ModifiedSincSmoother.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Sarah Najar $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/CONCEPT/Constants.h>
#include <OpenMS/CONCEPT/Exception.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/KERNEL/Mobilogram.h>
#include <OpenMS/KERNEL/MSExperiment.h>
 
#include <vector>
#include <cmath>
 
namespace OpenMS
{
  class OPENMS_DLLAPI ModifiedSincSmoother :
    public ProgressLogger,
    public DefaultParamHandler
  {
  public:
    ModifiedSincSmoother();
 
    ModifiedSincSmoother(bool isMS1, int degree, int m);
 
    std::vector<double> smooth(const std::vector<double>& data);
 
    std::vector<double> smoothExceptBoundaries(const std::vector<double>& data);
 
    static int bandwidthToM(bool isMS1, int degree, double bandwidth);
 
    static int noiseGainToM(bool isMS1, int degree, double noiseGain);
 
    static double savitzkyGolayBandwidth(int degree, int m);
 
    void filter(MSSpectrum& spectrum);
 
    void filter(MSChromatogram& chromatogram);
 
    void filter(Mobilogram& mobilogram);
 
    void filterExperiment(PeakMap& map);
 
  protected:
    void updateMembers_() override;
 
  private:
    void registerDefaults_();
 
    bool isMS1_;
    int degree_;
    int m_;
    std::vector<double> kernel_;
    std::vector<double> fit_weights_;
 
    std::vector<double> makeKernel(bool isMS1, int degree, int m, const std::vector<double>& coeffs);
 
    std::vector<double> getCoefficients(bool isMS1, int degree, int m);
 
    std::vector<double> makeFitWeights(bool isMS1, int degree, int m);
 
    std::vector<double> extendData(const std::vector<double>& data, int m);
 
    struct LinearRegression
    {
      double sum_weights = 0;  
      double sum_x = 0;        
      double sum_y = 0;        
      double sum_xy = 0;       
      double sum_x2 = 0;       
      double offset = NAN;     
      double slope = NAN;      
      bool calculated = false; 
 
      void clear();
 
      void addPointW(double x, double y, double weight);
 
      void calculate();
 
      double getOffset();
 
      double getSlope();
    };
 
    static double sqr(double x) { return x * x; }
  };
} // namespace OpenMS