OpenMS  3.0.0
GaussTraceFitter.h
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31 // $Maintainer: Timo Sachsenberg$
32 // $Authors: Stephan Aiche, Marc Sturm$
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34 
35 #pragma once
36 
38 
39 namespace OpenMS
40 {
41 
49  class OPENMS_DLLAPI GaussTraceFitter :
50  public TraceFitter
51  {
52 public:
54 
55  GaussTraceFitter(const GaussTraceFitter& other);
56 
57  GaussTraceFitter& operator=(const GaussTraceFitter& source);
58 
59  ~GaussTraceFitter() override;
60 
61  // override important methods
63 
64  double getLowerRTBound() const override;
65 
66  double getUpperRTBound() const override;
67 
68  double getHeight() const override;
69 
70  double getCenter() const override;
71 
72  double getFWHM() const override;
73 
77  double getSigma() const;
78 
79  bool checkMaximalRTSpan(const double max_rt_span) override;
80 
81  bool checkMinimalRTSpan(const std::pair<double, double>& rt_bounds, const double min_rt_span) override;
82 
83  double getValue(double rt) const override;
84 
85  double getArea() override;
86 
87  String getGnuplotFormula(const FeatureFinderAlgorithmPickedHelperStructs::MassTrace& trace, const char function_name, const double baseline, const double rt_shift) override;
88 
89 protected:
90  double sigma_;
91  double x0_;
92  double height_;
94 
95  static const Size NUM_PARAMS_;
96 
97  void getOptimizedParameters_(const Eigen::VectorXd& x_init) override;
98 
101  {
102 public:
103  GaussTraceFunctor(int dimensions,
104  const TraceFitter::ModelData* data);
105 
106  int operator()(const Eigen::VectorXd& x, Eigen::VectorXd& fvec) override;
107 
108  // compute Jacobian matrix for the different parameters
109  int df(const Eigen::VectorXd& x, Eigen::MatrixXd& J) override;
110 protected:
112  };
113 
114  void setInitialParameters_(FeatureFinderAlgorithmPickedHelperStructs::MassTraces& traces);
115 
116  void updateMembers_() override;
117 
118  };
119 
120 } // namespace OpenMS
121 
OpenMS::TraceFitter
Abstract fitter for RT profile fitting.
Definition: TraceFitter.h:62
TraceFitter.h
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::GaussTraceFitter::height_
double height_
Definition: GaussTraceFitter.h:92
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::GaussTraceFitter::x0_
double x0_
Definition: GaussTraceFitter.h:91
OpenMS::GaussTraceFitter::GaussTraceFunctor::m_data
const TraceFitter::ModelData * m_data
Definition: GaussTraceFitter.h:111
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::GaussTraceFitter::GaussTraceFunctor
Definition: GaussTraceFitter.h:99
OpenMS::GaussTraceFitter::sigma_
double sigma_
Definition: GaussTraceFitter.h:90
OpenMS::GaussTraceFitter::region_rt_span_
double region_rt_span_
Definition: GaussTraceFitter.h:93
OpenMS::TraceFitter::ModelData
Definition: TraceFitter.h:174
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::GaussTraceFitter
Fitter for RT profiles using a Gaussian background model.
Definition: GaussTraceFitter.h:49
OpenMS::GaussTraceFitter::NUM_PARAMS_
static const Size NUM_PARAMS_
Definition: GaussTraceFitter.h:95