Example usage for org.apache.commons.math3.optimization.direct NelderMeadSimplex NelderMeadSimplex

Introduction

In this page you can find the example usage for org.apache.commons.math3.optimization.direct NelderMeadSimplex NelderMeadSimplex.

Prototype

public NelderMeadSimplex(final double[][] referenceSimplex) 

Source Link

Document

Build a Nelder-Mead simplex with default coefficients.

Usage

From source file:edu.stanford.cfuller.imageanalysistools.fitting.GaussianFitter3D.java

/**
 * Fits a 3D Gaussian to a supplied object, starting from an initial guess of the parameters of that Gaussian.
 *
 * The Gaussian is contrained to be symmetric in the x and y dimensions (that is, it will have equal variance in both dimensions).
 *
 * @param toFit         The {@link ImageObject} to be fit to a Gaussian.
 * @param initialGuess  The initial guess at the parameters of the Gaussian.  These must be supplied in the order: amplitude, x-y stddev, z stddev, x position, y position, z position, background.  Positions should be supplied in absolute coordinates from the original image, not relative to the box around the object being fit.
 * @param ppg           The number of photons corresponding to one greylevel in the original image.
 * @return              The best fit Gaussian parameters, in the same order as the initial guess had to be supplied.
 *//* w ww .  j a va 2s  . c o m*/
public RealVector fit(ImageObject toFit, RealVector initialGuess, double ppg) {

    //parameter ordering: amplitude, stddev x-y, stddev z, x/y/z coords, background

    double tol = 1.0e-6;

    SimplexOptimizer nmm = new SimplexOptimizer(tol, tol);

    NelderMeadSimplex nms = new NelderMeadSimplex(initialGuess.getDimension());

    nmm.setSimplex(nms);

    PointValuePair pvp = nmm.optimize(10000000, new MLObjectiveFunction(toFit, ppg),
            org.apache.commons.math3.optimization.GoalType.MINIMIZE, initialGuess.toArray());

    RealVector result = new ArrayRealVector(pvp.getPoint());

    return result;

}

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