| OpenMS 2.5.0

LocalLinearMap.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/DATASTRUCTURES/Matrix.h>
38
39 namespace OpenMS
40 {
41
56 class OPENMS_DLLAPI LocalLinearMap
57 {
58
59 public:
60
68 struct OPENMS_DLLAPI LLMParam
69 {
70 UInt xdim;
71 UInt ydim;
72 double radius;
73 };
74
76 LocalLinearMap();
78 virtual ~LocalLinearMap();
79
81 const LLMParam & getLLMParam() const;
83 const Matrix<double> & getCodebooks() const;
85 const Matrix<double> & getMatrixA() const;
87 const std::vector<double> & getVectorWout() const;
89 const Matrix<UInt> & getCord() const;
91 void normalizeVector(std::vector<double> & aaIndexVariables);
93 std::vector<double> neigh(const Matrix<UInt> & cord, Size win, double radius);
94
95 private:
96
97 LLMParam param_;
98 Matrix<double> code_;
99 Matrix<double> A_;
100 std::vector<double> wout_;
101 Matrix<UInt> cord_;
102
104 Matrix<UInt> genCord_(Size xdim, Size ydim);
106 double dist_(const Matrix<UInt> & u, const Matrix<UInt> & v, Size a, Size b);
107
109 LocalLinearMap(LocalLinearMap & rhs);
111 LocalLinearMap & operator=(const LocalLinearMap & llm);
112
113 };
114
115
116 }
OpenMS::LocalLinearMap::wout_
std::vector< double > wout_
linear bias
Definition: LocalLinearMap.h:100
OpenMS::LocalLinearMap::code_
Matrix< double > code_
codebook vectors
Definition: LocalLinearMap.h:98
OpenMS::LocalLinearMap::cord_
Matrix< UInt > cord_
coordinates of codebooks on grid
Definition: LocalLinearMap.h:101
OpenMS::LocalLinearMap::LLMParam
Define parameters needed by the Local Linear Map (LLM) model.
Definition: LocalLinearMap.h:68
OpenMS::LocalLinearMap::LLMParam::xdim
UInt xdim
Definition: LocalLinearMap.h:70
OpenMS::LocalLinearMap
Trained Local Linear Map (LLM) model for peak intensity prediction.
Definition: LocalLinearMap.h:56
Matrix.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::LocalLinearMap::A_
Matrix< double > A_
linear mappings
Definition: LocalLinearMap.h:99
OpenMS::LocalLinearMap::param_
LLMParam param_
parameters of the model
Definition: LocalLinearMap.h:97
OpenMS::LocalLinearMap::LLMParam::ydim
UInt ydim
Definition: LocalLinearMap.h:71
OpenMS::LocalLinearMap::LLMParam::radius
double radius
Definition: LocalLinearMap.h:72
OpenMS::Matrix< double >
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127