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LinearResampler.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Eva Lange $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/KERNEL/StandardTypes.h>
38 #include <OpenMS/KERNEL/MSExperiment.h>
39 #include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
40 #include <OpenMS/CONCEPT/ProgressLogger.h>
41
42 #include <limits>
43 #include <cmath>
44
45 namespace OpenMS
46 {
61 class OPENMS_DLLAPI LinearResampler :
62 public DefaultParamHandler,
63 public ProgressLogger
64 {
65
66 public:
67
69 LinearResampler() :
70 DefaultParamHandler("LinearResampler")
71 {
72 defaults_.setValue("spacing", 0.05, "Spacing of the resampled output peaks.");
73 defaultsToParam_();
74 }
75
77 ~LinearResampler() override
78 {
79 }
80
84 void raster(MSSpectrum& spectrum)
85 {
86 //return if nothing to do
87 if (spectrum.empty()) return;
88
89 typename MSSpectrum::iterator first = spectrum.begin();
90 typename MSSpectrum::iterator last = spectrum.end();
91
92 double end_pos = (last - 1)->getMZ();
93 double start_pos = first->getMZ();
94 int number_raw_points = static_cast<int>(spectrum.size());
95 int number_resampled_points = static_cast<int>(ceil((end_pos - start_pos) / spacing_ + 1));
96
97 std::vector<Peak1D> resampled_peak_container;
98 resampled_peak_container.resize(number_resampled_points);
99
100 // generate the resampled peaks at positions origin+i*spacing_
101 std::vector<Peak1D>::iterator it = resampled_peak_container.begin();
102 for (int i = 0; i < number_resampled_points; ++i)
103 {
104 it->setMZ(start_pos + i * spacing_);
105 ++it;
106 }
107
108 // spread the intensity h of the data point at position x to the left and right
109 // adjacent resampled peaks
110 double distance_left = 0.;
111 double distance_right = 0.;
112 int left_index = 0;
113 int right_index = 0;
114
115 it = resampled_peak_container.begin();
116 for (int i = 0; i < number_raw_points; ++i)
117 {
118 int help = static_cast<int>(floor(((first + i)->getMZ() - start_pos) / spacing_));
119 left_index = (help < 0) ? 0 : help;
120 help = distance(first, last) - 1;
121 right_index = (left_index >= help) ? help : left_index + 1;
122
123 // compute the distance between x and the left adjacent resampled peak
124 distance_left = fabs((first + i)->getMZ() - (it + left_index)->getMZ()) / spacing_;
125 //std::cout << "Distance left " << distance_left << std::endl;
126 // compute the distance between x and the right adjacent resampled peak
127 distance_right = fabs((first + i)->getMZ() - (it + right_index)->getMZ());
128 //std::cout << "Distance right " << distance_right << std::endl;
129
130
131 // add the distance_right*h to the left resampled peak and distance_left*h to the right resampled peak
132 double intensity = static_cast<double>((it + left_index)->getIntensity());
133 intensity += static_cast<double>((first + i)->getIntensity()) * distance_right / spacing_;
134 (it + left_index)->setIntensity(intensity);
135 intensity = static_cast<double>((it + right_index)->getIntensity());
136 intensity += static_cast<double>((first + i)->getIntensity()) * distance_left;
137 (it + right_index)->setIntensity(intensity);
138 }
139
140 spectrum.swap(resampled_peak_container);
141 }
142
146 void rasterExperiment(PeakMap& exp)
147 {
148 startProgress(0, exp.size(), "resampling of data");
149 for (Size i = 0; i < exp.size(); ++i)
150 {
151 raster(exp[i]);
152 setProgress(i);
153 }
154 endProgress();
155 }
156
157 protected:
158
160 double spacing_;
161
162 void updateMembers_() override
163 {
164 spacing_ = param_.getValue("spacing");
165 }
166
167 };
168
169
170 } // namespace OpenMS
171
OpenMS::LinearResampler::raster
void raster(MSSpectrum &spectrum)
Applies the resampling algorithm to an MSSpectrum.
Definition: LinearResampler.h:84
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
OpenMS::LinearResampler::LinearResampler
LinearResampler()
Constructor.
Definition: LinearResampler.h:69
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
StandardTypes.h
OpenMS::LinearResampler::updateMembers_
void updateMembers_() override
This method is used to update extra member variables at the end of the setParameters() method...
Definition: LinearResampler.h:162
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
ProgressLogger.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
MSExperiment.h
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
DefaultParamHandler.h
OpenMS::LinearResampler
Linear Resampling of raw data.
Definition: LinearResampler.h:61
OpenMS::MSExperiment::size
Size size() const
Definition: MSExperiment.h:127
OpenMS::LinearResampler::rasterExperiment
void rasterExperiment(PeakMap &exp)
Resamples the data in an MSExperiment.
Definition: LinearResampler.h:146
OpenMS::LinearResampler::spacing_
double spacing_
Spacing of the resampled data.
Definition: LinearResampler.h:160
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::LinearResampler::~LinearResampler
~LinearResampler() override
Destructor.
Definition: LinearResampler.h:77