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

Example 11 with OptSolverResultSet

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

the class OptXmlReader method getOptimizationResultSet.

public static OptSolverResultSet getOptimizationResultSet(String xmlString) {
    Element optResultSetElement = stringToXML(xmlString);
    if (!optResultSetElement.getName().equals(OptXmlTags.OptSolverResultSet_Tag)) {
        throw new RuntimeException("unexpected element '" + optResultSetElement.getName() + "', expecting " + OptXmlTags.OptSolverResultSet_Tag);
    }
    List<Element> paramElementList = optResultSetElement.getChildren(OptXmlTags.Parameter_Tag);
    String[] parameterNames = new String[paramElementList.size()];
    int count = 0;
    for (Element parameterElement : paramElementList) {
        parameterNames[count] = parameterElement.getAttributeValue(OptXmlTags.ParameterName_Attr);
        count++;
    }
    Element bestRunElement = optResultSetElement.getChild(OptXmlTags.bestOptRunResultSet_Tag);
    try {
        OptRunResultSet bestResultSet = getOptRunResultSet(bestRunElement);
        OptSolverResultSet optResultSet = new OptSolverResultSet(parameterNames, bestResultSet);
        return optResultSet;
    } catch (DataConversionException e) {
        e.printStackTrace(System.out);
        throw new RuntimeException(e.getMessage());
    }
}

Example 12 with OptSolverResultSet

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

the class PowellOptimizationSolver method solve.

/**
 * Insert the method's description here.
 * Creation date: (3/5/00 11:15:15 PM)
 * @return double[]
 * @param optSpec cbit.vcell.opt.OptimizationSpec
 * @exception java.io.IOException The exception description.
 * @exception cbit.vcell.parser.ExpressionException The exception description.
 * @exception cbit.vcell.opt.OptimizationException The exception description.
 */
public OptimizationResultSet solve(OptimizationSpec os, OptimizationSolverSpec optSolverSpec, OptSolverCallbacks optSolverCallbacks) throws java.io.IOException, cbit.vcell.parser.ExpressionException, OptimizationException {
    final double power = 2.0;
    final double MU_START = 0.1;
    final double MU_END = 100000.0;
    final double MU_STEP = 10.0;
    AugmentedObjectiveFunction augmentedObjFunc = OptUtils.getAugmentedObjectiveFunction(os, power, MU_START, optSolverCallbacks);
    // 
    // initialize starting guess
    // 
    Parameter[] parameters = os.getParameters();
    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]);
    }
    // 
    // get initial direction set
    // 
    double[][] xi = new double[parameterValues.length][parameterValues.length];
    for (int i = 0; i < parameterValues.length; i++) {
        for (int j = 0; j < parameterValues.length; j++) {
            xi[i][j] = (i == j ? 1.0 : 0.0);
        }
    }
    final double ftol = 1e-6;
    double fret = augmentedObjFunc.f(parameterValues);
    PowellSolver powellSolver = new PowellSolver();
    for (double mu = MU_START; mu <= MU_END; mu *= MU_STEP) {
        try {
            if (optSolverCallbacks.getStopRequested()) {
                break;
            }
            augmentedObjFunc.setMu(mu);
            fret = powellSolver.powell(parameterValues.length, parameterValues, xi, ftol, augmentedObjFunc);
            System.out.println("mu=" + mu + ", function value=" + fret);
            if (augmentedObjFunc.getPenalty(parameterValues) == 0.0) {
                break;
            }
        } catch (Exception ex) {
            ex.printStackTrace();
            break;
        }
    }
    OptimizationStatus optStatus = new OptimizationStatus(OptimizationStatus.NORMAL_TERMINATION, "Normal Termination");
    ODESolverResultSet odeSolverResultSet = null;
    if (optSolverCallbacks.getStopRequested()) {
        optStatus = new OptimizationStatus(OptimizationStatus.STOPPED_BY_USER, "Stopped by user");
    }
    parameterValues = optSolverCallbacks.getBestEvaluation().getParameterValues();
    fret = optSolverCallbacks.getBestEvaluation().getObjectiveFunctionValue();
    odeSolverResultSet = optSolverCallbacks.getBestResultSet();
    for (int i = 0; i < parameters.length; i++) {
        System.out.println("final " + parameters[i].getName() + " = " + parameterValues[i]);
    }
    OptRunResultSet bestResult = new OptRunResultSet(parameterValues, new Double(fret), optSolverCallbacks.getEvaluationCount(), optStatus);
    return new OptimizationResultSet(new OptSolverResultSet(os.getParameterNames(), bestResult), odeSolverResultSet);
}

Example 13 with OptSolverResultSet

use of cbit.vcell.opt.OptSolverResultSet 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;
}