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

Example 1 with ObjectiveFunction

use of cbit.vcell.opt.ObjectiveFunction 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;
}