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MaxLikeliFitter1D.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: $
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34
35 #pragma once
36
37 #include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/Fitter1D.h>
38 #include <OpenMS/MATH/STATISTICS/StatisticFunctions.h>
39 #include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/InterpolationModel.h>
40
41 namespace OpenMS
42 {
43
47 class OPENMS_DLLAPI MaxLikeliFitter1D :
48 public Fitter1D
49 {
50
51 public:
52
54 MaxLikeliFitter1D() :
55 Fitter1D()
56 {
57 }
58
60 MaxLikeliFitter1D(const MaxLikeliFitter1D & source) :
61 Fitter1D(source)
62 {
63 }
64
66 ~MaxLikeliFitter1D() override
67 {
68 }
69
71 virtual MaxLikeliFitter1D & operator=(const MaxLikeliFitter1D & source)
72 {
73 if (&source == this) return *this;
74
75 Fitter1D::operator=(source);
76
77 return *this;
78 }
79
80 protected:
81
83 QualityType fitOffset_(InterpolationModel * model, const RawDataArrayType & set, const CoordinateType stdev1, const CoordinateType stdev2, const CoordinateType offset_step)
84 {
85 const CoordinateType offset_min = model->getInterpolation().supportMin() - stdev1;
86 const CoordinateType offset_max = model->getInterpolation().supportMin() + stdev2;
87
88 CoordinateType offset;
89 QualityType correlation;
90
91 //test model with default offset
92 std::vector<float> real_data;
93 real_data.reserve(set.size());
94 std::vector<float> model_data;
95 model_data.reserve(set.size());
96
97 for (Size i = 0; i < set.size(); ++i)
98 {
99 real_data.push_back(set[i].getIntensity());
100 model_data.push_back(model->getIntensity(DPosition<1>(set[i].getPosition())));
101 }
102
103 CoordinateType max_offset = model->getInterpolation().getOffset();
104 QualityType max_correlation = Math::pearsonCorrelationCoefficient(real_data.begin(), real_data.end(), model_data.begin(), model_data.end());
105
106 //test different offsets
107 for (offset = offset_min; offset <= offset_max; offset += offset_step)
108 {
109 // set offset
110 model->setOffset(offset);
111
112 // get samples
113 model_data.clear();
114 for (Size i = 0; i < set.size(); ++i)
115 {
116 model_data.push_back(model->getIntensity(DPosition<1>(set[i].getPosition())));
117 }
118
119 correlation = Math::pearsonCorrelationCoefficient(real_data.begin(), real_data.end(), model_data.begin(), model_data.end());
120
121 if (correlation > max_correlation)
122 {
123 max_correlation = correlation;
124 max_offset = offset;
125 }
126 }
127
128 model->setOffset(max_offset);
129
130 return max_correlation;
131 }
132
133 void updateMembers_() override
134 {
135 Fitter1D::updateMembers_();
136 }
137
138 };
139 }
140
Fitter1D.h
OpenMS::Math::LinearInterpolation::getOffset
KeyType const & getOffset() const
Accessor. "Offset" is the point (in "outside" units) which corresponds to "Data[0]".
Definition: LinearInterpolation.h:388
OpenMS::InterpolationModel::getInterpolation
const LinearInterpolation & getInterpolation() const
Returns the interpolation class.
Definition: InterpolationModel.h:113
OpenMS::Fitter1D::updateMembers_
void updateMembers_() override
This method is used to update extra member variables at the end of the setParameters() method...
OpenMS::Fitter1D
Abstract base class for all 1D-dimensional model fitter.
Definition: Fitter1D.h:58
OpenMS::InterpolationModel::setOffset
virtual void setOffset(CoordinateType offset)
set the offset of the model
Definition: InterpolationModel.h:133
OpenMS::MaxLikeliFitter1D::MaxLikeliFitter1D
MaxLikeliFitter1D(const MaxLikeliFitter1D &source)
copy constructor
Definition: MaxLikeliFitter1D.h:60
OpenMS::InterpolationModel
Abstract class for 1D-models that are approximated using linear interpolation.
Definition: InterpolationModel.h:54
OpenMS::MaxLikeliFitter1D::fitOffset_
QualityType fitOffset_(InterpolationModel *model, const RawDataArrayType &set, const CoordinateType stdev1, const CoordinateType stdev2, const CoordinateType offset_step)
fit an offset on the basis of the Pearson correlation coefficient
Definition: MaxLikeliFitter1D.h:83
OpenMS::Math::LinearInterpolation::supportMin
KeyType supportMin() const
Lower boundary of the support, in "outside" coordinates.
Definition: LinearInterpolation.h:459
OpenMS::MaxLikeliFitter1D
Abstract base class for all 1D-model fitters using maximum likelihood optimization.
Definition: MaxLikeliFitter1D.h:47
OpenMS::Math::pearsonCorrelationCoefficient
static double pearsonCorrelationCoefficient(IteratorType1 begin_a, IteratorType1 end_a, IteratorType2 begin_b, IteratorType2 end_b)
Calculates the Pearson correlation coefficient for the values in [begin_a, end_a) and [begin_b...
Definition: StatisticFunctions.h:505
OpenMS::Fitter1D::CoordinateType
Feature::CoordinateType CoordinateType
Single coordinate.
Definition: Fitter1D.h:69
OpenMS::InterpolationModel::getIntensity
IntensityType getIntensity(const PositionType &pos) const override
access model predicted intensity at position pos
Definition: InterpolationModel.h:101
InterpolationModel.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::MaxLikeliFitter1D::MaxLikeliFitter1D
MaxLikeliFitter1D()
default constructor
Definition: MaxLikeliFitter1D.h:54
OpenMS::DPosition< 1 >
float
StatisticFunctions.h
OpenMS::MaxLikeliFitter1D::operator=
virtual MaxLikeliFitter1D & operator=(const MaxLikeliFitter1D &source)
assignment operator
Definition: MaxLikeliFitter1D.h:71
OpenMS::MaxLikeliFitter1D::updateMembers_
void updateMembers_() override
This method is used to update extra member variables at the end of the setParameters() method...
Definition: MaxLikeliFitter1D.h:133
OpenMS::Fitter1D::operator=
virtual Fitter1D & operator=(const Fitter1D &source)
assignment operator
OpenMS::MaxLikeliFitter1D::~MaxLikeliFitter1D
~MaxLikeliFitter1D() override
destructor
Definition: MaxLikeliFitter1D.h:66
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