Gaussian distribution fitter (1-dim.) using Levenberg-Marquardt algorithm (GSL implementation) for parameter optimization. More...
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/LmaGaussFitter1D.h>
Classes | |
struct | Data |
Helper struct (contains the size of an area and a raw data container) More... | |
Public Member Functions | |
LmaGaussFitter1D () | |
Default constructor. More... | |
LmaGaussFitter1D (const LmaGaussFitter1D &source) | |
copy constructor More... | |
virtual | ~LmaGaussFitter1D () |
destructor More... | |
virtual LmaGaussFitter1D & | operator= (const LmaGaussFitter1D &source) |
assignment operator More... | |
QualityType | fit1d (const RawDataArrayType &range, InterpolationModel *&model) |
return interpolation model More... | |
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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... | |
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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... | |
Static Public Member Functions | |
static Fitter1D * | create () |
create new LmaGaussFitter1D object (function needed by Factory) More... | |
static const String | getProductName () |
name of the model (needed by Factory) More... | |
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static void | registerChildren () |
register all derived classes here More... | |
Protected Member Functions | |
void | setInitialParameters_ (const RawDataArrayType &set) |
Compute start parameter. More... | |
void | printState_ (Int iter, gsl_multifit_fdfsolver *s) |
void | updateMembers_ () |
This method is used to update extra member variables at the end of the setParameters() method. More... | |
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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... | |
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void | defaultsToParam_ () |
Updates the parameters after the defaults have been set in the constructor. More... | |
Static Protected Member Functions | |
static Int | residual_ (const gsl_vector *x, void *params, gsl_vector *f) |
Evaluation of the target function for nonlinear optimization. More... | |
static Int | jacobian_ (const gsl_vector *x, void *params, gsl_matrix *J) |
Compute the Jacobian matrix, where each row of the matrix corresponds to a point in the data. More... | |
static Int | evaluate_ (const gsl_vector *x, void *params, gsl_vector *f, gsl_matrix *J) |
Driver function for the evaluation of function and jacobian. More... | |
Protected Attributes | |
CoordinateType | standard_deviation_ |
parameter of gauss function: standard deviation More... | |
CoordinateType | scale_factor_ |
parameter of gauss function: scale factor More... | |
CoordinateType | expected_value_ |
parameter of gauss function: expected value More... | |
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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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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... | |
Gaussian distribution fitter (1-dim.) using Levenberg-Marquardt algorithm (GSL implementation) for parameter optimization.
Parameters of this class are:Name | Type | Default | Restrictions | Description |
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interpolation_step | float | 0.2 | Sampling rate for the interpolation of the model function. | |
tolerance_stdev_bounding_box | float | 3 | Bounding box has range [minimim of data, maximum of data] enlarged by tolerance_stdev_bounding_box times the standard deviation of the data. | |
max_iteration | int | 500 | Maximum number of iterations using by Levenberg-Marquardt algorithm. | |
deltaAbsError | float | 0.0001 | Absolute error used by the Levenberg-Marquardt algorithm. | |
deltaRelError | float | 0.0001 | Relative error used by the Levenberg-Marquardt algorithm. | |
statistics:mean | float | 1 | Centroid position of the model. | |
statistics:variance | float | 1 | Variance of the model. |
LmaGaussFitter1D | ( | ) |
Default constructor.
LmaGaussFitter1D | ( | const LmaGaussFitter1D & | source | ) |
copy constructor
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virtual |
destructor
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inlinestatic |
create new LmaGaussFitter1D object (function needed by Factory)
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staticprotected |
Driver function for the evaluation of function and jacobian.
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virtual |
return interpolation model
Reimplemented from Fitter1D.
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staticprotected |
Compute the Jacobian matrix, where each row of the matrix corresponds to a point in the data.
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virtual |
assignment operator
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protectedvirtual |
Diplay 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
Implements LevMarqFitter1D.
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staticprotected |
Evaluation of the target function for nonlinear optimization.
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protected |
Compute start parameter.
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protectedvirtual |
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 LevMarqFitter1D.
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protected |
parameter of gauss function: expected value
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protected |
parameter of gauss function: scale factor
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protected |
parameter of gauss function: standard deviation
OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:34 using doxygen 1.8.5 |