Example usage for org.apache.commons.math.optimization.fitting CurveFitter fit

Introduction

In this page you can find the example usage for org.apache.commons.math.optimization.fitting CurveFitter fit.

Prototype

public double[] fit(final ParametricRealFunction f, final double[] initialGuess)
        throws FunctionEvaluationException, OptimizationException, IllegalArgumentException 

Source Link

Document

Fit a curve.

Usage

From source file:net.bioclipse.brunn.ui.editors.plateEditor.model.HillCurveIC50Calculator.java

public double calculateIC50(double[] conc, double[] si) {

    LevenbergMarquardtOptimizer optimizer = new LevenbergMarquardtOptimizer();

    CurveFitter fitter = new CurveFitter(optimizer);

    for (int i = 0; i < si.length; i++) {
        fitter.addObservedPoint(conc[i], si[i] / 100);
        System.out.println("Added point: " + conc[i] + "; " + si[i] / 100);
    }/*from ww  w . ja  va 2 s  .  com*/

    ParametricRealFunction function = new ParametricRealFunction() {

        @Override
        public double value(double c, double[] paramaters) throws FunctionEvaluationException {

            double d = paramaters[0];
            double n = paramaters[1];
            double c_pow_n = Math.pow(c, n);

            return c_pow_n / (c_pow_n + Math.pow(d, n));
        }

        @Override
        public double[] gradient(double c, double[] paramaters) throws FunctionEvaluationException {

            double d = paramaters[0];
            double n = paramaters[1];
            double c_pow_n = Math.pow(c, n);
            double d_pow_n = Math.pow(d, n);

            double ddd = -n * c_pow_n * Math.pow(d, n - 1) / Math.pow(c_pow_n + d_pow_n, 2);

            double ddn = (c_pow_n * d_pow_n * (Math.log(c) - Math.log(d))) / Math.pow(c_pow_n + d_pow_n, 2);

            return new double[] { ddd, ddn };
        }

    };

    double[] params = null;
    try {
        params = fitter.fit(function, new double[] { 1, 1 });
    } catch (Exception e) {
        Logger.getLogger(HillCurveIC50Calculator.class)
                .debug("Caught Exception while fitting dose response curve", e);
        return Double.NaN;
    }

    double d = params[0];
    double n = params[1];

    System.out.println("d=" + d);
    System.out.println("n=" + n);

    return Math.pow(-(0.5 - 1) * Math.pow(d, -n) / 0.5, -1 / n);
}

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