Search in sources :

Example 21 with CSGObject

use of cbit.vcell.geometry.CSGObject in project vcell by virtualcell.

the class ClientRequestManager method createNewDocument.

/**
 * Insert the method's description here.
 * Creation date: (5/10/2004 3:48:16 PM)
 */
public AsynchClientTask[] createNewDocument(final TopLevelWindowManager requester, final VCDocument.DocumentCreationInfo documentCreationInfo) {
    // throws UserCancelException, Exception {
    /* asynchronous and not blocking any window */
    AsynchClientTask[] taskArray = null;
    final int createOption = documentCreationInfo.getOption();
    switch(documentCreationInfo.getDocumentType()) {
        case BIOMODEL_DOC:
            {
                AsynchClientTask task1 = new AsynchClientTask("creating biomodel", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

                    @Override
                    public void run(Hashtable<String, Object> hashTable) throws Exception {
                        BioModel bioModel = createDefaultBioModelDocument(null);
                        hashTable.put("doc", bioModel);
                    }
                };
                taskArray = new AsynchClientTask[] { task1 };
                break;
            }
        case MATHMODEL_DOC:
            {
                if ((createOption == VCDocument.MATH_OPTION_NONSPATIAL) || (createOption == VCDocument.MATH_OPTION_SPATIAL_EXISTS)) {
                    AsynchClientTask task2 = new AsynchClientTask("creating mathmodel", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

                        @Override
                        public void run(Hashtable<String, Object> hashTable) throws Exception {
                            Geometry geometry = null;
                            if (createOption == VCDocument.MATH_OPTION_NONSPATIAL) {
                                geometry = new Geometry("Untitled", 0);
                            } else {
                                geometry = (Geometry) hashTable.get(GEOMETRY_KEY);
                            }
                            MathModel mathModel = createMathModel("Untitled", geometry);
                            mathModel.setName("MathModel" + (getMdiManager().getNumCreatedDocumentWindows() + 1));
                            hashTable.put("doc", mathModel);
                        }
                    };
                    if (createOption == VCDocument.MATH_OPTION_SPATIAL_EXISTS) {
                        AsynchClientTask task1 = createSelectDocTask(requester);
                        AsynchClientTask task1b = createSelectLoadGeomTask(requester);
                        taskArray = new AsynchClientTask[] { task1, task1b, task2 };
                    } else {
                        taskArray = new AsynchClientTask[] { task2 };
                    }
                    break;
                } else if (createOption == VCDocument.MATH_OPTION_FROMBIOMODELAPP) {
                    AsynchClientTask task1 = new AsynchClientTask("select biomodel application", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

                        @Override
                        public void run(Hashtable<String, Object> hashTable) throws Exception {
                            // spatial or non-spatial
                            BioModelInfo bioModelInfo = (BioModelInfo) DialogUtils.getDBTreePanelSelection(requester.getComponent(), getMdiManager().getDatabaseWindowManager().getBioModelDbTreePanel(), "Open", "Select BioModel");
                            if (bioModelInfo != null) {
                                // may throw UserCancelException
                                hashTable.put("bioModelInfo", bioModelInfo);
                            }
                        }
                    };
                    AsynchClientTask task2 = new AsynchClientTask("find sim contexts in biomodel application", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

                        @Override
                        public void run(Hashtable<String, Object> hashTable) throws Exception {
                            // spatial or non-spatial
                            // Get the simContexts in the corresponding BioModel
                            BioModelInfo bioModelInfo = (BioModelInfo) hashTable.get("bioModelInfo");
                            SimulationContext[] simContexts = getDocumentManager().getBioModel(bioModelInfo).getSimulationContexts();
                            if (simContexts != null) {
                                // may throw UserCancelException
                                hashTable.put("simContexts", simContexts);
                            }
                        }
                    };
                    AsynchClientTask task3 = new AsynchClientTask("create math model from biomodel application", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

                        @Override
                        public void run(Hashtable<String, Object> hashTable) throws Exception {
                            SimulationContext[] simContexts = (SimulationContext[]) hashTable.get("simContexts");
                            String[] simContextNames = new String[simContexts.length];
                            if (simContextNames.length == 0) {
                                throw new RuntimeException("no application is available");
                            } else {
                                for (int i = 0; i < simContexts.length; i++) {
                                    simContextNames[i] = simContexts[i].getName();
                                }
                                Component component = requester.getComponent();
                                // Get the simContext names, so that user can choose which simContext math to import
                                String simContextChoice = (String) PopupGenerator.showListDialog(component, simContextNames, "Please select Application");
                                if (simContextChoice == null) {
                                    throw UserCancelException.CANCEL_DB_SELECTION;
                                }
                                SimulationContext chosenSimContext = null;
                                for (int i = 0; i < simContexts.length; i++) {
                                    if (simContexts[i].getName().equals(simContextChoice)) {
                                        chosenSimContext = simContexts[i];
                                        break;
                                    }
                                }
                                Objects.requireNonNull(chosenSimContext);
                                BioModelInfo bioModelInfo = (BioModelInfo) hashTable.get("bioModelInfo");
                                // Get corresponding mathDesc to create new mathModel and return.
                                String newName = bioModelInfo.getVersion().getName() + "_" + chosenSimContext.getName();
                                MathDescription bioMathDesc = chosenSimContext.getMathDescription();
                                MathDescription newMathDesc = null;
                                newMathDesc = new MathDescription(newName + "_" + (new Random()).nextInt());
                                newMathDesc.setGeometry(bioMathDesc.getGeometry());
                                newMathDesc.read_database(new CommentStringTokenizer(bioMathDesc.getVCML_database()));
                                newMathDesc.isValid();
                                MathModel newMathModel = new MathModel(null);
                                newMathModel.setName(newName);
                                newMathModel.setMathDescription(newMathDesc);
                                hashTable.put("doc", newMathModel);
                            }
                        }
                    };
                    taskArray = new AsynchClientTask[] { task1, task2, task3 };
                    break;
                } else {
                    throw new RuntimeException("Unknown MathModel Document creation option value=" + documentCreationInfo.getOption());
                }
            }
        case GEOMETRY_DOC:
            {
                if (createOption == VCDocument.GEOM_OPTION_1D || createOption == VCDocument.GEOM_OPTION_2D || createOption == VCDocument.GEOM_OPTION_3D) {
                    // analytic
                    AsynchClientTask task1 = new AsynchClientTask("creating analytic geometry", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

                        @Override
                        public void run(Hashtable<String, Object> hashTable) throws Exception {
                            Geometry geometry = new Geometry("Geometry" + (getMdiManager().getNumCreatedDocumentWindows() + 1), documentCreationInfo.getOption());
                            geometry.getGeometrySpec().addSubVolume(new AnalyticSubVolume("subdomain0", new Expression(1.0)));
                            geometry.precomputeAll(new GeometryThumbnailImageFactoryAWT());
                            hashTable.put("doc", geometry);
                        }
                    };
                    taskArray = new AsynchClientTask[] { task1 };
                    break;
                }
                if (createOption == VCDocument.GEOM_OPTION_CSGEOMETRY_3D) {
                    // constructed solid geometry
                    AsynchClientTask task1 = new AsynchClientTask("creating constructed solid geometry", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

                        @Override
                        public void run(Hashtable<String, Object> hashTable) throws Exception {
                            Geometry geometry = new Geometry("Geometry" + (getMdiManager().getNumCreatedDocumentWindows() + 1), 3);
                            Extent extent = geometry.getExtent();
                            if (extent != null) {
                                // create a CSGPrimitive of type cube and scale it to the 'extent' components. Use this as the default or background CSGObject (subdomain).
                                // This can be considered as the equivalent of subdomain (with expression) 1.0 for analyticSubvolume.
                                // basic cube
                                CSGPrimitive cube = new CSGPrimitive("cube", CSGPrimitive.PrimitiveType.CUBE);
                                // scaled cube
                                double x = extent.getX();
                                double y = extent.getY();
                                double z = extent.getZ();
                                CSGScale scaledCube = new CSGScale("scale", new Vect3d(x / 2.0, y / 2.0, z / 2.0));
                                scaledCube.setChild(cube);
                                // translated scaled cube
                                CSGTranslation translatedScaledCube = new CSGTranslation("translation", new Vect3d(x / 2, y / 2, z / 2));
                                translatedScaledCube.setChild(scaledCube);
                                CSGObject csgObject = new CSGObject(null, "subdomain0", 0);
                                csgObject.setRoot(translatedScaledCube);
                                geometry.getGeometrySpec().addSubVolume(csgObject, false);
                                geometry.precomputeAll(new GeometryThumbnailImageFactoryAWT());
                                hashTable.put("doc", geometry);
                            }
                        }
                    };
                    taskArray = new AsynchClientTask[] { task1 };
                    break;
                } else {
                    throw new RuntimeException("Unknown Geometry Document creation option value=" + documentCreationInfo.getOption());
                }
            }
        default:
            {
                throw new RuntimeException("Unknown default document type: " + documentCreationInfo.getDocumentType());
            }
    }
    return taskArray;
}
Also used : AsynchClientTask(cbit.vcell.client.task.AsynchClientTask) MathModel(cbit.vcell.mathmodel.MathModel) SetMathDescription(cbit.vcell.client.task.SetMathDescription) MathDescription(cbit.vcell.math.MathDescription) Extent(org.vcell.util.Extent) CSGPrimitive(cbit.vcell.geometry.CSGPrimitive) CSGScale(cbit.vcell.geometry.CSGScale) GeometryThumbnailImageFactoryAWT(cbit.vcell.geometry.GeometryThumbnailImageFactoryAWT) Random(java.util.Random) Component(java.awt.Component) CSGObject(cbit.vcell.geometry.CSGObject) CSGTranslation(cbit.vcell.geometry.CSGTranslation) Hashtable(java.util.Hashtable) BioModelInfo(org.vcell.util.document.BioModelInfo) SimulationContext(cbit.vcell.mapping.SimulationContext) ProgrammingException(org.vcell.util.ProgrammingException) GeometryException(cbit.vcell.geometry.GeometryException) IOException(java.io.IOException) DataAccessException(org.vcell.util.DataAccessException) PropertyVetoException(java.beans.PropertyVetoException) ImageException(cbit.image.ImageException) UtilCancelException(org.vcell.util.UtilCancelException) DataFormatException(java.util.zip.DataFormatException) UserCancelException(org.vcell.util.UserCancelException) Vect3d(cbit.vcell.render.Vect3d) Geometry(cbit.vcell.geometry.Geometry) Expression(cbit.vcell.parser.Expression) BioModel(cbit.vcell.biomodel.BioModel) CommentStringTokenizer(org.vcell.util.CommentStringTokenizer) CSGObject(cbit.vcell.geometry.CSGObject) AnalyticSubVolume(cbit.vcell.geometry.AnalyticSubVolume)

Example 22 with CSGObject

use of cbit.vcell.geometry.CSGObject 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
// }
}
Also used : Origin(org.vcell.util.Origin) CompartmentMapping(org.sbml.jsbml.ext.spatial.CompartmentMapping) Compartment(org.sbml.jsbml.Compartment) SpatialParameterPlugin(org.sbml.jsbml.ext.spatial.SpatialParameterPlugin) StructureMappingParameter(cbit.vcell.mapping.StructureMapping.StructureMappingParameter) AnalyticGeometry(org.sbml.jsbml.ext.spatial.AnalyticGeometry) ExpressionException(cbit.vcell.parser.ExpressionException) Boundary(org.sbml.jsbml.ext.spatial.Boundary) GeometrySpec(cbit.vcell.geometry.GeometrySpec) DomainType(org.sbml.jsbml.ext.spatial.DomainType) SampledVolume(org.sbml.jsbml.ext.spatial.SampledVolume) SubVolume(cbit.vcell.geometry.SubVolume) ImageSubVolume(cbit.vcell.geometry.ImageSubVolume) AnalyticSubVolume(cbit.vcell.geometry.AnalyticSubVolume) GeometryContext(cbit.vcell.mapping.GeometryContext) SpatialCompartmentPlugin(org.sbml.jsbml.ext.spatial.SpatialCompartmentPlugin) CoordinateComponent(org.sbml.jsbml.ext.spatial.CoordinateComponent) SimulationContext(cbit.vcell.mapping.SimulationContext) SpeciesContext(cbit.vcell.model.SpeciesContext) GeometryContext(cbit.vcell.mapping.GeometryContext) VolumeGeometricRegion(cbit.vcell.geometry.surface.VolumeGeometricRegion) SurfaceGeometricRegion(cbit.vcell.geometry.surface.SurfaceGeometricRegion) VolumeGeometricRegion(cbit.vcell.geometry.surface.VolumeGeometricRegion) GeometricRegion(cbit.vcell.geometry.surface.GeometricRegion) SpatialSymbolReference(org.sbml.jsbml.ext.spatial.SpatialSymbolReference) AnalyticVolume(org.sbml.jsbml.ext.spatial.AnalyticVolume) InteriorPoint(org.sbml.jsbml.ext.spatial.InteriorPoint) SampledField(org.sbml.jsbml.ext.spatial.SampledField) Domain(org.sbml.jsbml.ext.spatial.Domain) AnalyticSubVolume(cbit.vcell.geometry.AnalyticSubVolume) GeometryClass(cbit.vcell.geometry.GeometryClass) ImageException(cbit.image.ImageException) GeometrySurfaceDescription(cbit.vcell.geometry.surface.GeometrySurfaceDescription) Extent(org.vcell.util.Extent) SurfaceClass(cbit.vcell.geometry.SurfaceClass) ISize(org.vcell.util.ISize) CSGeometry(org.sbml.jsbml.ext.spatial.CSGeometry) RegionInfo(cbit.vcell.geometry.RegionImage.RegionInfo) VCImage(cbit.image.VCImage) StructureMapping(cbit.vcell.mapping.StructureMapping) GeometryThumbnailImageFactoryAWT(cbit.vcell.geometry.GeometryThumbnailImageFactoryAWT) ASTNode(org.sbml.jsbml.ASTNode) CSGObject(cbit.vcell.geometry.CSGObject) VCUnitDefinition(cbit.vcell.units.VCUnitDefinition) UnitDefinition(org.sbml.jsbml.UnitDefinition) ImageSubVolume(cbit.vcell.geometry.ImageSubVolume) SurfaceGeometricRegion(cbit.vcell.geometry.surface.SurfaceGeometricRegion) SampledFieldGeometry(org.sbml.jsbml.ext.spatial.SampledFieldGeometry) SpatialModelPlugin(org.sbml.jsbml.ext.spatial.SpatialModelPlugin) InteriorPoint(org.sbml.jsbml.ext.spatial.InteriorPoint) XMLStreamException(javax.xml.stream.XMLStreamException) SbmlException(org.vcell.sbml.SbmlException) ImageException(cbit.image.ImageException) SBMLException(org.sbml.jsbml.SBMLException) ExpressionException(cbit.vcell.parser.ExpressionException) AdjacentDomains(org.sbml.jsbml.ext.spatial.AdjacentDomains) Geometry(cbit.vcell.geometry.Geometry) SampledFieldGeometry(org.sbml.jsbml.ext.spatial.SampledFieldGeometry) AnalyticGeometry(org.sbml.jsbml.ext.spatial.AnalyticGeometry) CSGeometry(org.sbml.jsbml.ext.spatial.CSGeometry) Expression(cbit.vcell.parser.Expression) Model(cbit.vcell.model.Model) BioModel(cbit.vcell.biomodel.BioModel)

Example 23 with CSGObject

use of cbit.vcell.geometry.CSGObject in project vcell by virtualcell.

the class ComsolModelBuilder method getVCCModel.

public static VCCModel getVCCModel(SimulationJob vcellSimJob) throws ExpressionException {
    MathDescription vcellMathDesc = vcellSimJob.getSimulation().getMathDescription();
    Geometry vcellGeometry = vcellMathDesc.getGeometry();
    GeometrySpec vcellGeometrySpec = vcellGeometry.getGeometrySpec();
    int vcellDim = vcellGeometrySpec.getDimension();
    VCCModel model = new VCCModel("Model", vcellDim);
    model.modelpath = "D:\\Developer\\eclipse\\workspace_refactor\\comsol_java\\src";
    model.comments = "Untitled\n\n";
    VCCModelNode comp1 = new VCCModelNode("comp1");
    model.modelnodes.add(comp1);
    // if (vcellDim != 2){
    // throw new RuntimeException("expecting 2D simulation");
    // }
    // 
    // assume initial geometry is circle centered at 0.5, 0.5 of radius 0.3
    // 
    // String comsolOutsideDomainName = "dif1";
    // String comsolInsideDomainName = "c1";
    VCCGeomSequence geom1 = new VCCGeomSequence("geom1", vcellDim);
    model.geometrysequences.add(geom1);
    VCCMeshSequence mesh1 = new VCCMeshSequence("mesh1", geom1);
    model.meshes.add(mesh1);
    VCCStudy std1 = new VCCStudy("std1");
    model.study = std1;
    TimeBounds timeBounds = vcellSimJob.getSimulation().getSolverTaskDescription().getTimeBounds();
    TimeStep timeStep = vcellSimJob.getSimulation().getSolverTaskDescription().getTimeStep();
    String beginTime = Double.toString(timeBounds.getStartingTime());
    String endTime = Double.toString(timeBounds.getEndingTime());
    String step = Double.toString(timeStep.getDefaultTimeStep());
    VCCStudyFeature time = new VCCTransientStudyFeature("time", beginTime, step, endTime);
    std1.features.add(time);
    if (vcellGeometrySpec.getImage() != null) {
        throw new RuntimeException("image-based geometries not yet supported by VCell's COMSOL model builder");
    }
    if (vcellGeometrySpec.getNumSubVolumes() == 0) {
        throw new RuntimeException("no subvolumes defined in geometry");
    }
    if (vcellGeometrySpec.getNumAnalyticOrCSGSubVolumes() != vcellGeometrySpec.getNumSubVolumes()) {
        throw new RuntimeException("only analytic and CSG subvolumes currently supported by VCell's COMSOL model builder");
    }
    // 
    // add geometry for all subvolumes
    // 
    HashMap<String, VCCGeomFeature> subvolumeNameFeatureMap = new HashMap<String, VCCGeomFeature>();
    SubVolume[] subVolumes = vcellGeometrySpec.getSubVolumes();
    for (int i = 0; i < subVolumes.length; i++) {
        SubVolume subvolume = subVolumes[i];
        if (subvolume instanceof CSGObject) {
            CSGObject vcellCSGObject = (CSGObject) subvolume;
            CSGNode vcellCSGNode = vcellCSGObject.getRoot();
            ArrayList<VCCGeomFeature> geomFeatureList = new ArrayList<VCCGeomFeature>();
            VCCGeomFeature feature = csgVisitor(vcellCSGNode, geomFeatureList, subvolume.getName());
            geom1.geomfeatures.addAll(geomFeatureList);
            if (i == 0) {
                // first subvolume (on top in ordinals) doesn't need any differencing
                subvolumeNameFeatureMap.put(subvolume.getName(), feature);
            } else {
                // have to subtract union of prior subvolumes
                ArrayList<VCCGeomFeature> priorFeatures = new ArrayList<VCCGeomFeature>();
                for (int j = 0; j < i; j++) {
                    CSGObject priorCSGObject = (CSGObject) subVolumes[j];
                    CSGNode priorCSGNode = priorCSGObject.getRoot();
                    geomFeatureList.clear();
                    VCCGeomFeature priorFeature = csgVisitor(priorCSGNode, geomFeatureList, subvolume.getName());
                    priorFeatures.add(priorFeature);
                    geom1.geomfeatures.addAll(geomFeatureList);
                }
                VCCDifference diff = new VCCDifference("diff" + subvolume.getName(), Keep.off);
                diff.input.add(feature);
                diff.input2.addAll(priorFeatures);
                geom1.geomfeatures.add(diff);
                subvolumeNameFeatureMap.put(subvolume.getName(), diff);
            }
        } else {
            throw new RuntimeException("only CSG subvolumes currently supported by VCell's COMSOL model builder");
        }
    }
    // 
    // add geometry for all surfaceClasses
    // 
    HashMap<String, VCCGeomFeature> surfaceclassNameFeatureMap = new HashMap<String, VCCGeomFeature>();
    SurfaceClass[] surfaceClasses = vcellGeometry.getGeometrySurfaceDescription().getSurfaceClasses();
    for (int i = 0; i < surfaceClasses.length; i++) {
        SurfaceClass surfaceClass = surfaceClasses[i];
        Set<SubVolume> adjacentSubvolumes = surfaceClass.getAdjacentSubvolumes();
        if (adjacentSubvolumes.size() != 2) {
            throw new RuntimeException("expecting two adjacent subvolumes for surface " + surfaceClass.getName() + " in COMSOL model builder");
        }
        // find adjacent Geometry Features (for subvolumes)
        Iterator<SubVolume> svIter = adjacentSubvolumes.iterator();
        SubVolume subvolume0 = svIter.next();
        SubVolume subvolume1 = svIter.next();
        ArrayList<VCCGeomFeature> adjacentFeatures = new ArrayList<VCCGeomFeature>();
        adjacentFeatures.add(subvolumeNameFeatureMap.get(subvolume0.getName()));
        adjacentFeatures.add(subvolumeNameFeatureMap.get(subvolume1.getName()));
        String name = "inter_" + subvolume0.getName() + "_" + subvolume1.getName();
        // surfaces are dimension N-1
        int entitydim = vcellDim - 1;
        VCCIntersectionSelection intersect_subvolumes = new VCCIntersectionSelection(name, entitydim);
        intersect_subvolumes.input.addAll(adjacentFeatures);
        geom1.geomfeatures.add(intersect_subvolumes);
        surfaceclassNameFeatureMap.put(surfaceClass.getName(), intersect_subvolumes);
    }
    SimulationSymbolTable symbolTable = new SimulationSymbolTable(vcellSimJob.getSimulation(), vcellSimJob.getJobIndex());
    // 
    for (SubDomain subDomain : Collections.list(vcellMathDesc.getSubDomains())) {
        for (Equation equ : subDomain.getEquationCollection()) {
            if (equ instanceof PdeEquation || equ instanceof OdeEquation) {
                VCCGeomFeature geomFeature = null;
                final int dim;
                if (subDomain instanceof CompartmentSubDomain) {
                    geomFeature = subvolumeNameFeatureMap.get(subDomain.getName());
                    dim = vcellDim;
                } else if (subDomain instanceof MembraneSubDomain) {
                    geomFeature = surfaceclassNameFeatureMap.get(subDomain.getName());
                    dim = vcellDim - 1;
                } else {
                    throw new RuntimeException("subdomains of type '" + subDomain.getClass().getSimpleName() + "' not yet supported in COMSOL model builder");
                }
                if (geomFeature == null) {
                    throw new RuntimeException("cannot find COMSOL geometry feature named " + subDomain.getName() + " in COMSOL model builder");
                }
                VCCConvectionDiffusionEquation cdeq = new VCCConvectionDiffusionEquation("cdeq_" + equ.getVariable().getName(), geom1, geomFeature, dim);
                cdeq.fieldName = equ.getVariable().getName();
                cdeq.initial = MathUtilities.substituteModelParameters(equ.getInitialExpression(), symbolTable).flatten().infix();
                cdeq.sourceTerm_f = MathUtilities.substituteModelParameters(equ.getRateExpression(), symbolTable).flatten().infix();
                if (equ instanceof PdeEquation) {
                    PdeEquation pde = (PdeEquation) equ;
                    cdeq.diffTerm_c = MathUtilities.substituteModelParameters(pde.getDiffusionExpression(), symbolTable).flatten().infix();
                    if (subDomain instanceof CompartmentSubDomain) {
                        CompartmentSubDomain compartmentSubdomain = (CompartmentSubDomain) subDomain;
                        ArrayList<String> be = new ArrayList<String>();
                        if (pde.getVelocityX() != null) {
                            be.add(MathUtilities.substituteModelParameters(pde.getVelocityX(), symbolTable).flatten().infix());
                        } else {
                            be.add("0");
                        }
                        if (vcellDim >= 2) {
                            if (pde.getVelocityY() != null) {
                                be.add(MathUtilities.substituteModelParameters(pde.getVelocityY(), symbolTable).flatten().infix());
                            } else {
                                be.add("0");
                            }
                        }
                        if (vcellDim == 3) {
                            if (pde.getVelocityY() != null) {
                                be.add(MathUtilities.substituteModelParameters(pde.getVelocityZ(), symbolTable).flatten().infix());
                            } else {
                                be.add("0");
                            }
                        }
                        cdeq.advection_be = be.toArray(new String[vcellDim]);
                        // 
                        // look for membrane boundary conditions for this variable
                        // 
                        MembraneSubDomain[] membraneSubdomains = vcellMathDesc.getMembraneSubDomains(compartmentSubdomain);
                        for (MembraneSubDomain membraneSubdomain : membraneSubdomains) {
                            JumpCondition jumpCondition = membraneSubdomain.getJumpCondition((VolVariable) pde.getVariable());
                            if (jumpCondition != null) {
                                Expression fluxExpr = null;
                                if (membraneSubdomain.getInsideCompartment() == compartmentSubdomain) {
                                    fluxExpr = jumpCondition.getInFluxExpression();
                                } else if (membraneSubdomain.getOutsideCompartment() == compartmentSubdomain) {
                                    fluxExpr = jumpCondition.getOutFluxExpression();
                                }
                                String name = equ.getVariable().getName() + "_flux_" + membraneSubdomain.getName();
                                VCCGeomFeature selection = surfaceclassNameFeatureMap.get(membraneSubdomain.getName());
                                VCCFluxBoundary fluxBoundary = new VCCFluxBoundary(name, selection, vcellDim - 1);
                                fluxBoundary.flux_g = MathUtilities.substituteModelParameters(fluxExpr, symbolTable).flatten().infix();
                                cdeq.features.add(fluxBoundary);
                            }
                        }
                    }
                }
                model.physics.add(cdeq);
            }
        }
    }
    // 
    return model;
}
Also used : JumpCondition(cbit.vcell.math.JumpCondition) MembraneSubDomain(cbit.vcell.math.MembraneSubDomain) MathDescription(cbit.vcell.math.MathDescription) HashMap(java.util.HashMap) SurfaceClass(cbit.vcell.geometry.SurfaceClass) VCCConvectionDiffusionEquation(org.vcell.solver.comsol.model.VCCConvectionDiffusionEquation) CSGNode(cbit.vcell.geometry.CSGNode) ArrayList(java.util.ArrayList) VCCFluxBoundary(org.vcell.solver.comsol.model.VCCPhysicsFeature.VCCFluxBoundary) GeometrySpec(cbit.vcell.geometry.GeometrySpec) CompartmentSubDomain(cbit.vcell.math.CompartmentSubDomain) SubDomain(cbit.vcell.math.SubDomain) MembraneSubDomain(cbit.vcell.math.MembraneSubDomain) PdeEquation(cbit.vcell.math.PdeEquation) TimeBounds(cbit.vcell.solver.TimeBounds) TimeStep(cbit.vcell.solver.TimeStep) SubVolume(cbit.vcell.geometry.SubVolume) VCCStudyFeature(org.vcell.solver.comsol.model.VCCStudyFeature) CSGObject(cbit.vcell.geometry.CSGObject) VCCGeomFeature(org.vcell.solver.comsol.model.VCCGeomFeature) VCCDifference(org.vcell.solver.comsol.model.VCCGeomFeature.VCCDifference) VCCGeomSequence(org.vcell.solver.comsol.model.VCCGeomSequence) VCCIntersectionSelection(org.vcell.solver.comsol.model.VCCGeomFeature.VCCIntersectionSelection) SimulationSymbolTable(cbit.vcell.solver.SimulationSymbolTable) VCCConvectionDiffusionEquation(org.vcell.solver.comsol.model.VCCConvectionDiffusionEquation) OdeEquation(cbit.vcell.math.OdeEquation) PdeEquation(cbit.vcell.math.PdeEquation) Equation(cbit.vcell.math.Equation) VCCModelNode(org.vcell.solver.comsol.model.VCCModelNode) VCCTransientStudyFeature(org.vcell.solver.comsol.model.VCCTransientStudyFeature) VCCMeshSequence(org.vcell.solver.comsol.model.VCCMeshSequence) Geometry(cbit.vcell.geometry.Geometry) VCCStudy(org.vcell.solver.comsol.model.VCCStudy) OdeEquation(cbit.vcell.math.OdeEquation) Expression(cbit.vcell.parser.Expression) CompartmentSubDomain(cbit.vcell.math.CompartmentSubDomain) VCCModel(org.vcell.solver.comsol.model.VCCModel)

Aggregations

CSGObject (cbit.vcell.geometry.CSGObject)23 AnalyticSubVolume (cbit.vcell.geometry.AnalyticSubVolume)11 GeometryThumbnailImageFactoryAWT (cbit.vcell.geometry.GeometryThumbnailImageFactoryAWT)8 Expression (cbit.vcell.parser.Expression)7 CSGNode (cbit.vcell.geometry.CSGNode)6 CSGSetOperator (cbit.vcell.geometry.CSGSetOperator)6 SubVolume (cbit.vcell.geometry.SubVolume)6 AsynchClientTask (cbit.vcell.client.task.AsynchClientTask)5 BioModelNode (cbit.vcell.desktop.BioModelNode)5 CSGTransformation (cbit.vcell.geometry.CSGTransformation)5 Geometry (cbit.vcell.geometry.Geometry)5 ImageSubVolume (cbit.vcell.geometry.ImageSubVolume)5 Hashtable (java.util.Hashtable)5 BioModel (cbit.vcell.biomodel.BioModel)4 CSGPrimitive (cbit.vcell.geometry.CSGPrimitive)4 CSGScale (cbit.vcell.geometry.CSGScale)4 CSGTranslation (cbit.vcell.geometry.CSGTranslation)4 SimulationContext (cbit.vcell.mapping.SimulationContext)4 ImageException (cbit.image.ImageException)3 CSGRotation (cbit.vcell.geometry.CSGRotation)3