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