edu.ucsf.valelab.saim.calculations.TestSaimFitter.java Source code

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Here is the source code for edu.ucsf.valelab.saim.calculations.TestSaimFitter.java

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///////////////////////////////////////////////////////////////////////////////
//FILE:          TestSaimFitter.java
//PROJECT:       SAIM
//-----------------------------------------------------------------------------
//
// AUTHOR:       Nico Stuurman
//
// COPYRIGHT:    University of California, San Francisco 2015
//
// LICENSE:      This file is distributed under the BSD license.
//               License text is included with the source distribution.
//
//               This file is distributed in the hope that it will be useful,
//               but WITHOUT ANY WARRANTY; without even the implied warranty
//               of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
//
//               IN NO EVENT SHALL THE COPYRIGHT OWNER OR
//               CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
//               INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES.

package edu.ucsf.valelab.saim.calculations;

import java.util.ArrayList;
import junit.framework.TestCase;
import org.apache.commons.math3.fitting.WeightedObservedPoint;

/**
 *
 * @author nico
 */
public class TestSaimFitter extends TestCase {

    public TestSaimFitter(String testName) {
        super(testName);
    }

    public void test() throws Exception {
        double wavelength = 488.0;
        double nSample = 1.36;
        double dOx = 500.0;

        double A = 100.0;
        double B = 100.0;
        double h = 16.0;

        double fractionMaxError = 0.0000001;
        final int nrTries = 10;

        // make a collection of "observed" points
        ArrayList<WeightedObservedPoint> points = new ArrayList<WeightedObservedPoint>();
        for (int i = -50; i <= 50; i += 2) {
            double angle = Math.toRadians(i);
            double I = A * SaimCalc.fieldStrength(wavelength, angle, nSample, dOx, h) + B;
            WeightedObservedPoint point = new WeightedObservedPoint(1.0, angle, I);
            points.add(point);
        }

        // create the fitter
        SaimFunctionFitter sff = new SaimFunctionFitter(wavelength, dOx, nSample, false);
        double[] values = new double[] { A, B, h };

        // test by varying the input for height
        for (int i = 0; i < nrTries; i++) {
            double[] guess = values.clone();
            guess[0] = 50.0;
            guess[1] = 150.0;
            guess[2] = guess[2] + (guess[2] * (Math.random() - 0.5) * 10);
            if (guess[2] < 1.0)
                guess[2] = 1.0;
            for (int j = 0; j < guess.length; j++) {
                System.out.println("Guess: " + j + " " + guess[j]);
            }

            sff.setGuess(guess);

            final double[] coefficients = sff.fit(points);
            for (int j = 0; j < coefficients.length; j++) {
                System.out
                        .println("coefficient " + j + ", expected:  " + values[j] + ", found: " + coefficients[j]);
                assertEquals(values[j], coefficients[j], values[j] * fractionMaxError);
            }

            System.out.println("Value was calculated: " + sff.getCalcCount() + " times");
            sff.resetCalcCount();
        }

        // test by adding noise to the input
        // make a collection of "observed" points
        final double noiseFactor = 0.1; // 10% noise
        fractionMaxError = noiseFactor;

        double[] guess = values.clone();
        guess[0] = 50.0;
        guess[1] = 150.0;
        guess[2] = 50.0;
        for (int j = 0; j < guess.length; j++) {
            System.out.println("Guess: " + j + " " + guess[j]);
        }

        for (int i = 0; i < nrTries; i++) {
            ArrayList<WeightedObservedPoint> noisyPoints = new ArrayList<WeightedObservedPoint>();
            for (int j = -50; j <= 50; j += 2) {
                double angle = Math.toRadians(j);
                double I = A * SaimCalc.fieldStrength(wavelength, angle, nSample, dOx, h) + B;
                WeightedObservedPoint noisyPoint = new WeightedObservedPoint(1.0, angle,
                        I + I * (Math.random() - 0.5) * noiseFactor);
                noisyPoints.add(noisyPoint);
            }

            sff.setGuess(guess);

            final double[] coefficients = sff.fit(noisyPoints);
            for (int j = 0; j < coefficients.length; j++) {
                System.out
                        .println("coefficient " + j + ", expected:  " + values[j] + ", found: " + coefficients[j]);
                assertEquals(values[j], coefficients[j], values[j] * fractionMaxError);
            }

            System.out.println("Value was calculated: " + sff.getCalcCount() + " times");
            sff.resetCalcCount();
        }

    }
}