36 #ifndef OPENMS_TRANSFORMATIONS_RAW2PEAK_OPTIMIZEPEAKDECONVOLUTION_H
37 #define OPENMS_TRANSFORMATIONS_RAW2PEAK_OPTIMIZEPEAKDECONVOLUTION_H
41 #include <gsl/gsl_vector.h>
42 #include <gsl/gsl_multifit_nlin.h>
43 #include <gsl/gsl_blas.h>
57 namespace OptimizationFunctions
139 penalties_(opt.penalties_),
140 charge_(opt.charge_){}
169 penalties_ = penalties;
170 param_.setValue(
"penalties:left_width", penalties_.lWidth);
171 param_.setValue(
"penalties:right_width", penalties_.rWidth);
172 param_.setValue(
"penalties:height", penalties_.height);
173 param_.setValue(
"penalties:position", penalties_.pos);
184 bool optimize(std::vector<PeakShape> & peaks, Data & data);
197 Size getNumberOfPeaks_(
Int charge, std::vector<PeakShape> & temp_shapes,
Data & data);
200 bool checkFWHM_(std::vector<PeakShape> & peaks, gsl_multifit_fdfsolver * & fit);
202 void updateMembers_();
This class provides the deconvolution of peak regions using non-linear optimization.
Definition: OptimizePeakDeconvolution.h:105
~PenaltyFactorsIntensity()
Definition: OptimizePeakDeconvolution.h:83
OptimizePeakDeconvolution & operator=(const OptimizePeakDeconvolution &opt)
Definition: OptimizePeakDeconvolution.h:149
RawDataVector::iterator PeakIterator
Definition: OptimizePeakDeconvolution.h:113
void setPenalties(const OptimizationFunctions::PenaltyFactorsIntensity &penalties)
Mutable access to the penalty parameter.
Definition: OptimizePeakDeconvolution.h:167
OptimizationFunctions::PenaltyFactorsIntensity penalties
Definition: OptimizePeakDeconvolution.h:124
double lWidth
Penalty factor for the peak shape's left width parameter.
Definition: OptimizePick.h:91
std::vector< Peak1D > RawDataVector
Definition: OptimizePeakDeconvolution.h:112
void setCharge(const Int charge)
Mutable access to the charge.
Definition: OptimizePeakDeconvolution.h:179
std::vector< PeakShape > peaks
Definition: OptimizePeakDeconvolution.h:121
double pos
Penalty factor for the peak shape's position.
Definition: OptimizePick.h:89
double rWidth
Penalty factor for the peak shape's right width parameter.
Definition: OptimizePick.h:93
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:144
Class containing the data needed for optimization.
Definition: OptimizePeakDeconvolution.h:119
Class for the penalty factors used during the optimization.
Definition: OptimizePick.h:71
virtual ~OptimizePeakDeconvolution()
Destructor.
Definition: OptimizePeakDeconvolution.h:143
virtual DefaultParamHandler & operator=(const DefaultParamHandler &rhs)
Assignment operator.
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:90
static const DoubleReal dist_
distance between two isotopic peaks
Definition: OptimizePeakDeconvolution.h:194
Int charge
Definition: OptimizePeakDeconvolution.h:125
OptimizePeakDeconvolution(const OptimizePeakDeconvolution &opt)
Copy-Constructor.
Definition: OptimizePeakDeconvolution.h:137
Int charge_
Charge state of the current isotope pattern.
Definition: OptimizePeakDeconvolution.h:191
PenaltyFactorsIntensity & operator=(const PenaltyFactorsIntensity &p)
Definition: OptimizePeakDeconvolution.h:73
std::vector< DoubleReal > signal
Definition: OptimizePeakDeconvolution.h:123
DoubleReal height
Definition: OptimizePeakDeconvolution.h:85
int Int
Signed integer type.
Definition: Types.h:100
OptimizationFunctions::PenaltyFactorsIntensity penalties_
Definition: OptimizePeakDeconvolution.h:188
Int getCharge() const
Non-mutable access to the charge.
Definition: OptimizePeakDeconvolution.h:177
std::vector< DoubleReal > positions
Definition: OptimizePeakDeconvolution.h:122
Class for the penalty factors used during the optimization.
Definition: OptimizePeakDeconvolution.h:66
PenaltyFactorsIntensity(const PenaltyFactorsIntensity &p)
Definition: OptimizePeakDeconvolution.h:71
PenaltyFactorsIntensity()
Definition: OptimizePeakDeconvolution.h:69