36 #ifndef OPENMS_FILTERING_CALIBRATION_TOFCALIBRATION_H 
   37 #define OPENMS_FILTERING_CALIBRATION_TOFCALIBRATION_H 
   48 #include <gsl/gsl_multifit.h> 
   49 #include <gsl/gsl_spline.h> 
   87     template <
typename PeakType>
 
   96     template <
typename PeakType>
 
  100     inline const std::vector<double> & 
getML1s()
 const {
return ml1s_; }
 
  102     inline void setML1s(
const std::vector<double> & ml1s)
 
  108     inline const std::vector<double> & 
getML2s()
 const {
return ml2s_; }
 
  110     inline void setML2s(
const std::vector<double> & ml2s)
 
  116     inline const std::vector<double> & 
getML3s()
 const {
return ml3s_; }
 
  118     inline void setML3s(
const std::vector<double> & ml3s)
 
  132     std::map<double, std::vector<double> > 
errors_;
 
  161     void getMonoisotopicPeaks_(
MSExperiment<> & calib_peaks, std::vector<std::vector<unsigned int> > & monoiso_peaks);
 
  176     void matchMasses_(
MSExperiment<> & calib_peaks, std::vector<std::vector<unsigned int> > & monoiso_peaks, std::vector<unsigned int> & obs_masses, std::vector<double> & exp_masses, 
unsigned int idx);
 
  179     inline double mQ_(
double ft, 
unsigned int spec)
 
  181       return coeff_quad_fit_[3 * spec] + ft * coeff_quad_fit_[3 * spec + 1] + ft * ft * coeff_quad_fit_[3 * spec + 2];
 
  187       return a_ + ft * b_ + ft * ft * c_;
 
  191     void averageErrors_();
 
  194     void averageCoefficients_();
 
  197   template <
typename PeakType>
 
  208     calibrate(p_calib_spectra, exp, exp_masses);
 
  211   template <
typename PeakType>
 
  217     for (
unsigned int spec = 0; spec <  exp.
size(); ++spec)
 
  219       for (
unsigned int peak = 0; peak <  exp[spec].
size(); ++peak)
 
  221         m = 
mQAv_(exp[spec][peak].getMZ());
 
  222         exp[spec][peak].setPos(m - gsl_spline_eval(
spline_, m, 
acc_));
 
  229 #endif // OPENMS_FILTERING_CALIBRATION_TOFCALIBRATION_H 
void setML3s(const std::vector< double > &ml3s)
mutable access to the third calibration constant 
Definition: TOFCalibration.h:118
This class implements an external calibration for TOF data using external calibrant spectra...
Definition: TOFCalibration.h:68
gsl_interp_accel * acc_
Definition: TOFCalibration.h:152
std::vector< double > coeff_quad_fit_
all coefficients of the quadratic fit 
Definition: TOFCalibration.h:146
const std::vector< double > & getML2s() const 
Non-mutable access to the second calibration constant. 
Definition: TOFCalibration.h:108
Size size() const 
Definition: MSExperiment.h:117
gsl_spline * spline_
Definition: TOFCalibration.h:154
Param param_
Container for current parameters. 
Definition: DefaultParamHandler.h:148
std::vector< double > error_medians_
median errors 
Definition: TOFCalibration.h:135
This class implements a peak picking algorithm using wavelet techniques. 
Definition: PeakPickerCWT.h:77
std::vector< double > ml3s_
Definition: TOFCalibration.h:143
std::vector< double > ml2s_
Definition: TOFCalibration.h:142
void setML1s(const std::vector< double > &ml1s)
mutable access to the first calibration constant 
Definition: TOFCalibration.h:102
void setParameters(const Param ¶m)
Sets the parameters. 
std::vector< double > exp_masses_
the expected calibrant masses 
Definition: TOFCalibration.h:129
std::vector< double > ml1s_
calibration constants from the instrument needed for the conversion of the calibrant spectra ...
Definition: TOFCalibration.h:141
Param copy(const String &prefix, bool remove_prefix=false) const 
Returns a new Param object containing all entries that start with prefix. 
double c_
Definition: TOFCalibration.h:149
const std::vector< double > & getML3s() const 
Non-mutable access to the third calibration constant. 
Definition: TOFCalibration.h:116
const std::vector< double > & getML1s() const 
Non-mutable access to the first calibration constant. 
Definition: TOFCalibration.h:100
void pickExperiment(const MSExperiment<> &input, MSExperiment<> &output)
Picks the peaks in an MSExperiment. 
MSExperiment calib_peaks_ft_
the calibrant spectra still using flight times instead of m/z-values 
Definition: TOFCalibration.h:125
void pickAndCalibrate(MSExperiment< Peak1D > &calib_spectra, MSExperiment< PeakType > &exp, std::vector< double > &exp_masses)
Definition: TOFCalibration.h:198
void calculateCalibCoeffs_(MSExperiment<> &calib_peaks_ft)
Calculates the coefficients of the quadratic fit used for external calibration. 
std::map< double, std::vector< double > > errors_
error in ppm after quadratic fit 
Definition: TOFCalibration.h:132
double mQ_(double ft, unsigned int spec)
Calculate the mass value for a given flight time using the coefficients of the quadratic fit in a spe...
Definition: TOFCalibration.h:179
std::vector< double > calib_masses_
Definition: TOFCalibration.h:138
Base class for all classes that want to report their progess. 
Definition: ProgressLogger.h:56
A base class for all classes handling default parameters. 
Definition: DefaultParamHandler.h:90
void calibrate(MSExperiment< Peak1D > &calib_spectra, MSExperiment< PeakType > &exp, std::vector< double > &exp_masses)
Definition: TOFCalibration.h:212
double mQAv_(double ft)
Calculate the mass value for a given flight time using the averaged coefficients of the quadratic fit...
Definition: TOFCalibration.h:185
void setML2s(const std::vector< double > &ml2s)
mutable access to the second calibration constant 
Definition: TOFCalibration.h:110