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

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

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///////////////////////////////////////////////////////////////////////////////
//FILE:          SaimFunctionFitter.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.Collection;
import org.apache.commons.math3.exception.DimensionMismatchException;
import org.apache.commons.math3.fitting.AbstractCurveFitter;
import org.apache.commons.math3.fitting.WeightedObservedPoint;
import org.apache.commons.math3.fitting.leastsquares.LeastSquaresBuilder;
import org.apache.commons.math3.fitting.leastsquares.LeastSquaresProblem;
import org.apache.commons.math3.fitting.leastsquares.ParameterValidator;
import org.apache.commons.math3.linear.DiagonalMatrix;
import org.apache.commons.math3.optim.ConvergenceChecker;
import org.apache.commons.math3.optim.PointVectorValuePair;
import org.apache.commons.math3.optim.SimpleVectorValueChecker;

/**
 * Fits the Saim function using pre-defined wavelength, thickness of the oxide
 * layer, and refractive index of the sample
 *
 * @author nico
 */
public class SaimFunctionFitter extends AbstractCurveFitter {

    private final SaimFunction saimFunction_;
    private double[] guess_ = { 1.0, 1.0, 1.0 };
    private int maxIterations_ = 100;

    public SaimFunctionFitter(double wavelength, double dOx, double nSample, boolean useBAngle) {
        saimFunction_ = new SaimFunction(wavelength, dOx, nSample, useBAngle);
    }

    public void setGuess(double[] guess) {
        if (guess.length != 3) {
            throw new DimensionMismatchException(guess.length, 3);
        }
        guess_ = guess;
    }

    public void setMaxIterations(int val) {
        maxIterations_ = val;
    }

    public int getCalcCount() {
        return saimFunction_.counter;
    }

    public void resetCalcCount() {
        saimFunction_.counter = 0;
    }

    @Override
    protected LeastSquaresProblem getProblem(Collection<WeightedObservedPoint> points) {
        final int len = points.size();
        final double[] target = new double[len];
        final double[] weights = new double[len];

        int i = 0;
        for (WeightedObservedPoint point : points) {
            target[i] = point.getY();
            weights[i] = point.getWeight();
            i += 1;
        }

        final AbstractCurveFitter.TheoreticalValuesFunction model = new AbstractCurveFitter.TheoreticalValuesFunction(
                saimFunction_, points);

        ConvergenceChecker<PointVectorValuePair> checker = new SimpleVectorValueChecker(1.0e-6, 1.0e-10);

        // this parameter validator appears to have the same effect
        // as using the SaimFunctionFitterWithBounds
        double[] lowerBounds = { 0.0, 0.0, 0.0 };
        double[] upperBounds = { 64000, 64000, 1000 };
        ParameterValidator spv = new SaimParameterValidator(lowerBounds, upperBounds);

        return new LeastSquaresBuilder().maxEvaluations(Integer.MAX_VALUE).maxIterations(maxIterations_)
                .lazyEvaluation(true).
                //checker(checker).
                start(guess_).target(target).parameterValidator(spv).weight(new DiagonalMatrix(weights))
                .model(model.getModelFunction(), model.getModelFunctionJacobian()).build();
    }

}