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OpenMS::OptimizationFunctions Namespace Reference


Detailed Description

Namespace for all functions and classes needed for the gsl levenberg-marquard algorithm.

We have to use function pointers for the gsl and can't put them into a class, so we provide an extra namespace.


Classes

struct  PenaltyFactorsIntensity
 Class for the penalty factors used during the optimization. More...
struct  PenaltyFactors
 Class for the penalty factors used during the optimization. More...

Typedefs

typedef std::vector
< DRawDataPoint< 1 > > 
RawDataVector
 Raw data vector type.
typedef RawDataVector::iterator RawDataPointIterator
 Raw data iterator type.
typedef RawDataPoint1D RawDataPointType
 Raw data point type.
typedef MSExperiment
< PickedPeak1D
ExperimentPickedType
 MSExperiment with picked peaks.

Functions

int residual (const gsl_vector *x, void *, gsl_vector *f)
 Evaluation of the target function for nonlinear optimization.
int jacobian (const gsl_vector *x, void *, gsl_matrix *J)
 Compute the Jacobian of the residual, where each row of the matrix corresponds to a point in the data.
int evaluate (const gsl_vector *x, void *params, gsl_vector *f, gsl_matrix *J)
 Driver function for the evaluation of function and jacobian.
void printSignal (const gsl_vector *x, float resolution=0.25)
 Print all peak shapes.
Functions provided to the gsl Levenberg-Marquardt
int residual2D (const gsl_vector *x, void *params, gsl_vector *f)
 Function computing estimated signal and its deviation to the experimental signal*/.
int jacobian2D (const gsl_vector *x, void *params, gsl_matrix *J)
 Function computing the Jacobian */.
int evaluate2D (const gsl_vector *x, void *params, gsl_vector *f, gsl_matrix *J)
 Function that calls residual2D and jacobian2D*/.

Variables

std::vector< PeakShapepeaks_DC_
std::vector< double > positions_DC_
std::vector< double > signal_DC_
std::vector< double > positions_
 Positions and intensity values of the raw data.
std::vector< double > signal_
std::vector< PeakShapepeaks_
 This container contains the peak shapes to be optimized.
std::vector< std::pair< int,
int > > 
signal2D
std::multimap< double,
IsotopeCluster >::iterator 
iso_map_iter
unsigned int total_nr_peaks
std::map< int, std::vector
< ExperimentPickedType::SpectrumType::Iterator > > 
matching_peaks
MSExperiment< PickedPeak1D >
::Iterator 
picked_peaks_iter
MSExperiment< RawDataPointType >
::ConstIterator 
raw_data_first


Typedef Documentation

typedef MSExperiment<PickedPeak1D > ExperimentPickedType

MSExperiment with picked peaks.

typedef RawDataVector::iterator RawDataPointIterator

Raw data iterator type.

typedef RawDataPoint1D RawDataPointType

Raw data point type.

typedef std::vector<DRawDataPoint<1> > RawDataVector

Raw data vector type.


Function Documentation

int OpenMS::OptimizationFunctions::evaluate ( const gsl_vector *  x,
void *  params,
gsl_vector *  f,
gsl_matrix *  J 
)

Driver function for the evaluation of function and jacobian.

int OpenMS::OptimizationFunctions::evaluate2D ( const gsl_vector *  x,
void *  params,
gsl_vector *  f,
gsl_matrix *  J 
)

Function that calls residual2D and jacobian2D*/.

int OpenMS::OptimizationFunctions::jacobian ( const gsl_vector *  x,
void *  ,
gsl_matrix *  J 
)

Compute the Jacobian of the residual, where each row of the matrix corresponds to a point in the data.

int OpenMS::OptimizationFunctions::jacobian2D ( const gsl_vector *  x,
void *  params,
gsl_matrix *  J 
)

Function computing the Jacobian */.

void OpenMS::OptimizationFunctions::printSignal ( const gsl_vector *  x,
float  resolution = 0.25 
)

Print all peak shapes.

int OpenMS::OptimizationFunctions::residual ( const gsl_vector *  x,
void *  ,
gsl_vector *  f 
)

Evaluation of the target function for nonlinear optimization.

int OpenMS::OptimizationFunctions::residual2D ( const gsl_vector *  x,
void *  params,
gsl_vector *  f 
)

Function computing estimated signal and its deviation to the experimental signal*/.


Variable Documentation

std::multimap<double,IsotopeCluster>::iterator iso_map_iter

std::map<int, std::vector<ExperimentPickedType::SpectrumType::Iterator > > matching_peaks

std::vector<PeakShape> peaks_

This container contains the peak shapes to be optimized.

std::vector<PeakShape> peaks_DC_

MSExperiment<PickedPeak1D>::Iterator picked_peaks_iter

std::vector<double> positions_

Positions and intensity values of the raw data.

std::vector<double> positions_DC_

MSExperiment<RawDataPointType>::ConstIterator raw_data_first

std::vector<std::pair<int,int> > signal2D

std::vector<double> signal_

std::vector<double> signal_DC_

unsigned int total_nr_peaks


Generated Tue Apr 1 15:36:50 2008 -- using doxygen 1.5.4 OpenMS / TOPP 1.1