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

Example 1 with ProfileDistribution

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

the class ReactionDominantTest method solve.

private OptimizationResultSet solve() throws ExpressionException, IOException {
    Expression Fbleached_bleachFastExp = new Expression(Fbleached_bleachFast);
    Expression OmegaExp = new Expression(strOmega);
    Expression Omega_cExp = new Expression(strOmega_c);
    Expression WExp = new Expression(strW);
    Fbleached_bleachFastExp.substituteInPlace(OmegaExp, new Expression(Omega));
    Fbleached_bleachFastExp.substituteInPlace(Omega_cExp, new Expression(Omega_c));
    Fbleached_bleachFastExp.substituteInPlace(WExp, new Expression(W));
    Parameter[] parameters = new Parameter[] { para_alpha, para_Kon_star, para_Koff };
    // Expression Fbleached_bleachFast = Fbleached_bleachFastExp.flatten();
    // choose optimization solver, currently we have Powell and CFSQP
    PowellOptimizationSolver optService = new PowellOptimizationSolver();
    OptimizationSpec optSpec = new OptimizationSpec();
    // create simple reference data
    double[][] realData = new double[2][t.length];
    for (int i = 0; i < t.length; i++) {
        realData[0][i] = t[i];
        realData[1][i] = data_bleached[i];
    }
    String[] colNames = new String[] { "t", "intensity" };
    double[] weights = new double[] { 1.0, 1.0 };
    SimpleReferenceData refData = new SimpleReferenceData(colNames, weights, realData);
    // send to optimization service
    ExplicitFitObjectiveFunction.ExpressionDataPair oneExpDataPair = new ExplicitFitObjectiveFunction.ExpressionDataPair(Fbleached_bleachFastExp.flatten(), 1);
    ExplicitFitObjectiveFunction.ExpressionDataPair[] expDataPairs = new ExplicitFitObjectiveFunction.ExpressionDataPair[] { oneExpDataPair };
    optSpec.setObjectiveFunction(new ExplicitFitObjectiveFunction(expDataPairs, refData));
    optSpec.setComputeProfileDistributions(true);
    // 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);
    String[] paramNames = optResultSet.getOptSolverResultSet().getParameterNames();
    ArrayList<ProfileDistribution> profileDistributionList = optResultSet.getOptSolverResultSet().getProfileDistributionList();
    for (int i = 0; i < profileDistributionList.size(); i++) {
        outputProfileLikelihood(profileDistributionList.get(i), i, paramNames[i], new File(fileDir));
    }
    return optResultSet;
}