Home  · Classes  · Annotated Classes  · Modules  · Members  · Namespaces  · Related Pages
Public Types | Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
SignalToNoiseEstimatorMeanIterative< Container > Class Template Reference

Estimates the signal/noise (S/N) ratio of each data point in a scan based on an iterative scheme which discards high intensities. More...

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

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

Public Types

enum  IntensityThresholdCalculation { MANUAL = -1, AUTOMAXBYSTDEV = 0, AUTOMAXBYPERCENT = 1 }
 method to use for estimating the maximal intensity that is used for histogram calculation More...
 
typedef SignalToNoiseEstimator< Container >::PeakIterator PeakIterator
 
typedef SignalToNoiseEstimator< Container >::PeakType PeakType
 
typedef SignalToNoiseEstimator< Container >::GaussianEstimate GaussianEstimate
 
- Public Types inherited from SignalToNoiseEstimator< Container >
typedef Container::const_iterator PeakIterator
 
typedef PeakIterator::value_type PeakType
 
- Public Types inherited from ProgressLogger
enum  LogType { CMD, GUI, NONE }
 Possible log types. More...
 

Public Member Functions

 SignalToNoiseEstimatorMeanIterative ()
 default constructor More...
 
 SignalToNoiseEstimatorMeanIterative (const SignalToNoiseEstimatorMeanIterative &source)
 Copy Constructor. More...
 
virtual ~SignalToNoiseEstimatorMeanIterative ()
 Destructor. More...
 
Assignment
SignalToNoiseEstimatorMeanIterativeoperator= (const SignalToNoiseEstimatorMeanIterative &source)
 
- Public Member Functions inherited from SignalToNoiseEstimator< Container >
 SignalToNoiseEstimator ()
 Constructor. More...
 
 SignalToNoiseEstimator (const SignalToNoiseEstimator &source)
 Copy constructor. More...
 
SignalToNoiseEstimatoroperator= (const SignalToNoiseEstimator &source)
 Assignment operator. More...
 
virtual ~SignalToNoiseEstimator ()
 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)
 
- 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...
 

Protected Member Functions

virtual void computeSTN_ (const PeakIterator &scan_first_, const PeakIterator &scan_last_)
 
void updateMembers_ ()
 overridden function from DefaultParamHandler to keep members up to date, when a parameter is changed More...
 
- Protected Member Functions inherited from SignalToNoiseEstimator< Container >
GaussianEstimate estimate_ (const PeakIterator &scan_first_, const PeakIterator &scan_last_) const
 calculate mean & stdev of intensities of a spectrum More...
 
- Protected Member Functions inherited from DefaultParamHandler
void defaultsToParam_ ()
 Updates the parameters after the defaults have been set in the constructor. More...
 

Protected Attributes

double max_intensity_
 maximal intensity considered during binning (values above get discarded) More...
 
double auto_max_stdev_Factor_
 parameter for initial automatic estimation of "max_intensity_": a stdev multiplier More...
 
double auto_max_percentile_
 parameter for initial automatic estimation of "max_intensity_" percentile or a stdev More...
 
int auto_mode_
 determines which method shall be used for estimating "max_intensity_". valid are MANUAL=-1, AUTOMAXBYSTDEV=0 or AUTOMAXBYPERCENT=1 More...
 
double win_len_
 range of data points which belong to a window in Thomson More...
 
int bin_count_
 number of bins in the histogram More...
 
double stdev_
 multiplier for the stdev of intensities More...
 
int min_required_elements_
 minimal number of elements a window needs to cover to be used More...
 
double noise_for_empty_window_
 
- Protected Attributes inherited from SignalToNoiseEstimator< Container >
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...
 
- 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_
 

Additional Inherited Members

- 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

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

Estimates the signal/noise (S/N) ratio of each data point in a scan based on an iterative scheme which discards high intensities.

For each datapoint in the given scan, we collect a range of data points around it (param: win_len). The noise for a datapoint is estimated iteratively by discarding peaks which are more than (stdev_mp * StDev) above the mean value. After three iterations, the mean value is considered to be the noise level. If the number of elements in the current window is not sufficient (param: min_required_elements), the noise level is set to a default value (param: noise_for_empty_window).

The whole computation is histogram based, so the user will need to supply a number of bins (param: bin_count), which determines the level of error and runtime. The maximal intensity for a datapoint to be included in the histogram can be either determined automatically (param: auto_mode) by two different methods or can be set directly by the user (param: max_intensity).

Changing any of the parameters will invalidate the S/N values (which will invoke a recomputation on the next request).

Note
If more than 20 percent of windows have less than min_required_elements of elements, a warning is issued to stderr and noise estimates in those windows are set to the constant noise_for_empty_window.

Member Typedef Documentation

Member Enumeration Documentation

method to use for estimating the maximal intensity that is used for histogram calculation

Enumerator
MANUAL 
AUTOMAXBYSTDEV 
AUTOMAXBYPERCENT 

Constructor & Destructor Documentation

virtual ~SignalToNoiseEstimatorMeanIterative ( )
inlinevirtual

Destructor.

Member Function Documentation

virtual void computeSTN_ ( const PeakIterator scan_first_,
const PeakIterator scan_last_ 
)
inlineprotectedvirtual
SignalToNoiseEstimatorMeanIterative& operator= ( const SignalToNoiseEstimatorMeanIterative< Container > &  source)
inline
void updateMembers_ ( )
inlineprotectedvirtual

Member Data Documentation

double auto_max_percentile_
protected

parameter for initial automatic estimation of "max_intensity_" percentile or a stdev

Referenced by SignalToNoiseEstimatorMeanIterative< Container >::computeSTN_(), and SignalToNoiseEstimatorMeanIterative< Container >::updateMembers_().

double auto_max_stdev_Factor_
protected

parameter for initial automatic estimation of "max_intensity_": a stdev multiplier

Referenced by SignalToNoiseEstimatorMeanIterative< Container >::computeSTN_(), and SignalToNoiseEstimatorMeanIterative< Container >::updateMembers_().

int auto_mode_
protected

determines which method shall be used for estimating "max_intensity_". valid are MANUAL=-1, AUTOMAXBYSTDEV=0 or AUTOMAXBYPERCENT=1

Referenced by SignalToNoiseEstimatorMeanIterative< Container >::computeSTN_(), and SignalToNoiseEstimatorMeanIterative< Container >::updateMembers_().

int bin_count_
protected
double max_intensity_
protected

maximal intensity considered during binning (values above get discarded)

Referenced by SignalToNoiseEstimatorMeanIterative< Container >::computeSTN_(), and SignalToNoiseEstimatorMeanIterative< Container >::updateMembers_().

int min_required_elements_
protected
double noise_for_empty_window_
protected

used as noise value for windows which cover less than "min_required_elements_" use a very high value if you want to get a low S/N result

Referenced by SignalToNoiseEstimatorMeanIterative< Container >::computeSTN_(), and SignalToNoiseEstimatorMeanIterative< Container >::updateMembers_().

double stdev_
protected
double win_len_
protected

OpenMS / TOPP release 2.0.0 Documentation generated on Tue Nov 1 2016 16:34:46 using doxygen 1.8.11