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

Example 41 with VolVariable

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

the class DefaultODESolver method createIdentifiers.

/**
 * This method was created in VisualAge.
 */
private Vector<Variable> createIdentifiers() throws MathException, ExpressionException {
    SimulationSymbolTable simSymbolTable = simTask.getSimulationJob().getSimulationSymbolTable();
    // create list of possible identifiers (including reserved x,y,z,t)
    Vector<Variable> identifiers = new Vector<Variable>();
    // add reserved variables x,y,z,t
    identifiers.addElement(ReservedVariable.TIME);
    identifiers.addElement(ReservedVariable.X);
    identifiers.addElement(ReservedVariable.Y);
    identifiers.addElement(ReservedVariable.Z);
    // add regular variables
    Variable[] variables = simSymbolTable.getVariables();
    for (int i = 0; i < variables.length; i++) {
        if (variables[i] instanceof VolVariable) {
            identifiers.addElement(variables[i]);
        }
    }
    // Add sensitivity variables (for sensitivity equations)...
    fieldSensVariables = new Vector<SensVariable>();
    if (getSensitivityParameter() != null) {
        for (int i = 0; i < variables.length; i++) {
            if (variables[i] instanceof VolVariable) {
                VolVariable volVariable = (VolVariable) variables[i];
                SensVariable sv = new SensVariable(volVariable, getSensitivityParameter());
                identifiers.addElement(sv);
            }
        }
    }
    // Add pseudoConstants for fast system (if necessary)...
    if (getFastAlgebraicSystem() != null) {
        Enumeration<PseudoConstant> enum1 = fieldFastAlgebraicSystem.getPseudoConstants();
        while (enum1.hasMoreElements()) {
            identifiers.addElement(enum1.nextElement());
        }
    }
    // Assign indices...
    for (int i = 0; i < identifiers.size(); i++) {
        Variable variable = (Variable) identifiers.elementAt(i);
        variable.setIndex(i);
    }
    return (identifiers);
}

Example 42 with VolVariable

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

the class Jacobian method show.

/**
 * This method was created by a SmartGuide.
 */
public void show() throws MathException, ExpressionException {
    refresh();
    for (int rateIndex = 0; rateIndex < numVariables; rateIndex++) {
        for (int varIndex = 0; varIndex < numVariables; varIndex++) {
            Expression rateExp = rates[rateIndex];
            VolVariable var = vars[varIndex];
            Expression J = getJexp(rateIndex, varIndex);
            System.out.println("Jacobian of " + vars[rateIndex].getName() + "' wrt " + vars[varIndex].getName() + " is " + J);
        }
    }
}

Example 43 with VolVariable

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

the class OdeFileWriter method createSymbolTable.

/**
 * OdeFileCoder constructor comment.
 * @throws Exception
 */
private void createSymbolTable() throws Exception {
    // 
    // Create symbol table for binding sensitivity variable expressions. (Cannot bind to simulation,
    // since it does not have the sensitivity variables corresponding to the volume variables).
    // 
    varsSymbolTable = new VariableSymbolTable();
    // SymbolTableEntry.index doesn't matter ... just code generating binding by var names not index.
    varsSymbolTable.addVar(ReservedVariable.TIME);
    int count = 0;
    Variable[] variables = simTask.getSimulationJob().getSimulationSymbolTable().getVariables();
    for (int i = 0; i < variables.length; i++) {
        if (variables[i] instanceof VolVariable) {
            VolVariable vVar = (VolVariable) variables[i];
            vVar.setIndex(count);
            varsSymbolTable.addVar(vVar);
            count++;
        } else if (variables[i] instanceof Function) {
            Function func = (Function) variables[i];
            func.setIndex(count);
            varsSymbolTable.addVar(func);
            count++;
        } else if (variables[i] instanceof Constant) {
            Constant constant = (Constant) variables[i];
            constant.setIndex(count);
            varsSymbolTable.addVar(constant);
            count++;
        } else if (variables[i] instanceof ParameterVariable) {
            ParameterVariable param = (ParameterVariable) variables[i];
            param.setIndex(count);
            varsSymbolTable.addVar(param);
            count++;
        }
    }
    // Get the vector of sensVariables, needed for creating SensStateVariables
    Vector<SensStateVariable> sensVars = new Vector<SensStateVariable>();
    for (int i = 0; i < getStateVariableCount(); i++) {
        if (simTask.getSimulation().getSolverTaskDescription().getSensitivityParameter() != null) {
            if (getStateVariable(i) instanceof SensStateVariable) {
                sensVars.addElement((SensStateVariable) getStateVariable(i));
            }
        }
    }
    for (int j = count; j < (count + sensVars.size()); j++) {
        SensVariable sVar = (SensVariable) (sensVars.elementAt(j - count).getVariable());
        sVar.setIndex(j);
        varsSymbolTable.addVar(sVar);
    }
}

Example 44 with VolVariable

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

the class SensStateVariable method init.

/**
 * This method was created in VisualAge.
 * @param rateSensitivity cbit.vcell.math.RateSensitivity
 * @param jacobian cbit.vcell.math.Jacobian
 */
private void init(RateSensitivity rateSensitivity, Jacobian jacobian, SymbolTable symbolTable, Vector<SensVariable> sensVarArray) throws MathException, ExpressionException {
    // 
    // order sensVars according to the jacobian (rate index)
    // 
    sensVars = (Vector<SensVariable>) sensVarArray.clone();
    for (int i = 0; i < sensVarArray.size(); i++) {
        SensVariable sensVar = sensVarArray.elementAt(i);
        int index = jacobian.getRateIndex(sensVar.getVolVariable());
        sensVars.setElementAt(sensVar, index);
    }
    // 
    // given the system
    // 
    // 
    // d Ci
    // ------- = Fi(C1..Cn,P1..Pm)
    // d t
    // 
    // where:  C's are variables and P's are parameters
    // 
    // jacobian.show();
    VolVariable var = ((SensVariable) variable).getVolVariable();
    Constant parameter = ((SensVariable) variable).getParameter();
    // 
    // get list of jacobian expressions for this var (Ci)
    // 
    // d Fi
    // ------   for all j
    // d Cj
    // 
    optimizedJacobianExps = new Expression[jacobian.getNumRates()];
    int currIndex = jacobian.getRateIndex(var);
    for (int i = 0; i < optimizedJacobianExps.length; i++) {
        Expression exp = jacobian.getJexp(currIndex, i);
        exp.bindExpression(symbolTable);
        optimizedJacobianExps[i] = exp.flatten();
    }
    // 
    // get rate sensitivity for this variable (Ci) and the parameter under investigation (Pj)
    // 
    // d Fi
    // ------
    // d Pj
    // 
    // 
    Expression exp = rateSensitivity.getCPexp(var, parameter.getName());
    exp.bindExpression(symbolTable);
    optimizedRateSensExp = exp.flatten();
}

Example 45 with VolVariable

use of cbit.vcell.math.VolVariable 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());
    }
}