Example usage for org.apache.commons.math3.fitting GaussianFitter fit

Introduction

In this page you can find the example usage for org.apache.commons.math3.fitting GaussianFitter fit.

Prototype

public double[] fit(double[] initialGuess) 

Source Link

Document

Fits a Gaussian function to the observed points.

Usage

From source file:edu.ucsc.barrel.cdf_gen.SpectrumExtract.java

private static float find511(double[] x, double[] y) {
    GaussianFitter fitter = new GaussianFitter(new LevenbergMarquardtOptimizer());
    double[] fit_params = { 10, Constants.DOUBLE_FILL, 1 }, curve = new double[PEAK_511_WIDTH - 4];
    int[] high_area = new int[PEAK_511_WIDTH];
    double m, b, slope = 0, this_low = 0, last_low = 0;
    int apex = 0, high_cnt = 0;

    // guess at a linear background
    m = (y[PEAK_511_WIDTH - 1] - y[0]) / (x[PEAK_511_WIDTH - 1] - x[0]);
    b = y[0] - m * x[0];//  w w  w .java  2  s .c o m

    //convert y to cnts/bin_width
    for (int bin_i = 0; bin_i < x.length; bin_i++) {
        y[bin_i] /= (RAW_EDGES[2][bin_i + PEAK_511_START + 1] - RAW_EDGES[2][bin_i + PEAK_511_START]);
    }

    //take the second derivitave to find peak
    for (int bin_i = 2; bin_i < x.length - 2; bin_i++) {
        curve[bin_i - 2] = y[bin_i + 2] - (2 * y[bin_i]) + y[bin_i - 2];
    }

    //find low point of second derivitave using moving average
    this_low = (curve[0] + curve[1] + curve[2]);
    last_low = this_low;
    for (int bin_i = 2; bin_i < curve.length - 1; bin_i++) {
        this_low += (curve[bin_i + 1] - curve[bin_i - 2]);
        if (this_low < last_low) {
            apex = bin_i + 2;
            last_low = this_low;
        }
    }

    //do the curve fit
    try {
        fit_params[1] = x[apex]; //guess for peak location
        for (int bin_i = apex - 3; bin_i < apex + 3; bin_i++) {
            fitter.addObservedPoint(x[bin_i], y[bin_i]);
        }
        fit_params = fitter.fit(fit_params);
    } catch (ArrayIndexOutOfBoundsException ex) {
        System.out.println(
                "Payload ID: " + CDF_Gen.getSetting("currentPayload") + " Date: " + CDF_Gen.getSetting("date"));
        System.out.println("Gaussian out of bounds: " + apex);
        fit_params[1] = Constants.DOUBLE_FILL;
    }
    return (float) fit_params[1];
}

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