35 #ifndef OPENMS_TRANSFORMATIONS_FEATUREFINDER_TRACEFITTER_H 
   36 #define OPENMS_TRANSFORMATIONS_FEATUREFINDER_TRACEFITTER_H 
   44 #include <gsl/gsl_rng.h> 
   45 #include <gsl/gsl_vector.h> 
   46 #include <gsl/gsl_multifit_nlin.h> 
   47 #include <gsl/gsl_blas.h> 
   61   template <
class PeakType>
 
  200                    Int (* 
residual)(
const gsl_vector * x, 
void * params, gsl_vector * f),
 
  201                    Int (* 
jacobian)(
const gsl_vector * x, 
void * params, gsl_matrix * J),
 
  202                    Int (* 
evaluate)(
const gsl_vector * x, 
void * params, gsl_vector * f, gsl_matrix * J))
 
  204       const gsl_multifit_fdfsolver_type * T;
 
  205       gsl_multifit_fdfsolver * s;
 
  211       if (data_count < num_params) 
throw Exception::UnableToFit(__FILE__, __LINE__, __PRETTY_FUNCTION__, 
"UnableToFit-FinalSet", 
"Skipping feature, gsl always expects N>=p");
 
  213       gsl_multifit_function_fdf func;
 
  214       gsl_vector_view x = gsl_vector_view_array(x_init, num_params);
 
  221       func.params = &traces;
 
  222       T = gsl_multifit_fdfsolver_lmsder;
 
  223       s = gsl_multifit_fdfsolver_alloc(T, data_count, num_params);
 
  224       gsl_multifit_fdfsolver_set(s, &func, &x.vector);
 
  230         gsl_status_ = gsl_multifit_fdfsolver_iterate(s);
 
  232         if (gsl_status_) 
break;
 
  240       gsl_multifit_fdfsolver_free(s);
 
  255 #endif // #ifndef OPENMS_TRANSFORMATIONS_FEATUREFINDER_FEATUREFINDERALGORITHMPICKED_RTFITTING_H 
virtual DoubleReal getFeatureIntensityContribution()=0
virtual String getGnuplotFormula(FeatureFinderAlgorithmPickedHelperStructs::MassTrace< PeakType > const &trace, const char function_name, const DoubleReal baseline, const DoubleReal rt_shift)=0
Param defaults_
Container for default parameters. This member should be filled in the constructor of derived classes!...
Definition: DefaultParamHandler.h:155
void setValue(const String &key, const DataValue &value, const String &description="", const StringList &tags=StringList())
Sets a value. 
A more convenient string class. 
Definition: String.h:56
DoubleReal epsilon_rel_
Relative error. 
Definition: TraceFitter.h:247
void optimize_(FeatureFinderAlgorithmPickedHelperStructs::MassTraces< PeakType > &traces, const Size num_params, double x_init[], Int(*residual)(const gsl_vector *x, void *params, gsl_vector *f), Int(*jacobian)(const gsl_vector *x, void *params, gsl_matrix *J), Int(*evaluate)(const gsl_vector *x, void *params, gsl_vector *f, gsl_matrix *J))
Definition: TraceFitter.h:199
virtual void updateMembers_()
This method is used to update extra member variables at the end of the setParameters() method...
Definition: TraceFitter.h:182
Param param_
Container for current parameters. 
Definition: DefaultParamHandler.h:148
Helper struct for a collection of mass traces used in FeatureFinderAlgorithmPicked. 
Definition: FeatureFinderAlgorithmPickedHelperStructs.h:153
Abstract fitter for RT profile fitting. 
Definition: TraceFitter.h:62
virtual bool checkMinimalRTSpan(const std::pair< DoubleReal, DoubleReal > &rt_bounds, const DoubleReal min_rt_span)=0
virtual DoubleReal getLowerRTBound() const =0
virtual void getOptimizedParameters_(gsl_multifit_fdfsolver *s)=0
ptrdiff_t SignedSize
Signed Size type e.g. used as pointer difference. 
Definition: Types.h:151
Size getPeakCount() const 
Returns the peak count of all traces. 
Definition: FeatureFinderAlgorithmPickedHelperStructs.h:163
virtual DoubleReal computeTheoretical(const FeatureFinderAlgorithmPickedHelperStructs::MassTrace< PeakType > &trace, Size k)=0
int evaluate(const gsl_vector *x, void *params, gsl_vector *f, gsl_matrix *J)
Driver function for the evaluation of function and jacobian. 
virtual TraceFitter & operator=(const TraceFitter &source)
assignment operator 
Definition: TraceFitter.h:86
const DataValue & getValue(const String &key) const 
Returns a value of a parameter. 
TraceFitter(const TraceFitter &source)
copy constructor 
Definition: TraceFitter.h:77
virtual bool checkMaximalRTSpan(const DoubleReal max_rt_span)=0
virtual DoubleReal getHeight() const =0
SignedSize max_iterations_
Maximum number of iterations. 
Definition: TraceFitter.h:249
virtual DoubleReal getFWHM() const =0
virtual DoubleReal getUpperRTBound() const =0
static StringList create(const String &list, const char splitter= ',')
Returns a list that is created by splitting the given (comma-separated) string (String are not trimme...
TraceFitter()
default constructor. 
Definition: TraceFitter.h:68
int residual(const gsl_vector *x, void *params, gsl_vector *f)
Evaluation of the target function for nonlinear optimization. 
virtual void fit(FeatureFinderAlgorithmPickedHelperStructs::MassTraces< PeakType > &traces)=0
virtual ~TraceFitter()
destructor 
Definition: TraceFitter.h:98
virtual void printState_(SignedSize iter, gsl_multifit_fdfsolver *s)=0
Exception used if an error occurred while fitting a model to a given dataset. 
Definition: Exception.h:662
size_t Size
Size type e.g. used as variable which can hold result of size() 
Definition: Types.h:144
int jacobian(const gsl_vector *x, void *params, gsl_matrix *J)
Compute the Jacobian of the residual, where each row of the matrix corresponds to a point in the data...
DoubleReal epsilon_abs_
Absolute error. 
Definition: TraceFitter.h:245
virtual DefaultParamHandler & operator=(const DefaultParamHandler &rhs)
Assignment operator. 
A base class for all classes handling default parameters. 
Definition: DefaultParamHandler.h:90
virtual DoubleReal getCenter() const =0
int Int
Signed integer type. 
Definition: Types.h:100
Helper struct for mass traces used in FeatureFinderAlgorithmPicked. 
Definition: FeatureFinderAlgorithmPickedHelperStructs.h:83