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

Example 16 with SimpleReferenceData

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

the class CurveFitting method solve.

public static OptimizationResultSet solve(ExplicitFitObjectiveFunction.ExpressionDataPair[] expDataPairs, Parameter[] parameters, double[] time, double[][] data, String[] colNames, Weights weights) throws ExpressionException, OptimizationException, IOException {
    // choose optimization solver, currently we have Powell and CFSQP
    PowellOptimizationSolver optService = new PowellOptimizationSolver();
    OptimizationSpec optSpec = new OptimizationSpec();
    // create simple reference data, columns: t + dataColumns
    double[][] realData = new double[1 + data.length][time.length];
    for (// add time column
    int i = 0; // add time column
    i < time.length; // add time column
    i++) {
        realData[0][i] = time[i];
    }
    for (// add each data column to realData
    int i = 0; // add each data column to realData
    i < data.length; // add each data column to realData
    i++) {
        for (int j = 0; j < time.length; j++) {
            realData[1 + i][j] = data[i][j];
        }
    }
    SimpleReferenceData refData = new SimpleReferenceData(colNames, weights, realData);
    // send to optimization service
    optSpec.setObjectiveFunction(new ExplicitFitObjectiveFunction(expDataPairs, refData));
    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);
    return optResultSet;
}