OpenMS  3.0.0
EGHTraceFitter.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Stephan Aiche $
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34 
35 #pragma once
36 
38 
39 namespace OpenMS
40 {
41 
54  class OPENMS_DLLAPI EGHTraceFitter :
55  public TraceFitter
56  {
57 public:
61  {
62 public:
63 
64  EGHTraceFunctor(int dimensions,
65  const TraceFitter::ModelData* data);
66 
67  ~EGHTraceFunctor() override;
68 
69  int operator()(const Eigen::VectorXd& x, Eigen::VectorXd& fvec) override;
70 
71  // compute Jacobian matrix for the different parameters
72  int df(const Eigen::VectorXd& x, Eigen::MatrixXd& J) override;
73 
74 protected:
76  };
77 
79 
80  EGHTraceFitter(const EGHTraceFitter& other);
81 
82  EGHTraceFitter& operator=(const EGHTraceFitter& source);
83 
84  ~EGHTraceFitter() override;
85 
86  // override important methods
88 
89  double getLowerRTBound() const override;
90 
91  double getTau() const;
92 
93  double getUpperRTBound() const override;
94 
95  double getHeight() const override;
96 
97  double getSigma() const;
98 
99  double getCenter() const override;
100 
101  bool checkMaximalRTSpan(const double max_rt_span) override;
102 
103  bool checkMinimalRTSpan(const std::pair<double, double>& rt_bounds, const double min_rt_span) override;
104 
105  double getValue(double rt) const override;
106 
107  double getArea() override;
108 
109  double getFWHM() const override;
110 
111  String getGnuplotFormula(const FeatureFinderAlgorithmPickedHelperStructs::MassTrace& trace, const char function_name, const double baseline, const double rt_shift) override;
112 
113 protected:
114  double apex_rt_;
115  double height_;
116 
117  double sigma_;
118  double tau_;
119 
120  std::pair<double, double> sigma_5_bound_;
121 
123 
125  static const double EPSILON_COEFS_[];
126 
127  static const Size NUM_PARAMS_;
128 
134  std::pair<double, double> getAlphaBoundaries_(const double alpha) const;
135 
136  void getOptimizedParameters_(const Eigen::VectorXd& x_init) override;
137 
138  void setInitialParameters_(FeatureFinderAlgorithmPickedHelperStructs::MassTraces& traces);
139 
140  void updateMembers_() override;
141  };
142 
143 } // namespace OpenMS
144 
OpenMS::TraceFitter
Abstract fitter for RT profile fitting.
Definition: TraceFitter.h:62
OpenMS::EGHTraceFitter::apex_rt_
double apex_rt_
Definition: EGHTraceFitter.h:114
OpenMS::EGHTraceFitter::sigma_5_bound_
std::pair< double, double > sigma_5_bound_
Definition: EGHTraceFitter.h:120
OpenMS::EGHTraceFitter::EGHTraceFunctor::m_data
const TraceFitter::ModelData * m_data
Definition: EGHTraceFitter.h:75
TraceFitter.h
OpenMS::EGHTraceFitter::sigma_
double sigma_
Definition: EGHTraceFitter.h:117
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::EGHTraceFitter::region_rt_span_
double region_rt_span_
Definition: EGHTraceFitter.h:122
OpenMS::FeatureFinderAlgorithmPickedHelperStructs::MassTrace
Helper struct for mass traces used in FeatureFinderAlgorithmPicked.
Definition: FeatureFinderAlgorithmPickedHelperStructs.h:79
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
Eigen::Matrix
Definition: IsobaricIsotopeCorrector.h:43
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::EGHTraceFitter
A RT Profile fitter using an Exponential Gaussian Hybrid background model.
Definition: EGHTraceFitter.h:54
OpenMS::EGHTraceFitter::height_
double height_
Definition: EGHTraceFitter.h:115
OpenMS::EGHTraceFitter::NUM_PARAMS_
static const Size NUM_PARAMS_
Definition: EGHTraceFitter.h:127
OpenMS::TraceFitter::ModelData
Definition: TraceFitter.h:174
OpenMS::EGHTraceFitter::EGHTraceFunctor
Definition: EGHTraceFitter.h:59
OpenMS::TraceFitter::GenericFunctor
Definition: TraceFitter.h:69
OpenMS::FeatureFinderAlgorithmPickedHelperStructs::MassTraces
Helper struct for a collection of mass traces used in FeatureFinderAlgorithmPicked.
Definition: FeatureFinderAlgorithmPickedHelperStructs.h:109
OpenMS::EGHTraceFitter::tau_
double tau_
Definition: EGHTraceFitter.h:118