OpenMS  3.0.0
MZTrafoModel.h
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31 // $Maintainer: Chris Bielow $
32 // $Authors: Chris Bielow $
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34 
35 #pragma once
36 
39 
40 #include <vector>
41 
42 namespace OpenMS
43 {
44 
64  class OPENMS_DLLAPI MZTrafoModel
65  {
66 
67  private:
68  std::vector<double> coeff_;
69  bool use_ppm_;
70  double rt_;
71 
73  static int ransac_seed_;
74  static double limit_offset_;
75  static double limit_scale_;
76  static double limit_power_;
77 
78  public:
79 
83  MZTrafoModel();
84 
95  MZTrafoModel(bool ppm_model);
96 
97  enum MODELTYPE { LINEAR, LINEAR_WEIGHTED, QUADRATIC, QUADRATIC_WEIGHTED, SIZE_OF_MODELTYPE };
98  static const std::string names_of_modeltype[];
99 
106  static MODELTYPE nameToEnum(const std::string& name);
113  static const std::string& enumToName(MODELTYPE mt);
114 
115 
125  static void setRANSACParams(const Math::RANSACParam& p);
126 
130  static void setRANSACSeed(int seed);
131 
140  static void setCoefficientLimits(double offset, double scale, double power);
151  static bool isValidModel(const MZTrafoModel& trafo);
152 
159  bool isTrained() const;
160 
164  double getRT() const;
165 
178  double predict(double mz) const;
179 
191  static Size findNearest(const std::vector<MZTrafoModel>& tms, double rt);
192 
193 
195  struct RTLess
196  {
197  inline bool operator()(const double& left, const MZTrafoModel& right) const
198  {
199  return left < right.rt_;
200  }
201  inline bool operator()(const MZTrafoModel& left, const double& right) const
202  {
203  return left.rt_ < right;
204  }
205  inline bool operator()(const MZTrafoModel& left, const MZTrafoModel& right) const
206  {
207  return left.rt_ < right.rt_;
208  }
209  };
231  bool train(const CalibrationData& cd, MODELTYPE md, bool use_RANSAC,
232  double rt_left = -std::numeric_limits<double>::max(),
233  double rt_right = std::numeric_limits<double>::max()
234  );
235 
260  bool train(std::vector<double> error_mz,
261  std::vector<double> theo_mz,
262  std::vector<double> weights,
263  MODELTYPE md,
264  bool use_RANSAC);
265 
277  void getCoefficients(double& intercept, double& slope, double& power);
278 
282  void setCoefficients(const MZTrafoModel& rhs);
283 
295  void setCoefficients(double intercept, double slope, double power);
296 
303  String toString() const;
304 
305  }; // MZTrafoModel
306 
307 } // namespace OpenMS
308 
OpenMS::MZTrafoModel::limit_scale_
static double limit_scale_
acceptable boundary for the estimated scale; if estimated scale is larger (absolute) the model does n...
Definition: MZTrafoModel.h:75
OpenMS::toString
const std::string & toString(const DriftTimeUnit value)
OpenMS::MZTrafoModel::MODELTYPE
MODELTYPE
Definition: MZTrafoModel.h:97
OpenMS::Math::RANSACParam
A simple struct to carry all the parameters required for a RANSAC run.
Definition: RANSAC.h:58
OpenMS::MZTrafoModel::coeff_
std::vector< double > coeff_
Model coefficients (for both linear and quadratic models), estimated from the data.
Definition: MZTrafoModel.h:68
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::MZTrafoModel::use_ppm_
bool use_ppm_
during training, model is build on absolute or relative(ppm) predictions. predict(),...
Definition: MZTrafoModel.h:69
OpenMS::MZTrafoModel::ransac_seed_
static int ransac_seed_
seed used for all RANSAC invocations
Definition: MZTrafoModel.h:73
RANSAC.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::MZTrafoModel::RTLess::operator()
bool operator()(const double &left, const MZTrafoModel &right) const
Definition: MZTrafoModel.h:197
OpenMS::MZTrafoModel
Create and apply models of a mass recalibration function.
Definition: MZTrafoModel.h:64
OpenMS::MZTrafoModel::limit_offset_
static double limit_offset_
acceptable boundary for the estimated offset; if estimated offset is larger (absolute) the model does...
Definition: MZTrafoModel.h:74
OpenMS::MZTrafoModel::rt_
double rt_
retention time associated to the model (i.e. where the calibrant data was taken from)
Definition: MZTrafoModel.h:70
OpenMS::MZTrafoModel::RTLess
Comparator by position. As this class has dimension 1, this is basically an alias for MZLess.
Definition: MZTrafoModel.h:195
OpenMS::MZTrafoModel::RTLess::operator()
bool operator()(const MZTrafoModel &left, const MZTrafoModel &right) const
Definition: MZTrafoModel.h:205
CalibrationData.h
OpenMS::MZTrafoModel::ransac_params_
static Math::RANSACParam * ransac_params_
global pointer, init to NULL at startup; set class-global RANSAC params
Definition: MZTrafoModel.h:72
OpenMS::CalibrationData
A helper class, holding all calibration points.
Definition: CalibrationData.h:64
OpenMS::MZTrafoModel::limit_power_
static double limit_power_
acceptable boundary for the estimated power; if estimated power is larger (absolute) the model does n...
Definition: MZTrafoModel.h:76
OpenMS::MZTrafoModel::RTLess::operator()
bool operator()(const MZTrafoModel &left, const double &right) const
Definition: MZTrafoModel.h:201