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

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

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///////////////////////////////////////////////////////////////////////////////
//FILE:          TestSaimErrorFunctionFitter.java
//PROJECT:       SAIM
//SUBSYSTEM:     Tests  
//-----------------------------------------------------------------------------
//
// 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 edu.ucsf.valelab.saim.data.SaimData;
import java.util.ArrayList;
import junit.framework.TestCase;
import org.apache.commons.math3.fitting.WeightedObservedPoint;

/**
 *
 * @author nico
 */
public class TestSaimErrorFunctionFitter extends TestCase {
    public TestSaimErrorFunctionFitter(String testName) {
        super(testName);
    }

    public void test() throws Exception {
        SaimData data = new SaimData();

        data.wavelength_ = 488.0;
        data.nSample_ = 1.36;
        data.dOx_ = 500.0;
        data.A_ = 1000.0;
        data.B_ = 5000.0;
        data.heights_ = new double[] { 75.0 };

        double maxError = 0.00000000001;
        int nrRepeats = 5;

        // make a collection of "observed" points
        ArrayList<WeightedObservedPoint> points = new ArrayList<WeightedObservedPoint>();
        for (int i = -50; i <= 50; i += 1) {
            double angle = Math.toRadians(i);
            double I = data.A_
                    * SaimCalc.fieldStrength(data.wavelength_, angle, data.nSample_, data.dOx_, data.heights_[0])
                    + data.B_;
            WeightedObservedPoint point = new WeightedObservedPoint(1.0, angle, I);
            points.add(point);
        }
        System.out.println("BOBYQA Test results (TestSaimErrorFunctionFitter:");
        System.out.println("Goal: " + data.A_ + ", " + data.B_ + ", " + data.heights_[0]);

        for (int i = 0; i < nrRepeats; i++) {
            SaimErrorFunctionFitter sef = new SaimErrorFunctionFitter(data);
            double[] guess = { Math.random() * 4000.0, Math.random() * 10000.0, Math.random() * 300.0 };
            sef.setGuess(guess);
            double[] result = sef.fit(points);
            System.out.println("Guess: " + guess[0] + ", " + guess[1] + ", " + guess[2]);
            System.out.println("Result: " + result[0] + ", " + result[1] + ", " + result[2]);

        }
    }

}