Examples with DefaultOptSolverCallbacks org.vcell.optimization.DefaultOptSolverCallbacks used on opensource projects

Example 6 with DefaultOptSolverCallbacks

use of org.vcell.optimization.DefaultOptSolverCallbacks in project vcell by virtualcell.

the class AugmentedObjectiveFunctionTest method getExample2.

/**
 * Insert the method's description here.                    // Root-finding example
 * Creation date: (5/3/2002 2:49:06 PM)
 * @return opt.AugmentedObjectiveFunction
 */
public static AugmentedObjectiveFunction getExample2() {
    try {
        Expression scalarFn_exp = new Expression("1");
        Expression[] eqConstraints_exps = { new Expression("sin(x1+x2)-exp(x1-x2)"), new Expression("cos(x1+x2)-x1*x1*x2*x2") };
        Expression[] ineqConstraints_exps = {};
        String[] ids = { "x1", "x2" };
        ScalarFunction scalarFn = new DynamicScalarFunction(scalarFn_exp, ids);
        VectorFunction eqConstraints = new DynamicVectorFunction(eqConstraints_exps, ids);
        VectorFunction ineqConstraints = new DynamicVectorFunction(ineqConstraints_exps, ids);
        AugmentedObjectiveFunction aof = new AugmentedObjectiveFunction(scalarFn, eqConstraints, ineqConstraints, 2.0, 0.1, new DefaultOptSolverCallbacks());
        return aof;
    } catch (ExpressionException e) {
        e.printStackTrace();
        throw new RuntimeException(e.getMessage());
    }
}

Example 7 with DefaultOptSolverCallbacks

use of org.vcell.optimization.DefaultOptSolverCallbacks 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
    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;
}

Example 8 with DefaultOptSolverCallbacks

use of org.vcell.optimization.DefaultOptSolverCallbacks 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;
}

Example 9 with DefaultOptSolverCallbacks

use of org.vcell.optimization.DefaultOptSolverCallbacks 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;
}