Java example source code file (HarmonicFitter.java)

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Java - Java tags/keywords

deprecated, harmonicfitter, multivariatevectoroptimizer, parameterguesser, weightedobservedpoint, zeroexception

The HarmonicFitter.java Java example source code

/*
 * Licensed to the Apache Software Foundation (ASF) under one or more
 * contributor license agreements.  See the NOTICE file distributed with
 * this work for additional information regarding copyright ownership.
 * The ASF licenses this file to You under the Apache License, Version 2.0
 * (the "License"); you may not use this file except in compliance with
 * the License.  You may obtain a copy of the License at
 *
 *      http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */
package org.apache.commons.math3.fitting;

import org.apache.commons.math3.optim.nonlinear.vector.MultivariateVectorOptimizer;
import org.apache.commons.math3.analysis.function.HarmonicOscillator;
import org.apache.commons.math3.exception.ZeroException;
import org.apache.commons.math3.exception.NumberIsTooSmallException;
import org.apache.commons.math3.exception.MathIllegalStateException;
import org.apache.commons.math3.exception.util.LocalizedFormats;
import org.apache.commons.math3.util.FastMath;

/**
 * Class that implements a curve fitting specialized for sinusoids.
 *
 * Harmonic fitting is a very simple case of curve fitting. The
 * estimated coefficients are the amplitude a, the pulsation ? and
 * the phase ?: <code>f (t) = a cos (? t + ?). They are
 * searched by a least square estimator initialized with a rough guess
 * based on integrals.
 *
 * @since 2.0
 * @deprecated As of 3.3. Please use {@link HarmonicCurveFitter} and
 * {@link WeightedObservedPoints} instead.
 */
@Deprecated
public class HarmonicFitter extends CurveFitter<HarmonicOscillator.Parametric> {
    /**
     * Simple constructor.
     * @param optimizer Optimizer to use for the fitting.
     */
    public HarmonicFitter(final MultivariateVectorOptimizer optimizer) {
        super(optimizer);
    }

    /**
     * Fit an harmonic function to the observed points.
     *
     * @param initialGuess First guess values in the following order:
     * <ul>
     *  <li>Amplitude
     *  <li>Angular frequency
     *  <li>Phase
     * </ul>
     * @return the parameters of the harmonic function that best fits the
     * observed points (in the same order as above).
     */
    public double[] fit(double[] initialGuess) {
        return fit(new HarmonicOscillator.Parametric(), initialGuess);
    }

    /**
     * Fit an harmonic function to the observed points.
     * An initial guess will be automatically computed.
     *
     * @return the parameters of the harmonic function that best fits the
     * observed points (see the other {@link #fit(double[]) fit} method.
     * @throws NumberIsTooSmallException if the sample is too short for the
     * the first guess to be computed.
     * @throws ZeroException if the first guess cannot be computed because
     * the abscissa range is zero.
     */
    public double[] fit() {
        return fit((new ParameterGuesser(getObservations())).guess());
    }

    /**
     * This class guesses harmonic coefficients from a sample.
     * <p>The algorithm used to guess the coefficients is as follows:

     *
     * <p>We know f (t) at some sampling points ti and want to find a,
     * ? and ? such that f (t) = a cos (? t + ?).
     * </p>
     *
     * <p>From the analytical expression, we can compute two primitives :
     * <pre>
     *     If2  (t) = ? f<sup>2  = a2 × [t + S (t)] / 2
     *     If'2 (t) = ? f'<sup>2 = a2 ?2 × [t - S (t)] / 2
     *     where S (t) = sin (2 (? t + ?)) / (2 ?)
     * </pre>
     * </p>
     *
     * <p>We can remove S between these expressions :
     * <pre>
     *     If'2 (t) = a<sup>2 ?2 t - ?2 If2 (t)
     * </pre>
     * </p>
     *
     * <p>The preceding expression shows that If'2 (t) is a linear
     * combination of both t and If2 (t): If'2 (t) = A × t + B × If2 (t)
     * </p>
     *
     * <p>From the primitive, we can deduce the same form for definite
     * integrals between t<sub>1 and ti for each ti :
     * <pre>
     *   If2 (t<sub>i) - If2 (t1) = A × (ti - t1) + B × (If2 (ti) - If2 (t1))
     * </pre>
     * </p>
     *
     * <p>We can find the coefficients A and B that best fit the sample
     * to this linear expression by computing the definite integrals for
     * each sample points.
     * </p>
     *
     * <p>For a bilinear expression z (xi, yi) = A × xi + B × yi, the
     * coefficients A and B that minimize a least square criterion
     * ? (z<sub>i - z (xi, yi))2 are given by these expressions:

     * <pre>
     *
     *         ?y<sub>iyi ?xizi - ?xiyi ?yizi
     *     A = ------------------------
     *         ?x<sub>ixi ?yiyi - ?xiyi ?xiyi
     *
     *         ?x<sub>ixi ?yizi - ?xiyi ?xizi
     *     B = ------------------------
     *         ?x<sub>ixi ?yiyi - ?xiyi ?xiyi
     * </pre>
     * </p>
     *
     *
     * <p>In fact, we can assume both a and ? are positive and
     * compute them directly, knowing that A = a<sup>2 ?2 and that
     * B = - ?<sup>2. The complete algorithm is therefore:

     * <pre>
     *
     * for each t<sub>i from t1 to tn-1, compute:
     *   f  (t<sub>i)
     *   f' (t<sub>i) = (f (ti+1) - f(ti-1)) / (ti+1 - ti-1)
     *   x<sub>i = ti - t1
     *   y<sub>i = ? f2 from t1 to ti
     *   z<sub>i = ? f'2 from t1 to ti
     *   update the sums ?x<sub>ixi, ?yiyi, ?xiyi, ?xizi and ?yizi
     * end for
     *
     *            |--------------------------
     *         \  | ?y<sub>iyi ?xizi - ?xiyi ?yizi
     * a     =  \ | ------------------------
     *           \| ?x<sub>iyi ?xizi - ?xixi ?yizi
     *
     *
     *            |--------------------------
     *         \  | ?x<sub>iyi ?xizi - ?xixi ?yizi
     * ?     =  \ | ------------------------
     *           \| ?x<sub>ixi ?yiyi - ?xiyi ?xiyi
     *
     * </pre>
     * </p>
     *
     * <p>Once we know ?, we can compute:
     * <pre>
     *    fc = ? f (t) cos (? t) - f' (t) sin (? t)
     *    fs = ? f (t) sin (? t) + f' (t) cos (? t)
     * </pre>
     * </p>
     *
     * <p>It appears that fc = a ? cos (?) and
     * <code>fs = -a ? sin (?), so we can use these
     * expressions to compute ?. The best estimate over the sample is
     * given by averaging these expressions.
     * </p>
     *
     * <p>Since integrals and means are involved in the preceding
     * estimations, these operations run in O(n) time, where n is the
     * number of measurements.</p>
     */
    public static class ParameterGuesser {
        /** Amplitude. */
        private final double a;
        /** Angular frequency. */
        private final double omega;
        /** Phase. */
        private final double phi;

        /**
         * Simple constructor.
         *
         * @param observations Sampled observations.
         * @throws NumberIsTooSmallException if the sample is too short.
         * @throws ZeroException if the abscissa range is zero.
         * @throws MathIllegalStateException when the guessing procedure cannot
         * produce sensible results.
         */
        public ParameterGuesser(WeightedObservedPoint[] observations) {
            if (observations.length < 4) {
                throw new NumberIsTooSmallException(LocalizedFormats.INSUFFICIENT_OBSERVED_POINTS_IN_SAMPLE,
                                                    observations.length, 4, true);
            }

            final WeightedObservedPoint[] sorted = sortObservations(observations);

            final double aOmega[] = guessAOmega(sorted);
            a = aOmega[0];
            omega = aOmega[1];

            phi = guessPhi(sorted);
        }

        /**
         * Gets an estimation of the parameters.
         *
         * @return the guessed parameters, in the following order:
         * <ul>
         *  <li>Amplitude
         *  <li>Angular frequency
         *  <li>Phase
         * </ul>
         */
        public double[] guess() {
            return new double[] { a, omega, phi };
        }

        /**
         * Sort the observations with respect to the abscissa.
         *
         * @param unsorted Input observations.
         * @return the input observations, sorted.
         */
        private WeightedObservedPoint[] sortObservations(WeightedObservedPoint[] unsorted) {
            final WeightedObservedPoint[] observations = unsorted.clone();

            // Since the samples are almost always already sorted, this
            // method is implemented as an insertion sort that reorders the
            // elements in place. Insertion sort is very efficient in this case.
            WeightedObservedPoint curr = observations[0];
            for (int j = 1; j < observations.length; ++j) {
                WeightedObservedPoint prec = curr;
                curr = observations[j];
                if (curr.getX() < prec.getX()) {
                    // the current element should be inserted closer to the beginning
                    int i = j - 1;
                    WeightedObservedPoint mI = observations[i];
                    while ((i >= 0) && (curr.getX() < mI.getX())) {
                        observations[i + 1] = mI;
                        if (i-- != 0) {
                            mI = observations[i];
                        }
                    }
                    observations[i + 1] = curr;
                    curr = observations[j];
                }
            }

            return observations;
        }

        /**
         * Estimate a first guess of the amplitude and angular frequency.
         * This method assumes that the {@link #sortObservations(WeightedObservedPoint[])} method
         * has been called previously.
         *
         * @param observations Observations, sorted w.r.t. abscissa.
         * @throws ZeroException if the abscissa range is zero.
         * @throws MathIllegalStateException when the guessing procedure cannot
         * produce sensible results.
         * @return the guessed amplitude (at index 0) and circular frequency
         * (at index 1).
         */
        private double[] guessAOmega(WeightedObservedPoint[] observations) {
            final double[] aOmega = new double[2];

            // initialize the sums for the linear model between the two integrals
            double sx2 = 0;
            double sy2 = 0;
            double sxy = 0;
            double sxz = 0;
            double syz = 0;

            double currentX = observations[0].getX();
            double currentY = observations[0].getY();
            double f2Integral = 0;
            double fPrime2Integral = 0;
            final double startX = currentX;
            for (int i = 1; i < observations.length; ++i) {
                // one step forward
                final double previousX = currentX;
                final double previousY = currentY;
                currentX = observations[i].getX();
                currentY = observations[i].getY();

                // update the integrals of f<sup>2 and f'2
                // considering a linear model for f (and therefore constant f')
                final double dx = currentX - previousX;
                final double dy = currentY - previousY;
                final double f2StepIntegral =
                    dx * (previousY * previousY + previousY * currentY + currentY * currentY) / 3;
                final double fPrime2StepIntegral = dy * dy / dx;

                final double x = currentX - startX;
                f2Integral += f2StepIntegral;
                fPrime2Integral += fPrime2StepIntegral;

                sx2 += x * x;
                sy2 += f2Integral * f2Integral;
                sxy += x * f2Integral;
                sxz += x * fPrime2Integral;
                syz += f2Integral * fPrime2Integral;
            }

            // compute the amplitude and pulsation coefficients
            double c1 = sy2 * sxz - sxy * syz;
            double c2 = sxy * sxz - sx2 * syz;
            double c3 = sx2 * sy2 - sxy * sxy;
            if ((c1 / c2 < 0) || (c2 / c3 < 0)) {
                final int last = observations.length - 1;
                // Range of the observations, assuming that the
                // observations are sorted.
                final double xRange = observations[last].getX() - observations[0].getX();
                if (xRange == 0) {
                    throw new ZeroException();
                }
                aOmega[1] = 2 * Math.PI / xRange;

                double yMin = Double.POSITIVE_INFINITY;
                double yMax = Double.NEGATIVE_INFINITY;
                for (int i = 1; i < observations.length; ++i) {
                    final double y = observations[i].getY();
                    if (y < yMin) {
                        yMin = y;
                    }
                    if (y > yMax) {
                        yMax = y;
                    }
                }
                aOmega[0] = 0.5 * (yMax - yMin);
            } else {
                if (c2 == 0) {
                    // In some ill-conditioned cases (cf. MATH-844), the guesser
                    // procedure cannot produce sensible results.
                    throw new MathIllegalStateException(LocalizedFormats.ZERO_DENOMINATOR);
                }

                aOmega[0] = FastMath.sqrt(c1 / c2);
                aOmega[1] = FastMath.sqrt(c2 / c3);
            }

            return aOmega;
        }

        /**
         * Estimate a first guess of the phase.
         *
         * @param observations Observations, sorted w.r.t. abscissa.
         * @return the guessed phase.
         */
        private double guessPhi(WeightedObservedPoint[] observations) {
            // initialize the means
            double fcMean = 0;
            double fsMean = 0;

            double currentX = observations[0].getX();
            double currentY = observations[0].getY();
            for (int i = 1; i < observations.length; ++i) {
                // one step forward
                final double previousX = currentX;
                final double previousY = currentY;
                currentX = observations[i].getX();
                currentY = observations[i].getY();
                final double currentYPrime = (currentY - previousY) / (currentX - previousX);

                double omegaX = omega * currentX;
                double cosine = FastMath.cos(omegaX);
                double sine = FastMath.sin(omegaX);
                fcMean += omega * currentY * cosine - currentYPrime * sine;
                fsMean += omega * currentY * sine + currentYPrime * cosine;
            }

            return FastMath.atan2(-fsMean, fcMean);
        }
    }
}