Abstract class for 1D-model fitter using Levenberg-Marquardt algorithm for parameter optimization. More...
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/LevMarqFitter1D.h>
Public Types | |
typedef std::vector< double > | ContainerType |
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typedef IsotopeCluster::IndexSet | IndexSet |
IndexSet. More... | |
typedef IsotopeCluster::ChargedIndexSet | ChargedIndexSet |
IndexSet with charge information. More... | |
typedef Feature::CoordinateType | CoordinateType |
Single coordinate. More... | |
typedef Feature::QualityType | QualityType |
Quality of a feature. More... | |
typedef Peak1D | PeakType |
Raw data point type. More... | |
typedef std::vector< PeakType > | RawDataArrayType |
Raw data container type using for the temporary storage of the input data. More... | |
typedef RawDataArrayType::iterator | PeakIterator |
Raw data iterator. More... | |
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enum | Flag { UNUSED, USED } |
Flags that indicate if a peak is already used in a feature. More... | |
typedef IsotopeCluster::IndexPair | IndexPair |
Index to peak consisting of two UInts (scan index / peak index) More... | |
typedef IsotopeCluster::ChargedIndexSet | ChargedIndexSet |
Index to peak consisting of two UInts (scan index / peak index) with charge information. More... | |
typedef IsotopeCluster::IndexSet | IndexSet |
A set of peak indices. More... | |
Public Member Functions | |
LevMarqFitter1D () | |
Default constructor. More... | |
LevMarqFitter1D (const LevMarqFitter1D &source) | |
copy constructor More... | |
virtual | ~LevMarqFitter1D () |
destructor More... | |
virtual LevMarqFitter1D & | operator= (const LevMarqFitter1D &source) |
assignment operator More... | |
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Fitter1D () | |
Default constructor. More... | |
Fitter1D (const Fitter1D &source) | |
copy constructor More... | |
virtual | ~Fitter1D () |
destructor More... | |
virtual Fitter1D & | operator= (const Fitter1D &source) |
assignment operator More... | |
virtual QualityType | fit1d (const RawDataArrayType &, InterpolationModel *&) |
return interpolation model More... | |
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DefaultParamHandler (const String &name) | |
Constructor with name that is displayed in error messages. More... | |
DefaultParamHandler (const DefaultParamHandler &rhs) | |
Copy constructor. More... | |
virtual | ~DefaultParamHandler () |
Destructor. More... | |
virtual DefaultParamHandler & | operator= (const DefaultParamHandler &rhs) |
Assignment operator. More... | |
virtual bool | operator== (const DefaultParamHandler &rhs) const |
Equality operator. More... | |
void | setParameters (const Param ¶m) |
Sets the parameters. More... | |
const Param & | getParameters () const |
Non-mutable access to the parameters. More... | |
const Param & | getDefaults () const |
Non-mutable access to the default parameters. More... | |
const String & | getName () const |
Non-mutable access to the name. More... | |
void | setName (const String &name) |
Mutable access to the name. More... | |
const std::vector< String > & | getSubsections () const |
Non-mutable access to the registered subsections. More... | |
Protected Member Functions | |
virtual void | printState_ (Int iter, gsl_multifit_fdfsolver *s)=0 |
const String | getGslStatus_ () |
Return GSL status as string. More... | |
void | optimize_ (const RawDataArrayType &set, Int num_params, CoordinateType 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), void *advanced_params) |
Optimize start parameter. More... | |
void | updateMembers_ () |
This method is used to update extra member variables at the end of the setParameters() method. More... | |
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void | defaultsToParam_ () |
Updates the parameters after the defaults have been set in the constructor. More... | |
Protected Attributes | |
Int | gsl_status_ |
GSL status. More... | |
bool | symmetric_ |
Parameter indicates symmetric peaks. More... | |
Int | max_iteration_ |
Maximum number of iterations. More... | |
CoordinateType | abs_error_ |
Absolute error. More... | |
CoordinateType | rel_error_ |
Relative error. More... | |
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CoordinateType | tolerance_stdev_box_ |
standard derivation in bounding box More... | |
CoordinateType | min_ |
minimum of the bounding box More... | |
CoordinateType | max_ |
maximum of the bounding box More... | |
CoordinateType | stdev1_ |
standard derivation More... | |
CoordinateType | stdev2_ |
standard derivation More... | |
Math::BasicStatistics | statistics_ |
basic statistics More... | |
CoordinateType | interpolation_step_ |
interpolation step size More... | |
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Param | param_ |
Container for current parameters. More... | |
Param | defaults_ |
Container for default parameters. This member should be filled in the constructor of derived classes! More... | |
std::vector< String > | subsections_ |
Container for registered subsections. This member should be filled in the constructor of derived classes! More... | |
String | error_name_ |
Name that is displayed in error messages during the parameter checking. More... | |
bool | check_defaults_ |
If this member is set to false no checking if parameters in done;. More... | |
bool | warn_empty_defaults_ |
If this member is set to false no warning is emitted when defaults are empty;. More... | |
Additional Inherited Members | |
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static void | registerChildren () |
register all derived classes here More... | |
Abstract class for 1D-model fitter using Levenberg-Marquardt algorithm for parameter optimization.
typedef std::vector<double> ContainerType |
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inline |
Default constructor.
References StringList::create().
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inline |
copy constructor
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inlinevirtual |
destructor
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inlineprotected |
Return GSL status as string.
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inlinevirtual |
assignment operator
References LevMarqFitter1D::abs_error_, LevMarqFitter1D::max_iteration_, Fitter1D::operator=(), and LevMarqFitter1D::rel_error_.
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inlineprotected |
Optimize start parameter.
Exception::UnableToFit | is thrown if fitting cannot be performed |
References OpenMS::Constants::c, ERR, OpenMS::OptimizationFunctions::evaluate(), FIT, OpenMS::OptimizationFunctions::jacobian(), and OpenMS::OptimizationFunctions::residual().
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protectedpure virtual |
Display the intermediate state of the solution. The solver state contains the vector s->x which is the current position, and the vector s->f with corresponding function values
Implemented in LmaIsotopeFitter1D, EGHFitter1D, EmgFitter1D, and LmaGaussFitter1D.
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inlineprotectedvirtual |
This method is used to update extra member variables at the end of the setParameters() method.
Also call it at the end of the derived classes' copy constructor and assignment operator.
The default implementation is empty.
Reimplemented from Fitter1D.
Reimplemented in LmaIsotopeFitter1D, and LmaGaussFitter1D.
References Fitter1D::updateMembers_().
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protected |
Absolute error.
Test for the convergence of the sequence by comparing the last iteration step dx with the absolute error epsabs and relative error epsrel to the current position x
Referenced by LevMarqFitter1D::operator=().
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protected |
GSL status.
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protected |
Maximum number of iterations.
Referenced by LevMarqFitter1D::operator=().
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protected |
Relative error.
Referenced by LevMarqFitter1D::operator=().
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protected |
Parameter indicates symmetric peaks.
OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:34 using doxygen 1.8.5 |