| OpenMS 2.5.0

EGHFitter1D.h
Go to the documentation of this file.
1 // --------------------------------------------------------------------------
2 // OpenMS -- Open-Source Mass Spectrometry
3 // --------------------------------------------------------------------------
4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
6 //
7 // This software is released under a three-clause BSD license:
8 // * Redistributions of source code must retain the above copyright
9 // notice, this list of conditions and the following disclaimer.
10 // * Redistributions in binary form must reproduce the above copyright
11 // notice, this list of conditions and the following disclaimer in the
12 // documentation and/or other materials provided with the distribution.
13 // * Neither the name of any author or any participating institution
14 // may be used to endorse or promote products derived from this software
15 // without specific prior written permission.
16 // For a full list of authors, refer to the file AUTHORS.
17 // --------------------------------------------------------------------------
18 // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
19 // AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
20 // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
21 // ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
22 // INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
23 // EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
24 // PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
25 // OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
26 // WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
27 // OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
28 // ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
29 //
30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Stephan Aiche $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #define DEBUG_FEATUREFINDER
38
39 #include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/LevMarqFitter1D.h>
40
41 namespace OpenMS
42 {
48 class OPENMS_DLLAPI EGHFitter1D :
49 public LevMarqFitter1D
50 {
51 public:
53 EGHFitter1D();
54
56 EGHFitter1D(const EGHFitter1D & source);
57
59 ~EGHFitter1D() override;
60
62 virtual EGHFitter1D & operator=(const EGHFitter1D & source);
63
65 static Fitter1D * create()
66 {
67 return new EGHFitter1D();
68 }
69
71 static const String getProductName()
72 {
73 return "EGHFitter1D";
74 }
75
77 QualityType fit1d(const RawDataArrayType & range, InterpolationModel * & model) override;
78
79 protected:
80
82 struct Data
83 {
84 typedef Peak1D PeakType;
85 typedef std::vector<PeakType> RawDataArrayType;
86
87 Size n;
88 RawDataArrayType set;
89 };
90
91 class EGHFitterFunctor : public LevMarqFitter1D::GenericFunctor
92 {
93 public:
94 EGHFitterFunctor(int dimensions, const EGHFitter1D::Data * data)
95 : LevMarqFitter1D::GenericFunctor(dimensions, data->n), m_data(data) {}
96
97 int operator()(const Eigen::VectorXd &x, Eigen::VectorXd &fvec) override;
98 // compute Jacobian matrix for the different parameters
99 int df(const Eigen::VectorXd &x, Eigen::MatrixXd &J) override;
100
101 protected:
102 const EGHFitter1D::Data * m_data;
103 };
104
106 virtual void setInitialParameters_(const RawDataArrayType & set);
107
109 CoordinateType height_;
111 CoordinateType tau_;
113 CoordinateType sigma_square_;
115 CoordinateType retention_;
116
117 void updateMembers_() override;
118 };
119
120 }
121
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::EGHFitter1D::EGHFitterFunctor::m_data
const EGHFitter1D::Data * m_data
Definition: EGHFitter1D.h:102
OpenMS::EGHFitter1D::Data::n
Size n
Definition: EGHFitter1D.h:87
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
OpenMS::EGHFitter1D::EGHFitterFunctor::EGHFitterFunctor
EGHFitterFunctor(int dimensions, const EGHFitter1D::Data *data)
Definition: EGHFitter1D.h:94
LevMarqFitter1D.h
OpenMS::EGHFitter1D::Data::PeakType
Peak1D PeakType
Definition: EGHFitter1D.h:84
OpenMS::EGHFitter1D::retention_
CoordinateType retention_
Parameter of egh - peak retention time.
Definition: EGHFitter1D.h:115
OpenMS::InterpolationModel
Abstract class for 1D-models that are approximated using linear interpolation.
Definition: InterpolationModel.h:54
OpenMS::EGHFitter1D
Exponential-Gaussian hybrid distribution fitter (1-dim.) using Levenberg-Marquardt algorithm (Eigen i...
Definition: EGHFitter1D.h:48
OpenMS::Peak1D
A 1-dimensional raw data point or peak.
Definition: Peak1D.h:54
OpenMS::EGHFitter1D::EGHFitterFunctor
Definition: EGHFitter1D.h:91
OpenMS::EGHFitter1D::Data
Helper struct (contains the size of an area and a raw data container)
Definition: EGHFitter1D.h:82
OpenMS::EGHFitter1D::tau_
CoordinateType tau_
Parameter of egh - tau.
Definition: EGHFitter1D.h:111
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::LevMarqFitter1D::GenericFunctor
Definition: LevMarqFitter1D.h:61
OpenMS::EGHFitter1D::getProductName
static const String getProductName()
name of the model (needed by Factory)
Definition: EGHFitter1D.h:71
OpenMS::EGHFitter1D::height_
CoordinateType height_
Parameter of egh - peak height.
Definition: EGHFitter1D.h:109
OpenMS::EGHFitter1D::create
static Fitter1D * create()
create new EGHFitter1D object (function needed by Factory)
Definition: EGHFitter1D.h:65
OpenMS::EGHFitter1D::sigma_square_
CoordinateType sigma_square_
Parameter of egh - sigma-square.
Definition: EGHFitter1D.h:113
OpenMS::EGHFitter1D::Data::RawDataArrayType
std::vector< PeakType > RawDataArrayType
Definition: EGHFitter1D.h:85
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::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127