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

Example 1 with PdeObjectiveFunction

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

the class CurveFitting method solveSpatial.

public static OptimizationResultSet solveSpatial(Simulation sim, Parameter[] parameters, SpatialReferenceData refData, File dataDir, FieldDataIdentifierSpec[] fieldDataIDSs) throws ExpressionException, OptimizationException, IOException {
    // choose optimization solver, currently we have Powell
    PowellOptimizationSolver optService = new PowellOptimizationSolver();
    OptimizationSpec optSpec = new OptimizationSpec();
    // send to optimization service
    optSpec.setObjectiveFunction(new PdeObjectiveFunction(sim.getMathDescription(), refData, dataDir, fieldDataIDSs));
    double[] parameterValues = new double[parameters.length];
    for (int i = 0; i < parameters.length; i++) {
        parameterValues[i] = parameters[i].getInitialGuess();
        System.out.println("initial " + parameters[i].getName() + " = " + parameterValues[i] + ";\tLB = " + parameters[i].getLowerBound() + ";\tUB = " + parameters[i].getUpperBound());
    }
    // get the initial guess to send it to the f() function. ....
    for (int i = 0; i < parameters.length; i++) {
        optSpec.addParameter(parameters[i]);
    }
    // Parameters in OptimizationSolverSpec are solver type and objective function change tolerance.
    OptimizationSolverSpec optSolverSpec = new OptimizationSolverSpec(OptimizationSolverSpec.SOLVERTYPE_POWELL, 0.000001);
    OptSolverCallbacks optSolverCallbacks = new DefaultOptSolverCallbacks();
    OptimizationResultSet optResultSet = null;
    optResultSet = optService.solve(optSpec, optSolverSpec, optSolverCallbacks);
    OptSolverResultSet optSolverResultSet = optResultSet.getOptSolverResultSet();
    String[] paramNames = optSolverResultSet.getParameterNames();
    double[] paramValues = optSolverResultSet.getBestEstimates();
    for (int i = 0; i < paramNames.length; i++) {
        System.out.println("finally:   " + paramNames[i] + " = " + paramValues[i]);
    }
    return optResultSet;
}

Example 2 with PdeObjectiveFunction

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

the class CurveFitting method solveSpatial.

public static OptimizationResultSet solveSpatial(Simulation sim, Parameter[] parameters, SpatialReferenceData refData, File dataDir, FieldDataIdentifierSpec[] fieldDataIDSs) throws ExpressionException, OptimizationException, IOException {
    // choose optimization solver, currently we have Powell and CFSQP
    PowellOptimizationSolver optService = new PowellOptimizationSolver();
    OptimizationSpec optSpec = new OptimizationSpec();
    // send to optimization service
    optSpec.setObjectiveFunction(new PdeObjectiveFunction(sim.getMathDescription(), refData, dataDir, fieldDataIDSs));
    double[] parameterValues = new double[parameters.length];
    for (int i = 0; i < parameters.length; i++) {
        parameterValues[i] = parameters[i].getInitialGuess();
        System.out.println("initial " + parameters[i].getName() + " = " + parameterValues[i] + ";\tLB = " + parameters[i].getLowerBound() + ";\tUB = " + parameters[i].getUpperBound());
    }
    // get the initial guess to send it to the f() function. ....
    for (int i = 0; i < parameters.length; i++) {
        optSpec.addParameter(parameters[i]);
    }
    // Parameters in OptimizationSolverSpec are solver type and objective function change tolerance.
    OptimizationSolverSpec optSolverSpec = new OptimizationSolverSpec(OptimizationSolverSpec.SOLVERTYPE_POWELL, 0.000001);
    OptSolverCallbacks optSolverCallbacks = new DefaultOptSolverCallbacks();
    OptimizationResultSet optResultSet = null;
    optResultSet = optService.solve(optSpec, optSolverSpec, optSolverCallbacks);
    OptSolverResultSet optSolverResultSet = optResultSet.getOptSolverResultSet();
    String[] paramNames = optSolverResultSet.getParameterNames();
    double[] paramValues = optSolverResultSet.getBestEstimates();
    for (int i = 0; i < paramNames.length; i++) {
        System.out.println("finally:   " + paramNames[i] + " = " + paramValues[i]);
    }
    return optResultSet;
}

Example 3 with PdeObjectiveFunction

use of cbit.vcell.opt.PdeObjectiveFunction 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;
}