| OpenMS 2.5.0

InterpolationModel.h
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: $
33 // --------------------------------------------------------------------------
34
35
36 #pragma once
37
38 #include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/BaseModel.h>
39 #include <OpenMS/MATH/MISC/LinearInterpolation.h>
40
41 namespace OpenMS
42 {
54 class OPENMS_DLLAPI InterpolationModel :
55 public BaseModel<1>
56 {
57
58 public:
59 typedef double IntensityType;
60 typedef DPosition<1> PositionType;
61 typedef double CoordinateType;
62 typedef Math::LinearInterpolation<double> LinearInterpolation;
63
65 InterpolationModel() :
66 BaseModel<1>(),
67 interpolation_()
68 {
69 this->defaults_.setValue("interpolation_step", 0.1, "Sampling rate for the interpolation of the model function ");
70 this->defaults_.setValue("intensity_scaling", 1.0, "Scaling factor used to adjust the model distribution to the intensities of the data");
71 }
72
74 InterpolationModel(const InterpolationModel & source) :
75 BaseModel<1>(source),
76 interpolation_(source.interpolation_),
77 interpolation_step_(source.interpolation_step_),
78 scaling_(source.scaling_)
79 {
80 }
81
83 ~InterpolationModel() override
84 {
85 }
86
88 virtual InterpolationModel & operator=(const InterpolationModel & source)
89 {
90 if (&source == this) return *this;
91
92 BaseModel<1>::operator=(source);
93 interpolation_step_ = source.interpolation_step_;
94 interpolation_ = source.interpolation_;
95 scaling_ = source.scaling_;
96
97 return *this;
98 }
99
101 IntensityType getIntensity(const PositionType & pos) const override
102 {
103 return interpolation_.value(pos[0]);
104 }
105
107 IntensityType getIntensity(CoordinateType coord) const
108 {
109 return interpolation_.value(coord);
110 }
111
113 const LinearInterpolation & getInterpolation() const
114 {
115 return interpolation_;
116 }
117
123 CoordinateType getScalingFactor() const
124 {
125 return scaling_;
126 }
127
133 virtual void setOffset(CoordinateType offset)
134 {
135 interpolation_.setOffset(offset);
136 }
137
139 void getSamples(SamplesType & cont) const override
140 {
141 cont = SamplesType();
142 BaseModel<1>::PeakType peak;
143 for (Size i = 0; i < interpolation_.getData().size(); ++i)
144 {
145 #pragma clang diagnostic push
146 #pragma clang diagnostic ignored "-Wconversion"
147 peak.setIntensity(interpolation_.getData()[i]);
148 #pragma clang diagnostic pop
149 peak.getPosition()[0] = interpolation_.index2key(i);
150 cont.push_back(peak);
151 }
152 }
153
155 virtual CoordinateType getCenter() const
156 {
157 throw Exception::NotImplemented(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);
158 }
159
161 virtual void setSamples()
162 {
163 throw Exception::NotImplemented(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);
164 }
165
171 void setInterpolationStep(CoordinateType interpolation_step)
172 {
173 interpolation_step_ = interpolation_step;
174 this->param_.setValue("interpolation_step", interpolation_step_);
175 }
176
177 void setScalingFactor(CoordinateType scaling)
178 {
179 scaling_ = scaling;
180 this->param_.setValue("intensity_scaling", scaling_);
181 }
182
183 protected:
184 LinearInterpolation interpolation_;
185 CoordinateType interpolation_step_;
186 CoordinateType scaling_;
187
188 void updateMembers_() override
189 {
190 BaseModel<1>::updateMembers_();
191 interpolation_step_ = this->param_.getValue("interpolation_step");
192 scaling_ = this->param_.getValue("intensity_scaling");
193 }
194
195 };
196 }
197
OpenMS::InterpolationModel::operator=
virtual InterpolationModel & operator=(const InterpolationModel &source)
assignment operator
Definition: InterpolationModel.h:88
OpenMS::InterpolationModel::updateMembers_
void updateMembers_() override
This method is used to update extra member variables at the end of the setParameters() method...
Definition: InterpolationModel.h:188
OpenMS::InterpolationModel::getInterpolation
const LinearInterpolation & getInterpolation() const
Returns the interpolation class.
Definition: InterpolationModel.h:113
OpenMS::InterpolationModel::setOffset
virtual void setOffset(CoordinateType offset)
set the offset of the model
Definition: InterpolationModel.h:133
OpenMS::InterpolationModel::~InterpolationModel
~InterpolationModel() override
destructor
Definition: InterpolationModel.h:83
OpenMS::InterpolationModel::CoordinateType
double CoordinateType
Definition: InterpolationModel.h:61
OpenMS::BaseModel::updateMembers_
void updateMembers_() override
This method is used to update extra member variables at the end of the setParameters() method...
Definition: BaseModel.h:157
OpenMS::InterpolationModel
Abstract class for 1D-models that are approximated using linear interpolation.
Definition: InterpolationModel.h:54
OpenMS::Math::LinearInterpolation< double >
OpenMS::BaseModel
Abstract base class for all D-dimensional models.
Definition: BaseModel.h:50
OpenMS::InterpolationModel::PositionType
DPosition< 1 > PositionType
Definition: InterpolationModel.h:60
OpenMS::InterpolationModel::getSamples
void getSamples(SamplesType &cont) const override
get reasonable set of samples from the model (i.e. for printing)
Definition: InterpolationModel.h:139
OpenMS::InterpolationModel::getIntensity
IntensityType getIntensity(const PositionType &pos) const override
access model predicted intensity at position pos
Definition: InterpolationModel.h:101
OpenMS::InterpolationModel::IntensityType
double IntensityType
Definition: InterpolationModel.h:59
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::InterpolationModel::getIntensity
IntensityType getIntensity(CoordinateType coord) const
access model predicted intensity at position pos
Definition: InterpolationModel.h:107
OpenMS::BaseModel< 1 >::SamplesType
std::vector< PeakType > SamplesType
Definition: BaseModel.h:60
OpenMS::BaseModel::operator=
virtual BaseModel & operator=(const BaseModel &source)
assignment operator
Definition: BaseModel.h:83
OpenMS::InterpolationModel::InterpolationModel
InterpolationModel(const InterpolationModel &source)
copy constructor
Definition: InterpolationModel.h:74
OpenMS::DPosition< 1 >
double
OpenMS::InterpolationModel::setSamples
virtual void setSamples()
set sample/supporting points of interpolation wrt params.
Definition: InterpolationModel.h:161
BaseModel.h
OpenMS::InterpolationModel::setScalingFactor
void setScalingFactor(CoordinateType scaling)
Definition: InterpolationModel.h:177
OpenMS::Exception::NotImplemented
Not implemented exception.
Definition: Exception.h:436
OpenMS::InterpolationModel::scaling_
CoordinateType scaling_
Definition: InterpolationModel.h:186
OpenMS::InterpolationModel::LinearInterpolation
Math::LinearInterpolation< double > LinearInterpolation
Definition: InterpolationModel.h:62
OpenMS::InterpolationModel::interpolation_step_
CoordinateType interpolation_step_
Definition: InterpolationModel.h:185
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::InterpolationModel::getCenter
virtual CoordinateType getCenter() const
"center" of the model, particular definition (depends on the derived model)
Definition: InterpolationModel.h:155
LinearInterpolation.h
OpenMS::InterpolationModel::setInterpolationStep
void setInterpolationStep(CoordinateType interpolation_step)
Set the interpolation step for the linear interpolation of the model.
Definition: InterpolationModel.h:171
OpenMS::InterpolationModel::interpolation_
LinearInterpolation interpolation_
Definition: InterpolationModel.h:184
OpenMS::InterpolationModel::InterpolationModel
InterpolationModel()
Default constructor.
Definition: InterpolationModel.h:65
OpenMS::InterpolationModel::getScalingFactor
CoordinateType getScalingFactor() const
get the scaling for the model
Definition: InterpolationModel.h:123