OpenMS  3.0.0
PeakPickerCWT.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Eva Lange, Alexandra Zerck $
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34 //
35 #pragma once
36 
44 
45 //#define DEBUG_PEAK_PICKING
46 #undef DEBUG_PEAK_PICKING
47 //#define DEBUG_DECONV
48 namespace OpenMS
49 {
50  class PeakShape;
51 
78  class OPENMS_DLLAPI PeakPickerCWT :
79  public DefaultParamHandler,
80  public ProgressLogger
81  {
82 public:
84  typedef MSSpectrum::iterator PeakIterator;
86  typedef MSSpectrum::const_iterator ConstPeakIterator;
87 
89  PeakPickerCWT();
90 
92  ~PeakPickerCWT() override;
93 
99  void pick(const MSSpectrum & input, MSSpectrum & output) const;
100 
108  void pickExperiment(const PeakMap & input, PeakMap & output);
109 
120  double estimatePeakWidth(const PeakMap & input);
121 
122 protected:
123 
125  float peak_bound_;
126 
129 
132 
134  float fwhm_bound_;
135 
138 
140  float scale_;
141 
144 
147 
150 
153 
156 
157 
158  void updateMembers_() override;
159 
170  struct OPENMS_DLLAPI PeakArea_
171  {
172  typedef MSSpectrum::iterator PeakIterator;
177  };
178 
180  void getPeakArea_(const PeakArea_ & area, double & area_left, double & area_right) const;
181 
183  PeakShape fitPeakShape_(const PeakArea_ & area) const;
184 
191  double correlate_(const PeakShape & peak, const PeakArea_ & area, Int direction = 0) const;
192 
193 
202  bool getMaxPosition_(const PeakIterator first, const PeakIterator last, const ContinuousWaveletTransform & wt,
203  PeakArea_ & area, const Int distance_from_scan_border,
204  const double peak_bound_cwt, const double peak_bound_ms2_level_cwt, const Int direction = 1) const;
205 
206 
226  bool getPeakEndPoints_(PeakIterator first, PeakIterator last, PeakArea_ & area, Int distance_from_scan_border,
227  Int & peak_left_index, Int & peak_right_index, ContinuousWaveletTransformNumIntegration & wt) const;
228 
229 
236  void getPeakCentroid_(PeakArea_ & area) const;
237 
239  inline double lorentz_(const double height, const double lambda, const double pos, const double x) const
240  {
241  const double x2 = lambda * (x - pos);
242  return height / (1 + x2*x2);
243  }
244 
254  void initializeWT_(ContinuousWaveletTransformNumIntegration& wt, const double peak_bound_in, double& peak_bound_ms_cwt) const;
255 
259 
266  bool deconvolutePeak_(PeakShape & shape, std::vector<PeakShape> & peak_shapes, double peak_bound_cwt) const;
267 
269  Int getNumberOfPeaks_(ConstPeakIterator first, ConstPeakIterator last, std::vector<double> & peak_values,
270  Int direction, double resolution, ContinuousWaveletTransformNumIntegration & wt, double peak_bound_cwt) const;
271 
273  Int determineChargeState_(std::vector<double> & peak_values) const;
274 
276  void addPeak_(std::vector<PeakShape> & peaks_DC, PeakArea_ & area, double left_width, double right_width, OptimizePeakDeconvolution::Data & data) const;
278  }; // end PeakPickerCWT
279 
280 } // namespace OpenMS
281 
DefaultParamHandler.h
ContinuousWaveletTransformNumIntegration.h
OpenMS::ContinuousWaveletTransform
This class is the base class of the continuous wavelet transformation.
Definition: ContinuousWaveletTransform.h:46
OpenMS::PeakPickerCWT::lorentz_
double lorentz_(const double height, const double lambda, const double pos, const double x) const
Computes the value of a theoretical Lorentz peak at position x.
Definition: PeakPickerCWT.h:239
OpenMS::PeakPickerCWT
This class implements a peak picking algorithm using wavelet techniques.
Definition: PeakPickerCWT.h:78
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
OpenMS::PeakPickerCWT::PeakArea_
Class for the internal peak representation.
Definition: PeakPickerCWT.h:170
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
OpenMS::Int
int Int
Signed integer type.
Definition: Types.h:102
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::OptimizePeakDeconvolution::Data
Class containing the data needed for optimization.
Definition: OptimizePeakDeconvolution.h:110
OpenMS::PeakPickerCWT::two_d_optimization_
bool two_d_optimization_
Switch for the 2D optimization of peak parameters.
Definition: PeakPickerCWT.h:155
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:52
ProgressLogger.h
OpenMS::PeakPickerCWT::radius_
UInt radius_
The search radius for the determination of a peak's maximum position.
Definition: PeakPickerCWT.h:137
OpenMS::PeakShape
Internal representation of a peak shape (used by the PeakPickerCWT)
Definition: PeakShape.h:50
OpenMS::PeakPickerCWT::optimization_
bool optimization_
Switch for the optimization of peak parameters.
Definition: PeakPickerCWT.h:149
OpenMS::PeakPickerCWT::peak_bound_
float peak_bound_
Threshold for the peak height in the MS 1 level.
Definition: PeakPickerCWT.h:125
OpenMS::PeakPickerCWT::peak_bound_ms2_level_
float peak_bound_ms2_level_
Threshold for the peak height in the MS 2 level.
Definition: PeakPickerCWT.h:128
OpenMS::PeakPickerCWT::noise_level_
float noise_level_
The threshold for the noise level (TODO: Use the information of the signal to noise estimator)
Definition: PeakPickerCWT.h:146
OptimizePeakDeconvolution.h
OpenMS::PeakPickerCWT::peak_corr_bound_
float peak_corr_bound_
The threshold for correlation.
Definition: PeakPickerCWT.h:143
OpenMS::DPosition< 1 >
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::PeakPickerCWT::PeakArea_::max
PeakIterator max
iterator to the maximum position
Definition: PeakPickerCWT.h:174
OpenMS::PeakPickerCWT::scale_
float scale_
The dilation of the wavelet.
Definition: PeakPickerCWT.h:140
MSExperiment.h
OpenMS::PeakPickerCWT::fwhm_bound_
float fwhm_bound_
The minimal full width at half maximum.
Definition: PeakPickerCWT.h:134
OpenMS::PeakPickerCWT::PeakArea_::right
PeakIterator right
iterator to the rightmost valid point (inclusive)
Definition: PeakPickerCWT.h:175
OpenMS::PeakPickerCWT::deconvolution_
bool deconvolution_
Switch for the deconvolution of peak parameters.
Definition: PeakPickerCWT.h:152
OpenMS::PeakPickerCWT::PeakIterator
MSSpectrum::iterator PeakIterator
Profile data iterator type.
Definition: PeakPickerCWT.h:84
OpenMS::ContinuousWaveletTransformNumIntegration
This class computes the continuous wavelet transformation using a marr wavelet.
Definition: ContinuousWaveletTransformNumIntegration.h:56
OpenMS::PeakPickerCWT::PeakArea_::left
PeakIterator left
iterator to the leftmost valid point
Definition: PeakPickerCWT.h:173
OpenMS::PeakPickerCWT::PeakArea_::centroid_position
DPosition< 1 > centroid_position
The estimated centroid position in m/z.
Definition: PeakPickerCWT.h:176
ContinuousWaveletTransform.h
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
OpenMS::PeakPickerCWT::signal_to_noise_
float signal_to_noise_
Signal to noise threshold.
Definition: PeakPickerCWT.h:131
StandardTypes.h
OpenMS::PeakPickerCWT::ConstPeakIterator
MSSpectrum::const_iterator ConstPeakIterator
Const profile data iterator type.
Definition: PeakPickerCWT.h:86