Examples with VolumeRegionVariable cbit.vcell.math.VolumeRegionVariable used on opensource projects

Example 16 with VolumeRegionVariable

use of cbit.vcell.math.VolumeRegionVariable in project vcell by virtualcell.

the class MathTestingUtilities method substituteWithExactSolution.

/**
 * Insert the method's description here.
 * Creation date: (1/24/2003 10:18:14 AM)
 * @return cbit.vcell.parser.Expression
 * @param origExp cbit.vcell.parser.Expression
 * @param subDomain cbit.vcell.math.SubDomain
 */
private static Expression substituteWithExactSolution(Expression origExp, MembraneSubDomain subDomain, MathDescription exactMathDesc) throws ExpressionException {
    Expression substitutedExp = new Expression(origExp);
    substitutedExp.bindExpression(exactMathDesc);
    substitutedExp = MathUtilities.substituteFunctions(substitutedExp, exactMathDesc);
    substitutedExp.bindExpression(null);
    substitutedExp = substitutedExp.flatten();
    substitutedExp.bindExpression(exactMathDesc);
    String[] symbols = substitutedExp.getSymbols();
    for (int i = 0; symbols != null && i < symbols.length; i++) {
        Variable var = (Variable) substitutedExp.getSymbolBinding(symbols[i]);
        if (var instanceof MemVariable) {
            String exactVarName = var.getName() + "_" + subDomain.getName() + "_exact";
            substitutedExp.substituteInPlace(new Expression(var.getName()), new Expression(exactVarName));
        } else if (var instanceof InsideVariable) {
            String exactVarName = var.getName() + "_" + subDomain.getInsideCompartment().getName() + "_exact";
            substitutedExp.substituteInPlace(new Expression(var.getName()), new Expression(exactVarName));
        } else if (var instanceof OutsideVariable) {
            String exactVarName = var.getName() + "_" + subDomain.getOutsideCompartment().getName() + "_exact";
            substitutedExp.substituteInPlace(new Expression(var.getName()), new Expression(exactVarName));
        } else if (var instanceof VolumeRegionVariable || var instanceof MemVariable || var instanceof MembraneRegionVariable || var instanceof FilamentVariable || var instanceof FilamentRegionVariable) {
            throw new RuntimeException("variable substitution not yet implemented for Variable type " + var.getClass().getName() + "(" + var.getName() + ")");
        }
    }
    substitutedExp.bindExpression(null);
    return substitutedExp;
}

Example 17 with VolumeRegionVariable

use of cbit.vcell.math.VolumeRegionVariable in project vcell by virtualcell.

the class ModelOptimizationSpec method removeUncoupledParameters.

public void removeUncoupledParameters() {
    try {
        localIssueList.clear();
        MathMapping mathMapping = getSimulationContext().createNewMathMapping();
        MathDescription mathDesc = mathMapping.getMathDescription();
        MathSystemHash mathSystemHash = fromMath(mathDesc);
        Graph graph = mathSystemHash.getDependencyGraph(mathSystemHash.getSymbols());
        Tree[] spanningTrees = graph.getSpanningForest();
        // 
        for (int i = 0; i < spanningTrees.length; i++) {
            Node[] treeNodes = spanningTrees[i].getNodes();
            boolean bHasStateVariables = false;
            for (int j = 0; j < treeNodes.length; j++) {
                Node node = treeNodes[j];
                Variable var = mathDesc.getVariable(node.getName());
                if (var instanceof VolVariable || var instanceof MemVariable || var instanceof FilamentVariable || var instanceof VolumeRegionVariable || var instanceof MembraneRegionVariable || var instanceof FilamentRegionVariable) {
                    bHasStateVariables = true;
                    break;
                }
            }
            if (!bHasStateVariables) {
                spanningTrees = (Tree[]) BeanUtils.removeElement(spanningTrees, spanningTrees[i]);
                i--;
            }
        }
        // 
        // remove parameters not mapped to a surviving tree (not coupled to any state variables
        // 
        ArrayList<ParameterMappingSpec> paramMappingSpecsList = new ArrayList<ParameterMappingSpec>();
        paramMappingSpecsList.addAll(Arrays.asList(fieldParameterMappingSpecs));
        for (int i = 0; i < paramMappingSpecsList.size(); i++) {
            Parameter parameter = paramMappingSpecsList.get(i).getModelParameter();
            String mathName = mathMapping.getMathSymbolMapping().getVariable(parameter).getName();
            boolean bFoundInTree = false;
            for (int j = 0; j < spanningTrees.length; j++) {
                Node node = spanningTrees[j].getNode(mathName);
                if (node != null) {
                    bFoundInTree = true;
                }
            }
            if (!bFoundInTree) {
                paramMappingSpecsList.remove(i);
                i--;
            }
        }
        ParameterMappingSpec[] parameterMappingSpecs = new ParameterMappingSpec[paramMappingSpecsList.size()];
        paramMappingSpecsList.toArray(parameterMappingSpecs);
        setParameterMappingSpecs(parameterMappingSpecs);
    } catch (Exception e) {
        e.printStackTrace(System.out);
        localIssueList.add(new Issue(this, localIssueContext, IssueCategory.ParameterEstimationGeneralWarning, e.getMessage(), Issue.SEVERITY_WARNING));
    // throw new RuntimeException(e.getMessage());
    }
}