void readSpatialSBML() { SBMLDocument *document2 = readSBML("spatial_example2.xml"); Model *model2 = document2->getModel(); Compartment *comp; SpatialCompartmentPlugin* cplugin; for (unsigned int i = 0; i < model2->getNumCompartments(); i++) { comp = model2->getCompartment(i); cout << "Compartment" << i << ": " << comp->getId() << endl; cplugin = static_cast<SpatialCompartmentPlugin*>(comp->getPlugin("spatial")); if (cplugin->getCompartmentMapping()->isSetId()) { cout << "Comp" << i << " CMSpId: " << cplugin->getCompartmentMapping()->getId() << endl; cout << "Comp" << i << " CM_DType: " << cplugin->getCompartmentMapping()->getDomainType() << endl; cout << "Comp" << i << " CM_UnitSz: " << cplugin->getCompartmentMapping()->getUnitSize() << endl; } } Species *sp; SpatialSpeciesPlugin* srplugin; for (unsigned int i = 0; i < model2->getNumSpecies(); i++) { sp = model2->getSpecies(i); cout << "Species" << i << ": " << sp->getId() << endl; srplugin = static_cast<SpatialSpeciesPlugin*>(sp->getPlugin("spatial")); if (srplugin->getIsSpatial()) { cout << "species" << i << " isSpatial: " << srplugin->getIsSpatial() << endl; } } Parameter *param; SpatialParameterPlugin* pplugin; for (unsigned int i = 0; i < model2->getNumParameters(); i++) { param = model2->getParameter(i); cout << "Parameter" << i << ": " << param->getId() << endl; pplugin = static_cast<SpatialParameterPlugin*>(param->getPlugin("spatial")); if (pplugin->isSetSpatialSymbolReference()) { cout << "Parameter" << i << " SpRefId: " << pplugin->getSpatialSymbolReference()->getSpatialRef() << endl; } if (pplugin->isSetDiffusionCoefficient()) { cout << "Diff_" << i << " SpeciesVarId: " << pplugin->getDiffusionCoefficient()->getVariable() << endl; cout << "Diff_" << i << " Type: " << DiffusionKind_toString(pplugin->getDiffusionCoefficient()->getType()) << endl; for (unsigned int j = 0; j < pplugin->getDiffusionCoefficient()->getNumCoordinateReferences(); ++j) cout << "Diff_" << i << " SpCoordIndex " << j << " : " << CoordinateKind_toString(pplugin->getDiffusionCoefficient()->getCoordinateReference(j) ->getCoordinate()) << endl; } if (pplugin->isSetAdvectionCoefficient()) { cout << "Adv_" << i << " SpeciesVarId: " << pplugin->getAdvectionCoefficient()->getVariable() << endl; cout << "Adv_" << i << " SpCoordIndex: " << CoordinateKind_toString(pplugin->getAdvectionCoefficient()->getCoordinate()) << endl; } if (pplugin->isSetBoundaryCondition()) { cout << "BC_" << i << " SpeciesVarId: " << pplugin->getBoundaryCondition()->getVariable() << endl; cout << "BC_" << i << " SpCoordBoundary: " << pplugin->getBoundaryCondition()->getCoordinateBoundary() << endl; cout << "BC_" << i << " SpBoundaryType: " << pplugin->getBoundaryCondition()->getType() << endl; } } Reaction *rxn; SpatialReactionPlugin* rplugin; for (unsigned int i = 0; i < model2->getNumReactions(); i++) { rxn = model2->getReaction(i); cout << "Reaction" << i << ": " << rxn->getId() << endl; rplugin = static_cast<SpatialReactionPlugin*>(rxn->getPlugin("spatial")); if (rplugin->getIsLocal()) { cout << "rxn" << i << " isLocal: " << rplugin->getIsLocal() << endl; } } Rule *rule; for (unsigned int i = 0; i < model2->getNumRules(); i++) { rule = model2->getRule(i); cout << "Rule" << i << ": " << rule->getVariable() << endl; } // // Get a SpatialModelPlugin object plugged in the model object. // // The type of the returned value of SBase::getPlugin() function is // SBasePlugin*, and thus the value needs to be cast for the // corresponding derived class. // SpatialModelPlugin* mplugin2; mplugin2 = static_cast<SpatialModelPlugin*>(model2->getPlugin("spatial")); cout << "URI: " << mplugin2->getURI() << endl; cout << "prefix: " << mplugin2->getPrefix() << endl; // get a Geometry object via SpatialModelPlugin object. Geometry* geometry2 = mplugin2->getGeometry(); cout << "Geometry coordSystem: " << geometry2->getCoordinateSystem() << endl; // get a CoordComponent object via the Geometry object. CoordinateComponent* coordComp = geometry2->getCoordinateComponent(0); std::cout << "CoordComponent Id: " << coordComp->getId() << std::endl; std::cout << "CoordComponent type: " << CoordinateKind_toString( coordComp->getType()) << std::endl; std::cout << "CoordComponent sbmlUnit: " << coordComp->getUnit() << std::endl; if (coordComp->isSetBoundaryMin()) { Boundary* minX = coordComp->getBoundaryMin(); std::cout << "minX name: " << minX->getId() << std::endl; std::cout << "minX value: " << minX->getValue() << std::endl; } if (coordComp->isSetBoundaryMax()) { Boundary* maxX = coordComp->getBoundaryMax(); std::cout << "maxX name: " << maxX->getId() << std::endl; std::cout << "maxX value: " << maxX->getValue() << std::endl; } // get a DomainType object via the Geometry object. DomainType* domainType2 = geometry2->getDomainType(0); std::cout << "DomainType Id: " << domainType2->getId() << std::endl; std::cout << "DomainType spatialDim: " << domainType2->getSpatialDimension() << std::endl; // get a Domain object via the Geometry object. Domain* domain = geometry2->getDomain(0); std::cout << "Domain1 Id: " << domain->getId() << std::endl; std::cout << "Domain1 domainType: " << domain->getDomainType() << std::endl; // get an internal point via the domain object InteriorPoint* internalPt = domain->getInteriorPoint(0); std::cout << "InternalPt_1 coord1: " << internalPt->getCoord1() << std::endl; // get a Domain object via the Geometry object. domain = geometry2->getDomain(1); std::cout << "Domain2 Id: " << domain->getId() << std::endl; std::cout << "Domain2 domainType: " << domain->getDomainType() << std::endl; // get an internal point via the domain object internalPt = domain->getInteriorPoint(0); std::cout << "InternalPt_2 coord1: " << internalPt->getCoord1() << std::endl; // get an AdjacentDomains object via the Geometry object. AdjacentDomains* adjDomain = geometry2->getAdjacentDomains(0); std::cout << "AdjDomain Id: " << adjDomain->getId() << std::endl; std::cout << "AdjDomain domain1: " << adjDomain->getDomain1() << std::endl; std::cout << "AdjDomain domain2: " << adjDomain->getDomain2() << std::endl; // get an AnalyticGeometry object via the Geometry object. GeometryDefinition* gd; for (unsigned int i = 0; i < geometry2->getNumGeometryDefinitions(); i++) { gd = geometry2->getGeometryDefinition(i); if (gd->isAnalyticGeometry()) { AnalyticGeometry* analyticalGeom = static_cast<AnalyticGeometry*>(gd); std::cout << "AnalGeom Id: " << analyticalGeom->getId() << std::endl; // analVol from analGeom. AnalyticVolume* av = analyticalGeom->getAnalyticVolume(0); std::cout << "AnalVol Id: " << av->getId() << std::endl; std::cout << "AnalVol domainType: " << av->getDomainType() << std::endl; std::cout << "AnalVol funcType: " << av->getFunctionType() << std::endl; std::cout << "AnalVol ordinal: " << av->getOrdinal() << std::endl; const ASTNode* mathNode = av->getMath(); char* mathStr = writeMathMLToString(mathNode); std::cout << "AnalVol math: " << mathStr << std::endl; } if (gd->isSampledFieldGeometry()) { SampledFieldGeometry* sfGeom = static_cast<SampledFieldGeometry*>(gd); std::cout << "SampledFieldGeom Id: " << sfGeom->getId() << std::endl; // sampledField from sfGeom SampledField* sf = sfGeom->getSampledField(); std::cout << "SampledField Id: " << sf->getId() << std::endl; std::cout << "SampledField dataType: " << sf->getDataType() << std::endl; std::cout << "SampledField interpolation: " << sf->getInterpolationType() << std::endl; std::cout << "SampledField encoding: " << sf->getEncoding() << std::endl; std::cout << "SampledField numSamples1: " << sf->getNumSamples1() << std::endl; std::cout << "SampledField numSamples2: " << sf->getNumSamples2() << std::endl; std::cout << "SampledField numSamples3: " << sf->getNumSamples3() << std::endl; const ImageData* id = sf->getImageData(); int* samples = new int[id->getSamplesLength()]; id->getSamples(samples); std::cout << "ImageData samples[0]: " << samples[0] << std::endl; std::cout << "ImageData dtype: " << id->getDataType() << std::endl; std::cout << "ImageData samplesLen: " << id->getSamplesLength() << std::endl; // sampledVolVol from sfGeom. SampledVolume* sv = sfGeom->getSampledVolume(0); std::cout << "SampledVol Id: " << sv->getId() << std::endl; std::cout << "SampledVol domainType: " << sv->getDomainType() << std::endl; std::cout << "SampledVol sampledVal: " << sv->getSampledValue() << std::endl; std::cout << "SampledVol min: " << sv->getMinValue() << std::endl; std::cout << "SampledVol max: " << sv->getMaxValue() << std::endl; } } delete document2; }
END_TEST START_TEST (test_SpatialExtension_read_L3V1V1_defaultNS) { string file = TestDataDirectory; file += "/read_L3V1V1_defaultNS.xml"; SBMLDocument *document = readSBMLFromFile(file.c_str()); string sbmlDoc = writeSBMLToStdString(document); Model *model = document->getModel(); //document->printErrors(); fail_unless(model != NULL); //fail_unless(document->getNumErrors() == 0); // model : compartment fail_unless(model->getNumCompartments() == 1); Compartment *comp = model->getCompartment(0); // compartment : compartmentMapping SpatialCompartmentPlugin* cplugin = static_cast<SpatialCompartmentPlugin*>(comp->getPlugin("spatial")); fail_unless(cplugin != NULL); CompartmentMapping *cMapping = cplugin->getCompartmentMapping(); if (cMapping->isSetId()) { fail_unless(cMapping->getId() == "compMap1"); fail_unless(cMapping->getDomainType() == "dtype1"); fail_unless(cMapping->getUnitSize() == 1); } // model : species 1 fail_unless(model->getNumSpecies() == 2); Species *sp = model->getSpecies(0); SpatialSpeciesPlugin* srplugin = static_cast<SpatialSpeciesPlugin*>(sp->getPlugin("spatial")); fail_unless(srplugin != NULL); fail_unless(srplugin->getIsSpatial() == true); // model : species 2 sp = model->getSpecies(1); srplugin = static_cast<SpatialSpeciesPlugin*>(sp->getPlugin("spatial")); fail_unless(srplugin != NULL); fail_unless(srplugin->getIsSpatial() == true); // model : parameters (species diffusion, advection coeffs, species boundary conditions, coordinate components from Geometry fail_unless(model->getNumParameters() == 5); // parameter 0 : diffusionCoefficient Parameter *param = model->getParameter(0); SpatialParameterPlugin* pplugin = static_cast<SpatialParameterPlugin*>(param->getPlugin("spatial")); fail_unless(pplugin != NULL); fail_unless(pplugin->isSpatialParameter() == true); fail_unless(pplugin->getType() == SBML_SPATIAL_DIFFUSIONCOEFFICIENT); DiffusionCoefficient *diffCoeff = pplugin->getDiffusionCoefficient(); fail_unless(diffCoeff->getVariable() == "ATPc"); fail_unless(diffCoeff->isSetCoordinateReference1()); fail_unless(diffCoeff->getCoordinateReference1() == SPATIAL_COORDINATEKIND_CARTESIAN_X); // parameter 1 : advectionCoefficient param = model->getParameter(1); pplugin = static_cast<SpatialParameterPlugin*>(param->getPlugin("spatial")); fail_unless(pplugin != NULL); fail_unless(pplugin->isSpatialParameter() == true); fail_unless(pplugin->getType() == SBML_SPATIAL_ADVECTIONCOEFFICIENT); AdvectionCoefficient *advCoeff = pplugin->getAdvectionCoefficient(); fail_unless(advCoeff->getVariable() == "ATPc"); fail_unless(advCoeff->getCoordinate() == SPATIAL_COORDINATEKIND_CARTESIAN_X); // parameter 2 : boundaryCondition X param = model->getParameter(2); pplugin = static_cast<SpatialParameterPlugin*>(param->getPlugin("spatial")); fail_unless(pplugin != NULL); fail_unless(pplugin->isSpatialParameter() == true); fail_unless(pplugin->getType() == SBML_SPATIAL_BOUNDARYCONDITION); BoundaryCondition *bc = pplugin->getBoundaryCondition(); fail_unless(bc->getVariable() == "ATPc"); fail_unless(bc->getCoordinateBoundary() == "Xmin"); fail_unless(bc->getType() == SPATIAL_BOUNDARYKIND_DIRICHLET); // parameter 3 : SpatialSymbolReference (coordinateComponent from geometry) param = model->getParameter(3); pplugin = static_cast<SpatialParameterPlugin*>(param->getPlugin("spatial")); fail_unless(pplugin != NULL); SpatialSymbolReference *spSymRef = pplugin->getSpatialSymbolReference(); fail_unless(spSymRef->getSpatialRef() == "coordComp1"); // model : reaction fail_unless(model->getNumReactions() == 1); Reaction *rxn = model->getReaction(0); SpatialReactionPlugin* rplugin = static_cast<SpatialReactionPlugin*>(rxn->getPlugin("spatial")); fail_unless(rplugin != NULL); fail_unless(rplugin->getIsLocal() == true); // get the Geometry SpatialModelPlugin* mplugin = static_cast<SpatialModelPlugin*>(model->getPlugin("spatial")); fail_unless(mplugin != NULL); Geometry *geometry = mplugin->getGeometry(); fail_unless(geometry != NULL); fail_unless(geometry->getPackageName() == "spatial"); fail_unless(geometry->getCoordinateSystem() == SPATIAL_GEOMETRYKIND_CARTESIAN); // geometry coordinateComponent fail_unless(geometry->getNumCoordinateComponents() == 1); fail_unless(geometry->getListOfCoordinateComponents()->getPackageName() == "spatial"); CoordinateComponent* coordComp = geometry->getCoordinateComponent(0); fail_unless(coordComp->getId() == "coordComp1"); fail_unless(coordComp->getType() == SPATIAL_COORDINATEKIND_CARTESIAN_X); fail_unless(coordComp->getUnit() == "umeter"); fail_unless(coordComp->getPackageName() == "spatial"); // boundaryMin and boundayMax within coordinateComponent Boundary *minX = coordComp->getBoundaryMin(); fail_unless(minX->getId() == "Xmin"); fail_unless(minX->getValue() == 0); fail_unless(minX->getPackageName() == "spatial"); Boundary *maxX = coordComp->getBoundaryMax(); fail_unless(maxX->getId() == "Xmax"); fail_unless(maxX->getValue() == 10); fail_unless(maxX->getPackageName() == "spatial"); // geometry domainType fail_unless(geometry->getNumDomainTypes() == 1); fail_unless(geometry->getListOfDomainTypes()->getPackageName() == "spatial"); DomainType *domainType = geometry->getDomainType(0); fail_unless(domainType->getId() == "dtype1"); fail_unless(domainType->getSpatialDimensions() == 3); fail_unless(domainType->getPackageName() == "spatial"); // geometry domains fail_unless(geometry->getNumDomains() == 2); fail_unless(geometry->getListOfDomains()->getPackageName() == "spatial"); Domain* domain = geometry->getDomain(0); fail_unless(domain->getId() == "domain1"); fail_unless(domain->getDomainType() == "dtype1"); //fail_unless(domain->getImplicit() == false); //fail_unless(domain->getShapeId() == "circle"); fail_unless(domain->getPackageName() == "spatial"); // interiorPoints in Domain fail_unless(domain->getNumInteriorPoints() == 1); fail_unless(domain->getListOfInteriorPoints()->getPackageName() == "spatial"); InteriorPoint* interiorPt = domain->getInteriorPoint(0); fail_unless(interiorPt->getCoord1() == 1); fail_unless(interiorPt->getPackageName() == "spatial"); // second domain in geometry domain = geometry->getDomain(1); fail_unless(domain->getId() == "domain2"); fail_unless(domain->getDomainType() == "dtype1"); //fail_unless(domain->getImplicit() == false); //fail_unless(domain->getShapeId() == "square"); fail_unless(domain->getPackageName() == "spatial"); // Domain : interiorPoints fail_unless(domain->getNumInteriorPoints() == 1); fail_unless(domain->getListOfInteriorPoints()->getPackageName() == "spatial"); interiorPt = domain->getInteriorPoint(0); fail_unless(interiorPt->getCoord1() == 5); fail_unless(interiorPt->getPackageName() == "spatial"); // geometry adjacentDomains fail_unless(geometry->getNumAdjacentDomains() == 1); fail_unless(geometry->getListOfAdjacentDomains()->getPackageName() == "spatial"); AdjacentDomains* adjDomain = geometry->getAdjacentDomains(0); fail_unless(adjDomain->getId() == "adjDomain1"); fail_unless(adjDomain->getDomain1() == "domain1"); fail_unless(adjDomain->getDomain2() == "domain2"); fail_unless(adjDomain->getPackageName() == "spatial"); // geometry : geometryDefinitions fail_unless(geometry->getNumGeometryDefinitions() == 2); fail_unless(geometry->getListOfGeometryDefinitions()->getPackageName() == "spatial"); GeometryDefinition *gd = geometry->getGeometryDefinition(0); AnalyticGeometry *analyticGeom = static_cast<AnalyticGeometry*>(gd); fail_unless(analyticGeom->getId() == "analyticGeom1"); fail_unless(analyticGeom->getPackageName() == "spatial"); // AnalyticGeometry : analyticVolumes fail_unless(analyticGeom->getNumAnalyticVolumes() == 1); fail_unless(analyticGeom->getListOfAnalyticVolumes()->getPackageName() == "spatial"); AnalyticVolume* av = analyticGeom->getAnalyticVolume(0); fail_unless(av->getId() == "analyticVol1"); fail_unless(av->getDomainType() == "dtype1"); fail_unless(av->getFunctionType() == SPATIAL_FUNCTIONKIND_LAYERED); fail_unless(av->getOrdinal() == 1); fail_unless(av->getPackageName() == "spatial"); // ??????Math???? // geometry : sampledFieldGeometry gd = geometry->getGeometryDefinition(1); SampledFieldGeometry* sfGeom = static_cast<SampledFieldGeometry*>(gd); fail_unless(sfGeom->getId() == "sampledFieldGeom1"); fail_unless(sfGeom->getPackageName() == "spatial"); // sampledFieldGeometry : SampledVolumes fail_unless(sfGeom->getNumSampledVolumes() == 1); fail_unless(sfGeom->getListOfSampledVolumes()->getPackageName() == "spatial"); SampledVolume* sv = sfGeom->getSampledVolume(0); fail_unless(sv->getId() == "sv_1"); fail_unless(sv->getDomainType() == "dtype1"); fail_unless(sv->getSampledValue() == 128); fail_unless(sv->getMinValue() == 0); fail_unless(sv->getMaxValue() == 255); fail_unless(sv->getPackageName() == "spatial"); // sampledFieldGeometry : SampledField SampledField* sf = geometry->getSampledField( sfGeom->getSampledField() ); fail_unless(sf->getId() == "sampledField1"); fail_unless(sf->getDataType() == SPATIAL_DATAKIND_UINT8); fail_unless(sf->getInterpolationType() == SPATIAL_INTERPOLATIONKIND_LINEAR); fail_unless(sf->getCompression() == SPATIAL_COMPRESSIONKIND_UNCOMPRESSED); fail_unless(sf->getNumSamples1() == 4); fail_unless(sf->getNumSamples2() == 4); fail_unless(sf->getNumSamples3() == 2); fail_unless(sf->getPackageName() == "spatial"); // sampledField : ImageData fail_unless(sf->getSamplesLength() == 32); int* samples = new int[sf->getSamplesLength()]; sf->getSamples(samples); fail_unless(samples[0] == 0); string s2 = writeSBMLToStdString(document); fail_unless(sbmlDoc==s2); delete document; delete[] samples; }