Examples with VolumeGeometricRegion cbit.vcell.geometry.surface.VolumeGeometricRegion used on opensource projects

Example 6 with VolumeGeometricRegion

use of cbit.vcell.geometry.surface.VolumeGeometricRegion 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 7 with VolumeGeometricRegion

use of cbit.vcell.geometry.surface.VolumeGeometricRegion in project vcell by virtualcell.

the class Xmlproducer method getXML.

private Element getXML(GeometrySurfaceDescription param) throws XmlParseException {
    Element gsd = new Element(XMLTags.SurfaceDescriptionTag);
    // add attributes
    ISize isize = param.getVolumeSampleSize();
    if (isize == null) {
        throw new XmlParseException("Unable to retrieve dimensions for surface descriptions for Geometry: " + param.getGeometry().getName());
    }
    gsd.setAttribute(XMLTags.NumSamplesXAttrTag, String.valueOf(isize.getX()));
    gsd.setAttribute(XMLTags.NumSamplesYAttrTag, String.valueOf(isize.getY()));
    gsd.setAttribute(XMLTags.NumSamplesZAttrTag, String.valueOf(isize.getZ()));
    Double coFrequency = param.getFilterCutoffFrequency();
    if (coFrequency == null) {
        throw new XmlParseException("Unable to retrieve cutoff frequency for surface descriptions for Geometry: " + param.getGeometry().getName());
    }
    double cutoffFrequency = coFrequency.doubleValue();
    gsd.setAttribute(XMLTags.CutoffFrequencyAttrTag, String.valueOf(cutoffFrequency));
    // add subelements
    GeometricRegion[] geomRegions = param.getGeometricRegions();
    if (geomRegions != null) {
        for (int i = 0; i < geomRegions.length; i++) {
            if (geomRegions[i] instanceof SurfaceGeometricRegion) {
                SurfaceGeometricRegion sgr = (SurfaceGeometricRegion) geomRegions[i];
                Element membraneRegion = new Element(XMLTags.MembraneRegionTag);
                membraneRegion.setAttribute(XMLTags.NameAttrTag, sgr.getName());
                GeometricRegion[] adjacents = sgr.getAdjacentGeometricRegions();
                if (adjacents == null || adjacents.length != 2) {
                    throw new XmlParseException("Wrong number of adjacent regions for surface descriptions for location: " + sgr.getName() + " in Geometry: " + param.getGeometry().getName());
                }
                membraneRegion.setAttribute(XMLTags.VolumeRegion_1AttrTag, adjacents[0].getName());
                membraneRegion.setAttribute(XMLTags.VolumeRegion_2AttrTag, adjacents[1].getName());
                double size = sgr.getSize();
                if (size != -1) {
                    membraneRegion.setAttribute(XMLTags.SizeAttrTag, String.valueOf(size));
                    VCUnitDefinition unit = sgr.getSizeUnit();
                    if (unit != null) {
                        membraneRegion.setAttribute(XMLTags.VCUnitDefinitionAttrTag, unit.getSymbol());
                    }
                }
                gsd.addContent(membraneRegion);
            } else if (geomRegions[i] instanceof VolumeGeometricRegion) {
                VolumeGeometricRegion vgr = (VolumeGeometricRegion) geomRegions[i];
                Element volumeRegion = new Element(XMLTags.VolumeRegionTag);
                volumeRegion.setAttribute(XMLTags.NameAttrTag, vgr.getName());
                volumeRegion.setAttribute(XMLTags.RegionIDAttrTag, String.valueOf(vgr.getRegionID()));
                volumeRegion.setAttribute(XMLTags.SubVolumeAttrTag, vgr.getSubVolume().getName());
                double size = vgr.getSize();
                if (size != -1) {
                    volumeRegion.setAttribute(XMLTags.SizeAttrTag, String.valueOf(size));
                    VCUnitDefinition unit = vgr.getSizeUnit();
                    if (unit != null) {
                        volumeRegion.setAttribute(XMLTags.VCUnitDefinitionAttrTag, unit.getSymbol());
                    }
                }
                gsd.addContent(volumeRegion);
            }
        }
    }
    return gsd;
}

Example 8 with VolumeGeometricRegion

use of cbit.vcell.geometry.surface.VolumeGeometricRegion in project vcell by virtualcell.

the class VolumeRegionObject method gatherIssues.

@Override
public void gatherIssues(IssueContext issueContext, List<Issue> issueList) {
    if (simulationContext.getGeometry().getGeometrySurfaceDescription() != null && simulationContext.getGeometry().getGeometrySurfaceDescription().getGeometricRegions() != null) {
        GeometricRegion[] regions = simulationContext.getGeometry().getGeometrySurfaceDescription().getGeometricRegions();
        boolean bFound = false;
        for (GeometricRegion region : regions) {
            if (region instanceof VolumeGeometricRegion) {
                VolumeGeometricRegion vr = (VolumeGeometricRegion) region;
                if (getSubVolume() == vr.getSubVolume() && getRegionID() == vr.getRegionID()) {
                    bFound = true;
                    break;
                }
            }
        }
        if (!bFound) {
            issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, "geometry missing volume region (subvolume " + subVolume.getName() + " region " + regionID + ")", Issue.Severity.ERROR));
        }
    }
}

Example 9 with VolumeGeometricRegion

use of cbit.vcell.geometry.surface.VolumeGeometricRegion in project vcell by virtualcell.

the class MathDescription method gatherIssues.

/**
 * This method was created in VisualAge.
 * @return boolean
 */
public void gatherIssues(IssueContext issueContext, List<Issue> issueList) {
    issueContext = issueContext.newChildContext(ContextType.MathDescription, this);
    setWarning(null);
    if (geometry == null) {
        Issue issue = new Issue(this, issueContext, IssueCategory.MathDescription_NoGeometry, VCellErrorMessages.MATH_DESCRIPTION_GEOMETRY_1, Issue.SEVERITY_ERROR);
        issueList.add(issue);
    }
    if (isSpatialStoch() && geometry.getDimension() != 3) {
        Issue issue = new Issue(geometry, issueContext, IssueCategory.Smoldyn_Geometry_3DWarning, "VCell spatial stochastic models only support 3D geometry.", Issue.SEVERITY_ERROR);
        issueList.add(issue);
    }
    // check Constant are really constants
    for (int i = 0; i < variableList.size(); i++) {
        Variable var = variableList.get(i);
        if (var instanceof Constant) {
            try {
                ((Constant) var).getExpression().evaluateConstant();
            } catch (Exception ex) {
                ex.printStackTrace(System.out);
                Issue issue = new Issue(var, issueContext, IssueCategory.MathDescription_Constant_NotANumber, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_CONSTANT, var.getExpression().infix()), Issue.SEVERITY_ERROR);
                issueList.add(issue);
            }
        }
    }
    // 
    // count number of variables of each type
    // 
    int volVarCount = 0;
    int memVarCount = 0;
    int filVarCount = 0;
    int volRegionVarCount = 0;
    int memRegionVarCount = 0;
    int filRegionVarCount = 0;
    int stochVarCount = 0;
    int pointVarCount = 0;
    for (int i = 0; i < variableList.size(); i++) {
        Variable var = variableList.get(i);
        if (var instanceof VolVariable) {
            volVarCount++;
        } else if (var instanceof MemVariable) {
            memVarCount++;
        } else if (var instanceof FilamentVariable) {
            filVarCount++;
        } else if (var instanceof VolumeRegionVariable) {
            volRegionVarCount++;
        } else if (var instanceof MembraneRegionVariable) {
            memRegionVarCount++;
        } else if (var instanceof FilamentRegionVariable) {
            filRegionVarCount++;
        } else if (var instanceof StochVolVariable) {
            stochVarCount++;
        } else if (var instanceof PointVariable) {
            pointVarCount++;
        }
    }
    // 
    for (int i = 0; i < subDomainList.size(); i++) {
        try {
            SubDomain subDomain = subDomainList.get(i);
            Enumeration<Equation> equEnum = subDomain.getEquations();
            while (equEnum.hasMoreElements()) {
                Equation equ = equEnum.nextElement();
                equ.checkValid(this, subDomain);
                equ.bind(this);
            }
            FastSystem fastSystem = subDomain.getFastSystem();
            if (fastSystem != null) {
                Enumeration<FastRate> frEnum = fastSystem.getFastRates();
                while (frEnum.hasMoreElements()) {
                    FastRate fr = frEnum.nextElement();
                    fr.bind(this);
                }
                Enumeration<FastInvariant> fiEnum = fastSystem.getFastInvariants();
                while (fiEnum.hasMoreElements()) {
                    FastInvariant fi = fiEnum.nextElement();
                    fi.bind(this);
                }
            }
            for (ParticleProperties pp : subDomain.getParticleProperties()) {
                pp.bind(this);
            }
            for (ParticleJumpProcess pjp : subDomain.getParticleJumpProcesses()) {
                pjp.bind(this);
                Expression rateDefinition = null;
                JumpProcessRateDefinition jprd = pjp.getParticleRateDefinition();
                if (jprd instanceof MacroscopicRateConstant) {
                    rateDefinition = MathUtilities.substituteFunctions(((MacroscopicRateConstant) jprd).getExpression(), this);
                } else if (jprd instanceof InteractionRadius) {
                    rateDefinition = MathUtilities.substituteFunctions(((InteractionRadius) jprd).getExpression(), this);
                } else {
                    new RuntimeException("The jump process rate definition is not supported");
                }
                String[] symbols = rateDefinition.getSymbols();
                if (symbols != null) {
                    for (String symbol : symbols) {
                        // throw exception for particle variables, particle variable cannot be referenced
                        Variable var = getVariable(symbol);
                        if (var instanceof ParticleVariable) {
                            throw new MathException("Stochastic variables can not be referenced in functions and equations.");
                        }
                        if (subDomain instanceof CompartmentSubDomain) {
                            if ((var instanceof MembraneRegionVariable || var instanceof MemVariable)) {
                                throw new MathException("Volume reaction: " + pjp.getName() + " cannot reference membrane variable: " + var.getName() + ".");
                            }
                        }
                    }
                }
            }
        } catch (ExpressionBindingException e) {
            Issue issue = new Issue(this, issueContext, IssueCategory.MathDescription_ExpressionBindingException, e.getMessage(), Issue.SEVERITY_ERROR);
            issueList.add(issue);
        } catch (ExpressionException e) {
            Issue issue = new Issue(this, issueContext, IssueCategory.MathDescription_ExpressionException, e.getMessage(), Issue.SEVERITY_ERROR);
            issueList.add(issue);
        } catch (MathException e) {
            Issue issue = new Issue(this, issueContext, IssueCategory.MathDescription_MathException, e.getMessage(), Issue.SEVERITY_ERROR);
            issueList.add(issue);
        }
    }
    // 
    if (geometry.getDimension() == 0) {
        // 
        if (subDomainList.size() != 1) {
            Issue issue = new Issue(this, issueContext, IssueCategory.MathDescription_CompartmentalModel, VCellErrorMessages.MATH_DESCRIPTION_COMPARTMENT_MODEL_1, Issue.SEVERITY_ERROR);
            issueList.add(issue);
        } else if (subDomainList.size() == 1) {
            if (!(subDomainList.get(0) instanceof CompartmentSubDomain)) {
                Issue issue = new Issue(this, issueContext, IssueCategory.MathDescription_CompartmentalModel, VCellErrorMessages.MATH_DESCRIPTION_COMPARTMENT_MODEL_2, Issue.SEVERITY_ERROR);
                issueList.add(issue);
            }
            CompartmentSubDomain subDomain = (CompartmentSubDomain) subDomainList.get(0);
            // distinguish ODE model and stochastic model
            if (isNonSpatialStoch()) {
                if (stochVarCount == 0) {
                    Issue issue = new Issue(this, issueContext, IssueCategory.MathDescription_StochasticModel, VCellErrorMessages.MATH_DESCRIPTION_COMPARTMENT_STOCHASTIC_MODEL_1, Issue.SEVERITY_ERROR);
                    issueList.add(issue);
                }
                if (subDomain.getJumpProcesses().size() == 0) {
                    Issue issue = new Issue(this, issueContext, IssueCategory.MathDescription_StochasticModel, VCellErrorMessages.MATH_DESCRIPTION_COMPARTMENT_STOCHASTIC_MODEL_2, Issue.SEVERITY_ERROR);
                    issueList.add(issue);
                }
                // check variable initial condition
                for (VarIniCondition varIniCondition : subDomain.getVarIniConditions()) {
                    Expression iniExp = varIniCondition.getIniVal();
                    try {
                        iniExp.bindExpression(this);
                    } catch (Exception ex) {
                        ex.printStackTrace(System.out);
                        setWarning(ex.getMessage());
                    }
                }
                // check probability rate
                for (JumpProcess jumpProcess : subDomain.getJumpProcesses()) {
                    Expression probExp = jumpProcess.getProbabilityRate();
                    try {
                        probExp.bindExpression(this);
                    } catch (Exception ex) {
                        ex.printStackTrace(System.out);
                        setWarning(ex.getMessage());
                    }
                }
            } else if (isRuleBased()) {
            } else {
                // ODE model
                // 
                // Check that all equations are ODEs
                // 
                int odeCount = 0;
                Enumeration<Equation> enum_equ = subDomain.getEquations();
                while (enum_equ.hasMoreElements()) {
                    Equation equ = enum_equ.nextElement();
                    if (equ instanceof OdeEquation) {
                        odeCount++;
                    } else {
                        Issue issue = new Issue(this, issueContext, IssueCategory.MathDescription_CompartmentalModel, VCellErrorMessages.MATH_DESCRIPTION_COMPARTMENT_MODEL_3, Issue.SEVERITY_ERROR);
                        issueList.add(issue);
                    }
                }
                if (odeCount == 0) {
                    Issue issue = new Issue(this, issueContext, IssueCategory.MathDescription_CompartmentalModel, VCellErrorMessages.MATH_DESCRIPTION_COMPARTMENT_MODEL_4, Issue.SEVERITY_ERROR);
                    issueList.add(issue);
                }
                if (volVarCount != odeCount) {
                    Issue issue = new Issue(this, issueContext, IssueCategory.MathDescription_CompartmentalModel, VCellErrorMessages.MATH_DESCRIPTION_COMPARTMENT_MODEL_5, Issue.SEVERITY_ERROR);
                    issueList.add(issue);
                }
                if (memVarCount > 0) {
                    Issue issue = new Issue(this, issueContext, IssueCategory.MathDescription_CompartmentalModel, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_COMPARTMENT_MODEL_6, VCML.MembraneVariable), Issue.SEVERITY_ERROR);
                    issueList.add(issue);
                }
                if (filVarCount > 0) {
                    Issue issue = new Issue(this, issueContext, IssueCategory.MathDescription_CompartmentalModel, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_COMPARTMENT_MODEL_6, VCML.FilamentVariable), Issue.SEVERITY_ERROR);
                    issueList.add(issue);
                }
                if (volRegionVarCount > 0) {
                    Issue issue = new Issue(this, issueContext, IssueCategory.MathDescription_CompartmentalModel, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_COMPARTMENT_MODEL_6, VCML.VolumeRegionVariable), Issue.SEVERITY_ERROR);
                    issueList.add(issue);
                }
                if (memRegionVarCount > 0) {
                    Issue issue = new Issue(this, issueContext, IssueCategory.MathDescription_CompartmentalModel, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_COMPARTMENT_MODEL_6, VCML.MembraneRegionVariable), Issue.SEVERITY_ERROR);
                    issueList.add(issue);
                }
                if (filRegionVarCount > 0) {
                    Issue issue = new Issue(this, issueContext, IssueCategory.MathDescription_CompartmentalModel, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_COMPARTMENT_MODEL_6, VCML.FilamentRegionVariable), Issue.SEVERITY_ERROR);
                    issueList.add(issue);
                }
            }
        }
    // 
    // spatial (PDE and ODE)
    // 
    } else {
        // 
        // Check that the number of CompartmentSubdomains equals the number of VolumeSubVolumes in the Geometry
        // Check that the number of FilamentSubdomains equals the number of Filaments in the Geometry
        // 
        int compartmentCount = 0;
        int membraneCount = 0;
        int filamentCount = 0;
        int pointCount = 0;
        for (int i = 0; i < subDomainList.size(); i++) {
            SubDomain subDomain = (SubDomain) subDomainList.get(i);
            if (subDomain instanceof CompartmentSubDomain) {
                if (geometry.getGeometrySpec().getSubVolume(subDomain.getName()) == null) {
                    Issue issue = new Issue(subDomain, issueContext, IssueCategory.MathDescription_SpatialModel_Subdomain, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_SPATIAL_MODEL_1, subDomain.getName()), Issue.SEVERITY_ERROR);
                    issueList.add(issue);
                }
                compartmentCount++;
            } else if (subDomain instanceof MembraneSubDomain) {
                membraneCount++;
            } else if (subDomain instanceof FilamentSubDomain) {
                filamentCount++;
            } else if (subDomain instanceof PointSubDomain) {
                pointCount++;
            } else {
                Issue issue = new Issue(subDomain, issueContext, IssueCategory.MathDescription_SpatialModel_Subdomain, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_SPATIAL_MODEL_2, subDomain.getName()), Issue.SEVERITY_ERROR);
                issueList.add(issue);
            }
        }
        if (geometry.getGeometrySpec().getNumSubVolumes() != compartmentCount) {
            Issue issue = new Issue(this, issueContext, IssueCategory.MathDescription_SpatialModel, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_SPATIAL_MODEL_3, geometry.getGeometrySpec().getNumSubVolumes(), compartmentCount), Issue.SEVERITY_ERROR);
            issueList.add(issue);
        }
        if (geometry.getGeometrySpec().getFilamentGroup().getFilamentCount() != filamentCount) {
        // setWarning("Spatial model, there are "+geometry.getGeometrySpec().getFilamentGroup().getFilamentCount()+" filaments in geometry, but "+filamentCount+" "+VCML.FilamentSubDomain+"'s, must be equal");
        // return false;
        }
        if (filamentCount == 0 && (filVarCount > 0 || filRegionVarCount > 0)) {
            Issue issue = new Issue(this, issueContext, IssueCategory.MathDescription_SpatialModel, VCellErrorMessages.MATH_DESCRIPTION_SPATIAL_MODEL_4, Issue.SEVERITY_ERROR);
            issueList.add(issue);
        }
        if (membraneCount == 0 && (memVarCount > 0 || memRegionVarCount > 0)) {
            Issue issue = new Issue(this, issueContext, IssueCategory.MathDescription_SpatialModel, VCellErrorMessages.MATH_DESCRIPTION_SPATIAL_MODEL_5, Issue.SEVERITY_ERROR);
            issueList.add(issue);
        }
        // 
        for (int i = 0; i < subDomainList.size(); i++) {
            SubDomain subDomain1 = (SubDomain) subDomainList.get(i);
            for (int j = 0; j < subDomainList.size(); j++) {
                if (i != j) {
                    SubDomain subDomain2 = (SubDomain) subDomainList.get(j);
                    if (subDomain1.getName().equals(subDomain2.getName())) {
                        Issue issue = new Issue(subDomain1, issueContext, IssueCategory.MathDescription_SpatialModel_Subdomain, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_SPATIAL_MODEL_6, subDomain1.getName(), subDomain2.getName()), Issue.SEVERITY_ERROR);
                        issueList.add(issue);
                    }
                    if (subDomain1 instanceof MembraneSubDomain && subDomain2 instanceof MembraneSubDomain) {
                        MembraneSubDomain memSubDomain1 = (MembraneSubDomain) subDomain1;
                        MembraneSubDomain memSubDomain2 = (MembraneSubDomain) subDomain2;
                        if ((memSubDomain1.getInsideCompartment() == memSubDomain2.getInsideCompartment() && memSubDomain1.getOutsideCompartment() == memSubDomain2.getOutsideCompartment()) || (memSubDomain1.getInsideCompartment() == memSubDomain2.getOutsideCompartment() && memSubDomain1.getOutsideCompartment() == memSubDomain2.getInsideCompartment())) {
                            Issue issue = new Issue(subDomain1, issueContext, IssueCategory.MathDescription_SpatialModel_Subdomain, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_SPATIAL_MODEL_7, memSubDomain1.getInsideCompartment().getName(), memSubDomain1.getOutsideCompartment().getName()), Issue.SEVERITY_ERROR);
                            issueList.add(issue);
                        }
                    }
                }
            }
        }
        // check periodic boundary conditons
        for (int i = 0; i < subDomainList.size(); i++) {
            SubDomain subDomain = (SubDomain) subDomainList.get(i);
            if (subDomain instanceof CompartmentSubDomain) {
                CompartmentSubDomain compartmentSubDomain = (CompartmentSubDomain) subDomain;
                BoundaryConditionType bctM = compartmentSubDomain.getBoundaryConditionXm();
                BoundaryConditionType bctP = compartmentSubDomain.getBoundaryConditionXp();
                if (bctM.isPERIODIC() && !bctP.isPERIODIC() || !bctM.isPERIODIC() && bctP.isPERIODIC()) {
                    Issue issue = new Issue(subDomain, issueContext, IssueCategory.MathDescription_SpatialModel_Subdomain, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_SPATIAL_MODEL_9, "Xm", "Xp", subDomain.getName()), Issue.SEVERITY_ERROR);
                    issueList.add(issue);
                }
                bctM = compartmentSubDomain.getBoundaryConditionYm();
                bctP = compartmentSubDomain.getBoundaryConditionYp();
                if (bctM.isPERIODIC() && !bctP.isPERIODIC() || !bctM.isPERIODIC() && bctP.isPERIODIC()) {
                    Issue issue = new Issue(subDomain, issueContext, IssueCategory.MathDescription_SpatialModel_Subdomain, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_SPATIAL_MODEL_9, "Ym", "Yp", subDomain.getName()), Issue.SEVERITY_ERROR);
                    issueList.add(issue);
                }
                bctM = compartmentSubDomain.getBoundaryConditionZm();
                bctP = compartmentSubDomain.getBoundaryConditionZp();
                if (bctM.isPERIODIC() && !bctP.isPERIODIC() || !bctM.isPERIODIC() && bctP.isPERIODIC()) {
                    Issue issue = new Issue(subDomain, issueContext, IssueCategory.MathDescription_SpatialModel_Subdomain, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_SPATIAL_MODEL_9, "Zm", "Zp", subDomain.getName()), Issue.SEVERITY_ERROR);
                    issueList.add(issue);
                }
            } else if (subDomain instanceof MembraneSubDomain) {
                MembraneSubDomain membraneSubDomain = (MembraneSubDomain) subDomain;
                BoundaryConditionType bctM = membraneSubDomain.getBoundaryConditionXm();
                BoundaryConditionType bctP = membraneSubDomain.getBoundaryConditionXp();
                if (bctM.isPERIODIC() && !bctP.isPERIODIC() || !bctM.isPERIODIC() && bctP.isPERIODIC()) {
                    Issue issue = new Issue(subDomain, issueContext, IssueCategory.MathDescription_SpatialModel_Subdomain, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_SPATIAL_MODEL_9, "Xm", "Xp", subDomain.getName()), Issue.SEVERITY_ERROR);
                    issueList.add(issue);
                }
                bctM = membraneSubDomain.getBoundaryConditionYm();
                bctP = membraneSubDomain.getBoundaryConditionYp();
                if (bctM.isPERIODIC() && !bctP.isPERIODIC() || !bctM.isPERIODIC() && bctP.isPERIODIC()) {
                    Issue issue = new Issue(subDomain, issueContext, IssueCategory.MathDescription_SpatialModel_Subdomain, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_SPATIAL_MODEL_9, "Ym", "Yp", subDomain.getName()), Issue.SEVERITY_ERROR);
                    issueList.add(issue);
                }
                bctM = membraneSubDomain.getBoundaryConditionZm();
                bctP = membraneSubDomain.getBoundaryConditionZp();
                if (bctM.isPERIODIC() && !bctP.isPERIODIC() || !bctM.isPERIODIC() && bctP.isPERIODIC()) {
                    Issue issue = new Issue(subDomain, issueContext, IssueCategory.MathDescription_SpatialModel_Subdomain, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_SPATIAL_MODEL_9, "Zm", "Zp", subDomain.getName()), Issue.SEVERITY_ERROR);
                    issueList.add(issue);
                }
            }
        }
        try {
            if (geometry.getGeometrySpec().getDimension() > 0) {
                // 
                // Check that there is a MembraneSubdomain for each unique subVolume-subVolume interface in Geometry
                // each ResolvedSurfaceLocation is an instance of a subVolume-subVolume interface (one-to-one with region boundaries).
                // 
                GeometricRegion[] regions = geometry.getGeometrySurfaceDescription().getGeometricRegions();
                // }
                if (regions == null) {
                    Issue issue = new Issue(geometry, issueContext, IssueCategory.MathDescription_SpatialModel_Geometry, VCellErrorMessages.MATH_DESCRIPTION_GEOMETRY_2, Issue.SEVERITY_ERROR);
                    issueList.add(issue);
                } else {
                    for (int i = 0; i < regions.length; i++) {
                        if (regions[i] instanceof SurfaceGeometricRegion) {
                            SurfaceGeometricRegion surfaceRegion = (SurfaceGeometricRegion) regions[i];
                            SubVolume subVolume1 = ((VolumeGeometricRegion) surfaceRegion.getAdjacentGeometricRegions()[0]).getSubVolume();
                            CompartmentSubDomain compartment1 = getCompartmentSubDomain(subVolume1.getName());
                            if (compartment1 == null) {
                                Issue issue = new Issue(geometry, issueContext, IssueCategory.MathDescription_SpatialModel_Geometry, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_GEOMETRY_3, getGeometry().getName(), subVolume1.getName()), Issue.SEVERITY_ERROR);
                                issueList.add(issue);
                            }
                            SubVolume subVolume2 = ((VolumeGeometricRegion) surfaceRegion.getAdjacentGeometricRegions()[1]).getSubVolume();
                            CompartmentSubDomain compartment2 = getCompartmentSubDomain(subVolume2.getName());
                            if (compartment2 == null) {
                                Issue issue = new Issue(geometry, issueContext, IssueCategory.MathDescription_SpatialModel_Geometry, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_GEOMETRY_3, getGeometry().getName(), subVolume2.getName()), Issue.SEVERITY_ERROR);
                                issueList.add(issue);
                            }
                            MembraneSubDomain membraneSubDomain = getMembraneSubDomain(compartment1, compartment2);
                            if (compartment2 != null && compartment1 != null && membraneSubDomain == null) {
                                Issue issue = new Issue(geometry, issueContext, IssueCategory.MathDescription_SpatialModel_Geometry, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_GEOMETRY_4, compartment1.getName(), compartment2.getName()), Issue.SEVERITY_ERROR);
                                issueList.add(issue);
                            }
                        }
                    }
                    // 
                    for (int i = 0; i < subDomainList.size(); i++) {
                        if (subDomainList.get(i) instanceof MembraneSubDomain) {
                            MembraneSubDomain membraneSubDomain = (MembraneSubDomain) subDomainList.get(i);
                            boolean bFoundSurfaceInGeometry = false;
                            for (int j = 0; j < regions.length; j++) {
                                if (regions[j] instanceof SurfaceGeometricRegion) {
                                    SurfaceGeometricRegion surfaceRegion = (SurfaceGeometricRegion) regions[j];
                                    VolumeGeometricRegion volumeRegion1 = (VolumeGeometricRegion) surfaceRegion.getAdjacentGeometricRegions()[0];
                                    VolumeGeometricRegion volumeRegion2 = (VolumeGeometricRegion) surfaceRegion.getAdjacentGeometricRegions()[1];
                                    String memInsideName = membraneSubDomain.getInsideCompartment().getName();
                                    String memOutsideName = membraneSubDomain.getOutsideCompartment().getName();
                                    if ((memInsideName.equals(volumeRegion1.getSubVolume().getName()) && memOutsideName.equals(volumeRegion2.getSubVolume().getName())) || (memInsideName.equals(volumeRegion2.getSubVolume().getName()) && memOutsideName.equals(volumeRegion1.getSubVolume().getName()))) {
                                        bFoundSurfaceInGeometry = true;
                                        break;
                                    }
                                }
                            }
                            if (!bFoundSurfaceInGeometry) {
                                Issue issue = new Issue(geometry, issueContext, IssueCategory.MathDescription_SpatialModel_Geometry, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_GEOMETRY_5, membraneSubDomain.getInsideCompartment().getName(), membraneSubDomain.getOutsideCompartment().getName()), Issue.SEVERITY_ERROR);
                                issueList.add(issue);
                            }
                        }
                    }
                }
            }
        // }catch (GeometryException e){
        // e.printStackTrace(System.out);
        // setWarning("error validating MathDescription: "+e.getMessage());
        // return false;
        // }catch (ImageException e){
        // e.printStackTrace(System.out);
        // setWarning("error validating MathDescription: "+e.getMessage());
        // return false;
        // }catch (ExpressionException e){
        // e.printStackTrace(System.out);
        // setWarning("error validating MathDescription: "+e.getMessage());
        // return false;
        } catch (Exception e) {
            e.printStackTrace(System.out);
            Issue issue = new Issue(geometry, issueContext, IssueCategory.MathDescription_SpatialModel_Geometry, e.getMessage(), Issue.SEVERITY_ERROR);
            issueList.add(issue);
        }
        // 
        for (int i = 0; i < variableList.size(); i++) {
            Variable var = variableList.get(i);
            String varName = var.getName();
            if (var instanceof VolVariable) {
                VolVariable volVar = (VolVariable) var;
                int pdeRefCount = 0;
                int odeRefCount = 0;
                int steadyPdeCount = 0;
                int measureCount = 0;
                for (int j = 0; j < subDomainList.size(); j++) {
                    SubDomain subDomain = subDomainList.get(j);
                    Equation equ = subDomain.getEquation(volVar);
                    if (equ instanceof PdeEquation) {
                        if (((PdeEquation) equ).isSteady()) {
                            steadyPdeCount++;
                        } else {
                            pdeRefCount++;
                        }
                        // 
                        for (int k = 0; k < subDomainList.size(); k++) {
                            SubDomain subDomain2 = subDomainList.get(k);
                            if (subDomain2 instanceof MembraneSubDomain) {
                                MembraneSubDomain membraneSubDomain = (MembraneSubDomain) subDomain2;
                                if (membraneSubDomain.getInsideCompartment() == subDomain || membraneSubDomain.getOutsideCompartment() == subDomain) {
                                    JumpCondition jumpCondition = membraneSubDomain.getJumpCondition(volVar);
                                    BoundaryConditionValue boundaryValue = ((PdeEquation) equ).getBoundaryConditionValue(membraneSubDomain.getName());
                                    // if PDE variable does not have jump condition OR boundaryValue (neither or both are not allowed), its an error.
                                    if ((jumpCondition == null && boundaryValue == null) || (jumpCondition != null && boundaryValue != null)) {
                                        Issue issue = new Issue(equ, issueContext, IssueCategory.MathDescription_SpatialModel_Equation, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_SPATIAL_MODEL_10, varName, subDomain.getName(), membraneSubDomain.getName()), Issue.SEVERITY_ERROR);
                                        issueList.add(issue);
                                    }
                                    if (boundaryValue != null && (subDomain.getBoundaryConditionSpec(membraneSubDomain.getName()) == null)) {
                                        Issue issue = new Issue(equ, issueContext, IssueCategory.MathDescription_SpatialModel_Equation, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_SPATIAL_MODEL_10A, varName, subDomain.getName(), membraneSubDomain.getName(), membraneSubDomain.getName(), subDomain.getName()), Issue.SEVERITY_ERROR);
                                        issueList.add(issue);
                                    }
                                }
                            }
                        }
                    } else if (equ instanceof OdeEquation) {
                        odeRefCount++;
                    } else if (equ instanceof MeasureEquation) {
                        measureCount++;
                    }
                    // 
                    if (subDomain instanceof MembraneSubDomain) {
                        MembraneSubDomain memSubDomain = (MembraneSubDomain) subDomain;
                        JumpCondition jumpCondition = memSubDomain.getJumpCondition(volVar);
                        if (jumpCondition != null) {
                            boolean bInsidePresent = (memSubDomain.getInsideCompartment().getEquation(volVar) instanceof PdeEquation);
                            boolean bOutsidePresent = (memSubDomain.getOutsideCompartment().getEquation(volVar) instanceof PdeEquation);
                            if (!bInsidePresent && !bOutsidePresent) {
                                Issue issue = new Issue(equ, issueContext, IssueCategory.MathDescription_SpatialModel_Equation, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_SPATIAL_MODEL_11, varName, memSubDomain.getName(), memSubDomain.getInsideCompartment().getName(), memSubDomain.getOutsideCompartment().getName()), Issue.SEVERITY_ERROR);
                                issueList.add(issue);
                            }
                            // 
                            if (!bInsidePresent && !jumpCondition.getInFluxExpression().isZero()) {
                                Issue issue = new Issue(equ, issueContext, IssueCategory.MathDescription_SpatialModel_Equation, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_SPATIAL_MODEL_12, varName, memSubDomain.getName(), memSubDomain.getInsideCompartment().getName()), Issue.SEVERITY_ERROR);
                                issueList.add(issue);
                            }
                            if (!bOutsidePresent && !jumpCondition.getOutFluxExpression().isZero()) {
                                Issue issue = new Issue(equ, issueContext, IssueCategory.MathDescription_SpatialModel_Equation, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_SPATIAL_MODEL_13, varName, memSubDomain.getName(), memSubDomain.getOutsideCompartment().getName()), Issue.SEVERITY_ERROR);
                                issueList.add(issue);
                            }
                        }
                    }
                }
                if (odeRefCount > 0 && pdeRefCount > 0) {
                    Issue issue = new Issue(this, issueContext, IssueCategory.MathDescription_SpatialModel, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_SPATIAL_MODEL_14, varName), Issue.SEVERITY_ERROR);
                    issueList.add(issue);
                }
                if (steadyPdeCount > 0 && pdeRefCount > 0) {
                    Issue issue = new Issue(this, issueContext, IssueCategory.MathDescription_SpatialModel, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_SPATIAL_MODEL_15, varName), Issue.SEVERITY_ERROR);
                    issueList.add(issue);
                }
                if (odeRefCount == 0 && pdeRefCount == 0 && steadyPdeCount == 0 && measureCount == 0) {
                    Issue issue = new Issue(this, issueContext, IssueCategory.MathDescription_SpatialModel, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_SPATIAL_MODEL_16, varName), Issue.SEVERITY_ERROR);
                    issueList.add(issue);
                }
            } else // 
            if (var instanceof MemVariable) {
                int pdeRefCount = 0;
                int odeRefCount = 0;
                int steadyPdeCount = 0;
                for (int j = 0; j < subDomainList.size(); j++) {
                    SubDomain subDomain = subDomainList.get(j);
                    Equation equ = subDomain.getEquation(var);
                    if (equ instanceof PdeEquation) {
                        if (((PdeEquation) equ).isSteady()) {
                            steadyPdeCount++;
                        } else {
                            pdeRefCount++;
                        }
                    } else if (equ instanceof OdeEquation) {
                        odeRefCount++;
                    }
                }
                if (odeRefCount > 0 && pdeRefCount > 0) {
                    Issue issue = new Issue(var, issueContext, IssueCategory.MathDescription_SpatialModel_Variable, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_SPATIAL_MODEL_14, varName), Issue.SEVERITY_ERROR);
                    issueList.add(issue);
                }
                if (steadyPdeCount > 0 && pdeRefCount > 0) {
                    Issue issue = new Issue(var, issueContext, IssueCategory.MathDescription_SpatialModel_Variable, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_SPATIAL_MODEL_15, varName), Issue.SEVERITY_ERROR);
                    issueList.add(issue);
                }
                if (odeRefCount == 0 && pdeRefCount == 0 && steadyPdeCount == 0) {
                    Issue issue = new Issue(var, issueContext, IssueCategory.MathDescription_SpatialModel_Variable, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_SPATIAL_MODEL_16, varName), Issue.SEVERITY_ERROR);
                    issueList.add(issue);
                }
            } else // 
            if (var instanceof FilamentVariable) {
                for (int j = 0; j < subDomainList.size(); j++) {
                    SubDomain subDomain = subDomainList.get(j);
                    if (subDomain instanceof FilamentSubDomain) {
                        Equation equ = subDomain.getEquation(var);
                        if (!(equ instanceof OdeEquation)) {
                            Issue issue = new Issue(var, issueContext, IssueCategory.MathDescription_SpatialModel_Variable, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_SPATIAL_MODEL_21, varName, subDomain.getName()), Issue.SEVERITY_ERROR);
                            issueList.add(issue);
                        }
                    }
                }
            } else // 
            if (var instanceof VolumeRegionVariable) {
                VolumeRegionVariable volRegionVar = (VolumeRegionVariable) var;
                int count = 0;
                for (int j = 0; j < subDomainList.size(); j++) {
                    SubDomain subDomain = subDomainList.get(j);
                    if (subDomain instanceof CompartmentSubDomain) {
                        Equation equ = subDomain.getEquation(volRegionVar);
                        if (equ instanceof VolumeRegionEquation) {
                            count++;
                            // 
                            for (int k = 0; k < subDomainList.size(); k++) {
                                SubDomain subDomain2 = subDomainList.get(k);
                                if (subDomain2 instanceof MembraneSubDomain) {
                                    MembraneSubDomain membraneSubDomain = (MembraneSubDomain) subDomain2;
                                    if (membraneSubDomain.getInsideCompartment() == subDomain || membraneSubDomain.getOutsideCompartment() == subDomain) {
                                        if (membraneSubDomain.getJumpCondition(volRegionVar) == null) {
                                            Issue issue = new Issue(var, issueContext, IssueCategory.MathDescription_SpatialModel_Variable, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_SPATIAL_MODEL_17, varName, subDomain.getName(), membraneSubDomain.getName()), Issue.SEVERITY_ERROR);
                                            issueList.add(issue);
                                        }
                                    }
                                }
                            }
                        }
                    }
                }
                if (count == 0) {
                    Issue issue = new Issue(var, issueContext, IssueCategory.MathDescription_SpatialModel_Variable, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_SPATIAL_MODEL_18, varName), Issue.SEVERITY_ERROR);
                    issueList.add(issue);
                }
            } else // 
            if (var instanceof MembraneRegionVariable) {
                int count = 0;
                for (int j = 0; j < subDomainList.size(); j++) {
                    SubDomain subDomain = subDomainList.get(j);
                    if (subDomain instanceof MembraneSubDomain) {
                        Equation equ = subDomain.getEquation(var);
                        if (equ instanceof MembraneRegionEquation) {
                            count++;
                        }
                    }
                }
                if (count == 0) {
                    Issue issue = new Issue(var, issueContext, IssueCategory.MathDescription_SpatialModel_Variable, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_SPATIAL_MODEL_19, varName), Issue.SEVERITY_ERROR);
                    issueList.add(issue);
                }
            } else // 
            if (var instanceof FilamentRegionVariable) {
                for (int j = 0; j < subDomainList.size(); j++) {
                    SubDomain subDomain = subDomainList.get(j);
                    if (subDomain instanceof FilamentSubDomain) {
                        Equation equ = subDomain.getEquation(var);
                        if (!(equ instanceof FilamentRegionEquation)) {
                            Issue issue = new Issue(var, issueContext, IssueCategory.MathDescription_SpatialModel_Variable, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_SPATIAL_MODEL_20, varName, subDomain.getName()), Issue.SEVERITY_ERROR);
                            issueList.add(issue);
                        }
                    }
                }
            }
        }
    }
    if (eventList.size() > 0 && isSpatial()) {
        Issue issue = new Issue(this, issueContext, IssueCategory.MathDescription_SpatialModel, VCellErrorMessages.MATH_DESCRIPTION_SPATIAL_MODEL_22, Issue.SEVERITY_ERROR);
        issueList.add(issue);
    }
    for (Event event : eventList) {
        try {
            event.bind(this);
        } catch (ExpressionBindingException e) {
            Issue issue = new Issue(event, issueContext, IssueCategory.MathDescription_SpatialModel_Event, e.getMessage(), Issue.SEVERITY_ERROR);
            issueList.add(issue);
        }
    }
    for (DataGenerator dataGenerator : postProcessingBlock.getDataGeneratorList()) {
        try {
            dataGenerator.bind(this);
        } catch (ExpressionBindingException e) {
            Issue issue = new Issue(dataGenerator, issueContext, IssueCategory.MathDescription_SpatialModel_PostProcessingBlock, e.getMessage(), Issue.SEVERITY_ERROR);
            issueList.add(issue);
        }
    }
}

Example 10 with VolumeGeometricRegion

use of cbit.vcell.geometry.surface.VolumeGeometricRegion in project vcell by virtualcell.

the class CartesianMesh method createSimpleCartesianMesh.

public static CartesianMesh createSimpleCartesianMesh(Geometry geometry, Map<Polygon, MembraneElement> polygonMembaneElementMap) throws IOException, MathFormatException {
    GeometrySurfaceDescription geometrySurfaceDescription = geometry.getGeometrySurfaceDescription();
    RegionImage regionImage = geometrySurfaceDescription.getRegionImage();
    ISize iSize = new ISize(regionImage.getNumX(), regionImage.getNumY(), regionImage.getNumZ());
    CartesianMesh mesh = createSimpleCartesianMesh(geometry.getOrigin(), geometry.getExtent(), iSize, regionImage);
    GeometricRegion[] geometricRegions = geometrySurfaceDescription.getGeometricRegions();
    if (geometricRegions != null) {
        int memRegionCount = 0;
        for (int i = 0; i < geometricRegions.length; i++) {
            if (geometricRegions[i] instanceof VolumeGeometricRegion) {
                VolumeGeometricRegion vgr = (VolumeGeometricRegion) geometricRegions[i];
                mesh.meshRegionInfo.mapVolumeRegionToSubvolume(vgr.getRegionID(), vgr.getSubVolume().getHandle(), vgr.getSize(), vgr.getName());
            } else if (geometricRegions[i] instanceof SurfaceGeometricRegion) {
                SurfaceGeometricRegion sgr = (SurfaceGeometricRegion) geometricRegions[i];
                GeometricRegion[] neighbors = sgr.getAdjacentGeometricRegions();
                VolumeGeometricRegion insideRegion = (VolumeGeometricRegion) neighbors[0];
                VolumeGeometricRegion outsideRegion = (VolumeGeometricRegion) neighbors[1];
                mesh.meshRegionInfo.mapMembraneRegionToVolumeRegion(memRegionCount, insideRegion.getRegionID(), outsideRegion.getRegionID(), sgr.getSize());
                memRegionCount++;
            }
        }
    }
    SurfaceCollection surfaceCollection = geometrySurfaceDescription.getSurfaceCollection();
    if (surfaceCollection != null) {
        int numMembraneElement = surfaceCollection.getTotalPolygonCount();
        mesh.membraneElements = new MembraneElement[numMembraneElement];
        boolean bMembraneEdgeNeighborsAvailable = surfaceCollection.getMembraneEdgeNeighbors() != null && surfaceCollection.getMembraneEdgeNeighbors().length == surfaceCollection.getSurfaceCount();
        int[] membraneElementMapMembraneRegion = new int[numMembraneElement];
        mesh.meshRegionInfo.mapMembraneElementsToMembraneRegions(membraneElementMapMembraneRegion);
        int memCount = 0;
        // original values when no membraneedgeneighbors
        int[] membraneNeighbors = new int[] { 0, 0, 0, 0 };
        for (int i = 0; i < surfaceCollection.getSurfaceCount(); i++) {
            Surface surface = surfaceCollection.getSurfaces(i);
            bMembraneEdgeNeighborsAvailable = bMembraneEdgeNeighborsAvailable && surfaceCollection.getMembraneEdgeNeighbors()[i].length == surface.getPolygonCount();
            for (int j = 0; j < surface.getPolygonCount(); j++) {
                if (bMembraneEdgeNeighborsAvailable) {
                    membraneNeighbors = new int[MembraneElement.MAX_POSSIBLE_NEIGHBORS];
                    Arrays.fill(membraneNeighbors, MembraneElement.NEIGHBOR_UNDEFINED);
                    for (int k = 0; k < surfaceCollection.getMembraneEdgeNeighbors()[i][j].size(); k++) {
                        membraneNeighbors[k] = surfaceCollection.getMembraneEdgeNeighbors()[i][j].get(k).getMasterPolygonIndex();
                    }
                }
                Quadrilateral polygon = (Quadrilateral) surface.getPolygons(j);
                int volNeighbor1Region = regionImage.getRegionInfoFromOffset(polygon.getVolIndexNeighbor1()).getRegionIndex();
                int volNeighbor2Region = regionImage.getRegionInfoFromOffset(polygon.getVolIndexNeighbor2()).getRegionIndex();
                HashMap<Integer, int[]> map = mesh.getMembraneRegionMapSubvolumesInOut();
                Set<Entry<Integer, int[]>> entries = map.entrySet();
                for (Entry<Integer, int[]> entry : entries) {
                    int[] volNeighbors = entry.getValue();
                    if (volNeighbors[0] == volNeighbor1Region && volNeighbors[1] == volNeighbor2Region || volNeighbors[1] == volNeighbor1Region && volNeighbors[0] == volNeighbor2Region) {
                        membraneElementMapMembraneRegion[memCount] = entry.getKey();
                        break;
                    }
                }
                mesh.membraneElements[memCount] = new MembraneElement(memCount, polygon.getVolIndexNeighbor1(), polygon.getVolIndexNeighbor2(), membraneNeighbors[0], membraneNeighbors[1], membraneNeighbors[2], membraneNeighbors[3], MembraneElement.AREA_UNDEFINED, 0, 0, 0, 0, 0, 0);
                if (polygonMembaneElementMap != null) {
                    polygonMembaneElementMap.put(polygon, mesh.membraneElements[memCount]);
                }
                memCount++;
            }
        }
    }
    return mesh;
}