OpenMS
2.6.0
|
Exponentially modified gaussian distribution fitter (1-dim.) using Levenberg-Marquardt algorithm (Eigen implementation) for parameter optimization. More...
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/EmgFitter1D.h>
Classes | |
struct | Data |
Helper struct (contains the size of an area and a raw data container) More... | |
class | EgmFitterFunctor |
Public Member Functions | |
EmgFitter1D () | |
Default constructor. More... | |
EmgFitter1D (const EmgFitter1D &source) | |
copy constructor More... | |
~EmgFitter1D () override | |
destructor More... | |
virtual EmgFitter1D & | operator= (const EmgFitter1D &source) |
assignment operator More... | |
QualityType | fit1d (const RawDataArrayType &range, InterpolationModel *&model) override |
return interpolation model More... | |
Public Member Functions inherited from LevMarqFitter1D | |
LevMarqFitter1D () | |
Default constructor. More... | |
LevMarqFitter1D (const LevMarqFitter1D &source) | |
copy constructor More... | |
~LevMarqFitter1D () override | |
destructor More... | |
virtual LevMarqFitter1D & | operator= (const LevMarqFitter1D &source) |
assignment operator More... | |
Public Member Functions inherited from Fitter1D | |
Fitter1D () | |
Default constructor. More... | |
Fitter1D (const Fitter1D &source) | |
copy constructor More... | |
~Fitter1D () override | |
destructor More... | |
virtual Fitter1D & | operator= (const Fitter1D &source) |
assignment operator More... | |
Public Member Functions inherited from DefaultParamHandler | |
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 EmgFitter1D object (function needed by Factory) More... | |
static const String | getProductName () |
name of the model (needed by Factory) More... | |
Static Public Member Functions inherited from Fitter1D | |
static void | registerChildren () |
register all derived classes here More... | |
Static Public Member Functions inherited from DefaultParamHandler | |
static void | writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &prefix="") |
Writes all parameters to meta values. More... | |
Protected Member Functions | |
virtual void | setInitialParameters_ (const RawDataArrayType &set) |
Compute start parameter. More... | |
void | updateMembers_ () override |
This method is used to update extra member variables at the end of the setParameters() method. More... | |
Protected Member Functions inherited from LevMarqFitter1D | |
void | optimize_ (Eigen::VectorXd &x_init, GenericFunctor &functor) |
Optimize start parameter. More... | |
void | updateMembers_ () override |
This method is used to update extra member variables at the end of the setParameters() method. More... | |
Protected Member Functions inherited from DefaultParamHandler | |
void | defaultsToParam_ () |
Updates the parameters after the defaults have been set in the constructor. More... | |
Protected Attributes | |
CoordinateType | height_ |
Parameter of emg - peak height. More... | |
CoordinateType | width_ |
Parameter of emg - peak width. More... | |
CoordinateType | symmetry_ |
Parameter of emg - peak symmetry. More... | |
CoordinateType | retention_ |
Parameter of emg - peak retention time. More... | |
Protected Attributes inherited from LevMarqFitter1D | |
bool | symmetric_ |
Parameter indicates symmetric peaks. More... | |
Int | max_iteration_ |
Maximum number of iterations. More... | |
Protected Attributes inherited from Fitter1D | |
CoordinateType | tolerance_stdev_box_ |
standard derivation in bounding box More... | |
Math::BasicStatistics | statistics_ |
basic statistics More... | |
CoordinateType | interpolation_step_ |
interpolation step size More... | |
Protected Attributes inherited from DefaultParamHandler | |
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 | |
Public Types inherited from LevMarqFitter1D | |
typedef std::vector< double > | ContainerType |
Public Types inherited from Fitter1D | |
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 |
Peak type data point type. More... | |
typedef std::vector< PeakType > | RawDataArrayType |
Peak type data container type using for the temporary storage of the input data. More... | |
typedef RawDataArrayType::iterator | PeakIterator |
Peak type data iterator. More... | |
Public Types inherited from FeatureFinderDefs | |
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... | |
Exponentially modified gaussian distribution fitter (1-dim.) using Levenberg-Marquardt algorithm (Eigen implementation) for parameter optimization.
Parameters of this class are:Name | Type | Default | Restrictions | Description |
---|---|---|---|---|
interpolation_step | float | 0.2 | Sampling rate for the interpolation of the model function. | |
tolerance_stdev_bounding_box | float | 3.0 | 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. | |
statistics:mean | float | 1.0 | Centroid position of the model. | |
statistics:variance | float | 1.0 | Variance of the model. |
struct OpenMS::EmgFitter1D::Data |
Helper struct (contains the size of an area and a raw data container)
Class Members | ||
---|---|---|
typedef Peak1D | PeakType | |
typedef vector< PeakType > | RawDataArrayType |
Class Members | ||
---|---|---|
Size | n | |
RawDataArrayType | set |
EmgFitter1D | ( | ) |
Default constructor.
EmgFitter1D | ( | const EmgFitter1D & | source | ) |
copy constructor
|
override |
destructor
|
inlinestatic |
create new EmgFitter1D object (function needed by Factory)
|
overridevirtual |
|
virtual |
assignment operator
|
protectedvirtual |
Compute start parameter.
|
overrideprotectedvirtual |
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 DefaultParamHandler.
|
protected |
Parameter of emg - peak height.
|
protected |
Parameter of emg - peak retention time.
|
protected |
Parameter of emg - peak symmetry.
|
protected |
Parameter of emg - peak width.