Fitter for RT profiles using a gaussian background model. More...

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

Inheritance diagram for GaussTraceFitter< PeakType >:

Public Member Functions
	GaussTraceFitter ()
	GaussTraceFitter (const GaussTraceFitter &other)
GaussTraceFitter &	operator= (const GaussTraceFitter &source)
virtual	~GaussTraceFitter ()
void	fit (FeatureFinderAlgorithmPickedHelperStructs::MassTraces< PeakType > &traces)
DoubleReal	getLowerRTBound () const
DoubleReal	getUpperRTBound () const
DoubleReal	getHeight () const
DoubleReal	getCenter () const
DoubleReal	getFWHM () const
DoubleReal	getSigma () const
	Returns the sigma of the fitted gaussian model.
bool	checkMaximalRTSpan (const DoubleReal max_rt_span)
bool	checkMinimalRTSpan (const std::pair< DoubleReal, DoubleReal > &rt_bounds, const DoubleReal min_rt_span)
DoubleReal	computeTheoretical (const FeatureFinderAlgorithmPickedHelperStructs::MassTrace< PeakType > &trace, Size k)
DoubleReal	getFeatureIntensityContribution ()
String	getGnuplotFormula (FeatureFinderAlgorithmPickedHelperStructs::MassTrace< PeakType > const &trace, const char function_name, const DoubleReal baseline, const DoubleReal rt_shift)
Protected Member Functions
void	getOptimizedParameters_ (gsl_multifit_fdfsolver *s)
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	sigma_
DoubleReal	x0_
DoubleReal	height_
DoubleReal	region_rt_span_
Static Protected Attributes
static const Size	NUM_PARAMS_ = 3

Detailed Description

template<typename PeakType>
class OpenMS::GaussTraceFitter< PeakType >

Fitter for RT profiles using a gaussian background model.

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.

Todo:: More docu

Constructor & Destructor Documentation

GaussTraceFitter ( ) [inline]

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

References GaussTraceFitter< PeakType >::height_, GaussTraceFitter< PeakType >::sigma_, GaussTraceFitter< PeakType >::updateMembers_(), and GaussTraceFitter< PeakType >::x0_.

virtual ~GaussTraceFitter ( ) [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 GaussTraceFitter< PeakType >::region_rt_span_, and GaussTraceFitter< PeakType >::sigma_.

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 GaussTraceFitter< PeakType >::sigma_.

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 GaussTraceFitter< PeakType >::height_, FeatureFinderAlgorithmPickedHelperStructs::MassTrace< PeakType >::peaks, GaussTraceFitter< PeakType >::sigma_, FeatureFinderAlgorithmPickedHelperStructs::MassTrace< PeakType >::theoretical_int, and GaussTraceFitter< PeakType >::x0_.

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

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

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

Main method of the TraceFitter which triggers the actual fitting.

Implements TraceFitter< PeakType >.

References GaussTraceFitter< PeakType >::height_, LOG_DEBUG, GaussTraceFitter< PeakType >::NUM_PARAMS_, TraceFitter< PeakType >::optimize_(), GaussTraceFitter< PeakType >::setInitialParameters_(), GaussTraceFitter< PeakType >::sigma_, and GaussTraceFitter< PeakType >::x0_.

DoubleReal getCenter ( ) const [inline, virtual]

Returns the center position of the fitted model

Implements TraceFitter< PeakType >.

References GaussTraceFitter< PeakType >::x0_.

DoubleReal getFeatureIntensityContribution ( ) [inline, virtual]

???

Todo:: docu needs update

Implements TraceFitter< PeakType >.

References GaussTraceFitter< PeakType >::height_, and GaussTraceFitter< PeakType >::sigma_.

DoubleReal getFWHM ( ) const [inline, virtual]

Returns the mass trace width at half max (FWHM)

Implements TraceFitter< PeakType >.

References GaussTraceFitter< PeakType >::sigma_.

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.