Examples with SpatialSymbolReference org.sbml.jsbml.ext.spatial.SpatialSymbolReference used on opensource projects

Example 1 with SpatialSymbolReference

use of org.sbml.jsbml.ext.spatial.SpatialSymbolReference in project vcell by virtualcell.

the class SBMLImporter method addParameters.

/**
 * addParameters : Adds global parameters from SBML model to VCell model. If
 * expression for global parameter contains species, creates a conc_factor
 * parameter (conversion from SBML - VCell conc units) and adds this factor
 * to VC global params list, and replaces occurances of 'sp' with
 * 'sp*concFactor' in original param expression.
 *
 * @throws PropertyVetoException
 */
protected void addParameters() throws Exception {
    ListOf listofGlobalParams = sbmlModel.getListOfParameters();
    if (listofGlobalParams == null) {
        System.out.println("No Global Parameters");
        return;
    }
    Model vcModel = vcBioModel.getSimulationContext(0).getModel();
    ArrayList<ModelParameter> vcModelParamsList = new ArrayList<Model.ModelParameter>();
    // create a hash of reserved symbols so that if there is any reserved
    // symbol occurring as a global parameter in the SBML model,
    // the hash can be used to check for reserved symbols, so that it will
    // not be added as a global parameter in VCell,
    // since reserved symbols cannot be used as other variables (species,
    // structureSize, parameters, reactions, etc.).
    HashSet<String> reservedSymbolHash = new HashSet<String>();
    for (ReservedSymbol rs : vcModel.getReservedSymbols()) {
        reservedSymbolHash.add(rs.getName());
    }
    ModelUnitSystem modelUnitSystem = vcModel.getUnitSystem();
    for (int i = 0; i < sbmlModel.getNumParameters(); i++) {
        Parameter sbmlGlobalParam = (Parameter) listofGlobalParams.get(i);
        String paramName = sbmlGlobalParam.getId();
        SpatialParameterPlugin spplugin = null;
        if (bSpatial) {
            // check if parameter id is x/y/z : if so, check if its
            // 'spatialSymbolRef' child's spatial id and type are non-empty.
            // If so, the parameter represents a spatial element.
            // If not, throw an exception, since a parameter that does not
            // represent a spatial element cannot have an id of x/y/z
            spplugin = (SpatialParameterPlugin) sbmlGlobalParam.getPlugin(SBMLUtils.SBML_SPATIAL_NS_PREFIX);
            if (paramName.equals("x") || paramName.equals("y") || paramName.equals("z")) {
                boolean bSpatialParam = (spplugin != null && spplugin.getParamType() instanceof SpatialSymbolReference);
                // if (a) and (b) are true, continue with the next parameter
                if (!bSpatialParam) {
                    throw new RuntimeException("Parameter '" + paramName + "' is not a spatial parameter : Cannot have a variable in VCell named '" + paramName + "' unless it is a spatial variable.");
                } else {
                    // parameter to the list of vcell parameters.
                    continue;
                }
            }
        }
        // 
        // Get param value if set or get its expression from rule
        // 
        // Check if param is defined by an assignment rule or initial
        // assignment. If so, that value overrides the value existing in the
        // param element.
        // assignment rule, first
        Expression valueExpr = getValueFromAssignmentRule(paramName);
        if (valueExpr == null) {
            if (sbmlGlobalParam.isSetValue()) {
                double value = sbmlGlobalParam.getValue();
                valueExpr = new Expression(value);
            } else {
                // if value for global param is not set and param has a rate
                // rule, need to set an init value for param (else, there
                // will be a problem in reaction which uses this parameter).
                // use a 'default' initial value of '0'
                valueExpr = new Expression(0.0);
            // logger.sendMessage(VCLogger.Priority.MediumPriority,
            // VCLogger.Priority.LowPriority,
            // "Parameter did not have an initial value, but has a rate rule specified. Using a default value of 0.0.");
            }
        }
        if (valueExpr != null) {
            // valueExpr will be changed
            valueExpr = adjustExpression(valueExpr, vcModel);
        }
        // extension
        if (bSpatial) {
            VCAssert.assertTrue(spplugin != null, "invalid initialization logic");
            ParameterType sbmlParamType = spplugin.getParamType();
            SpeciesContext paramSpContext = null;
            SpeciesContextSpec vcSpContextsSpec = null;
            // Check for diffusion coefficient(s)
            if (sbmlParamType instanceof DiffusionCoefficient) {
                DiffusionCoefficient diffCoeff = (DiffusionCoefficient) sbmlParamType;
                if (diffCoeff != null && diffCoeff.isSetVariable()) {
                    // get the var of diffCoeff; find appropriate spContext
                    // in vcell; set its diff param to param value.
                    paramSpContext = vcModel.getSpeciesContext(diffCoeff.getVariable());
                    if (paramSpContext != null) {
                        vcSpContextsSpec = vcBioModel.getSimulationContext(0).getReactionContext().getSpeciesContextSpec(paramSpContext);
                        vcSpContextsSpec.getDiffusionParameter().setExpression(valueExpr);
                    }
                    // coeff parameter to the list of vcell parameters.
                    continue;
                }
            }
            // Check for advection coefficient(s)
            if (sbmlParamType instanceof AdvectionCoefficient) {
                AdvectionCoefficient advCoeff = (AdvectionCoefficient) sbmlParamType;
                if (advCoeff != null && advCoeff.isSetVariable()) {
                    // get the var of advCoeff; find appropriate spContext
                    // in vcell; set its adv param to param value.
                    paramSpContext = vcModel.getSpeciesContext(advCoeff.getVariable());
                    if (paramSpContext != null) {
                        vcSpContextsSpec = vcBioModel.getSimulationContext(0).getReactionContext().getSpeciesContextSpec(paramSpContext);
                        CoordinateKind coordKind = advCoeff.getCoordinate();
                        SpeciesContextSpecParameter param = null;
                        switch(coordKind) {
                            case cartesianX:
                                {
                                    param = vcSpContextsSpec.getParameterFromRole(SpeciesContextSpec.ROLE_VelocityX);
                                    break;
                                }
                            case cartesianY:
                                {
                                    param = vcSpContextsSpec.getParameterFromRole(SpeciesContextSpec.ROLE_VelocityY);
                                    break;
                                }
                            case cartesianZ:
                                {
                                    param = vcSpContextsSpec.getParameterFromRole(SpeciesContextSpec.ROLE_VelocityZ);
                                    break;
                                }
                        }
                        param.setExpression(valueExpr);
                    }
                    // coeff parameter to the list of vcell parameters.
                    continue;
                }
            }
            // Check for Boundary condition(s)
            if (sbmlParamType instanceof BoundaryCondition) {
                BoundaryCondition bCondn = (BoundaryCondition) sbmlParamType;
                if (bCondn != null && bCondn.isSetVariable()) {
                    // get the var of boundaryCondn; find appropriate
                    // spContext in vcell;
                    // set the BC param of its speciesContextSpec to param
                    // value.
                    paramSpContext = vcModel.getSpeciesContext(bCondn.getVariable());
                    if (paramSpContext == null) {
                        throw new RuntimeException("unable to process boundary condition for variable " + bCondn.getVariable());
                    }
                    StructureMapping sm = vcBioModel.getSimulationContext(0).getGeometryContext().getStructureMapping(paramSpContext.getStructure());
                    vcSpContextsSpec = vcBioModel.getSimulationContext(0).getReactionContext().getSpeciesContextSpec(paramSpContext);
                    for (CoordinateComponent coordComp : getSbmlGeometry().getListOfCoordinateComponents()) {
                        if (bCondn.getSpatialRef().equals(coordComp.getBoundaryMinimum().getSpatialId())) {
                            switch(coordComp.getType()) {
                                case cartesianX:
                                    {
                                        vcSpContextsSpec.getBoundaryXmParameter().setExpression(valueExpr);
                                    }
                                case cartesianY:
                                    {
                                        vcSpContextsSpec.getBoundaryYmParameter().setExpression(valueExpr);
                                    }
                                case cartesianZ:
                                    {
                                        vcSpContextsSpec.getBoundaryZmParameter().setExpression(valueExpr);
                                    }
                            }
                        }
                        if (bCondn.getSpatialRef().equals(coordComp.getBoundaryMaximum().getSpatialId())) {
                            switch(coordComp.getType()) {
                                case cartesianX:
                                    {
                                        vcSpContextsSpec.getBoundaryXpParameter().setExpression(valueExpr);
                                    }
                                case cartesianY:
                                    {
                                        vcSpContextsSpec.getBoundaryYpParameter().setExpression(valueExpr);
                                    }
                                case cartesianZ:
                                    {
                                        vcSpContextsSpec.getBoundaryZpParameter().setExpression(valueExpr);
                                    }
                            }
                        }
                    }
                    continue;
                }
            }
            // Check for Boundary condition(s)
            if (sbmlParamType instanceof SpatialSymbolReference) {
                SpatialSymbolReference spatialSymbolRef = (SpatialSymbolReference) sbmlParamType;
                throw new RuntimeException("generic Spatial Symbol References not yet supported, unresolved spatial reference '" + spatialSymbolRef.getSpatialRef() + "'");
            }
        }
        // doesn't exist.
        if (vcModel.getModelParameter(paramName) == null) {
            VCUnitDefinition glParamUnitDefn = sbmlUnitIdentifierHash.get(sbmlGlobalParam.getUnits());
            // set it to TBD or check if it was dimensionless.
            if (glParamUnitDefn == null) {
                glParamUnitDefn = modelUnitSystem.getInstance_TBD();
            }
            // VCell : cannot add reserved symbol to model params.
            if (!reservedSymbolHash.contains(paramName)) {
                ModelParameter vcGlobalParam = vcModel.new ModelParameter(paramName, valueExpr, Model.ROLE_UserDefined, glParamUnitDefn);
                if (paramName.length() > 64) {
                    // record global parameter name in annotation if it is
                    // longer than 64 characeters
                    vcGlobalParam.setDescription("Parameter Name : " + paramName);
                }
                vcModelParamsList.add(vcGlobalParam);
            }
        }
    }
    // end for - sbmlModel.parameters
    vcModel.setModelParameters(vcModelParamsList.toArray(new ModelParameter[0]));
}

Example 2 with SpatialSymbolReference

use of org.sbml.jsbml.ext.spatial.SpatialSymbolReference in project vcell by virtualcell.

the class SBMLImporter method addParameters.

/**
 * addParameters : Adds global parameters from SBML model to VCell model. If
 * expression for global parameter contains species, creates a conc_factor
 * parameter (conversion from SBML - VCell conc units) and adds this factor
 * to VC global params list, and replaces occurances of 'sp' with
 * 'sp*concFactor' in original param expression.
 *
 * @throws PropertyVetoException
 */
protected void addParameters(Map<String, String> vcToSbmlNameMap, Map<String, String> sbmlToVcNameMap) throws Exception {
    ListOf listofGlobalParams = sbmlModel.getListOfParameters();
    if (listofGlobalParams == null) {
        System.out.println("No Global Parameters");
        return;
    }
    Model vcModel = vcBioModel.getSimulationContext(0).getModel();
    ArrayList<ModelParameter> vcModelParamsList = new ArrayList<Model.ModelParameter>();
    // create a hash of reserved symbols so that if there is any reserved
    // symbol occurring as a global parameter in the SBML model,
    // the hash can be used to check for reserved symbols, so that it will
    // not be added as a global parameter in VCell,
    // since reserved symbols cannot be used as other variables (species,
    // structureSize, parameters, reactions, etc.).
    HashSet<String> reservedSymbolHash = new HashSet<String>();
    for (ReservedSymbol rs : vcModel.getReservedSymbols()) {
        reservedSymbolHash.add(rs.getName());
    }
    ModelUnitSystem modelUnitSystem = vcModel.getUnitSystem();
    for (int i = 0; i < sbmlModel.getNumParameters(); i++) {
        Parameter sbmlGlobalParam = (Parameter) listofGlobalParams.get(i);
        String paramName = sbmlGlobalParam.getId();
        String sbmlParamName = sbmlGlobalParam.getName();
        SpatialParameterPlugin spplugin = null;
        if (bSpatial) {
            // check if parameter id is x/y/z : if so, check if its
            // 'spatialSymbolRef' child's spatial id and type are non-empty.
            // If so, the parameter represents a spatial element.
            // If not, throw an exception, since a parameter that does not
            // represent a spatial element cannot have an id of x/y/z
            spplugin = (SpatialParameterPlugin) sbmlGlobalParam.getPlugin(SBMLUtils.SBML_SPATIAL_NS_PREFIX);
            if (paramName.equals("x") || paramName.equals("y") || paramName.equals("z")) {
                boolean bSpatialParam = (spplugin != null && spplugin.getParamType() instanceof SpatialSymbolReference);
                // if (a) and (b) are true, continue with the next parameter
                if (!bSpatialParam) {
                    throw new RuntimeException("Parameter '" + paramName + "' is not a spatial parameter : Cannot have a variable in VCell named '" + paramName + "' unless it is a spatial variable.");
                } else {
                    // parameter to the list of vcell parameters.
                    continue;
                }
            }
        }
        // 
        // Get param value if set or get its expression from rule
        // 
        // Check if param is defined by an assignment rule or initial
        // assignment. If so, that value overrides the value existing in the
        // param element.
        // assignment rule, first
        Expression valueExpr = getValueFromAssignmentRule(paramName);
        if (valueExpr == null) {
            if (sbmlGlobalParam.isSetValue()) {
                double value = sbmlGlobalParam.getValue();
                valueExpr = new Expression(value);
            } else {
                // if value for global param is not set and param has a rate
                // rule, need to set an init value for param (else, there
                // will be a problem in reaction which uses this parameter).
                // use a 'default' initial value of '0'
                valueExpr = new Expression(0.0);
            // logger.sendMessage(VCLogger.Priority.MediumPriority,
            // VCLogger.Priority.LowPriority,
            // "Parameter did not have an initial value, but has a rate rule specified. Using a default value of 0.0.");
            }
        }
        if (valueExpr != null) {
            // valueExpr will be changed
            valueExpr = adjustExpression(valueExpr, vcModel);
        }
        // extension
        if (bSpatial) {
            VCAssert.assertTrue(spplugin != null, "invalid initialization logic");
            ParameterType sbmlParamType = spplugin.getParamType();
            SpeciesContext paramSpContext = null;
            SpeciesContextSpec vcSpContextsSpec = null;
            // Check for diffusion coefficient(s)
            if (sbmlParamType instanceof DiffusionCoefficient) {
                DiffusionCoefficient diffCoeff = (DiffusionCoefficient) sbmlParamType;
                if (diffCoeff != null && diffCoeff.isSetVariable()) {
                    // get the var of diffCoeff; find appropriate spContext
                    // in vcell; set its diff param to param value.
                    paramSpContext = vcModel.getSpeciesContext(diffCoeff.getVariable());
                    if (paramSpContext != null) {
                        vcSpContextsSpec = vcBioModel.getSimulationContext(0).getReactionContext().getSpeciesContextSpec(paramSpContext);
                        vcSpContextsSpec.getDiffusionParameter().setExpression(valueExpr);
                    }
                    // coeff parameter to the list of vcell parameters.
                    continue;
                }
            }
            // Check for advection coefficient(s)
            if (sbmlParamType instanceof AdvectionCoefficient) {
                AdvectionCoefficient advCoeff = (AdvectionCoefficient) sbmlParamType;
                if (advCoeff != null && advCoeff.isSetVariable()) {
                    // get the var of advCoeff; find appropriate spContext
                    // in vcell; set its adv param to param value.
                    paramSpContext = vcModel.getSpeciesContext(advCoeff.getVariable());
                    if (paramSpContext != null) {
                        vcSpContextsSpec = vcBioModel.getSimulationContext(0).getReactionContext().getSpeciesContextSpec(paramSpContext);
                        CoordinateKind coordKind = advCoeff.getCoordinate();
                        SpeciesContextSpecParameter param = null;
                        switch(coordKind) {
                            case cartesianX:
                                {
                                    param = vcSpContextsSpec.getParameterFromRole(SpeciesContextSpec.ROLE_VelocityX);
                                    break;
                                }
                            case cartesianY:
                                {
                                    param = vcSpContextsSpec.getParameterFromRole(SpeciesContextSpec.ROLE_VelocityY);
                                    break;
                                }
                            case cartesianZ:
                                {
                                    param = vcSpContextsSpec.getParameterFromRole(SpeciesContextSpec.ROLE_VelocityZ);
                                    break;
                                }
                        }
                        param.setExpression(valueExpr);
                    }
                    // coeff parameter to the list of vcell parameters.
                    continue;
                }
            }
            // Check for Boundary condition(s)
            if (sbmlParamType instanceof BoundaryCondition) {
                BoundaryCondition bCondn = (BoundaryCondition) sbmlParamType;
                if (bCondn != null && bCondn.isSetVariable()) {
                    // get the var of boundaryCondn; find appropriate
                    // spContext in vcell;
                    // set the BC param of its speciesContextSpec to param
                    // value.
                    paramSpContext = vcModel.getSpeciesContext(bCondn.getVariable());
                    if (paramSpContext == null) {
                        throw new RuntimeException("unable to process boundary condition for variable " + bCondn.getVariable());
                    }
                    StructureMapping sm = vcBioModel.getSimulationContext(0).getGeometryContext().getStructureMapping(paramSpContext.getStructure());
                    vcSpContextsSpec = vcBioModel.getSimulationContext(0).getReactionContext().getSpeciesContextSpec(paramSpContext);
                    for (CoordinateComponent coordComp : getSbmlGeometry().getListOfCoordinateComponents()) {
                        if (bCondn.getSpatialRef().equals(coordComp.getBoundaryMinimum().getSpatialId())) {
                            switch(coordComp.getType()) {
                                case cartesianX:
                                    {
                                        vcSpContextsSpec.getBoundaryXmParameter().setExpression(valueExpr);
                                    }
                                case cartesianY:
                                    {
                                        vcSpContextsSpec.getBoundaryYmParameter().setExpression(valueExpr);
                                    }
                                case cartesianZ:
                                    {
                                        vcSpContextsSpec.getBoundaryZmParameter().setExpression(valueExpr);
                                    }
                            }
                        }
                        if (bCondn.getSpatialRef().equals(coordComp.getBoundaryMaximum().getSpatialId())) {
                            switch(coordComp.getType()) {
                                case cartesianX:
                                    {
                                        vcSpContextsSpec.getBoundaryXpParameter().setExpression(valueExpr);
                                    }
                                case cartesianY:
                                    {
                                        vcSpContextsSpec.getBoundaryYpParameter().setExpression(valueExpr);
                                    }
                                case cartesianZ:
                                    {
                                        vcSpContextsSpec.getBoundaryZpParameter().setExpression(valueExpr);
                                    }
                            }
                        }
                    }
                    continue;
                }
            }
            // Check for Boundary condition(s)
            if (sbmlParamType instanceof SpatialSymbolReference) {
                SpatialSymbolReference spatialSymbolRef = (SpatialSymbolReference) sbmlParamType;
                throw new RuntimeException("generic Spatial Symbol References not yet supported, unresolved spatial reference '" + spatialSymbolRef.getSpatialRef() + "'");
            }
        }
        // doesn't exist.
        if (vcModel.getModelParameter(paramName) == null) {
            VCUnitDefinition glParamUnitDefn = sbmlUnitIdentifierHash.get(sbmlGlobalParam.getUnits());
            // set it to TBD or check if it was dimensionless.
            if (glParamUnitDefn == null) {
                glParamUnitDefn = modelUnitSystem.getInstance_TBD();
            }
            // special treatment for x,y,z
            if (isRestrictedXYZT(paramName)) {
                String vcSpeciesId = "s_" + paramName;
                vcToSbmlNameMap.put(vcSpeciesId, paramName);
                sbmlToVcNameMap.put(paramName, vcSpeciesId);
                ModelParameter vcGlobalParam = vcModel.new ModelParameter(vcSpeciesId, valueExpr, Model.ROLE_UserDefined, glParamUnitDefn);
                if (vcSpeciesId.length() > 64) {
                    vcGlobalParam.setDescription("Parameter Name : " + vcSpeciesId);
                }
                if (sbmlParamName != null && !sbmlParamName.isEmpty()) {
                    vcGlobalParam.setSbmlName(sbmlParamName);
                }
                vcModelParamsList.add(vcGlobalParam);
            } else if (!reservedSymbolHash.contains(paramName)) {
                // Also check if the SBML global param is a reserved symbol in
                // VCell : cannot add reserved symbol to model params.
                // we dealt with x,y,z above
                ModelParameter vcGlobalParam = vcModel.new ModelParameter(paramName, valueExpr, Model.ROLE_UserDefined, glParamUnitDefn);
                if (paramName.length() > 64) {
                    // record global parameter name in annotation if it is
                    // longer than 64 characeters
                    vcGlobalParam.setDescription("Parameter Name : " + paramName);
                }
                if (sbmlParamName != null && !sbmlParamName.isEmpty()) {
                    vcGlobalParam.setSbmlName(sbmlParamName);
                }
                vcModelParamsList.add(vcGlobalParam);
            }
        }
    }
    // end for - sbmlModel.parameters
    vcModel.setModelParameters(vcModelParamsList.toArray(new ModelParameter[0]));
}

Example 3 with SpatialSymbolReference

use of org.sbml.jsbml.ext.spatial.SpatialSymbolReference 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());
        }
    }
}

Example 4 with SpatialSymbolReference

use of org.sbml.jsbml.ext.spatial.SpatialSymbolReference in project vcell by virtualcell.

the class SBMLExporter method addGeometry.

private void addGeometry() throws SbmlException {
    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.createGeometry();
    sbmlGeometry.setCoordinateSystem(GeometryKind.cartesian);
    sbmlGeometry.setSpatialId("vcell");
    Geometry vcGeometry = getSelectedSimContext().getGeometry();
    Model vcModel = getSelectedSimContext().getModel();
    // 
    // 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 xComp = sbmlGeometry.createCoordinateComponent();
    xComp.setSpatialId(vcModel.getX().getName());
    xComp.setType(CoordinateKind.cartesianX);
    final UnitDefinition sbmlUnitDef_length = getOrCreateSBMLUnit(vcModel.getUnitSystem().getLengthUnit());
    xComp.setUnits(sbmlUnitDef_length);
    Boundary minX = new Boundary();
    xComp.setBoundaryMinimum(minX);
    minX.setSpatialId("Xmin");
    minX.setValue(vcOrigin.getX());
    Boundary maxX = new Boundary();
    xComp.setBoundaryMaximum(maxX);
    maxX.setSpatialId("Xmax");
    maxX.setValue(vcOrigin.getX() + (vcExtent.getX()));
    org.sbml.jsbml.Parameter pX = sbmlModel.createParameter();
    pX.setId(vcModel.getX().getName());
    pX.setValue(0.0);
    pX.setConstant(false);
    pX.setUnits(sbmlUnitDef_length);
    SpatialParameterPlugin spPluginPx = (SpatialParameterPlugin) pX.getPlugin(SBMLUtils.SBML_SPATIAL_NS_PREFIX);
    SpatialSymbolReference spSymRefPx = new SpatialSymbolReference();
    spPluginPx.setParamType(spSymRefPx);
    spSymRefPx.setSpatialRef(xComp.getSpatialId());
    // add y coordinate component
    if (dimension == 2 || dimension == 3) {
        CoordinateComponent yComp = sbmlGeometry.createCoordinateComponent();
        yComp.setSpatialId(vcModel.getY().getName());
        yComp.setType(CoordinateKind.cartesianY);
        yComp.setUnits(sbmlUnitDef_length);
        Boundary minY = new Boundary();
        yComp.setBoundaryMinimum(minY);
        minY.setSpatialId("Ymin");
        minY.setValue(vcOrigin.getY());
        Boundary maxY = new Boundary();
        yComp.setBoundaryMaximum(maxY);
        maxY.setSpatialId("Ymax");
        maxY.setValue(vcOrigin.getY() + (vcExtent.getY()));
        org.sbml.jsbml.Parameter pY = sbmlModel.createParameter();
        pY.setId(vcModel.getY().getName());
        pY.setValue(0.0);
        pY.setConstant(false);
        pY.setUnits(sbmlUnitDef_length);
        SpatialParameterPlugin spPluginPy = (SpatialParameterPlugin) pY.getPlugin(SBMLUtils.SBML_SPATIAL_NS_PREFIX);
        SpatialSymbolReference spSymRefPy = new SpatialSymbolReference();
        spPluginPy.setParamType(spSymRefPy);
        spSymRefPy.setSpatialRef(yComp.getSpatialId());
    }
    // add z coordinate component
    if (dimension == 3) {
        CoordinateComponent zComp = sbmlGeometry.createCoordinateComponent();
        zComp.setSpatialId(vcModel.getZ().getName());
        zComp.setType(CoordinateKind.cartesianZ);
        zComp.setUnits(sbmlUnitDef_length);
        Boundary minZ = new Boundary();
        zComp.setBoundaryMinimum(minZ);
        minZ.setSpatialId("Zmin");
        minZ.setValue(vcOrigin.getZ());
        Boundary maxZ = new Boundary();
        zComp.setBoundaryMaximum(maxZ);
        maxZ.setSpatialId("Zmax");
        maxZ.setValue(vcOrigin.getZ() + (vcExtent.getZ()));
        org.sbml.jsbml.Parameter pZ = sbmlModel.createParameter();
        pZ.setId(vcModel.getZ().getName());
        pZ.setValue(0.0);
        pZ.setConstant(false);
        pZ.setUnits(sbmlUnitDef_length);
        SpatialParameterPlugin spPluginPz = (SpatialParameterPlugin) pZ.getPlugin(SBMLUtils.SBML_SPATIAL_NS_PREFIX);
        SpatialSymbolReference spSymRefPz = new SpatialSymbolReference();
        spPluginPz.setParamType(spSymRefPz);
        spSymRefPz.setSpatialRef(zComp.getSpatialId());
    }
    // 
    // list of compartmentMappings : VC structureMappings
    // 
    GeometryContext vcGeoContext = getSelectedSimContext().getGeometryContext();
    StructureMapping[] vcStrucMappings = vcGeoContext.getStructureMappings();
    for (int i = 0; i < vcStrucMappings.length; i++) {
        StructureMapping vcStructMapping = vcStrucMappings[i];
        String structName = vcStructMapping.getStructure().getName();
        Compartment comp = sbmlModel.getCompartment(TokenMangler.mangleToSName(structName));
        SpatialCompartmentPlugin cplugin = (SpatialCompartmentPlugin) comp.getPlugin(SBMLUtils.SBML_SPATIAL_NS_PREFIX);
        GeometryClass gc = vcStructMapping.getGeometryClass();
        if (!goodPointer(gc, GeometryClass.class, structName)) {
            continue;
        }
        CompartmentMapping compMapping = new CompartmentMapping();
        cplugin.setCompartmentMapping(compMapping);
        String geomClassName = gc.getName();
        String id = TokenMangler.mangleToSName(geomClassName + structName);
        compMapping.setSpatialId(id);
        compMapping.setDomainType(TokenMangler.mangleToSName(DOMAIN_TYPE_PREFIX + geomClassName));
        try {
            StructureMappingParameter usp = vcStructMapping.getUnitSizeParameter();
            Expression e = usp.getExpression();
            if (goodPointer(e, Expression.class, id)) {
                compMapping.setUnitSize(e.evaluateConstant());
            }
        } catch (ExpressionException e) {
            e.printStackTrace(System.out);
            throw new RuntimeException("Unable to create compartment mapping for structureMapping '" + compMapping.getId() + "' : " + e.getMessage());
        }
    }
    // 
    // list of domain types : subvolumes and surface classes from VC
    // 
    boolean bAnyAnalyticSubvolumes = false;
    boolean bAnyImageSubvolumes = false;
    boolean bAnyCSGSubvolumes = false;
    GeometryClass[] vcGeomClasses = vcGeometry.getGeometryClasses();
    int numSubVols = 0;
    for (int i = 0; i < vcGeomClasses.length; i++) {
        DomainType domainType = sbmlGeometry.createDomainType();
        domainType.setSpatialId(DOMAIN_TYPE_PREFIX + vcGeomClasses[i].getName());
        if (vcGeomClasses[i] instanceof SubVolume) {
            if (((SubVolume) vcGeomClasses[i]) instanceof AnalyticSubVolume) {
                bAnyAnalyticSubvolumes = true;
            } else if (((SubVolume) vcGeomClasses[i]) instanceof ImageSubVolume) {
                bAnyImageSubvolumes = true;
            } else if (((SubVolume) vcGeomClasses[i]) instanceof CSGObject) {
                bAnyCSGSubvolumes = true;
            }
            domainType.setSpatialDimensions(3);
            numSubVols++;
        } 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();
    for (int i = 0; i < vcGeometricRegions.length; i++) {
        // domains
        Domain domain = sbmlGeometry.createDomain();
        domain.setSpatialId(vcGeometricRegions[i].getName());
        if (vcGeometricRegions[i] instanceof VolumeGeometricRegion) {
            domain.setDomainType(DOMAIN_TYPE_PREFIX + ((VolumeGeometricRegion) vcGeometricRegions[i]).getSubVolume().getName());
            // 
            // get a list of interior points ... should probably use the distance map to find a point
            // furthest inside (or several points associated with the morphological skeleton).
            // 
            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(DOMAIN_TYPE_PREFIX + surfaceClass.getName());
            // adjacent domains : 2 adjacent domain objects for each surfaceClass in VC.
            // adjacent domain 1
            GeometricRegion adjGeomRegion0 = vcSurfaceGeomReg.getAdjacentGeometricRegions()[0];
            GeometricRegion adjGeomRegion1 = vcSurfaceGeomReg.getAdjacentGeometricRegions()[1];
            AdjacentDomains adjDomain = new AdjacentDomains();
            adjDomain.setSpatialId(TokenMangler.mangleToSName(vcSurfaceGeomReg.getName() + "_" + adjGeomRegion0.getName()));
            adjDomain.setDomain1(vcSurfaceGeomReg.getName());
            adjDomain.setDomain2(adjGeomRegion0.getName());
            sbmlGeometry.addAdjacentDomain(adjDomain);
            // adj domain 2
            adjDomain = new AdjacentDomains();
            adjDomain.setSpatialId(TokenMangler.mangleToSName(vcSurfaceGeomReg.getName() + "_" + adjGeomRegion1.getName()));
            adjDomain.setDomain1(vcSurfaceGeomReg.getName());
            adjDomain.setDomain2(adjGeomRegion1.getName());
            sbmlGeometry.addAdjacentDomain(adjDomain);
        }
    }
    // 
    if (bAnyAnalyticSubvolumes && !bAnyImageSubvolumes && !bAnyCSGSubvolumes) {
        AnalyticGeometry sbmlAnalyticGeomDefinition = sbmlGeometry.createAnalyticGeometry();
        sbmlAnalyticGeomDefinition.setSpatialId(TokenMangler.mangleToSName("Analytic_" + vcGeometry.getName()));
        sbmlAnalyticGeomDefinition.setIsActive(true);
        for (int i = 0; i < vcGeomClasses.length; i++) {
            if (vcGeomClasses[i] instanceof AnalyticSubVolume) {
                AnalyticVolume analyticVol = sbmlAnalyticGeomDefinition.createAnalyticVolume();
                analyticVol.setSpatialId(vcGeomClasses[i].getName());
                analyticVol.setDomainType(DOMAIN_TYPE_PREFIX + vcGeomClasses[i].getName());
                analyticVol.setFunctionType(FunctionKind.layered);
                analyticVol.setOrdinal(numSubVols - (i + 1));
                Expression expr = ((AnalyticSubVolume) vcGeomClasses[i]).getExpression();
                try {
                    String mathMLStr = ExpressionMathMLPrinter.getMathML(expr, true, MathType.BOOLEAN);
                    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());
                }
            }
        }
    }
    // 
    if (!bAnyAnalyticSubvolumes && !bAnyImageSubvolumes && bAnyCSGSubvolumes) {
        CSGeometry sbmlCSGeomDefinition = new CSGeometry();
        sbmlGeometry.addGeometryDefinition(sbmlCSGeomDefinition);
        sbmlCSGeomDefinition.setSpatialId(TokenMangler.mangleToSName("CSG_" + vcGeometry.getName()));
        for (int i = 0; i < vcGeomClasses.length; i++) {
            if (vcGeomClasses[i] instanceof CSGObject) {
                CSGObject vcellCSGObject = (CSGObject) vcGeomClasses[i];
                org.sbml.jsbml.ext.spatial.CSGObject sbmlCSGObject = new org.sbml.jsbml.ext.spatial.CSGObject();
                sbmlCSGeomDefinition.addCSGObject(sbmlCSGObject);
                sbmlCSGObject.setSpatialId(vcellCSGObject.getName());
                sbmlCSGObject.setDomainType(DOMAIN_TYPE_PREFIX + vcellCSGObject.getName());
                // the ordinal should the the least for the default/background subVolume
                sbmlCSGObject.setOrdinal(numSubVols - (i + 1));
                org.sbml.jsbml.ext.spatial.CSGNode sbmlcsgNode = getSBMLCSGNode(vcellCSGObject.getRoot());
                sbmlCSGObject.setCSGNode(sbmlcsgNode);
            }
        }
    }
    // 
    // add "Segmented" and "DistanceMap" SampledField Geometries
    // 
    final boolean bVCGeometryIsImage = bAnyImageSubvolumes && !bAnyAnalyticSubvolumes && !bAnyCSGSubvolumes;
    // 55if (bAnyAnalyticSubvolumes || bAnyImageSubvolumes || bAnyCSGSubvolumes){
    if (bVCGeometryIsImage) {
        // 
        // add "Segmented" SampledFieldGeometry
        // 
        SampledFieldGeometry segmentedImageSampledFieldGeometry = sbmlGeometry.createSampledFieldGeometry();
        segmentedImageSampledFieldGeometry.setSpatialId(TokenMangler.mangleToSName("SegmentedImage_" + vcGeometry.getName()));
        segmentedImageSampledFieldGeometry.setIsActive(true);
        // 55boolean bVCGeometryIsImage = bAnyImageSubvolumes && !bAnyAnalyticSubvolumes && !bAnyCSGSubvolumes;
        Geometry vcImageGeometry = null;
        {
            if (bVCGeometryIsImage) {
                // make a resampled image;
                if (dimension == 3) {
                    try {
                        ISize imageSize = vcGeometry.getGeometrySpec().getDefaultSampledImageSize();
                        vcGeometry.precomputeAll(new GeometryThumbnailImageFactoryAWT());
                        vcImageGeometry = RayCaster.resampleGeometry(new GeometryThumbnailImageFactoryAWT(), vcGeometry, imageSize);
                    } catch (Throwable e) {
                        e.printStackTrace(System.out);
                        throw new RuntimeException("Unable to convert the original analytic or constructed solid geometry to image-based geometry : " + e.getMessage());
                    }
                } else {
                    try {
                        vcGeometry.precomputeAll(new GeometryThumbnailImageFactoryAWT(), true, false);
                        GeometrySpec origGeometrySpec = vcGeometry.getGeometrySpec();
                        VCImage newVCImage = origGeometrySpec.getSampledImage().getCurrentValue();
                        // 
                        // construct the new geometry with the sampled VCImage.
                        // 
                        vcImageGeometry = new Geometry(vcGeometry.getName() + "_asImage", newVCImage);
                        vcImageGeometry.getGeometrySpec().setExtent(vcGeometry.getExtent());
                        vcImageGeometry.getGeometrySpec().setOrigin(vcGeometry.getOrigin());
                        vcImageGeometry.setDescription(vcGeometry.getDescription());
                        vcImageGeometry.getGeometrySurfaceDescription().setFilterCutoffFrequency(vcGeometry.getGeometrySurfaceDescription().getFilterCutoffFrequency());
                        vcImageGeometry.precomputeAll(new GeometryThumbnailImageFactoryAWT(), true, true);
                    } catch (Exception e) {
                        e.printStackTrace(System.out);
                        throw new RuntimeException("Unable to convert the original analytic or constructed solid geometry to image-based geometry : " + e.getMessage());
                    }
                }
                GeometryClass[] vcImageGeomClasses = vcImageGeometry.getGeometryClasses();
                for (int j = 0; j < vcImageGeomClasses.length; j++) {
                    if (vcImageGeomClasses[j] instanceof ImageSubVolume) {
                        SampledVolume sampledVol = segmentedImageSampledFieldGeometry.createSampledVolume();
                        sampledVol.setSpatialId(vcGeomClasses[j].getName());
                        sampledVol.setDomainType(DOMAIN_TYPE_PREFIX + vcGeomClasses[j].getName());
                        sampledVol.setSampledValue(((ImageSubVolume) vcImageGeomClasses[j]).getPixelValue());
                    }
                }
                // add sampledField to sampledFieldGeometry
                SampledField segmentedImageSampledField = sbmlGeometry.createSampledField();
                VCImage vcImage = vcImageGeometry.getGeometrySpec().getImage();
                segmentedImageSampledField.setSpatialId("SegmentedImageSampledField");
                segmentedImageSampledField.setNumSamples1(vcImage.getNumX());
                segmentedImageSampledField.setNumSamples2(vcImage.getNumY());
                segmentedImageSampledField.setNumSamples3(vcImage.getNumZ());
                segmentedImageSampledField.setInterpolationType(InterpolationKind.nearestNeighbor);
                segmentedImageSampledField.setCompression(CompressionKind.uncompressed);
                segmentedImageSampledField.setDataType(DataKind.UINT8);
                segmentedImageSampledFieldGeometry.setSampledField(segmentedImageSampledField.getId());
                try {
                    byte[] vcImagePixelsBytes = vcImage.getPixels();
                    // imageData.setCompression("");
                    StringBuffer sb = new StringBuffer();
                    for (int i = 0; i < vcImagePixelsBytes.length; i++) {
                        int uint8_sample = ((int) vcImagePixelsBytes[i]) & 0xff;
                        sb.append(uint8_sample + " ");
                    }
                    segmentedImageSampledField.setSamplesLength(vcImage.getNumXYZ());
                    segmentedImageSampledField.setSamples(sb.toString().trim());
                } catch (ImageException e) {
                    e.printStackTrace(System.out);
                    throw new RuntimeException("Unable to export image from VCell to SBML : " + e.getMessage());
                }
            }
        }
    /*		
		//
		// add "DistanceMap" SampledFieldGeometry if there are exactly two subvolumes (else need more fields) and geometry is 3d.
		//
		if (numSubVols==2 && dimension == 3){
			SignedDistanceMap[] distanceMaps = null;
			try {
				distanceMaps = DistanceMapGenerator.computeDistanceMaps(vcImageGeometry, vcImageGeometry.getGeometrySpec().getImage(), false, false);
			} catch (ImageException e) {
				e.printStackTrace(System.out);
				System.err.println("Unable to export distance map sampled field from VCell to SBML : " + e.getMessage());
				// throw new RuntimeException("Unable to export distance map sampled field from VCell to SBML : " + e.getMessage());
				
				// don't want to throw an exception and stop export because distance map geometry couldn't be exported. 
				// just 'return' from method (since this is the last thing that is being done in this method).
				return;
			}
			//
			// the two distanceMaps should be redundant (one is negation of the other) ... so choose first one for field.
			//
			double[] signedDistances = distanceMaps[0].getSignedDistances();
			SampledFieldGeometry distanceMapSampledFieldGeometry = sbmlGeometry.createSampledFieldGeometry();
			distanceMapSampledFieldGeometry.setSpatialId(TokenMangler.mangleToSName("DistanceMap_"+vcGeometry.getName()));
			SampledField distanceMapSampledField = distanceMapSampledFieldGeometry.createSampledField();
			distanceMapSampledField.setSpatialId("DistanceMapSampledField");
			distanceMapSampledField.setNumSamples1(distanceMaps[0].getSamplesX().length);
			distanceMapSampledField.setNumSamples2(distanceMaps[0].getSamplesY().length);
			distanceMapSampledField.setNumSamples3(distanceMaps[0].getSamplesZ().length);
			distanceMapSampledField.setDataType("real");
System.err.println("do we need distanceMapSampleField.setDataType()?");
			distanceMapSampledField.setInterpolationType("linear");
			ImageData distanceMapImageData = distanceMapSampledField.createImageData();
			distanceMapImageData.setDataType("int16");
System.err.println("should be:\n  distanceMapImageData.setDataType(\"float32\")");
//					distanceMapImageData.setCompression("");

			double maxAbsValue = 0;
			for (int i = 0; i < signedDistances.length; i++) {
				maxAbsValue = Math.max(maxAbsValue,Math.abs(signedDistances[i]));
			}
			if (maxAbsValue==0.0){
				throw new RuntimeException("computed distance map all zeros");
			}
			double scale = (Short.MAX_VALUE-1)/maxAbsValue;
			int[] scaledIntegerDistanceMap = new int[signedDistances.length];
			for (int i = 0; i < signedDistances.length; i++) {
				scaledIntegerDistanceMap[i] = (int)(scale * signedDistances[i]);
			}
			distanceMapImageData.setSamples(scaledIntegerDistanceMap, signedDistances.length);
System.err.println("should be:\n  distanceMapImageData.setSamples((float[])signedDistances,signedDistances.length)");
			SampledVolume sampledVol = distanceMapSampledFieldGeometry.createSampledVolume();
			sampledVol.setSpatialId(distanceMaps[0].getInsideSubvolumeName());
			sampledVol.setDomainType(DOMAIN_TYPE_PREFIX+distanceMaps[0].getInsideSubvolumeName());
			sampledVol.setSampledValue(255);
			sampledVol = distanceMapSampledFieldGeometry.createSampledVolume();
			sampledVol.setSpatialId(distanceMaps[1].getInsideSubvolumeName());
			sampledVol.setDomainType(DOMAIN_TYPE_PREFIX+distanceMaps[1].getInsideSubvolumeName());
			sampledVol.setSampledValue(1);
		}
*/
    }
// 
// add "SurfaceMesh" ParametricGeometry
// 
// if (bAnyAnalyticSubvolumes || bAnyImageSubvolumes || bAnyCSGSubvolumes){
// ParametricGeometry sbmlParametricGeomDefinition = sbmlGeometry.createParametricGeometry();
// sbmlParametricGeomDefinition.setSpatialId(TokenMangler.mangleToSName("SurfaceMesh_"+vcGeometry.getName()));
// xxxx
// }
}