A RT Profile fitter using an Exponential Gaussian Hybrid background model. More...

#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/EGHTraceFitter.h>

Inheritance diagram for EGHTraceFitter< PeakType >:

Public Member Functions
	EGHTraceFitter ()
	EGHTraceFitter (const EGHTraceFitter &other)
EGHTraceFitter &	operator= (const EGHTraceFitter &source)
virtual	~EGHTraceFitter ()
void	fit (FeatureFinderAlgorithmPickedHelperStructs::MassTraces< PeakType > &traces)
DoubleReal	getLowerRTBound () const
DoubleReal	getTau () const
DoubleReal	getUpperRTBound () const
DoubleReal	getHeight () const
DoubleReal	getSigmaSquare () const
DoubleReal	getCenter () const
bool	checkMaximalRTSpan (const DoubleReal max_rt_span)
virtual bool	checkMinimalRTSpan (const std::pair< DoubleReal, DoubleReal > &rt_bounds, const DoubleReal min_rt_span)
DoubleReal	computeTheoretical (const FeatureFinderAlgorithmPickedHelperStructs::MassTrace< PeakType > &trace, Size k)
virtual DoubleReal	getFeatureIntensityContribution ()
DoubleReal	getFWHM () const
virtual String	getGnuplotFormula (FeatureFinderAlgorithmPickedHelperStructs::MassTrace< PeakType > const &trace, const char function_name, const DoubleReal baseline, const DoubleReal rt_shift)
Protected Member Functions
std::pair< DoubleReal, DoubleReal >	getAlphaBoundaries_ (const DoubleReal alpha) const
	Return an ordered pair of the positions where the EGH reaches a height of alpha * height of the EGH.
void	getOptimizedParameters_ (gsl_multifit_fdfsolver *fdfsolver)
void	setInitialParameters_ (FeatureFinderAlgorithmPickedHelperStructs::MassTraces< PeakType > &traces)
virtual void	updateMembers_ ()
	This method is used to update extra member variables at the end of the setParameters() method.
void	printState_ (SignedSize iter, gsl_multifit_fdfsolver *s)
Static Protected Member Functions
static Int	residual_ (const gsl_vector param, void data, gsl_vector *f)
static Int	jacobian_ (const gsl_vector param, void data, gsl_matrix *J)
static Int	evaluate_ (const gsl_vector param, void data, gsl_vector f, gsl_matrix J)
Protected Attributes
DoubleReal	apex_rt_
DoubleReal	height_
DoubleReal	sigma_square_
DoubleReal	tau_
std::pair< DoubleReal, DoubleReal >	sigma_5_bound_
std::pair< DoubleReal, DoubleReal >	fwhm_bound_
DoubleReal	region_rt_span_
Static Protected Attributes
static const Size	NUM_PARAMS_ = 4

Detailed Description

template<class PeakType>
class OpenMS::EGHTraceFitter< PeakType >

A RT Profile fitter using an Exponential Gaussian Hybrid background model.

Lan K, Jorgenson JW. A hybrid of exponential and gaussian functions as a simple model of asymmetric chromatographic peaks. Journal of Chromatography A. 915 (1-2)p. 1-13. Available at: http://linkinghub.elsevier.com/retrieve/pii/S0021967301005945

Parameters of this class are:

Name	Type	Default	Description
max_iteration	int	500	Maximum number of iterations using by Levenberg-Marquardt algorithm.
epsilon_abs	float	0.0001	Absolute error used by the Levenberg-Marquardt algorithm.
epsilon_rel	float	0.0001	Relative error used by the Levenberg-Marquardt algorithm.

Note:

If a section name is documented, the documentation is displayed as tooltip.
Advanced parameter names are italic.

Experimental classes:: Needs further testing on real data. Note that the tests are currently also focused on testing the EGH as replacement for the gaussian.

Constructor & Destructor Documentation

EGHTraceFitter ( ) [inline]

EGHTraceFitter ( const EGHTraceFitter< PeakType > & other ) [inline]

References EGHTraceFitter< PeakType >::apex_rt_, EGHTraceFitter< PeakType >::fwhm_bound_, EGHTraceFitter< PeakType >::height_, EGHTraceFitter< PeakType >::sigma_5_bound_, EGHTraceFitter< PeakType >::sigma_square_, EGHTraceFitter< PeakType >::tau_, and EGHTraceFitter< PeakType >::updateMembers_().

virtual ~EGHTraceFitter ( ) [inline, virtual]

Member Function Documentation

bool checkMaximalRTSpan ( const DoubleReal max_rt_span ) [inline, virtual]

Checks if the fitted model is not to big

Parameters:

max_rt_span

Maximum RT span in relation to extended area that the model is allowed to have

Implements TraceFitter< PeakType >.

References EGHTraceFitter< PeakType >::region_rt_span_, and EGHTraceFitter< PeakType >::sigma_5_bound_.

virtual bool checkMinimalRTSpan	(	const std::pair< DoubleReal, DoubleReal > &	rt_bounds,
		const DoubleReal	min_rt_span
	)			`[inline, virtual]`

Checks if the fitted model fills out at least 'min_rt_span' of the RT span

Parameters:

	rt_bounds	RT boundaries of the fitted model
	min_rt_span	Minimum RT span in relation to extended area that has to remain after model fitting

Implements TraceFitter< PeakType >.

References EGHTraceFitter< PeakType >::sigma_5_bound_.

DoubleReal computeTheoretical	(	const FeatureFinderAlgorithmPickedHelperStructs::MassTrace< PeakType > &	trace,
		Size	k
	)			`[inline, virtual]`

Returns the theoretical value of the fitted model at position k in the passed Mass Trace

Parameters:

	trace	the mass trace for which the value should be computed
	k	use the position of the k-th peak to compute the value

Implements TraceFitter< PeakType >.

References EGHTraceFitter< PeakType >::apex_rt_, EGHTraceFitter< PeakType >::height_, FeatureFinderAlgorithmPickedHelperStructs::MassTrace< PeakType >::peaks, EGHTraceFitter< PeakType >::sigma_square_, EGHTraceFitter< PeakType >::tau_, and FeatureFinderAlgorithmPickedHelperStructs::MassTrace< PeakType >::theoretical_int.

static Int evaluate_	(	const gsl_vector *	param,
		void *	data,
		gsl_vector *	f,
		gsl_matrix *	J
	)			`[inline, static, protected]`

References EGHTraceFitter< PeakType >::jacobian_(), and EGHTraceFitter< PeakType >::residual_().

void fit ( FeatureFinderAlgorithmPickedHelperStructs::MassTraces< PeakType > & traces ) [inline, virtual]

Main method of the TraceFitter which triggers the actual fitting.

Implements TraceFitter< PeakType >.

References EGHTraceFitter< PeakType >::apex_rt_, EGHTraceFitter< PeakType >::height_, EGHTraceFitter< PeakType >::NUM_PARAMS_, TraceFitter< PeakType >::optimize_(), EGHTraceFitter< PeakType >::setInitialParameters_(), EGHTraceFitter< PeakType >::sigma_square_, and EGHTraceFitter< PeakType >::tau_.

std::pair<DoubleReal, DoubleReal> getAlphaBoundaries_ ( const DoubleReal alpha ) const [inline, protected]

Return an ordered pair of the positions where the EGH reaches a height of alpha * height of the EGH.

Parameters:

alpha

The alpha at which the boundaries should be computed

References EGHTraceFitter< PeakType >::apex_rt_, EGHTraceFitter< PeakType >::sigma_square_, and EGHTraceFitter< PeakType >::tau_.

Referenced by EGHTraceFitter< PeakType >::getFWHM(), and EGHTraceFitter< PeakType >::getOptimizedParameters_().

DoubleReal getCenter ( ) const [inline, virtual]

Returns the center position of the fitted model

Implements TraceFitter< PeakType >.

References EGHTraceFitter< PeakType >::apex_rt_.

virtual DoubleReal getFeatureIntensityContribution ( ) [inline, virtual]

???

Todo:: docu needs update

Implements TraceFitter< PeakType >.

References EGHTraceFitter< PeakType >::fwhm_bound_, and EGHTraceFitter< PeakType >::height_.

DoubleReal getFWHM ( ) const [inline, virtual]

Returns the mass trace width at half max (FWHM)

Implements TraceFitter< PeakType >.

References EGHTraceFitter< PeakType >::getAlphaBoundaries_().

virtual String getGnuplotFormula	(	FeatureFinderAlgorithmPickedHelperStructs::MassTrace< PeakType > const &	trace,
		const char	function_name,
		const DoubleReal	baseline,
		const DoubleReal	rt_shift
	)			`[inline, virtual]`

Returns a textual representation of the fitted model function, that can be plotted using Gnuplot

Parameters:

	trace	The MassTrace that should be plotted
	function_name	The name of the function (e.g. f(x) -> function_name = f)
	baseline	The intensity of the baseline
	rt_shift	A shift value, that allows to plot all RT profiles side by side, even if they would overlap in reality. This should be 0 for the first mass trace and increase by a fixed value for each mass trace.