimeException("Unable to export image from VCell to SBML : " + e.getMessage());
        }
    }
}