Examples with StructureMapping cbit.vcell.mapping.StructureMapping used on opensource projects

Example 36 with StructureMapping

use of cbit.vcell.mapping.StructureMapping in project vcell by virtualcell.

the class MathMapping_4_8 method refreshVariables.

/**
 * This method was created in VisualAge.
 */
private void refreshVariables() throws MappingException {
    // System.out.println("MathMapping.refreshVariables()");
    // 
    // non-constant dependent variables require a function
    // 
    Enumeration<SpeciesContextMapping> enum1 = getSpeciesContextMappings();
    while (enum1.hasMoreElements()) {
        SpeciesContextMapping scm = enum1.nextElement();
        SpeciesContextSpec scs = simContext.getReactionContext().getSpeciesContextSpec(scm.getSpeciesContext());
        if (scm.getDependencyExpression() != null && !scs.isConstant()) {
            // scm.setVariable(new Function(scm.getSpeciesContext().getName(),scm.getDependencyExpression()));
            scm.setVariable(null);
        }
    }
    enum1 = getSpeciesContextMappings();
    while (enum1.hasMoreElements()) {
        SpeciesContextMapping scm = enum1.nextElement();
        SpeciesContextSpec scs = simContext.getReactionContext().getSpeciesContextSpec(scm.getSpeciesContext());
        if (getSimulationContext().hasEventAssignment(scs.getSpeciesContext())) {
            scm.setDependencyExpression(null);
        }
    }
    // 
    // non-constant independent variables require either a membrane or volume variable
    // 
    enum1 = getSpeciesContextMappings();
    while (enum1.hasMoreElements()) {
        SpeciesContextMapping scm = (SpeciesContextMapping) enum1.nextElement();
        SpeciesContextSpec scs = simContext.getReactionContext().getSpeciesContextSpec(scm.getSpeciesContext());
        if (scm.getDependencyExpression() == null && (!scs.isConstant() || getSimulationContext().hasEventAssignment(scs.getSpeciesContext()))) {
            StructureMapping sm = simContext.getGeometryContext().getStructureMapping(scm.getSpeciesContext().getStructure());
            Structure struct = scm.getSpeciesContext().getStructure();
            if (struct instanceof Feature) {
                if (getResolved(sm)) {
                    scm.setVariable(getResolvedVolVariable(scm.getSpeciesContext().getSpecies()));
                } else {
                    scm.setVariable(new VolVariable(scm.getSpeciesContext().getName(), nullDomain));
                }
            } else if (struct instanceof Membrane) {
                if (getResolved(sm)) {
                    scm.setVariable(new MemVariable(scm.getSpeciesContext().getName(), nullDomain));
                } else {
                    scm.setVariable(new VolVariable(scm.getSpeciesContext().getName(), nullDomain));
                }
            } else {
                throw new MappingException("class " + scm.getSpeciesContext().getStructure().getClass() + " not supported");
            }
            mathSymbolMapping.put(scm.getSpeciesContext(), scm.getVariable().getName());
        }
    }
}

Example 37 with StructureMapping

use of cbit.vcell.mapping.StructureMapping in project vcell by virtualcell.

the class StructureAnalyzer method refreshTotalDependancies.

/**
 * This method was created by a SmartGuide.
 * @param b cbit.vcell.math.Matrix
 * @param vars java.lang.String[]
 */
static StructureAnalyzer.Dependency[] refreshTotalDependancies(RationalMatrix nullSpaceMatrix, SpeciesContextMapping[] speciesContextMappings, MathMapping_4_8 argMathMapping, boolean bFast) throws Exception {
    // System.out.println("StructureAnalyzer.refreshTotalDependancies()");
    SimulationContext argSimContext = argMathMapping.getSimulationContext();
    if (nullSpaceMatrix == null) {
        // System.out.println("the matrix has full rank, there are no dependencies");
        return new StructureAnalyzer.Dependency[0];
    }
    if (speciesContextMappings.length != nullSpaceMatrix.getNumCols()) {
        // throw new Exception("varName array not same dimension as b matrix");
        System.out.println("varName array not same dimension as b matrix");
        nullSpaceMatrix.show();
        for (int i = 0; i < speciesContextMappings.length; i++) {
            System.out.println("scm[" + i + "] is " + speciesContextMappings[i].getSpeciesContext().getName());
        }
    }
    // System.out.println("there are "+nullSpaceMatrix.rows+" dependencies");
    Vector<Dependency> dependencyList = new Vector<Dependency>();
    for (int i = 0; i < nullSpaceMatrix.getNumRows(); i++) {
        // 
        // find first variable
        // 
        Expression exp = null;
        Expression constantExp = null;
        String constantName = null;
        SpeciesContextMapping firstSCM = null;
        boolean bFirst = true;
        for (int j = 0; j < nullSpaceMatrix.getNumCols(); j++) {
            RationalNumber coeff = nullSpaceMatrix.get_elem(i, j);
            if (coeff.doubleValue() != 0.0) {
                if (bFirst) {
                    if (coeff.doubleValue() != 1.0) {
                        System.out.println("i=" + i + " j=" + j);
                        nullSpaceMatrix.show();
                        throw new Exception("expecting a coefficient of 1.0, instead coeff = " + coeff.infix());
                    }
                    firstSCM = speciesContextMappings[j];
                    // 
                    // first term of dependancy expression   ("K_CalciumCyt")
                    // 
                    SpeciesContext firstSC = firstSCM.getSpeciesContext();
                    constantName = "K_" + firstSC.getName() + "_total";
                    exp = new Expression(constantName);
                    // 
                    // first term of K expression
                    // 
                    StructureMapping firstSM = argSimContext.getGeometryContext().getStructureMapping(firstSC.getStructure());
                    SpeciesContextSpec firstSCS = argSimContext.getReactionContext().getSpeciesContextSpec(firstSC);
                    SymbolTableEntry scSTE = null;
                    if (bFast) {
                        scSTE = firstSCS.getSpeciesContext();
                    } else {
                        scSTE = firstSCS.getParameterFromRole(SpeciesContextSpec.ROLE_InitialConcentration);
                    }
                    constantExp = Expression.mult(new Expression(coeff), firstSM.getNormalizedConcentrationCorrection(argSimContext, argMathMapping), new Expression(scSTE, argMathMapping.getNameScope()));
                    bFirst = false;
                } else {
                    // 
                    // add term to dependancy expression     (" - 2*IP3Cyt ")
                    // 
                    SpeciesContextMapping scm = speciesContextMappings[j];
                    SpeciesContext sc = scm.getSpeciesContext();
                    StructureMapping sm = argSimContext.getGeometryContext().getStructureMapping(sc.getStructure());
                    SpeciesContextSpec scs = argSimContext.getReactionContext().getSpeciesContextSpec(sc);
                    exp = Expression.add(exp, Expression.negate(Expression.mult(new Expression(coeff), sm.getNormalizedConcentrationCorrection(argSimContext, argMathMapping), new Expression(sc, argMathMapping.getNameScope()))));
                    // 
                    // add term to K expression
                    // 
                    SymbolTableEntry scSTE = null;
                    if (bFast) {
                        scSTE = sc;
                    } else {
                        scSTE = scs.getParameterFromRole(SpeciesContextSpec.ROLE_InitialConcentration);
                    }
                    constantExp = Expression.add(constantExp, Expression.mult(new Expression(coeff), sm.getNormalizedConcentrationCorrection(argSimContext, argMathMapping), new Expression(scSTE, argMathMapping.getNameScope())));
                }
            }
        }
        if (firstSCM != null) {
            // 
            // store totalMass parameter (e.g. K_xyz_total = xyz_init + wzy_init)
            // 
            // MathMapping.MathMappingParameter totalMassParameter = mathMapping.addMathMappingParameter(constantName,constantExp.flatten(),MathMapping.PARAMETER_ROLE_TOTALMASS,cbit.vcell.units.VCUnitDefinition.UNIT_uM);
            // 
            // store dependency parameter (e.g. xyz = K_xyz_total - wzy)
            // 
            StructureMapping sm = argSimContext.getGeometryContext().getStructureMapping(firstSCM.getSpeciesContext().getStructure());
            exp = Expression.mult(exp, Expression.invert(sm.getNormalizedConcentrationCorrection(argSimContext, argMathMapping)));
            exp = exp.flatten();
            // exp.bindExpression(mathMapping_temp);
            // firstSCM.setDependencyExpression(exp);
            Dependency dependency = new Dependency();
            dependency.dependencyExpression = exp;
            dependency.speciesContextMapping = firstSCM;
            dependency.invariantSymbolName = constantName;
            dependency.conservedMoietyExpression = constantExp.flatten();
            dependencyList.add(dependency);
        }
    }
    return (StructureAnalyzer.Dependency[]) BeanUtils.getArray(dependencyList, StructureAnalyzer.Dependency.class);
}

Example 38 with StructureMapping

use of cbit.vcell.mapping.StructureMapping in project vcell by virtualcell.

the class MathMapping_4_8 method getResolved.

boolean getResolved(StructureMapping structureMapping) {
    if (simContext == null || structureMapping.getStructure() == null) {
        throw new RuntimeException("failed to process getResolved()");
    }
    if (structureMapping.getGeometryClass() == null) {
        return false;
    }
    StructureTopology structureTopology = simContext.getModel().getStructureTopology();
    Structure parentStructure = structureTopology.getParentStructure(structureMapping.getStructure());
    if (parentStructure != null) {
        StructureMapping outsideSM = simContext.getGeometryContext().getStructureMapping(parentStructure);
        if (outsideSM.getGeometryClass() != null && outsideSM.getGeometryClass() == structureMapping.getGeometryClass()) {
            return false;
        }
    }
    return true;
}

Example 39 with StructureMapping

use of cbit.vcell.mapping.StructureMapping in project vcell by virtualcell.

the class MathMapping_4_8 method getResolvedVolVariable.

/**
 * Find the defined variable (VolVariable) for the resolved compartments.
 * This method is used to assure only one variable is created.
 * @return cbit.vcell.math.VolVariable
 * @param species cbit.vcell.model.Species
 */
private VolVariable getResolvedVolVariable(Species species) {
    Enumeration<SpeciesContextMapping> enum1 = getSpeciesContextMappings();
    while (enum1.hasMoreElements()) {
        SpeciesContextMapping scm = enum1.nextElement();
        if (scm.getSpeciesContext().getSpecies() == species) {
            Variable var = scm.getVariable();
            if (var instanceof VolVariable) {
                Structure structure = scm.getSpeciesContext().getStructure();
                StructureMapping sm = simContext.getGeometryContext().getStructureMapping(structure);
                if (structure instanceof Feature && getResolved(sm)) {
                    return (VolVariable) var;
                }
            }
        }
    }
    return new VolVariable(TokenMangler.fixTokenStrict(species.getCommonName()), nullDomain);
}

Example 40 with StructureMapping

use of cbit.vcell.mapping.StructureMapping in project vcell by virtualcell.

the class ModelOptimizationSpec method getModelParameters.

/**
 * Insert the method's description here.
 * Creation date: (8/22/2005 10:38:04 AM)
 * @return cbit.vcell.model.Parameter[]
 */
private Parameter[] getModelParameters() {
    java.util.Vector<Parameter> modelParameterList = new java.util.Vector<Parameter>();
    Model model = getSimulationContext().getModel();
    // 
    // get Model (global) parameters
    // 
    ModelParameter[] globalParams = model.getModelParameters();
    for (int i = 0; i < globalParams.length; i++) {
        if (globalParams[i] != null && globalParams[i].getExpression() != null && globalParams[i].getExpression().isNumeric()) {
            modelParameterList.add(globalParams[i]);
        }
    }
    // 
    // get kinetic parameters that are numbers
    // 
    ReactionStep[] reactionSteps = model.getReactionSteps();
    for (int i = 0; i < reactionSteps.length; i++) {
        // 
        // make sure ReactionSteps are "enabled"
        // 
        ReactionSpec reactionSpec = getSimulationContext().getReactionContext().getReactionSpec(reactionSteps[i]);
        if (reactionSpec == null || reactionSpec.isExcluded()) {
            continue;
        }
        Kinetics.KineticsParameter[] kineticsParameters = reactionSteps[i].getKinetics().getKineticsParameters();
        for (int j = 0; j < kineticsParameters.length; j++) {
            if (kineticsParameters[j].getExpression() != null && kineticsParameters[j].getExpression().isNumeric()) {
                if (((kineticsParameters[j].getRole() == Kinetics.ROLE_CurrentDensity) || (kineticsParameters[j].getRole() == Kinetics.ROLE_LumpedCurrent)) && reactionSteps[i].getPhysicsOptions() == ReactionStep.PHYSICS_MOLECULAR_ONLY) {
                    continue;
                }
                if (((kineticsParameters[j].getRole() == Kinetics.ROLE_ReactionRate) || (kineticsParameters[j].getRole() == Kinetics.ROLE_LumpedReactionRate)) && reactionSteps[i].getPhysicsOptions() == ReactionStep.PHYSICS_ELECTRICAL_ONLY) {
                    continue;
                }
                modelParameterList.add(kineticsParameters[j]);
            }
        }
    }
    // 
    // get initial conditions that are numbers
    // 
    SpeciesContextSpec[] speciesContextSpecs = getSimulationContext().getReactionContext().getSpeciesContextSpecs();
    for (int i = 0; i < speciesContextSpecs.length; i++) {
        SpeciesContextSpec.SpeciesContextSpecParameter initParam = speciesContextSpecs[i].getInitialConditionParameter();
        if (initParam != null && initParam.getExpression() != null && initParam.getExpression().isNumeric()) {
            modelParameterList.add(initParam);
        }
    }
    // 
    // get structure parameters
    // 
    StructureMapping[] structureMappings = getSimulationContext().getGeometryContext().getStructureMappings();
    for (int i = 0; i < structureMappings.length; i++) {
        StructureMapping.StructureMappingParameter[] parameters = structureMappings[i].getParameters();
        for (int j = 0; j < parameters.length; j++) {
            if (parameters[j].getRole() == StructureMapping.ROLE_SpecificCapacitance && structureMappings[i] instanceof MembraneMapping && !((MembraneMapping) structureMappings[i]).getCalculateVoltage()) {
                continue;
            }
            if (parameters[j].getExpression() != null && parameters[j].getExpression().isNumeric()) {
                modelParameterList.add(parameters[j]);
            }
        }
    }
    Parameter[] modelParameters = (Parameter[]) BeanUtils.getArray(modelParameterList, Parameter.class);
    return modelParameters;
}