peakfinding.h

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/*******************************************************************************
    Copyright (C) 2014-2016 Wright State University - All Rights Reserved
    Daniel P. Foose - Maintainer/Lead Developer

    This file is part of Vespucci.

    Vespucci is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.

    Vespucci 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.  See the
    GNU General Public License for more details.

    You should have received a copy of the GNU General Public License
    along with Vespucci.  If not, see <http://www.gnu.org/licenses/>.
*******************************************************************************/
#ifndef PEAKFINDING_H
#define PEAKFINDING_H
#if !defined( SWIG )
    // SWIG should not see #inlcude<armadillo> as it can not handle it
    #include "Math/VespucciMath.h"
    #include "Global/libvespucci.h"
#endif
namespace Vespucci
{
    namespace Math
    {
        //Peak detection (SPF)
        namespace PeakFinding
        {

            VESPUCCI_EXPORT arma::vec FindPeaks(arma::vec X, arma::vec dX,
                          double sel,
                          double threshold,
                          arma::vec &peak_magnitudes);

            VESPUCCI_EXPORT arma::uvec FindPeakPositions(arma::vec X, arma::vec dX,
                                   double sel,
                                   double threshold,
                                   arma::uvec &local_minima);

            VESPUCCI_EXPORT arma::mat FindPeaksMat(arma::mat X,
                             double sel,
                             double threshold,
                             arma::uword poly_order, arma::uword window_size,
                             arma::mat &peak_magnitudes);


            VESPUCCI_EXPORT arma::vec EstimateBaseline(arma::vec X,
                                 arma::umat peaks,
                                 arma::uword window_size);
            VESPUCCI_EXPORT arma::umat FindPeakPositions(arma::vec X, arma::vec dX,
                                   double threshold,
                                   std::string threshold_method,
                                   arma::vec &peak_magnitudes);
            VESPUCCI_EXPORT arma::vec PeakPopulation(arma::uword vector_size, arma::umat peak_positions);
            VESPUCCI_EXPORT arma::vec PeakExtrema(arma::uword vector_size, arma::umat peak_positions);

        }
    }
}
#endif // PEAKFINDING_H