OpenMS  3.0.0
LinearResampler.h
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34 
35 #pragma once
36 
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 
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) const
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 
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 
DefaultParamHandler.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::LinearResampler::spacing_
double spacing_
Spacing of the resampled data.
Definition: LinearResampler.h:160
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::MetaInfoInterface::swap
void swap(MetaInfoInterface &rhs)
Swap contents.
OpenMS::LinearResampler::rasterExperiment
void rasterExperiment(PeakMap &exp)
Resamples the data in an MSExperiment.
Definition: LinearResampler.h:146
OpenMS::MSExperiment::size
Size size() const
Definition: MSExperiment.h:120
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
OpenMS::LinearResampler
Linear Resampling of raw data.
Definition: LinearResampler.h:61
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:52
ProgressLogger.h
OpenMS::LinearResampler::~LinearResampler
~LinearResampler() override
Destructor.
Definition: LinearResampler.h:77
MSExperiment.h
OpenMS::LinearResampler::raster
void raster(MSSpectrum &spectrum) const
Applies the resampling algorithm to an MSSpectrum.
Definition: LinearResampler.h:84
OpenMS::LinearResampler::LinearResampler
LinearResampler()
Constructor.
Definition: LinearResampler.h:69
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
StandardTypes.h