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

Introduction

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

Prototype

public CurveFitter(final DifferentiableMultivariateVectorialOptimizer optimizer) 

Source Link

Document

Simple constructor.

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 w  w  w.  j  a va 2 s.  co  m

    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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