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

Introduction

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

Source

///////////////////////////////////////////////////////////////////////////////
//FILE:          TestSaimErrorFunction.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 TestSaimErrorFunction extends TestCase {

    public TestSaimErrorFunction(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 = 0.0000000001;

        // 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);
        }
        // calculate the error with these ideal points (shoudle be 0)
        SaimErrorFunction sef = new SaimErrorFunction(data, points);
        double[] parameters = { data.A_, data.B_, data.heights_[0] };
        double error = sef.value(parameters);

        System.out.println("SaimError error: " + error);
        assertEquals(0.0, error, maxError);

        // now add 1 to all the data points.  Error should be number of data points
        ArrayList<WeightedObservedPoint> newPoints = new ArrayList<WeightedObservedPoint>();
        for (WeightedObservedPoint point : points) {
            newPoints.add(new WeightedObservedPoint(1.0, point.getX(), point.getY() + 1.0));
        }
        SaimErrorFunction sef2 = new SaimErrorFunction(data, newPoints);
        error = sef2.value(parameters);

        System.out.println("SaimError error: " + error);
        assertEquals(points.size(), error, maxError);

    }
}