de.bund.bfr.math.VectorFunction.java Source code

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Here is the source code for de.bund.bfr.math.VectorFunction.java

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/*******************************************************************************
 * Copyright (c) 2016 German Federal Institute for Risk Assessment (BfR)
 *
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 *
 * Contributors:
 *     Department Biological Safety - BfR
 *******************************************************************************/
package de.bund.bfr.math;

import java.util.ArrayList;
import java.util.List;
import java.util.Map;

import org.apache.commons.math3.analysis.MultivariateMatrixFunction;
import org.sbml.jsbml.ASTNode;
import org.sbml.jsbml.text.parser.ParseException;

import com.google.common.primitives.Doubles;

public class VectorFunction implements ValueAndJacobianFunction {

    private String formula;
    private List<String> parameters;
    private Map<String, List<Double>> variableValues;

    private Parser parser;
    private ASTNode function;

    public VectorFunction(String formula, List<String> parameters, Map<String, List<Double>> variableValues)
            throws ParseException {
        this.formula = formula;
        this.parameters = parameters;
        this.variableValues = variableValues;

        parser = new Parser();
        function = parser.parse(formula);
    }

    @Override
    public double[] value(double[] point) throws IllegalArgumentException {
        List<Double> result = new ArrayList<>();

        for (int i = 0; i < parameters.size(); i++) {
            parser.setVarValue(parameters.get(i), point[i]);
        }

        int n = variableValues.values().stream().findAny().get().size();

        for (int i = 0; i < n; i++) {
            for (Map.Entry<String, List<Double>> entry : variableValues.entrySet()) {
                parser.setVarValue(entry.getKey(), entry.getValue().get(i));
            }

            try {
                double value = parser.evaluate(function);

                result.add(Double.isFinite(value) ? value : Double.NaN);
            } catch (ParseException e) {
                e.printStackTrace();
                result.add(Double.NaN);
            }
        }

        return Doubles.toArray(result);
    }

    @Override
    public MultivariateMatrixFunction createJacobian() {
        List<VectorFunction> diffFunctions = new ArrayList<>();

        for (int i = 0; i < parameters.size(); i++) {
            try {
                diffFunctions.add(new VectorFunction(formula, parameters, variableValues));
            } catch (ParseException e) {
            }
        }

        return point -> MathUtils.aproxJacobianParallel(diffFunctions, point,
                variableValues.values().stream().findAny().get().size());
    }
}