de.biomedical_imaging.traJ.features.AsymmetryFeature.java Source code

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Here is the source code for de.biomedical_imaging.traJ.features.AsymmetryFeature.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.features;

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

import de.biomedical_imaging.traJ.Trajectory;
import de.biomedical_imaging.traj.math.RadiusGyrationTensor2D;

/**
 * The features characterizes  the asymetry of the trajectory. 
 * It is equal to 0 for circularly symmetric trajectories and 
 * 1 for linear trajectories.
 * 
 * It was implemented according to
 * 
 * Saxton, M.J., 1993. Lateral diffusion in an archipelago. 
 * Single-particle diffusion. Biophysical Journal, 64(6), pp.17661780.
 * @author Thorsten Wagner
 *
 */
public class AsymmetryFeature extends AbstractTrajectoryFeature {

    private Trajectory t;

    /**
     * 
     * @param t Trajectory for which the asymmetry is to be calculated.
     */
    public AsymmetryFeature(Trajectory t) {
        this.t = t;
    }

    /**
     * @return Returns an double array with the following elements [0]=Asymmetry
     */
    @Override
    public double[] evaluate() {
        Array2DRowRealMatrix gyr = RadiusGyrationTensor2D.getRadiusOfGyrationTensor(t);
        EigenDecomposition eigdec = new EigenDecomposition(gyr);
        double e1 = eigdec.getRealEigenvalue(0);
        double e2 = eigdec.getRealEigenvalue(1);

        double asym = Math.pow(e1 * e1 - e2 * e2, 2) / (Math.pow(e1 * e1 + e2 * e2, 2)); //-1*Math.log(1-Math.pow(e1-e2, 2)/(2*Math.pow(e1+e2, 2)));
        result = new double[] { asym };
        return result;
    }

    @Override
    public String getName() {
        return "Assymetry";
    }

    @Override
    public String getShortName() {
        return "ASYM";
    }

    @Override
    public void setTrajectory(Trajectory t) {
        this.t = t;
        result = null;

    }

}