Examples with ExplicitObjectiveFunction cbit.vcell.opt.ExplicitObjectiveFunction used on opensource projects

Example 1 with ExplicitObjectiveFunction

use of cbit.vcell.opt.ExplicitObjectiveFunction in project vcell by virtualcell.

the class OptXmlWriter method getObjectiveFunctionXML.

public static Element getObjectiveFunctionXML(OptimizationSpec optimizationSpec) {
    Element objectiveFunctionElement = new Element(OptXmlTags.ObjectiveFunction_Tag);
    ObjectiveFunction objectiveFunction = optimizationSpec.getObjectiveFunction();
    if (objectiveFunction instanceof ExplicitObjectiveFunction) {
        ExplicitObjectiveFunction explicitObjectiveFunction = (ExplicitObjectiveFunction) objectiveFunction;
        objectiveFunctionElement.setAttribute(OptXmlTags.ObjectiveFunctionType_Attr, OptXmlTags.ObjectiveFunctionType_Attr_Explicit);
        Element expressionElement = new Element(OptXmlTags.Expression_Tag);
        expressionElement.addContent(explicitObjectiveFunction.getExpression().infix());
        objectiveFunctionElement.addContent(expressionElement);
    } else if (objectiveFunction instanceof ExplicitFitObjectiveFunction) {
        ExplicitFitObjectiveFunction explicitFitObjectiveFunction = (ExplicitFitObjectiveFunction) objectiveFunction;
        objectiveFunctionElement.setAttribute(OptXmlTags.ObjectiveFunctionType_Attr, OptXmlTags.ObjectiveFunctionType_Attr_ExplicitFit);
        // add expression list
        Element expressionListElement = new Element(OptXmlTags.ExpressionList_Tag);
        objectiveFunctionElement.addContent(expressionListElement);
        ExplicitFitObjectiveFunction.ExpressionDataPair[] expDataPairs = explicitFitObjectiveFunction.getExpressionDataPairs();
        for (int i = 0; i < expDataPairs.length; i++) {
            Element expressionElement = new Element(OptXmlTags.Expression_Tag);
            expressionElement.setAttribute(OptXmlTags.ExpRefDataColumnIndex_Attr, expDataPairs[i].getReferenceDataIndex() + "");
            expressionElement.addContent(expDataPairs[i].getFitFunction().infix());
            expressionListElement.addContent(expressionElement);
        }
        if (explicitFitObjectiveFunction.getReferenceData() instanceof SimpleReferenceData) {
            Element dataElement = getDataXML(explicitFitObjectiveFunction.getReferenceData());
            objectiveFunctionElement.addContent(dataElement);
        } else {
            throw new OptimizationException("Optimization XML Writer exports SimpleReferenceData only.");
        }
    } else if (objectiveFunction instanceof PdeObjectiveFunction) {
        PdeObjectiveFunction pdeObjectiveFunction = (PdeObjectiveFunction) objectiveFunction;
        objectiveFunctionElement.setAttribute(OptXmlTags.ObjectiveFunctionType_Attr, OptXmlTags.ObjectiveFunctionType_Attr_PDE);
        SpatialReferenceData refData = pdeObjectiveFunction.getReferenceData();
        Element dataElement = getDataXML(refData);
        objectiveFunctionElement.addContent(dataElement);
        Element modelElement = getModelXML(pdeObjectiveFunction, optimizationSpec.getParameterNames());
        objectiveFunctionElement.addContent(modelElement);
        Simulation tempSim = new Simulation(pdeObjectiveFunction.getMathDescription());
        SimulationSymbolTable simSymbolTable = new SimulationSymbolTable(tempSim, 0);
        // 
        for (int i = 1; i < refData.getNumVariables(); i++) {
            Element modelMappingElement = new Element(OptXmlTags.ModelMapping_Tag);
            modelMappingElement.setAttribute(OptXmlTags.ModelMappingDataColumn_Attr, refData.getVariableNames()[i]);
            modelMappingElement.setAttribute(OptXmlTags.ModelMappingWeight_Attr, String.valueOf(refData.getVariableWeights()[i]));
            Expression mappingExpression = null;
            try {
                Variable var = pdeObjectiveFunction.getMathDescription().getVariable(refData.getVariableNames()[i]);
                if (var instanceof Function) {
                    Expression exp = new Expression(var.getExpression());
                    exp.bindExpression(simSymbolTable);
                    exp = MathUtilities.substituteFunctions(exp, simSymbolTable);
                    mappingExpression = exp.flatten();
                } else {
                    mappingExpression = new Expression(var.getName());
                }
            } catch (ExpressionException e) {
                e.printStackTrace();
                throw new OptimizationException(e.getMessage());
            }
            modelMappingElement.addContent(mappingExpression.infix());
            objectiveFunctionElement.addContent(modelMappingElement);
        }
    }
    return objectiveFunctionElement;
}

Example 2 with ExplicitObjectiveFunction

use of cbit.vcell.opt.ExplicitObjectiveFunction in project vcell by virtualcell.

the class OptUtils method getAugmentedObjectiveFunction.

/**
 * Insert the method's description here.
 * Creation date: (8/4/2005 3:26:14 PM)
 * @return function.AugmentedObjectiveFunction
 * @param optSpec cbit.vcell.opt.OptimizationSpec
 * @param power double
 * @param mu double
 */
public static AugmentedObjectiveFunction getAugmentedObjectiveFunction(OptimizationSpec optSpec, double power, double mu, OptSolverCallbacks optSolverCallbacks) throws cbit.vcell.parser.ExpressionException {
    Parameter[] parameters = optSpec.getParameters();
    // 
    // build symbol list
    // 
    String[] origSymbols = optSpec.getParameterNames();
    String[] scaledSymbols = optSpec.getScaledParameterNames();
    double[] scaleFactors = optSpec.getScaleFactors();
    ScalarFunction objFunction = null;
    if (optSpec.getObjectiveFunction() instanceof ExplicitObjectiveFunction) {
        ExplicitObjectiveFunction explicitObjectiveFunction = (ExplicitObjectiveFunction) optSpec.getObjectiveFunction();
        // 
        // build objective function
        // 
        objFunction = new DynamicScalarFunction(explicitObjectiveFunction.getScaledExpression(origSymbols, scaledSymbols, scaleFactors), scaledSymbols);
    } else if (optSpec.getObjectiveFunction() instanceof ImplicitObjectiveFunction) {
        ImplicitObjectiveFunction implicitObjectiveFunction = (ImplicitObjectiveFunction) optSpec.getObjectiveFunction();
        // 
        // build objective function
        // 
        objFunction = implicitObjectiveFunction.getObjectiveFunction();
    } else if (optSpec.getObjectiveFunction() instanceof ExplicitFitObjectiveFunction) {
        ExplicitFitObjectiveFunction explicitFitObjectiveFunction = (ExplicitFitObjectiveFunction) optSpec.getObjectiveFunction();
        objFunction = explicitFitObjectiveFunction.getScalarFunction();
    } else {
        throw new RuntimeException("unsupported objective function type : " + optSpec.getObjectiveFunction().getClass().getName());
    }
    // 
    // build equality and inequality constraints
    // 
    DynamicVectorFunction equalityConstraints = null;
    DynamicVectorFunction inequalityConstraints = null;
    Constraint[] constraints = optSpec.getConstraints();
    Vector equExpList = new Vector();
    Vector inequExpList = new Vector();
    // 
    for (int i = 0; i < constraints.length; i++) {
        ConstraintType type = constraints[i].getConstraintType();
        if (type.equals(ConstraintType.LinearEquality) || type.equals(ConstraintType.NonlinearEquality)) {
            equExpList.add(constraints[i].getExpression());
        } else {
            inequExpList.add(constraints[i].getExpression());
        }
    }
    // 
    for (int i = 0; i < parameters.length; i++) {
        if (!Double.isInfinite(parameters[i].getLowerBound())) {
            inequExpList.add(new Expression("(" + parameters[i].getLowerBound() + " - " + parameters[i].getName() + ")/" + scaleFactors[i]));
        }
        if (!Double.isInfinite(parameters[i].getUpperBound())) {
            inequExpList.add(new Expression("(" + parameters[i].getName() + " - " + parameters[i].getUpperBound() + ")/" + scaleFactors[i]));
        }
    }
    if (equExpList.size() > 0) {
        Expression[] exps = (Expression[]) org.vcell.util.BeanUtils.getArray(equExpList, Expression.class);
        equalityConstraints = new DynamicVectorFunction(exps, origSymbols);
    }
    if (inequExpList.size() > 0) {
        Expression[] exps = (Expression[]) org.vcell.util.BeanUtils.getArray(inequExpList, Expression.class);
        inequalityConstraints = new DynamicVectorFunction(exps, origSymbols);
    }
    AugmentedObjectiveFunction augmentedObjFunc = new AugmentedObjectiveFunction(objFunction, equalityConstraints, inequalityConstraints, power, mu, optSolverCallbacks);
    return augmentedObjFunc;
}