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EmgFitter1D.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/LevMarqFitter1D.h>
38
39 namespace OpenMS
40 {
46 class OPENMS_DLLAPI EmgFitter1D :
47 public LevMarqFitter1D
48 {
49 public:
50
52 EmgFitter1D();
53
55 EmgFitter1D(const EmgFitter1D& source);
56
58 ~EmgFitter1D() override;
59
61 virtual EmgFitter1D& operator=(const EmgFitter1D& source);
62
64 static Fitter1D* create()
65 {
66 return new EmgFitter1D();
67 }
68
70 static const String getProductName()
71 {
72 return "EmgFitter1D";
73 }
74
76 QualityType fit1d(const RawDataArrayType& range, InterpolationModel*& model) override;
77
78 protected:
80 struct Data
81 {
82 typedef Peak1D PeakType;
83 typedef std::vector<PeakType> RawDataArrayType;
84
85 Size n;
86 RawDataArrayType set;
87 };
88
89 class EgmFitterFunctor :
90 public LevMarqFitter1D::GenericFunctor
91 {
92 public:
93 EgmFitterFunctor(int dimensions, const EmgFitter1D::Data* data) :
94 LevMarqFitter1D::GenericFunctor(dimensions,
95 static_cast<int>(data->n)),
96 m_data(data)
97 {}
98
99 int operator()(const Eigen::VectorXd& x, Eigen::VectorXd& fvec) override;
100 // compute Jacobian matrix for the different parameters
101 int df(const Eigen::VectorXd& x, Eigen::MatrixXd& J) override;
102
103 protected:
104 const EmgFitter1D::Data* m_data;
105 };
106
108 virtual void setInitialParameters_(const RawDataArrayType& set);
109
111 CoordinateType height_;
113 CoordinateType width_;
115 CoordinateType symmetry_;
117 CoordinateType retention_;
118
119 void updateMembers_() override;
120 };
121
122 }
123
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::Fitter1D
Abstract base class for all 1D-dimensional model fitter.
Definition: Fitter1D.h:58
OpenMS::LevMarqFitter1D
Abstract class for 1D-model fitter using Levenberg-Marquardt algorithm for parameter optimization...
Definition: LevMarqFitter1D.h:51
LevMarqFitter1D.h
OpenMS::InterpolationModel
Abstract class for 1D-models that are approximated using linear interpolation.
Definition: InterpolationModel.h:54
OpenMS::EmgFitter1D::retention_
CoordinateType retention_
Parameter of emg - peak retention time.
Definition: EmgFitter1D.h:117
OpenMS::EmgFitter1D::EgmFitterFunctor::m_data
const EmgFitter1D::Data * m_data
Definition: EmgFitter1D.h:104
OpenMS::EmgFitter1D::Data
Helper struct (contains the size of an area and a raw data container)
Definition: EmgFitter1D.h:80
OpenMS::EmgFitter1D::Data::PeakType
Peak1D PeakType
Definition: EmgFitter1D.h:82
OpenMS::EmgFitter1D::EgmFitterFunctor::EgmFitterFunctor
EgmFitterFunctor(int dimensions, const EmgFitter1D::Data *data)
Definition: EmgFitter1D.h:93
OpenMS::Peak1D
A 1-dimensional raw data point or peak.
Definition: Peak1D.h:54
OpenMS::Fitter1D::CoordinateType
Feature::CoordinateType CoordinateType
Single coordinate.
Definition: Fitter1D.h:69
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::EmgFitter1D::height_
CoordinateType height_
Parameter of emg - peak height.
Definition: EmgFitter1D.h:111
OpenMS::LevMarqFitter1D::GenericFunctor
Definition: LevMarqFitter1D.h:61
OpenMS::EmgFitter1D
Exponentially modified gaussian distribution fitter (1-dim.) using Levenberg-Marquardt algorithm (Eig...
Definition: EmgFitter1D.h:46
OpenMS::EmgFitter1D::width_
CoordinateType width_
Parameter of emg - peak width.
Definition: EmgFitter1D.h:113
OpenMS::EmgFitter1D::getProductName
static const String getProductName()
name of the model (needed by Factory)
Definition: EmgFitter1D.h:70
OpenMS::EmgFitter1D::Data::n
Size n
Definition: EmgFitter1D.h:85
int
OpenMS::EmgFitter1D::EgmFitterFunctor
Definition: EmgFitter1D.h:89
OpenMS::EmgFitter1D::create
static Fitter1D * create()
create new EmgFitter1D object (function needed by Factory)
Definition: EmgFitter1D.h:64
OpenMS::Fitter1D::RawDataArrayType
std::vector< PeakType > RawDataArrayType
Peak type data container type using for the temporary storage of the input data.
Definition: Fitter1D.h:75
OpenMS::EmgFitter1D::symmetry_
CoordinateType symmetry_
Parameter of emg - peak symmetry.
Definition: EmgFitter1D.h:115
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::EmgFitter1D::Data::RawDataArrayType
std::vector< PeakType > RawDataArrayType
Definition: EmgFitter1D.h:83