TraceFitter.h

Go to the documentation of this file.

// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2020.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
//  * Neither the name of any author or any participating institution
//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg$
// $Authors: Stephan Aiche, Marc Sturm $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinderAlgorithmPickedHelperStructs.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/KERNEL/Peak1D.h>
 
#include <Eigen/Core>
 
namespace OpenMS
{
 
  class OPENMS_DLLAPI TraceFitter :
    public DefaultParamHandler
  {
 
public:
    //TODO: This is copy and paste from LevMarqFitter1d.h. Make a generic wrapper for LM optimization
    class GenericFunctor
    {
public:
      int inputs() const;
      int values() const;
 
      GenericFunctor(int dimensions, int num_data_points);
 
      virtual ~GenericFunctor();
 
      virtual int operator()(const Eigen::VectorXd& x, Eigen::VectorXd& fvec) = 0;
      // compute Jacobian matrix for the different parameters
      virtual int df(const Eigen::VectorXd& x, Eigen::MatrixXd& J) = 0;
 
protected:
      const int m_inputs, m_values;
    };
 
    TraceFitter();
 
    TraceFitter(const TraceFitter& source);
 
    virtual TraceFitter& operator=(const TraceFitter& source);
 
    ~TraceFitter() override;
 
    virtual void fit(FeatureFinderAlgorithmPickedHelperStructs::MassTraces& traces) = 0;
 
    virtual double getLowerRTBound() const = 0;
 
    virtual double getUpperRTBound() const = 0;
 
    virtual double getHeight() const = 0;
 
    virtual double getCenter() const = 0;
 
    virtual double getFWHM() const = 0;
 
    virtual double getValue(double rt) const = 0;
 
    double computeTheoretical(const FeatureFinderAlgorithmPickedHelperStructs::MassTrace& trace, Size k);
 
    virtual bool checkMinimalRTSpan(const std::pair<double, double>& rt_bounds, const double min_rt_span) = 0;
 
    virtual bool checkMaximalRTSpan(const double max_rt_span) = 0;
 
    virtual double getArea() = 0;
 
    virtual String getGnuplotFormula(const FeatureFinderAlgorithmPickedHelperStructs::MassTrace& trace, const char function_name, const double baseline, const double rt_shift) = 0;
 
protected:
    struct ModelData
    {
      FeatureFinderAlgorithmPickedHelperStructs::MassTraces* traces_ptr;
      bool weighted;
    };
 
    void updateMembers_() override;
 
    virtual void getOptimizedParameters_(const Eigen::VectorXd&) = 0;
    void optimize_(Eigen::VectorXd& x_init, GenericFunctor& functor);
 
    SignedSize max_iterations_;
    bool weighted_;
 
  };
 
}