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

Example 46 with Function

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

the class SimulationSymbolTable method getLocalFunction.

/**
 * Insert the method's description here.
 * Creation date: (6/6/2001 7:52:15 PM)
 * @return cbit.vcell.math.Function
 * @param functionName java.lang.String
 */
private Function getLocalFunction(Function referenceFunction) throws ExpressionException {
    if (localVariableHash == null) {
        localVariableHash = new HashMap<String, Variable>();
    }
    Variable var = localVariableHash.get(referenceFunction.getName());
    if (var instanceof Function) {
        Function localFunction = (Function) var;
        if (localFunction.compareEqual(referenceFunction)) {
            // localFunction.bind(this); // update bindings to latest mathOverrides
            return localFunction;
        }
    } else if (var != null) {
        throw new RuntimeException("Variable " + var + " expected to be a Function");
    }
    // 
    // if local Function not found, create new one, bind it to the Simulation (which ensures MathOverrides), and add to list
    // 
    Function newLocalFunction = new Function(referenceFunction.getName(), referenceFunction.getExpression(), referenceFunction.getDomain());
    // newLocalFunction.bind(this);
    localVariableHash.put(newLocalFunction.getName(), newLocalFunction);
    return newLocalFunction;
}

Example 47 with Function

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

the class SimulationSymbolTable method getVariables.

/**
 * Insert the method's description here.
 * Creation date: (5/25/01 11:34:08 AM)
 * @return cbit.vcell.math.Variable[]
 */
public Variable[] getVariables() {
    Vector<Variable> varList = new Vector<Variable>();
    // 
    // get all variables from MathDescription, but replace MathOverrides
    // 
    Enumeration<Variable> enum1 = simulation.getMathDescription().getVariables();
    while (enum1.hasMoreElements()) {
        Variable mathDescriptionVar = enum1.nextElement();
        // 
        if (mathDescriptionVar instanceof Constant) {
            try {
                Constant overriddenConstant = getLocalConstant((Constant) mathDescriptionVar);
                varList.addElement(overriddenConstant);
            } catch (ExpressionException e) {
                e.printStackTrace(System.out);
                throw new RuntimeException("local Constant " + mathDescriptionVar.getName() + " not found for Simulation");
            }
        // 
        // replace all Functions with local Functions that are bound to this Simulation
        // 
        } else if (mathDescriptionVar instanceof Function) {
            try {
                Function overriddenFunction = getLocalFunction((Function) mathDescriptionVar);
                varList.addElement(overriddenFunction);
            } catch (ExpressionException e) {
                e.printStackTrace(System.out);
                throw new RuntimeException("local Function " + mathDescriptionVar.getName() + " not found for Simulation");
            }
        // 
        // pass all other Variables through
        // 
        } else {
            varList.addElement(mathDescriptionVar);
        }
    }
    Variable[] variables = (Variable[]) BeanUtils.getArray(varList, Variable.class);
    return variables;
}

Example 48 with Function

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

the class SundialsSolver method createFunctionList.

public Vector<AnnotatedFunction> createFunctionList() {
    // 
    // add appropriate Function columns to result set
    // 
    Vector<AnnotatedFunction> funcList = super.createFunctionList();
    SimulationSymbolTable simSymbolTable = simTask.getSimulationJob().getSimulationSymbolTable();
    if (getSensitivityParameter() != null) {
        try {
            AnnotatedFunction saf = new AnnotatedFunction(getSensitivityParameter().getName(), new Expression(getSensitivityParameter().getConstantValue()), getSensitivityParameter().getDomain(), "", VariableType.NONSPATIAL, FunctionCategory.PREDEFINED);
            if (!funcList.contains(saf)) {
                funcList.add(saf);
            }
            Variable[] variables = simSymbolTable.getVariables();
            StateVariable[] stateVars = createStateVariables();
            for (int i = 0; i < variables.length; i++) {
                if (variables[i] instanceof Function && SimulationSymbolTable.isFunctionSaved((Function) variables[i])) {
                    Function depSensFunction = (Function) variables[i];
                    Expression depSensFnExpr = new Expression(depSensFunction.getExpression());
                    depSensFnExpr = simSymbolTable.substituteFunctions(depSensFnExpr);
                    depSensFnExpr = getFunctionSensitivity(depSensFnExpr, getSensitivityParameter(), stateVars);
                    // depSensFnExpr = depSensFnExpr.flatten(); 	// already bound and flattened in getFunctionSensitivity, no need here.....
                    String depSensFnName = new String("sens_" + depSensFunction.getName() + "_wrt_" + getSensitivityParameter().getName());
                    if (depSensFunction != null) {
                        AnnotatedFunction af = new AnnotatedFunction(depSensFnName, depSensFnExpr.flatten(), variables[i].getDomain(), "", VariableType.NONSPATIAL, FunctionCategory.PREDEFINED);
                        funcList.add(af);
                    }
                }
            }
        } catch (MathException e) {
            e.printStackTrace(System.out);
            throw new RuntimeException("Error adding function to resultSet: " + e.getMessage());
        } catch (ExpressionException e) {
            e.printStackTrace(System.out);
            throw new RuntimeException("Error adding function to resultSet: " + e.getMessage());
        }
    }
    return funcList;
}

Example 49 with Function

use of cbit.vcell.math.Function 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 50 with Function

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

the class NFsimXMLWriter method isFunction.

private static boolean isFunction(String candidate, MathDescription mathDesc, SimulationSymbolTable simulationSymbolTable) throws SolverException {
    Element listOfParametersElement = new Element("ListOfFunctions");
    for (Variable var : simulationSymbolTable.getVariables()) {
        Double value = null;
        if (var instanceof Constant || var instanceof Function) {
            Expression valExpression = var.getExpression();
            Expression substitutedValExpr = null;
            try {
                substitutedValExpr = simulationSymbolTable.substituteFunctions(valExpression);
            } catch (Exception e) {
                e.printStackTrace(System.out);
                throw new SolverException("Constant or Function " + var.getName() + " substitution failed : exp = \"" + var.getExpression().infix() + "\": " + e.getMessage());
            }
            try {
                value = substitutedValExpr.evaluateConstant();
            } catch (ExpressionException e) {
                System.out.println("constant or function " + var.getName() + " = " + substitutedValExpr.infix() + " does not have a constant value");
            }
            if (value != null) {
                // parameter, see getListOfParameters() above
                continue;
            } else {
                String current = var.getName();
                if (candidate.equals(current)) {
                    return true;
                }
            }
        }
    }
    return false;
}