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

Introduction

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

Prototype

public void addObservedPoint(double x, double y) 

Source Link

Document

Add an observed (x,y) point to the sample with unit weight.

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);
    }/* w  ww . ja  v  a  2s.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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