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

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///////////////////////////////////////////////////////////////////////////////
//FILE:          SaimErrorFunction.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 edu.ucsf.valelab.saim.data.SaimData;
import java.util.Collection;
import java.util.HashMap;
import java.util.Map;
import org.apache.commons.math3.analysis.MultivariateFunction;
import org.apache.commons.math3.complex.Complex;
import org.apache.commons.math3.exception.DimensionMismatchException;
import org.apache.commons.math3.fitting.WeightedObservedPoint;

/**
 * Calculates the error (as sum of absolute errors) between given set of 
 * data points and theoretical prediction given A, B, and h).
 * 
 * @author nico
 */
public class SaimErrorFunction implements MultivariateFunction {

    private final Collection<WeightedObservedPoint> observedPoints_;
    // note that we only use wavelength, dOx and nSample from SaimData
    private final SaimData data_;
    private final Map<Double, Complex> fresnelTE_;

    public SaimErrorFunction(SaimData data, Collection<WeightedObservedPoint> observedPoints) {
        data_ = data;
        observedPoints_ = observedPoints;
        fresnelTE_ = new HashMap<Double, Complex>(observedPoints_.size());
        // pre-calculate all the fresnel coefficients
        for (WeightedObservedPoint observedPoint : observedPoints_) {
            double angle = observedPoint.getX();
            Complex val = SaimCalc.fresnelTE(data_.wavelength_, angle, data_.dOx_, data_.nSample_);
            fresnelTE_.put(angle, val);
        }
    }

    /**
     * For each observedPoint.getX calculates the predicted intensity
     * Returns the sum of absolute errors
     * @param point {A, B, h}
     * @return sum of absolute errors
     */
    @Override
    public double value(double[] point) {
        if (point.length != 3) {
            throw new DimensionMismatchException(point.length, 3);
        }

        double A = point[0];
        double B = point[1];
        double h = point[2];

        double error = 0.0;
        for (WeightedObservedPoint observedPoint : observedPoints_) {
            double angle = observedPoint.getX();
            Complex rTE = fresnelTE_.get(angle);
            double phaseDiff = SaimCalc.PhaseDiff(data_.wavelength_, angle, data_.nSample_, h);
            double c = rTE.getReal();
            double d = rTE.getImaginary();
            double val = 1 + 2 * c * Math.cos(phaseDiff) - 2 * d * Math.sin(phaseDiff) + c * c + d * d;
            error += Math.abs(A * val + B - observedPoint.getY());
        }
        return error;
    }

}