OpenMS  2.5.0
Classes | List of all members
SignalToNoiseEstimator< Container > Class Template Referenceabstract

This class represents the abstract base class of a signal to noise estimator. More...

#include <OpenMS/FILTERING/NOISEESTIMATION/SignalToNoiseEstimator.h>

Inheritance diagram for SignalToNoiseEstimator< Container >:
DefaultParamHandler ProgressLogger SignalToNoiseEstimatorMeanIterative< Container > SignalToNoiseEstimatorMedian< Container >

Classes

struct  GaussianEstimate
 protected struct to store parameters my, sigma for a Gaussian distribution More...
 

Type definitions

typedef Container::const_iterator PeakIterator
 
typedef PeakIterator::value_type PeakType
 
std::map< PeakType, double, typename PeakType::PositionLessstn_estimates_
 stores the noise estimate for each peak More...
 
PeakIterator first_
 points to the first raw data point in the interval More...
 
PeakIterator last_
 points to the right position next to the last raw data point in the interval More...
 
bool is_result_valid_
 flag: set to true if SignalToNoise estimates are calculated and none of the params were changed. otherwise false. More...
 
 SignalToNoiseEstimator ()
 Constructor. More...
 
 SignalToNoiseEstimator (const SignalToNoiseEstimator &source)
 Copy constructor. More...
 
SignalToNoiseEstimatoroperator= (const SignalToNoiseEstimator &source)
 Assignment operator. More...
 
 ~SignalToNoiseEstimator () override
 Destructor. More...
 
virtual void init (const PeakIterator &it_begin, const PeakIterator &it_end)
 Set the start and endpoint of the raw data interval, for which signal to noise ratios will be estimated immediately. More...
 
virtual void init (const Container &c)
 Set the start and endpoint of the raw data interval, for which signal to noise ratios will be estimated immediately. More...
 
virtual double getSignalToNoise (const PeakIterator &data_point)
 
virtual double getSignalToNoise (const PeakType &data_point)
 
virtual void computeSTN_ (const PeakIterator &scan_first_, const PeakIterator &scan_last_)=0
 computes the S/N values when init() is called More...
 
GaussianEstimate estimate_ (const PeakIterator &scan_first_, const PeakIterator &scan_last_) const
 calculate mean & stdev of intensities of a spectrum More...
 

Additional Inherited Members

- Public Types inherited from ProgressLogger
enum  LogType { CMD, GUI, NONE }
 Possible log types. 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 DefaultParamHandleroperator= (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 ParamgetParameters () const
 Non-mutable access to the parameters. More...
 
const ParamgetDefaults () const
 Non-mutable access to the default parameters. More...
 
const StringgetName () 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...
 
- Public Member Functions inherited from ProgressLogger
 ProgressLogger ()
 Constructor. More...
 
 ~ProgressLogger ()
 Destructor. More...
 
 ProgressLogger (const ProgressLogger &other)
 Copy constructor. More...
 
ProgressLoggeroperator= (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 () const
 Ends the progress display. More...
 
void nextProgress () const
 increment progress by 1 (according to range begin-end) More...
 
- Protected Member Functions inherited from DefaultParamHandler
virtual void updateMembers_ ()
 This method is used to update extra member variables at the end of the setParameters() method. More...
 
void defaultsToParam_ ()
 Updates the parameters after the defaults have been set in the constructor. 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...
 
- 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< Stringsubsections_
 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...
 
- Protected Attributes inherited from ProgressLogger
LogType type_
 
time_t last_invoke_
 
ProgressLoggerImplcurrent_logger_
 
- Static Protected Attributes inherited from ProgressLogger
static int recursion_depth_
 

Detailed Description

template<typename Container = MSSpectrum>
class OpenMS::SignalToNoiseEstimator< Container >

This class represents the abstract base class of a signal to noise estimator.

A signal to noise estimator should provide the signal to noise ratio of all raw data points in a given interval [first_,last_).


Class Documentation

◆ OpenMS::SignalToNoiseEstimator::GaussianEstimate

struct OpenMS::SignalToNoiseEstimator::GaussianEstimate

template<typename Container = MSSpectrum>
struct OpenMS::SignalToNoiseEstimator< Container >::GaussianEstimate

protected struct to store parameters my, sigma for a Gaussian distribution

Accessors are : mean and variance

Class Members
double mean mean of estimated Gaussian
double variance variance of estimated Gaussian

Member Typedef Documentation

◆ PeakIterator

typedef Container::const_iterator PeakIterator

◆ PeakType

typedef PeakIterator::value_type PeakType

Constructor & Destructor Documentation

◆ SignalToNoiseEstimator() [1/2]

Constructor.

◆ SignalToNoiseEstimator() [2/2]

SignalToNoiseEstimator ( const SignalToNoiseEstimator< Container > &  source)
inline

Copy constructor.

◆ ~SignalToNoiseEstimator()

~SignalToNoiseEstimator ( )
inlineoverride

Destructor.

Member Function Documentation

◆ computeSTN_()

virtual void computeSTN_ ( const PeakIterator scan_first_,
const PeakIterator scan_last_ 
)
protectedpure virtual

◆ estimate_()

GaussianEstimate estimate_ ( const PeakIterator scan_first_,
const PeakIterator scan_last_ 
) const
inlineprotected

◆ getSignalToNoise() [1/2]

virtual double getSignalToNoise ( const PeakIterator data_point)
inlinevirtual

Return to signal/noise estimate for data point data_point

Note
the first query to this function will take longer, as all SignalToNoise values are calculated
you will get a warning to stderr if more than 20% of the noise estimates used sparse windows

Referenced by SignalToNoiseOpenMS< ContainerT >::getValueAtRT(), and PeakPickerIterative::pickRecenterPeaks_().

◆ getSignalToNoise() [2/2]

virtual double getSignalToNoise ( const PeakType data_point)
inlinevirtual

◆ init() [1/2]

virtual void init ( const Container &  c)
inlinevirtual

Set the start and endpoint of the raw data interval, for which signal to noise ratios will be estimated immediately.

◆ init() [2/2]

virtual void init ( const PeakIterator it_begin,
const PeakIterator it_end 
)
inlinevirtual

Set the start and endpoint of the raw data interval, for which signal to noise ratios will be estimated immediately.

Referenced by SignalToNoiseEstimator< ContainerT >::getSignalToNoise(), SignalToNoiseEstimator< ContainerT >::init(), and SignalToNoiseOpenMS< ContainerT >::SignalToNoiseOpenMS().

◆ operator=()

SignalToNoiseEstimator& operator= ( const SignalToNoiseEstimator< Container > &  source)
inline

Assignment operator.

Member Data Documentation

◆ first_

PeakIterator first_
protected

◆ is_result_valid_

bool is_result_valid_
mutableprotected

◆ last_

PeakIterator last_
protected

points to the right position next to the last raw data point in the interval

Referenced by SignalToNoiseEstimator< ContainerT >::getSignalToNoise(), SignalToNoiseEstimator< ContainerT >::init(), and SignalToNoiseEstimator< ContainerT >::operator=().

◆ stn_estimates_

std::map<PeakType, double, typename PeakType::PositionLess> stn_estimates_
protected