コード例 #1
0
/*
 * Copy constructor.
 */
SampledFieldGeometry::SampledFieldGeometry(const SampledFieldGeometry& source) : GeometryDefinition(source)
{
  this->setSpatialId(source.getSpatialId());
  this->mSampledVolumes = source.mSampledVolumes;

  if (source.mSampledField)
  {
	  mSampledField = static_cast<SampledField*>( source.mSampledField->clone() );
  }

  connectToChild();
}
コード例 #2
0
void readSpatialSBML() {
	SBMLDocument *document2 = readSBML("spatial_example0.xml");
  
	Model *model2 = document2->getModel();
	Compartment *comp;
	SpatialCompartmentPlugin* cplugin;
	RequiredElementsSBasePlugin* reqplugin;
	for (unsigned int i = 0; i < model2->getNumCompartments(); i++) {
		comp = model2->getCompartment(i);
		cout << "Compartment" << i << ": "  << comp->getId() << endl;
		reqplugin = static_cast<RequiredElementsSBasePlugin*>(comp->getPlugin("req"));
		if (!reqplugin->getMathOverridden().empty()) {
			cout << "Comp" << i << "  req mathOverridden: "  << reqplugin->getMathOverridden() << endl;
		}
		cplugin = static_cast<SpatialCompartmentPlugin*>(comp->getPlugin("spatial"));
		if (cplugin->getCompartmentMapping()->isSetSpatialId()) {
			cout << "Comp" << i << "  CMSpId: "  << cplugin->getCompartmentMapping()->getSpatialId() << endl;
			cout << "Comp" << i << "  CM_Comp: "  << cplugin->getCompartmentMapping()->getCompartment() << endl;
			cout << "Comp" << i << "  CM_DType: "  << cplugin->getCompartmentMapping()->getDomainType() << endl;
			cout << "Comp" << i << "  CM_UnitSz: "  << cplugin->getCompartmentMapping()->getUnitSize() << endl;
		}
	}

	Species *sp;
	SpatialSpeciesRxnPlugin* srplugin;
	for (unsigned int i = 0; i < model2->getNumSpecies(); i++) {
		sp = model2->getSpecies(i);
		cout << "Species" << i << ": "      << sp->getId()      << endl;
		srplugin = static_cast<SpatialSpeciesRxnPlugin*>(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;
		reqplugin = static_cast<RequiredElementsSBasePlugin*>(param->getPlugin("req"));
		if (!reqplugin->getMathOverridden().empty()) {
			cout << "Parameter" << i << "  req mathOverridden: "  << reqplugin->getMathOverridden() << endl;
		}
		pplugin = static_cast<SpatialParameterPlugin*>(param->getPlugin("spatial"));
		if (pplugin->getSpatialSymbolReference()->isSetSpatialId()) {
			cout << "Parameter" << i << "  SpRefId: "  << pplugin->getSpatialSymbolReference()->getSpatialId() << endl;
			cout << "Parameter" << i << "  SpRefType: "  << pplugin->getSpatialSymbolReference()->getType() << endl;
		}
		if (pplugin->getDiffusionCoefficient()->isSetVariable()) {
			cout << "Diff_" << i << "  SpeciesVarId: "  << pplugin->getDiffusionCoefficient()->getVariable() << endl;
			cout << "Diff_" << i << "  SpCoordIndex: "  << pplugin->getDiffusionCoefficient()->getCoordinateIndex() << endl;
		}
		if (pplugin->getAdvectionCoefficient()->isSetVariable()) {
			cout << "Adv_" << i << "  SpeciesVarId: "  << pplugin->getAdvectionCoefficient()->getVariable() << endl;
			cout << "Adv_" << i << "  SpCoordIndex: "  << pplugin->getAdvectionCoefficient()->getCoordinateIndex() << endl;
		}
		if (pplugin->getBoundaryCondition()->isSetVariable()) {
			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;
	for (unsigned int i = 0; i < model2->getNumReactions(); i++) {
		rxn = model2->getReaction(i);
		cout << "Reaction" << i << ": "      << rxn->getId()      << endl;
		srplugin = static_cast<SpatialSpeciesRxnPlugin*>(rxn->getPlugin("spatial"));
		if (srplugin->getIsLocal()) {
			cout << "rxn" << i << "  isLocal: "  << srplugin->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 spatialId: " << coordComp->getSpatialId() << std::endl;
	std::cout << "CoordComponent compType: " << coordComp->getComponentType() << std::endl;
	std::cout << "CoordComponent sbmlUnit: " << coordComp->getSbmlUnit() << std::endl;
	std::cout << "CoordComponent index: " << coordComp->getIndex() << std::endl;
	BoundaryMin* minX = coordComp->getBoundaryMin();
	std::cout << "minX name: " << minX->getSpatialId() << std::endl;
	std::cout << "minX value: " << minX->getValue() << std::endl;
	BoundaryMax* maxX = coordComp->getBoundaryMax();
	std::cout << "maxX name: " << maxX->getSpatialId() << 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 spatialId: " << domainType2->getSpatialId() << std::endl;
	std::cout << "DomainType spatialDim: " << domainType2->getSpatialDimensions() << std::endl;

	// get a Domain object via the Geometry object.	
	Domain* domain = geometry2->getDomain(0);
	std::cout << "Domain1 spatialId: " << domain->getSpatialId() << std::endl;
	std::cout << "Domain1 implicit: " << domain->getImplicit() << std::endl;
	std::cout << "Domain1 domainType: " << domain->getDomainType() << std::endl;
	std::cout << "Domain1 Shape: " << domain->getShapeId() << 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 spatialId: " << domain->getSpatialId() << std::endl;
	std::cout << "Domain2 implicit: " << domain->getImplicit() << std::endl;
	std::cout << "Domain2 domainType: " << domain->getDomainType() << std::endl;
	std::cout << "Domain2 Shape: " << domain->getShapeId() << 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 spatialId: " << adjDomain->getSpatialId() << std::endl;
	std::cout << "AdjDomain domain1: " << adjDomain->getDomain1() << std::endl;
	std::cout << "AdjDomain domain2: " << adjDomain->getDomain2() << std::endl;

	// get the different GeometryDefinition objects 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 spatialId: " << analyticalGeom->getSpatialId() << std::endl;

			// analVol from analGeom.
			AnalyticVolume* av = analyticalGeom->getAnalyticVolume(0);
			std::cout << "AnalVol spatialId: " << av->getSpatialId() << 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 spatialId: " << sfGeom->getSpatialId() << std::endl;
			
			// sampledField from sfGeom
			SampledField* sf = sfGeom->getSampledField();
			std::cout << "SampledField spatialId: " << sf->getSpatialId() << 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 samplesLen: " << id->getSamplesLength() << std::endl;
			std::cout << "ImageData dataType: " << id->getDataType() << std::endl;

			// sampledVolVol from sfGeom.
			SampledVolume* sv = sfGeom->getSampledVolume(0);
			std::cout << "SampledVol spatialId: " << sv->getSpatialId() << 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;
		}
		if (gd->isParametricGeometry()) {
			ParametricGeometry* pGeom = static_cast<ParametricGeometry*>(gd);
			std::cout << "ParametricGeometry spatialId: " << pGeom->getSpatialId() << std::endl;
			
			// parametricObject from pGeom
			ParametricObject* pObj = pGeom->getParametricObject(0);
			std::cout << "ParametricObj spatialId: " << pObj->getSpatialId() << std::endl;
			std::cout << "ParametricObj domain: " << pObj->getDomain() << std::endl;
			std::cout << "ParametricObj polygonType: " << pObj->getPolygonType() << std::endl;
			const PolygonObject* po = pObj->getPolygonObject();
			int* ptInd = new int[po->getIndicesLength()];
			po->getPointIndices(ptInd);
			std::cout << "PolygonObj ptIndices[0]: " << ptInd[0] << std::endl;
			std::cout << "PolygonObj indLen: " << po->getIndicesLength() << std::endl;

			// SpatialPoint from pGeom.
			SpatialPoint* sp = pGeom->getSpatialPoint(0);
			std::cout << "SpatialPt spatialId: " << sp->getSpatialId() << std::endl;
			std::cout << "SpatialPt domain: " << sp->getDomain() << std::endl;
			std::cout << "SpatialPt coord1: " << sp->getCoord1() << std::endl;
			std::cout << "SpatialPt coord2: " << sp->getCoord2() << std::endl;
			std::cout << "SpatialPt coord3: " << sp->getCoord3() << std::endl;
		}
		if (gd->isCSGeometry()) {
			CSGeometry* csGeom = static_cast<CSGeometry*>(gd);
			std::cout << "CSGeometry spatialId: " << csGeom->getSpatialId() << std::endl;
			
			// CSGObject-CSGOperator from csGeom
			CSGObject* csgo;
			for (unsigned int i = 0; i < csGeom->getNumCSGObjects(); i++) {
				csgo = csGeom->getCSGObject(i);
				std::cout << "CSGObject spatialId: " << csgo->getSpatialId() << std::endl;
				std::cout << "CSGObject domainType: " << csgo->getDomainType() << std::endl;
				const CSGNode* csgnode = csgo->getCSGNodeRoot();
				if (csgnode->isCSGTransformation()) {
					CSGTransformation* transf = (CSGTransformation*)csgnode;
					if (transf->isCSGScale()) {
						CSGScale* scale = static_cast<CSGScale*>(transf);
						std::cout << "CSGScale scaleX: " << scale->getScaleX() << std::endl;
						std::cout << "CSGScale scaleY: " << scale->getScaleY() << std::endl;
						std::cout << "CSGScale scaleZ: " << scale->getScaleZ() << std::endl;
						const CSGNode* scaleChild = scale->getChild();
						if (scaleChild->isCSGPrimitive()) {
							CSGPrimitive* prim = (CSGPrimitive*)scaleChild;
							std::cout << "CSGPrimitive primitiveType: " << prim->getPrimitiveType() << std::endl;
						}
					}
				}
				if (csgnode->isCSGSetOperator()) {
					CSGSetOperator* setop = (CSGSetOperator*)(csgnode);
					std::cout << "CSGSetOperator opType: " << setop->getOperationType() << std::endl;
					for (unsigned int k = 0; k < setop->getNumCSGNodeChildren(); k++) {
						CSGNode* csgNode = setop->getCSGNodeChild(k);
						std::cout << "CSGNode type: " << csgNode->getTypeCode() << std::endl;
					}
				}
			}
		}
	}

	delete document2;
}