Examples with Model cbit.vcell.model.Model used on opensource projects

Example 16 with Model

use of cbit.vcell.model.Model in project vcell by virtualcell.

the class SBPAXParameterExtractor method extractParameter.

public static Map<SBOTerm, ModelParameter> extractParameter(ReactionStep reaction, SBMeasurable measurable) throws PropertyVetoException {
    Map<SBOTerm, ModelParameter> sboToParameters = new HashMap<SBOTerm, ModelParameter>();
    Set<SBOTerm> sboTerms = SBPAXSBOExtractor.extractSBOTerms(measurable);
    String symbol = null;
    VCUnitDefinition targetUnit = null;
    Model model = reaction.getModel();
    ModelUnitSystem modelUnitSystem = model.getUnitSystem();
    Set<SBOTerm> termsWithUnituM = SetUtil.newSet(SBOList.sbo0000027MichaelisConstant, SBOList.sbo0000322MichaelisConstantForSubstrate);
    for (SBOTerm sboTerm : sboTerms) {
        if (termsWithUnituM.contains(sboTerm)) {
            targetUnit = modelUnitSystem.getVolumeConcentrationUnit();
        // targetUnit = VCUnitDefinition.UNIT_uM;
        }
        if (StringUtil.notEmpty(sboTerm.getSymbol())) {
            symbol = sboTerm.getSymbol();
        }
        for (int i = 0; i < symbol.length(); ++i) {
            char charAt = symbol.charAt(i);
            if (!Character.isJavaIdentifierPart(charAt)) {
                symbol = symbol.replace(charAt, '_');
            }
        }
    }
    VCUnitDefinition unit = UOMEUnitExtractor.extractVCUnitDefinition(measurable, modelUnitSystem);
    double conversionFactor = 1.0;
    if (targetUnit != null && unit != null && unit != modelUnitSystem.getInstance_TBD() && !targetUnit.equals(unit)) {
        // if(unit.equals(VCUnitDefinition.UNIT_M) && targetUnit.equals(VCUnitDefinition.UNIT_uM)) {
        if (unit.isCompatible(targetUnit)) {
            conversionFactor = unit.convertTo(conversionFactor, targetUnit);
            unit = targetUnit;
        }
    }
    ArrayList<Double> numbers = measurable.getNumber();
    if (StringUtil.isEmpty(symbol)) {
        symbol = "p" + (++nParameter);
    }
    for (Double number : numbers) {
        String parameterName = symbol + "_" + reaction.getName();
        if (model.getModelParameter(parameterName) != null) {
            int count = 0;
            while (model.getModelParameter(parameterName + "_" + count) != null) {
                ++count;
            }
            parameterName = parameterName + "_" + count;
        }
        ModelParameter parameter = model.new ModelParameter(parameterName, new Expression(conversionFactor * number.doubleValue()), Model.ROLE_UserDefined, unit);
        model.addModelParameter(parameter);
        for (SBOTerm sboTerm : sboTerms) {
            sboToParameters.put(sboTerm, parameter);
        }
    }
    return sboToParameters;
}

Example 17 with Model

use of cbit.vcell.model.Model in project vcell by virtualcell.

the class StochMathMapping method refreshMathDescription.

/**
 * set up a math description based on current simulationContext.
 */
@Override
protected void refreshMathDescription() throws MappingException, MatrixException, MathException, ExpressionException, ModelException {
    // use local variable instead of using getter all the time.
    SimulationContext simContext = getSimulationContext();
    GeometryClass geometryClass = simContext.getGeometry().getGeometrySpec().getSubVolumes()[0];
    Domain domain = new Domain(geometryClass);
    // local structure mapping list
    StructureMapping[] structureMappings = simContext.getGeometryContext().getStructureMappings();
    // We have to check if all the reactions are able to tranform to stochastic jump processes before generating the math.
    String stochChkMsg = simContext.getModel().isValidForStochApp();
    if (!(stochChkMsg.equals(""))) {
        throw new ModelException("Problem updating math description: " + simContext.getName() + "\n" + stochChkMsg);
    }
    simContext.checkValidity();
    // 
    if (simContext.getGeometry().getDimension() > 0) {
        throw new MappingException("nonspatial stochastic math mapping requires 0-dimensional geometry");
    }
    // 
    for (int i = 0; i < structureMappings.length; i++) {
        if (structureMappings[i] instanceof MembraneMapping) {
            if (((MembraneMapping) structureMappings[i]).getCalculateVoltage()) {
                throw new MappingException("electric potential not yet supported for particle models");
            }
        }
    }
    // 
    // fail if any events
    // 
    BioEvent[] bioEvents = simContext.getBioEvents();
    if (bioEvents != null && bioEvents.length > 0) {
        throw new MappingException("events not yet supported for particle-based models");
    }
    // 
    // verify that all structures are mapped to subvolumes and all subvolumes are mapped to a structure
    // 
    Structure[] structures = simContext.getGeometryContext().getModel().getStructures();
    for (int i = 0; i < structures.length; i++) {
        StructureMapping sm = simContext.getGeometryContext().getStructureMapping(structures[i]);
        if (sm == null || (sm instanceof FeatureMapping && ((FeatureMapping) sm).getGeometryClass() == null)) {
            throw new MappingException("model structure '" + structures[i].getName() + "' not mapped to a geometry subVolume");
        }
        if (sm != null && (sm instanceof MembraneMapping) && ((MembraneMapping) sm).getVolumeFractionParameter() != null) {
            Expression volFractExp = ((MembraneMapping) sm).getVolumeFractionParameter().getExpression();
            try {
                if (volFractExp != null) {
                    double volFract = volFractExp.evaluateConstant();
                    if (volFract >= 1.0) {
                        throw new MappingException("model structure '" + (getSimulationContext().getModel().getStructureTopology().getInsideFeature(((MembraneMapping) sm).getMembrane()).getName() + "' has volume fraction >= 1.0"));
                    }
                }
            } catch (ExpressionException e) {
                e.printStackTrace(System.out);
            }
        }
    }
    SubVolume[] subVolumes = simContext.getGeometryContext().getGeometry().getGeometrySpec().getSubVolumes();
    for (int i = 0; i < subVolumes.length; i++) {
        Structure[] mappedStructures = simContext.getGeometryContext().getStructuresFromGeometryClass(subVolumes[i]);
        if (mappedStructures == null || mappedStructures.length == 0) {
            throw new MappingException("geometry subVolume '" + subVolumes[i].getName() + "' not mapped from a model structure");
        }
    }
    // 
    // gather only those reactionSteps that are not "excluded"
    // 
    ReactionSpec[] reactionSpecs = simContext.getReactionContext().getReactionSpecs();
    Vector<ReactionStep> rsList = new Vector<ReactionStep>();
    for (int i = 0; i < reactionSpecs.length; i++) {
        if (!reactionSpecs[i].isExcluded()) {
            rsList.add(reactionSpecs[i].getReactionStep());
        }
    }
    // 
    for (ReactionStep reactionStep : rsList) {
        Kinetics.UnresolvedParameter[] unresolvedParameters = reactionStep.getKinetics().getUnresolvedParameters();
        if (unresolvedParameters != null && unresolvedParameters.length > 0) {
            StringBuffer buffer = new StringBuffer();
            for (int j = 0; j < unresolvedParameters.length; j++) {
                if (j > 0) {
                    buffer.append(", ");
                }
                buffer.append(unresolvedParameters[j].getName());
            }
            throw new MappingException("In Application '" + simContext.getName() + "', " + reactionStep.getDisplayType() + " '" + reactionStep.getName() + "' contains unresolved identifier(s): " + buffer);
        }
    }
    // 
    // create new MathDescription (based on simContext's previous MathDescription if possible)
    // 
    MathDescription oldMathDesc = simContext.getMathDescription();
    mathDesc = null;
    if (oldMathDesc != null) {
        if (oldMathDesc.getVersion() != null) {
            mathDesc = new MathDescription(oldMathDesc.getVersion());
        } else {
            mathDesc = new MathDescription(oldMathDesc.getName());
        }
    } else {
        mathDesc = new MathDescription(simContext.getName() + "_generated");
    }
    // 
    // temporarily place all variables in a hashtable (before binding) and discarding duplicates
    // 
    VariableHash varHash = new VariableHash();
    // 
    // conversion factors
    // 
    Model model = simContext.getModel();
    varHash.addVariable(new Constant(getMathSymbol(model.getKMOLE(), null), getIdentifierSubstitutions(model.getKMOLE().getExpression(), model.getKMOLE().getUnitDefinition(), null)));
    varHash.addVariable(new Constant(getMathSymbol(model.getN_PMOLE(), null), getIdentifierSubstitutions(model.getN_PMOLE().getExpression(), model.getN_PMOLE().getUnitDefinition(), null)));
    varHash.addVariable(new Constant(getMathSymbol(model.getPI_CONSTANT(), null), getIdentifierSubstitutions(model.getPI_CONSTANT().getExpression(), model.getPI_CONSTANT().getUnitDefinition(), null)));
    varHash.addVariable(new Constant(getMathSymbol(model.getFARADAY_CONSTANT(), null), getIdentifierSubstitutions(model.getFARADAY_CONSTANT().getExpression(), model.getFARADAY_CONSTANT().getUnitDefinition(), null)));
    varHash.addVariable(new Constant(getMathSymbol(model.getFARADAY_CONSTANT_NMOLE(), null), getIdentifierSubstitutions(model.getFARADAY_CONSTANT_NMOLE().getExpression(), model.getFARADAY_CONSTANT_NMOLE().getUnitDefinition(), null)));
    varHash.addVariable(new Constant(getMathSymbol(model.getGAS_CONSTANT(), null), getIdentifierSubstitutions(model.getGAS_CONSTANT().getExpression(), model.getGAS_CONSTANT().getUnitDefinition(), null)));
    varHash.addVariable(new Constant(getMathSymbol(model.getTEMPERATURE(), null), getIdentifierSubstitutions(new Expression(simContext.getTemperatureKelvin()), model.getTEMPERATURE().getUnitDefinition(), null)));
    Enumeration<SpeciesContextMapping> enum1 = getSpeciesContextMappings();
    while (enum1.hasMoreElements()) {
        SpeciesContextMapping scm = enum1.nextElement();
        if (scm.getVariable() instanceof StochVolVariable) {
            varHash.addVariable(scm.getVariable());
        }
    }
    // deals with model parameters
    ModelParameter[] modelParameters = simContext.getModel().getModelParameters();
    for (int j = 0; j < modelParameters.length; j++) {
        Expression expr = getSubstitutedExpr(modelParameters[j].getExpression(), true, false);
        expr = getIdentifierSubstitutions(expr, modelParameters[j].getUnitDefinition(), geometryClass);
        varHash.addVariable(newFunctionOrConstant(getMathSymbol(modelParameters[j], geometryClass), expr, geometryClass));
    }
    // added July 2009, ElectricalStimulusParameter electric mapping tab
    ElectricalStimulus[] elecStimulus = simContext.getElectricalStimuli();
    if (elecStimulus.length > 0) {
        throw new MappingException("Modles with electrophysiology are not supported for stochastic applications.");
    }
    for (int j = 0; j < structureMappings.length; j++) {
        if (structureMappings[j] instanceof MembraneMapping) {
            MembraneMapping memMapping = (MembraneMapping) structureMappings[j];
            Parameter initialVoltageParm = memMapping.getInitialVoltageParameter();
            try {
                Expression exp = initialVoltageParm.getExpression();
                exp.evaluateConstant();
                varHash.addVariable(newFunctionOrConstant(getMathSymbol(memMapping.getMembrane().getMembraneVoltage(), memMapping.getGeometryClass()), getIdentifierSubstitutions(memMapping.getInitialVoltageParameter().getExpression(), memMapping.getInitialVoltageParameter().getUnitDefinition(), memMapping.getGeometryClass()), memMapping.getGeometryClass()));
            } catch (ExpressionException e) {
                e.printStackTrace(System.out);
                throw new MappingException("Membrane initial voltage: " + initialVoltageParm.getName() + " cannot be evaluated as constant.");
            }
        }
    }
    // 
    for (ReactionStep rs : rsList) {
        if (rs.getKinetics() instanceof LumpedKinetics) {
            throw new RuntimeException("Lumped Kinetics not yet supported for Stochastic Math Generation");
        }
        Kinetics.KineticsParameter[] parameters = rs.getKinetics().getKineticsParameters();
        for (KineticsParameter parameter : parameters) {
            // 
            if ((parameter.getRole() == Kinetics.ROLE_CurrentDensity) && (parameter.getExpression() == null || parameter.getExpression().isZero())) {
                continue;
            }
            // 
            // don't add rate, we'll do it later when creating the jump processes
            // 
            // if (parameter.getRole() == Kinetics.ROLE_ReactionRate) {
            // continue;
            // }
            // 
            // don't add mass action reverse parameter if irreversible
            // 
            // if (!rs.isReversible() && parameters[i].getRole() == Kinetics.ROLE_KReverse){
            // continue;
            // }
            Expression expr = getSubstitutedExpr(parameter.getExpression(), true, false);
            varHash.addVariable(newFunctionOrConstant(getMathSymbol(parameter, geometryClass), getIdentifierSubstitutions(expr, parameter.getUnitDefinition(), geometryClass), geometryClass));
        }
    }
    // the parameter "Size" is already put into mathsymbolmapping in refreshSpeciesContextMapping()
    for (int i = 0; i < structureMappings.length; i++) {
        StructureMapping sm = structureMappings[i];
        StructureMapping.StructureMappingParameter parm = sm.getParameterFromRole(StructureMapping.ROLE_Size);
        if (parm.getExpression() != null) {
            try {
                double value = parm.getExpression().evaluateConstant();
                varHash.addVariable(new Constant(getMathSymbol(parm, sm.getGeometryClass()), new Expression(value)));
            } catch (ExpressionException e) {
                // varHash.addVariable(new Function(getMathSymbol0(parm,sm),getIdentifierSubstitutions(parm.getExpression(),parm.getUnitDefinition(),sm)));
                e.printStackTrace(System.out);
                throw new MappingException("Size of structure:" + sm.getNameScope().getName() + " cannot be evaluated as constant.");
            }
        }
    }
    SpeciesContextSpec[] speciesContextSpecs = getSimulationContext().getReactionContext().getSpeciesContextSpecs();
    addInitialConditions(domain, speciesContextSpecs, varHash);
    // 
    // constant species (either function or constant)
    // 
    enum1 = getSpeciesContextMappings();
    while (enum1.hasMoreElements()) {
        SpeciesContextMapping scm = (SpeciesContextMapping) enum1.nextElement();
        if (scm.getVariable() instanceof Constant) {
            varHash.addVariable(scm.getVariable());
        }
    }
    // 
    if (simContext.getGeometryContext().getGeometry() != null) {
        try {
            mathDesc.setGeometry(simContext.getGeometryContext().getGeometry());
        } catch (java.beans.PropertyVetoException e) {
            e.printStackTrace(System.out);
            throw new MappingException("failure setting geometry " + e.getMessage());
        }
    } else {
        throw new MappingException("Geometry must be defined in Application " + simContext.getName());
    }
    // 
    // create subDomains
    // 
    SubVolume subVolume = simContext.getGeometry().getGeometrySpec().getSubVolumes()[0];
    SubDomain subDomain = new CompartmentSubDomain(subVolume.getName(), 0);
    mathDesc.addSubDomain(subDomain);
    // 
    // functions: species which is not a variable, but has dependency expression
    // 
    enum1 = getSpeciesContextMappings();
    while (enum1.hasMoreElements()) {
        SpeciesContextMapping scm = (SpeciesContextMapping) enum1.nextElement();
        if (scm.getVariable() == null && scm.getDependencyExpression() != null) {
            StructureMapping sm = simContext.getGeometryContext().getStructureMapping(scm.getSpeciesContext().getStructure());
            Expression exp = scm.getDependencyExpression();
            exp.bindExpression(this);
            SpeciesCountParameter spCountParam = getSpeciesCountParameter(scm.getSpeciesContext());
            varHash.addVariable(new Function(getMathSymbol(spCountParam, sm.getGeometryClass()), getIdentifierSubstitutions(exp, spCountParam.getUnitDefinition(), sm.getGeometryClass()), domain));
        }
    }
    addJumpProcesses(varHash, geometryClass, subDomain);
    // 
    for (int i = 0; i < fieldMathMappingParameters.length; i++) {
        if (fieldMathMappingParameters[i] instanceof UnitFactorParameter) {
            varHash.addVariable(newFunctionOrConstant(getMathSymbol(fieldMathMappingParameters[i], geometryClass), getIdentifierSubstitutions(fieldMathMappingParameters[i].getExpression(), fieldMathMappingParameters[i].getUnitDefinition(), geometryClass), fieldMathMappingParameters[i].getGeometryClass()));
        }
    }
    // 
    // set Variables to MathDescription all at once with the order resolved by "VariableHash"
    // 
    mathDesc.setAllVariables(varHash.getAlphabeticallyOrderedVariables());
    // 
    // set up variable initial conditions in subDomain
    // 
    SpeciesContextSpec[] scSpecs = simContext.getReactionContext().getSpeciesContextSpecs();
    for (int i = 0; i < speciesContextSpecs.length; i++) {
        // get stochastic variable by name
        SpeciesCountParameter spCountParam = getSpeciesCountParameter(speciesContextSpecs[i].getSpeciesContext());
        StructureMapping sm = simContext.getGeometryContext().getStructureMapping(speciesContextSpecs[i].getSpeciesContext().getStructure());
        String varName = getMathSymbol(spCountParam, sm.getGeometryClass());
        StochVolVariable var = (StochVolVariable) mathDesc.getVariable(varName);
        // stochastic use initial number of particles
        SpeciesContextSpec.SpeciesContextSpecParameter initParm = scSpecs[i].getInitialCountParameter();
        // stochastic variables initial expression.
        if (initParm != null) {
            VarIniCondition varIni = null;
            if (!scSpecs[i].isConstant() && getSimulationContext().isRandomizeInitCondition()) {
                varIni = new VarIniPoissonExpectedCount(var, new Expression(getMathSymbol(initParm, sm.getGeometryClass())));
            } else {
                varIni = new VarIniCount(var, new Expression(getMathSymbol(initParm, sm.getGeometryClass())));
            }
            subDomain.addVarIniCondition(varIni);
        }
    }
    // 
    for (int i = 0; i < fieldMathMappingParameters.length; i++) {
        if (fieldMathMappingParameters[i] instanceof UnitFactorParameter) {
            Variable variable = newFunctionOrConstant(getMathSymbol(fieldMathMappingParameters[i], geometryClass), getIdentifierSubstitutions(fieldMathMappingParameters[i].getExpression(), fieldMathMappingParameters[i].getUnitDefinition(), geometryClass), fieldMathMappingParameters[i].getGeometryClass());
            if (mathDesc.getVariable(variable.getName()) == null) {
                mathDesc.addVariable(variable);
            }
        }
        if (fieldMathMappingParameters[i] instanceof ObservableCountParameter) {
            Variable variable = newFunctionOrConstant(getMathSymbol(fieldMathMappingParameters[i], geometryClass), getIdentifierSubstitutions(fieldMathMappingParameters[i].getExpression(), fieldMathMappingParameters[i].getUnitDefinition(), geometryClass), fieldMathMappingParameters[i].getGeometryClass());
            if (mathDesc.getVariable(variable.getName()) == null) {
                mathDesc.addVariable(variable);
            }
        }
    }
    if (!mathDesc.isValid()) {
        System.out.println(mathDesc.getVCML_database());
        throw new MappingException("generated an invalid mathDescription: " + mathDesc.getWarning());
    }
}

Example 18 with Model

use of cbit.vcell.model.Model in project vcell by virtualcell.

the class StructureAnalyzer method refreshTotalSpeciesContextMappings.

/**
 * This method was created in VisualAge.
 */
private void refreshTotalSpeciesContextMappings() throws java.beans.PropertyVetoException {
    if (structures == null) {
        return;
    }
    // System.out.println("StructureAnalyzer.refreshSpeciesContextMappings()");
    // GeometryContext geoContext = mathMapping.getSimulationContext().getGeometryContext();
    SimulationContext simContext = mathMapping.getSimulationContext();
    Model model = simContext.getReactionContext().getModel();
    // 
    // note, the order of species is specified such that the first species have priority
    // when the null space is solved for dependent variables.  So the order of priority
    // for elimination are as follows:
    // 
    // 1) Species involved with fast reactions.
    // 2) Species not involved with fast reactions.
    // 
    Vector<SpeciesContextMapping> scmList = new Vector<SpeciesContextMapping>();
    // 
    for (int i = 0; i < structures.length; i++) {
        SpeciesContext[] speciesContexts = model.getSpeciesContexts(structures[i]);
        for (int j = 0; j < speciesContexts.length; j++) {
            SpeciesContext sc = speciesContexts[j];
            SpeciesContextMapping scm = mathMapping.getSpeciesContextMapping(sc);
            SpeciesContextSpec scs = simContext.getReactionContext().getSpeciesContextSpec(sc);
            if (scm.isFastParticipant() && !scs.isConstant()) {
                scmList.addElement(scm);
            }
        }
    }
    // 
    for (int i = 0; i < structures.length; i++) {
        SpeciesContext[] speciesContexts = model.getSpeciesContexts(structures[i]);
        for (int j = 0; j < speciesContexts.length; j++) {
            SpeciesContext sc = speciesContexts[j];
            SpeciesContextMapping scm = mathMapping.getSpeciesContextMapping(sc);
            SpeciesContextSpec scs = simContext.getReactionContext().getSpeciesContextSpec(sc);
            if (!scm.isFastParticipant() && !scs.isConstant()) {
                scmList.addElement(scm);
            }
        }
    }
    if (scmList.size() > 0) {
        speciesContextMappings = new SpeciesContextMapping[scmList.size()];
        scmList.copyInto(speciesContextMappings);
        for (int i = 0; i < speciesContextMappings.length; i++) {
            speciesContextMappings[i].setRate(new Expression(0.0));
        // System.out.println("speciesContextMappings["+i+"] = "+speciesContextMappings[i].getSpeciesContext().getName());
        }
    } else {
        speciesContextMappings = null;
    }
    // System.out.println("StructureAnalyzer.refreshTotalSpeciesContextMapping(), speciesContextMappings.length = "+scmList.size());
    // 
    // get all reactionSteps associated with these structures
    // 
    Vector<ReactionStep> rsList = new Vector<ReactionStep>();
    ReactionSpec[] allReactionSpecs = simContext.getReactionContext().getReactionSpecs();
    for (int i = 0; i < allReactionSpecs.length; i++) {
        if (allReactionSpecs[i].isExcluded()) {
            continue;
        }
        ReactionStep rs = allReactionSpecs[i].getReactionStep();
        for (int j = 0; j < structures.length; j++) {
            if (rs.getStructure() == structures[j]) {
                rsList.addElement(rs);
            }
        }
    }
    // 
    for (int i = 0; i < scmList.size(); i++) {
        SpeciesContextMapping scm = (SpeciesContextMapping) scmList.elementAt(i);
        if (!simContext.isUsingMassConservationModelReduction()) {
            // 
            // break mass conservation on all species (disables model reduction).
            // 
            rsList.addElement(new DisableModelReductionReactionStep("DisableModelReductionReactionStep" + i, model, scm.getSpeciesContext().getStructure(), scm.getSpeciesContext()));
        } else {
            // 
            if (scm.isPDERequired() || simContext.getReactionContext().getSpeciesContextSpec(scm.getSpeciesContext()).isWellMixed()) {
                rsList.addElement(new DiffusionDummyReactionStep("DiffusionDummyReactionStep" + i, model, scm.getSpeciesContext().getStructure(), scm.getSpeciesContext()));
            }
            if (scm.hasEventAssignment()) {
                rsList.addElement(new EventDummyReactionStep("EventDummyReactionStep" + i, model, scm.getSpeciesContext().getStructure(), scm.getSpeciesContext()));
            }
            if (scm.hasHybridReaction()) {
                rsList.addElement(new HybridDummyReactionStep("HybridDummyReactionStep" + i, model, scm.getSpeciesContext().getStructure(), scm.getSpeciesContext()));
            }
            if (simContext.isStoch() && simContext.getGeometry().getDimension() > 0 && !simContext.getReactionContext().getSpeciesContextSpec(scm.getSpeciesContext()).isForceContinuous()) {
                rsList.addElement(new ParticleDummyReactionStep("ParticleDummyReactionStep" + i, model, scm.getSpeciesContext().getStructure(), scm.getSpeciesContext()));
            }
        }
    }
    if (rsList.size() > 0) {
        reactionSteps = new ReactionStep[rsList.size()];
        rsList.copyInto(reactionSteps);
    } else {
        reactionSteps = null;
    }
// System.out.println("StructureAnalyzer.refreshTotalSpeciesContextMapping(), reactionSteps.length = "+scmList.size());
}

Example 19 with Model

use of cbit.vcell.model.Model in project vcell by virtualcell.

the class ElectricalCircuitGraph method getCircuitGraph.

/**
 * Insert the method's description here.
 * Creation date: (2/19/2002 11:24:04 AM)
 * @return cbit.vcell.mapping.potential.Graph
 * @param simContext cbit.vcell.mapping.SimulationContext
 */
public static Graph getCircuitGraph(SimulationContext simContext, AbstractMathMapping mathMapping) throws ExpressionException {
    Graph graph = new Graph();
    Model model = simContext.getModel();
    // 
    // add nodes to the graph (one for each Feature)
    // 
    Structure[] structures = model.getStructures();
    for (int i = 0; i < structures.length; i++) {
        if (structures[i] instanceof Feature) {
            graph.addNode(new Node(structures[i].getName(), structures[i]));
        }
    }
    // 
    // add edges for all current clamp electrodes (always have dependent voltages)
    // 
    ElectricalStimulus[] stimuli = simContext.getElectricalStimuli();
    Electrode groundElectrode = simContext.getGroundElectrode();
    for (int i = 0; i < stimuli.length; i++) {
        ElectricalStimulus stimulus = stimuli[i];
        // 
        // get electrodes
        // 
        Electrode probeElectrode = stimulus.getElectrode();
        if (probeElectrode == null) {
            throw new RuntimeException("null electrode for electrical stimulus");
        }
        if (groundElectrode == null) {
            throw new RuntimeException("null ground electrode for electrical stimulus");
        }
        // if (!membraneMapping.getResolved()){
        Node groundNode = graph.getNode(groundElectrode.getFeature().getName());
        Node probeNode = graph.getNode(probeElectrode.getFeature().getName());
        if (stimulus instanceof CurrentDensityClampStimulus) {
            CurrentDensityClampStimulus ccStimulus = (CurrentDensityClampStimulus) stimulus;
            ElectricalDevice device = new CurrentClampElectricalDevice(ccStimulus, mathMapping);
            Edge edge = new Edge(probeNode, groundNode, device);
            graph.addEdge(edge);
        } else if (stimulus instanceof TotalCurrentClampStimulus) {
            TotalCurrentClampStimulus ccStimulus = (TotalCurrentClampStimulus) stimulus;
            ElectricalDevice device = new CurrentClampElectricalDevice(ccStimulus, mathMapping);
            Edge edge = new Edge(probeNode, groundNode, device);
            graph.addEdge(edge);
        }
    // }
    }
    // 
    // add edges for all membranes
    // 
    ElectricalTopology electricalTopology = simContext.getModel().getElectricalTopology();
    for (int i = 0; i < structures.length; i++) {
        if (structures[i] instanceof Membrane) {
            Membrane membrane = (Membrane) structures[i];
            MembraneMapping membraneMapping = (MembraneMapping) simContext.getGeometryContext().getStructureMapping(membrane);
            Feature positiveFeature = electricalTopology.getPositiveFeature(membrane);
            Feature negativeFeature = electricalTopology.getNegativeFeature(membrane);
            if (positiveFeature != null && negativeFeature != null) {
                Node insideNode = graph.getNode(positiveFeature.getName());
                Node outsideNode = graph.getNode(negativeFeature.getName());
                // 
                // getTotalMembraneCurrent() already converts to "outwardCurrent" so that same convention as voltage
                // 
                Expression currentSource = getTotalMembraneCurrent(simContext, membrane, mathMapping);
                MembraneElectricalDevice device = new MembraneElectricalDevice(membraneMapping, mathMapping);
                device.getParameterFromRole(ElectricalDevice.ROLE_TransmembraneCurrent).setExpression(currentSource);
                Edge edge = new Edge(insideNode, outsideNode, device);
                graph.addEdge(edge);
            }
        }
    }
    // 
    for (int i = 0; i < stimuli.length; i++) {
        ElectricalStimulus stimulus = stimuli[i];
        // 
        // get electrodes
        // 
        Electrode probeElectrode = stimulus.getElectrode();
        if (probeElectrode == null) {
            throw new RuntimeException("null electrode for electrical stimulus");
        }
        if (groundElectrode == null) {
            throw new RuntimeException("null ground electrode for electrical stimulus");
        }
        // if (!membraneMapping.getResolved()){
        Node groundNode = graph.getNode(groundElectrode.getFeature().getName());
        Node probeNode = graph.getNode(probeElectrode.getFeature().getName());
        if (stimulus instanceof VoltageClampStimulus) {
            VoltageClampStimulus vcStimulus = (VoltageClampStimulus) stimulus;
            ElectricalDevice device = new VoltageClampElectricalDevice(vcStimulus, mathMapping);
            Edge edge = new Edge(probeNode, groundNode, device);
            graph.addEdge(edge);
        }
    // }
    }
    // System.out.println(graph);
    return graph;
}

Example 20 with Model

use of cbit.vcell.model.Model in project vcell by virtualcell.

the class MathMapping_4_8 method getMathSymbol0.

/**
 * Substitutes appropriate variables for speciesContext bindings
 *
 * @return cbit.vcell.parser.Expression
 * @param origExp cbit.vcell.parser.Expression
 * @param structureMapping cbit.vcell.mapping.StructureMapping
 */
private String getMathSymbol0(SymbolTableEntry ste, StructureMapping structureMapping) throws MappingException {
    String steName = ste.getName();
    if (ste instanceof Kinetics.KineticsParameter) {
        Integer count = localNameCountHash.get(steName);
        if (count == null) {
            throw new MappingException("KineticsParameter " + steName + " not found in local name count");
        }
        if (count > 1 || steName.equals("J")) {
            return steName + "_" + ste.getNameScope().getName();
        // return getNameScope().getSymbolName(ste);
        } else {
            return steName;
        }
    }
    if (ste instanceof MathMapping_4_8.ProbabilityParameter) {
        // be careful here, to see if we need mangle the reaction name
        MathMapping_4_8.ProbabilityParameter probParm = (MathMapping_4_8.ProbabilityParameter) ste;
        return probParm.getName();
    }
    if (ste instanceof MathMapping_4_8.SpeciesConcentrationParameter) {
        MathMapping_4_8.SpeciesConcentrationParameter concParm = (MathMapping_4_8.SpeciesConcentrationParameter) ste;
        return concParm.getSpeciesContextSpec().getSpeciesContext().getName() + MATH_FUNC_SUFFIX_SPECIES_CONCENTRATION;
    }
    if (ste instanceof MathMapping_4_8.SpeciesCountParameter) {
        MathMapping_4_8.SpeciesCountParameter countParm = (MathMapping_4_8.SpeciesCountParameter) ste;
        return countParm.getSpeciesContextSpec().getSpeciesContext().getName() + MATH_VAR_SUFFIX_SPECIES_COUNT;
    }
    if (ste instanceof MathMapping_4_8.EventAssignmentInitParameter) {
        MathMapping_4_8.EventAssignmentInitParameter eventInitParm = (MathMapping_4_8.EventAssignmentInitParameter) ste;
        return eventInitParm.getName() + MATH_FUNC_SUFFIX_EVENTASSIGN_INIT;
    }
    if (ste instanceof Model.ReservedSymbol) {
        return steName;
    }
    if (ste instanceof Membrane.MembraneVoltage) {
        return steName;
    }
    if (ste instanceof Structure.StructureSize) {
        Structure structure = ((Structure.StructureSize) ste).getStructure();
        StructureMapping.StructureMappingParameter sizeParameter = simContext.getGeometryContext().getStructureMapping(structure).getSizeParameter();
        return getMathSymbol(sizeParameter, structureMapping);
    }
    if (ste instanceof ProxyParameter) {
        ProxyParameter pp = (ProxyParameter) ste;
        return getMathSymbol0(pp.getTarget(), structureMapping);
    }
    // 
    Model model = simContext.getModel();
    if (ste instanceof ModelParameter) {
        ModelParameter mp = (ModelParameter) ste;
        if (simContext.getGeometry().getDimension() == 0) {
            return mp.getName();
        } else {
            if (mp.getExpression().getSymbols() == null) {
                return mp.getName();
            }
            // check if global param variant name exists in globalVarsHash. If so, return it, else, throw exception.
            Hashtable<String, Expression> smVariantsHash = globalParamVariantsHash.get(mp);
            String variantName = mp.getName() + "_" + TokenMangler.fixTokenStrict(structureMapping.getStructure().getName());
            if (smVariantsHash.get(variantName) != null) {
                return variantName;
            } else {
                // global param variant doesn't exist in the hash, so get the substituted expression for global param and
                // gather all symbols (speciesContexts) that do not match with arg 'structureMapping' to display a proper error message.
                Expression expr = null;
                try {
                    expr = substituteGlobalParameters(mp.getExpression());
                } catch (ExpressionException e) {
                    e.printStackTrace(System.out);
                    throw new RuntimeException("Could not substitute expression for global parameter '" + mp.getName() + "' with expression '" + "'" + e.getMessage());
                }
                // find symbols (typically speciesContexts) in 'exp' that do not match with the arg 'structureMapping'
                String[] symbols = expr.getSymbols();
                String msg = "";
                if (symbols != null) {
                    Vector<String> spContextNamesVector = new Vector<String>();
                    for (int j = 0; j < symbols.length; j++) {
                        SpeciesContext sc = model.getSpeciesContext(symbols[j]);
                        if (sc != null) {
                            if (!sc.getStructure().compareEqual(structureMapping.getStructure())) {
                                spContextNamesVector.addElement(sc.getName());
                            }
                        }
                    }
                    for (int i = 0; (spContextNamesVector != null && i < spContextNamesVector.size()); i++) {
                        if (i == 0) {
                            msg += "'" + spContextNamesVector.elementAt(i) + ", ";
                        } else if (i == spContextNamesVector.size() - 1) {
                            msg += spContextNamesVector.elementAt(i) + "'";
                        } else {
                            msg += spContextNamesVector.elementAt(i) + ", ";
                        }
                    }
                }
                throw new RuntimeException("Global parameter '" + mp.getName() + "' is not defined in compartment '" + structureMapping.getStructure().getName() + "', but was referenced in that compartment." + "\n\nExpression '" + mp.getExpression().infix() + "' for global parameter '" + mp.getName() + "' expands to '" + expr.infix() + "' " + "and contains species " + msg + " that is/are not in adjacent compartments.");
            }
        // return (mp.getName()+"_"+TokenMangler.fixTokenStrict(structureMapping.getStructure().getName()));
        }
    }
    if (ste instanceof SpeciesContextSpec.SpeciesContextSpecParameter) {
        SpeciesContextSpec.SpeciesContextSpecParameter scsParm = (SpeciesContextSpec.SpeciesContextSpecParameter) ste;
        if (scsParm.getRole() == SpeciesContextSpec.ROLE_InitialConcentration) {
            return ((SpeciesContextSpec) (scsParm.getNameScope().getScopedSymbolTable())).getSpeciesContext().getName() + MATH_FUNC_SUFFIX_SPECIES_INIT_CONCENTRATION;
        }
        if (scsParm.getRole() == SpeciesContextSpec.ROLE_InitialCount) {
            return ((SpeciesContextSpec) (scsParm.getNameScope().getScopedSymbolTable())).getSpeciesContext().getName() + MATH_FUNC_SUFFIX_SPECIES_INIT_COUNT;
        }
        if (scsParm.getRole() == SpeciesContextSpec.ROLE_DiffusionRate) {
            return ((SpeciesContextSpec) (scsParm.getNameScope().getScopedSymbolTable())).getSpeciesContext().getName() + "_diffusionRate";
        }
        if (scsParm.getRole() == SpeciesContextSpec.ROLE_BoundaryValueXm) {
            return ((SpeciesContextSpec) (scsParm.getNameScope().getScopedSymbolTable())).getSpeciesContext().getName() + "_boundaryXm";
        }
        if (scsParm.getRole() == SpeciesContextSpec.ROLE_BoundaryValueXp) {
            return ((SpeciesContextSpec) (scsParm.getNameScope().getScopedSymbolTable())).getSpeciesContext().getName() + "_boundaryXp";
        }
        if (scsParm.getRole() == SpeciesContextSpec.ROLE_BoundaryValueYm) {
            return ((SpeciesContextSpec) (scsParm.getNameScope().getScopedSymbolTable())).getSpeciesContext().getName() + "_boundaryYm";
        }
        if (scsParm.getRole() == SpeciesContextSpec.ROLE_BoundaryValueYp) {
            return ((SpeciesContextSpec) (scsParm.getNameScope().getScopedSymbolTable())).getSpeciesContext().getName() + "_boundaryYp";
        }
        if (scsParm.getRole() == SpeciesContextSpec.ROLE_BoundaryValueZm) {
            return ((SpeciesContextSpec) (scsParm.getNameScope().getScopedSymbolTable())).getSpeciesContext().getName() + "_boundaryZm";
        }
        if (scsParm.getRole() == SpeciesContextSpec.ROLE_BoundaryValueZp) {
            return ((SpeciesContextSpec) (scsParm.getNameScope().getScopedSymbolTable())).getSpeciesContext().getName() + "_boundaryZp";
        }
        if (scsParm.getRole() == SpeciesContextSpec.ROLE_VelocityX) {
            return ((SpeciesContextSpec) (scsParm.getNameScope().getScopedSymbolTable())).getSpeciesContext().getName() + "_velocityX";
        }
        if (scsParm.getRole() == SpeciesContextSpec.ROLE_VelocityY) {
            return ((SpeciesContextSpec) (scsParm.getNameScope().getScopedSymbolTable())).getSpeciesContext().getName() + "_velocityY";
        }
        if (scsParm.getRole() == SpeciesContextSpec.ROLE_VelocityZ) {
            return ((SpeciesContextSpec) (scsParm.getNameScope().getScopedSymbolTable())).getSpeciesContext().getName() + "_velocityZ";
        }
    }
    if (ste instanceof ElectricalDevice.ElectricalDeviceParameter) {
        ElectricalDevice.ElectricalDeviceParameter edParm = (ElectricalDevice.ElectricalDeviceParameter) ste;
        ElectricalDevice electricalDevice = (ElectricalDevice) edParm.getNameScope().getScopedSymbolTable();
        if (electricalDevice instanceof MembraneElectricalDevice) {
            String nameWithScope = ((MembraneElectricalDevice) electricalDevice).getMembraneMapping().getMembrane().getNameScope().getName();
            if (edParm.getRole() == ElectricalDevice.ROLE_TotalCurrent) {
                return "I_" + nameWithScope;
            }
            if (edParm.getRole() == ElectricalDevice.ROLE_TransmembraneCurrent) {
                return "F_" + nameWithScope;
            }
        // }else if (electricalDevice instanceof CurrentClampElectricalDevice) {
        // if (edParm.getRole()==ElectricalDevice.ROLE_TotalCurrentDensity){
        // return "I_"+((CurrentClampElectricalDevice)electricalDevice).getCurrentClampStimulus().getNameScope().getName();
        // }
        // if (edParm.getRole()==ElectricalDevice.ROLE_TransmembraneCurrentDensity){
        // return "F_"+((CurrentClampElectricalDevice)electricalDevice).getCurrentClampStimulus().getNameScope().getName();
        // }
        // }else if (electricalDevice instanceof VoltageClampElectricalDevice) {
        // if (edParm.getRole()==ElectricalDevice.ROLE_TotalCurrentDensity){
        // return "I_"+((VoltageClampElectricalDevice)electricalDevice).getVoltageClampStimulus().getNameScope().getName();
        // }
        // if (edParm.getRole()==ElectricalDevice.ROLE_TransmembraneCurrentDensity){
        // return "F_"+((VoltageClampElectricalDevice)electricalDevice).getVoltageClampStimulus().getNameScope().getName();
        // }
        }
    }
    if (ste instanceof LocalParameter && ((LocalParameter) ste).getNameScope() instanceof ElectricalStimulus.ElectricalStimulusNameScope) {
        LocalParameter esParm = (LocalParameter) ste;
        String nameWithScope = esParm.getNameScope().getName();
        if (esParm.getRole() == ElectricalStimulusParameterType.TotalCurrent) {
            return "I_" + nameWithScope;
        } else if (esParm.getRole() == ElectricalStimulusParameterType.Voltage) {
            return "V_" + nameWithScope;
        }
    }
    StructureTopology structTopology = model.getStructureTopology();
    if (ste instanceof StructureMapping.StructureMappingParameter) {
        StructureMapping.StructureMappingParameter smParm = (StructureMapping.StructureMappingParameter) ste;
        Structure structure = ((StructureMapping) (smParm.getNameScope().getScopedSymbolTable())).getStructure();
        int role = smParm.getRole();
        if (role == StructureMapping.ROLE_VolumeFraction) {
            return "VolFract_" + (structTopology.getInsideFeature((Membrane) structure)).getNameScope().getName();
        } else {
            String nameWithScope = structure.getNameScope().getName();
            if (role == StructureMapping.ROLE_SurfaceToVolumeRatio) {
                return "SurfToVol_" + nameWithScope;
            } else if (role == StructureMapping.ROLE_InitialVoltage) {
                return smParm.getName();
            } else if (role == StructureMapping.ROLE_SpecificCapacitance) {
                return "C_" + nameWithScope;
            } else if (role == StructureMapping.ROLE_AreaPerUnitArea) {
                return "AreaPerUnitArea_" + nameWithScope;
            } else if (role == StructureMapping.ROLE_AreaPerUnitVolume) {
                return "AreaPerUnitVolume_" + nameWithScope;
            } else if (role == StructureMapping.ROLE_VolumePerUnitArea) {
                return "VolumePerUnitArea_" + nameWithScope;
            } else if (role == StructureMapping.ROLE_VolumePerUnitVolume) {
                return "VolumePerUnitVolume_" + nameWithScope;
            } else if (role == StructureMapping.ROLE_Size) {
                if (simContext.getGeometry().getDimension() == 0) {
                    // if geometry is compartmental, make sure compartment sizes are set if referenced in model.
                    if (smParm.getExpression() == null || smParm.getExpression().isZero()) {
                        throw new MappingException("\nIn non-spatial application '" + getSimulationContext().getName() + "', " + "size of structure '" + structure.getName() + "' must be assigned a " + "positive value if referenced in the model.\n\nPlease go to 'Structure Mapping' tab to check the size.");
                    }
                }
                return "Size_" + nameWithScope;
            }
        }
    }
    // 
    if (ste instanceof SpeciesContext) {
        SpeciesContext sc = (SpeciesContext) ste;
        SpeciesContextMapping scm = getSpeciesContextMapping(sc);
        // 
        if (structureMapping instanceof FeatureMapping) {
            // 
            if (scm.getVariable() != null && !scm.getVariable().getName().equals(steName)) {
                return scm.getVariable().getName();
            }
        // 
        // for reactions within a spatially resolved membrane, may need "_INSIDE" or "_OUTSIDE" for jump condition
        // 
        // if the membrane is distributed, then always use the plain variable.
        // 
        } else if (structureMapping instanceof MembraneMapping) {
            Membrane membrane = ((MembraneMapping) structureMapping).getMembrane();
            // 
            if (sc.getStructure() instanceof Membrane || getResolved(structureMapping) == false) {
                if (scm.getVariable() != null && !(scm.getVariable().getName().equals(steName))) {
                    return scm.getVariable().getName();
                }
            // 
            // if the speciesContext is outside the membrane
            // 
            } else {
                SpeciesContextSpec scs = simContext.getReactionContext().getSpeciesContextSpec(sc);
                if (sc.getStructure() == structTopology.getInsideFeature(membrane) || sc.getStructure() == structTopology.getOutsideFeature(membrane)) {
                    if (getResolved(structureMapping) && !scs.isConstant()) {
                        if (!scs.isDiffusing()) {
                            throw new MappingException("Enable diffusion in Application '" + simContext.getName() + "'. This must be done for any species (e.g '" + sc.getName() + "') in flux reactions.\n\n" + "To save or run simulations, set the diffusion rate to a non-zero " + "value in Initial Conditions or disable those reactions in Specifications->Reactions.");
                        }
                        return scm.getVariable().getName() + (sc.getStructure() == structTopology.getInsideFeature(membrane) ? "_INSIDE" : "_OUTSIDE");
                    } else {
                        return scm.getSpeciesContext().getName();
                    }
                } else {
                    throw new MappingException(sc.getName() + " shouldn't be involved with structure " + structureMapping.getStructure().getName());
                }
            }
        }
    }
    return getNameScope().getSymbolName(ste);
}