de.biomedical_imaging.traj.math.RadiusGyrationTensor2D.java Source code

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Here is the source code for de.biomedical_imaging.traj.math.RadiusGyrationTensor2D.java

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/*
 * The MIT License (MIT)
 * Copyright (c) 2015-2016 Thorsten Wagner (wagner@biomedical-imaging.de)
 * 
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the Software is
 * furnished to do so, subject to the following conditions:
 * 
 * The above copyright notice and this permission notice shall be included in all
 * copies or substantial portions of the Software.
 * 
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 * SOFTWARE.
 */

package de.biomedical_imaging.traj.math;

import org.apache.commons.math3.linear.Array2DRowRealMatrix;

import de.biomedical_imaging.traJ.Trajectory;

public class RadiusGyrationTensor2D {

    private Trajectory t;

    public RadiusGyrationTensor2D(Trajectory t) {
        this.t = t;
    }

    /**
     * Calculates the radius of gyration tensor according to formula (6.3) in
     * 
     * ELEMENTS OF THE RANDOM WALK by Rudnick and Gaspari
     * 
     * @return Radius of gyration tensor
     */
    public Array2DRowRealMatrix getRadiusOfGyrationTensor() {
        return getRadiusOfGyrationTensor(t);
    }

    /**
     * Calculates the radius of gyration tensor according to formula (6.3) in
     * 
     * ELEMENTS OF THE RANDOM WALK by Rudnick and Gaspari
     * 
     * @return Radius of gyration tensor
     */
    public static Array2DRowRealMatrix getRadiusOfGyrationTensor(Trajectory t) {
        double meanx = 0;
        double meany = 0;
        for (int i = 0; i < t.size(); i++) {
            meanx += t.get(i).x;
            meany += t.get(i).y;
        }
        meanx = meanx / t.size();
        meany = meany / t.size();

        double e11 = 0;
        double e12 = 0;
        double e21 = 0;
        double e22 = 0;

        for (int i = 0; i < t.size(); i++) {
            e11 += Math.pow(t.get(i).x - meanx, 2);
            e12 += (t.get(i).x - meanx) * (t.get(i).y - meany);
            e22 += Math.pow(t.get(i).y - meany, 2);
        }
        e11 = e11 / t.size();
        e12 = e12 / t.size();
        e21 = e12;
        e22 = e22 / t.size();
        int rows = 2;
        int columns = 2;
        Array2DRowRealMatrix gyr = new Array2DRowRealMatrix(rows, columns);

        gyr.addToEntry(0, 0, e11);
        gyr.addToEntry(0, 1, e12);
        gyr.addToEntry(1, 0, e21);
        gyr.addToEntry(1, 1, e22);

        return gyr;
    }

}