GaussFilter Class Reference

This class represents a Gaussian lowpass-filter which works on uniform as well as on non-uniform profile data. More...

#include <OpenMS/FILTERING/SMOOTHING/GaussFilter.h>

Inheritance diagram for GaussFilter:

Collaboration diagram for GaussFilter:

Public Member Functions
	GaussFilter ()
	Constructor. More...
	~GaussFilter () override=default
	Destructor. More...
void	filter (MSSpectrum &spectrum)
	Smoothes an MSSpectrum containing profile data. More...
void	filter (MSChromatogram &chromatogram)
void	filterExperiment (PeakMap &map)
	Smoothes an MSExperiment containing profile data. More...
Public Member Functions inherited from ProgressLogger
	ProgressLogger ()
	Constructor. More...
virtual	~ProgressLogger ()
	Destructor. More...
	ProgressLogger (const ProgressLogger &other)
	Copy constructor. More...
ProgressLogger &	operator= (const ProgressLogger &other)
	Assignment Operator. More...
void	setLogType (LogType type) const
	Sets the progress log that should be used. The default type is NONE! More...
LogType	getLogType () const
	Returns the type of progress log being used. More...
void	startProgress (SignedSize begin, SignedSize end, const String &label) const
	Initializes the progress display. More...
void	setProgress (SignedSize value) const
	Sets the current progress. More...
void	endProgress (UInt64 bytes_processed=0) const
void	nextProgress () const
	increment progress by 1 (according to range begin-end) 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...
DefaultParamHandler &	operator= (const DefaultParamHandler &rhs)
	Assignment operator. More...
virtual bool	operator== (const DefaultParamHandler &rhs) const
	Equality operator. More...
void	setParameters (const Param &param)
	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
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
GaussFilterAlgorithm	gauss_algo_
double	spacing_
	The spacing of the pre-tabulated kernel coefficients. More...
bool	write_log_messages_ = false
Protected Attributes inherited from ProgressLogger
LogType	type_
time_t	last_invoke_
ProgressLoggerImpl *	current_logger_
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 ProgressLogger
enum	LogType { CMD , GUI , NONE }
	Possible log types. More...
Static Public Member Functions inherited from DefaultParamHandler
static void	writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")
	Writes all parameters to meta values. More...
Static Protected Member Functions inherited from ProgressLogger
static String	logTypeToFactoryName_ (LogType type)
	Return the name of the factory product used for this log type. More...
Static Protected Attributes inherited from ProgressLogger
static int	recursion_depth_

Detailed Description

This class represents a Gaussian lowpass-filter which works on uniform as well as on non-uniform profile data.

Gaussian filters are important in many signal processing, image processing, and communication applications. These filters are characterized by narrow bandwidths, sharp cutoffs, and low passband ripple. A key feature of Gaussian filters is that the Fourier transform of a Gaussian is also a Gaussian, so the filter has the same response shape in both the time and frequency domains. The coefficients \( \emph{coeffs} \) of the Gaussian-window with length \( \emph{frameSize} \) are calculated from the gaussian distribution

\[ \emph{coeff}(x) = \frac{1}{\sigma \sqrt{2\pi}} e^{\frac{-x^2}{2\sigma^2}} \]

where \( x=[-\frac{frameSize}{2},...,\frac{frameSize}{2}] \) represents the window area and \( \sigma \) is the standard derivation.

Note

The wider the kernel width the smoother the signal (the more detail information get lost!). Use a Gaussian filter kernel which has approximately the same width as your mass peaks, whereas the Gaussian peak width corresponds approximately to 8*sigma.

The data must be sorted according to ascending m/z!

Parameters of this class are:

Name	Type	Default	Restrictions	Description
gaussian_width	float	0.2		Use a gaussian filter width which has approximately the same width as your mass peaks (FWHM in m/z).
ppm_tolerance	float	10.0		Gaussian width, depending on the m/z position. The higher the value, the wider the peak and therefore the wider the gaussian.
use_ppm_tolerance	string	false	true, false	If true, instead of the gaussian_width value, the ppm_tolerance is used. The gaussian is calculated in each step anew, so this is much slower.
write_log_messages	string	false	true, false	true: Warn if no signal was found by the Gauss filter algorithm.

Note:

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

Constructor & Destructor Documentation

GaussFilter()

GaussFilter

(

)

Constructor.

~GaussFilter()

~GaussFilter ( )

overridedefault

Destructor.

Member Function Documentation

filter() [1/2]

void filter

(

MSChromatogram &

chromatogram

)

filter() [2/2]

void filter

(

MSSpectrum &

spectrum

)

Smoothes an MSSpectrum containing profile data.

Convolutes the filter and the profile data and writes the result back to the spectrum.

Exceptions

Exception::IllegalArgument

is thrown, if the gaussian_width parameter is too small.

Referenced by EmgScoring::prepareFit_().

filterExperiment()

void filterExperiment

(

PeakMap &

map

)

Smoothes an MSExperiment containing profile data.

Exceptions

Exception::IllegalArgument

is thrown, if the gaussian_width parameter is too small.

updateMembers_()

void updateMembers_ ( )

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.

Member Data Documentation

gauss_algo_

GaussFilterAlgorithm gauss_algo_

protected

spacing_

double spacing_

protected

The spacing of the pre-tabulated kernel coefficients.

write_log_messages_

bool write_log_messages_ = false

protected