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SignalToNoiseEstimatorMedian< Container > Class Template Reference

Estimates the signal/noise (S/N) ratio of each data point in a scan by using the median (histogram based) More...

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

Inheritance diagram for SignalToNoiseEstimatorMedian< 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

 SignalToNoiseEstimatorMedian ()
 default constructor More...
 
 SignalToNoiseEstimatorMedian (const SignalToNoiseEstimatorMedian &source)
 Copy Constructor. More...
 
virtual ~SignalToNoiseEstimatorMedian ()
 Destructor. More...
 
Assignment
SignalToNoiseEstimatorMedianoperator= (const SignalToNoiseEstimatorMedian &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...
 
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

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...
 
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::PositionLess
stn_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_
 
SignedSize begin_
 
SignedSize end_
 
SignedSize value_
 
QProgressDialog * dlg_
 
StopWatch stop_watch_
 
time_t last_invoke_
 

Additional Inherited Members

- Static Protected Attributes inherited from ProgressLogger
static int recursion_depth_
 

Detailed Description

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

Estimates the signal/noise (S/N) ratio of each data point in a scan by using the median (histogram based)

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 to be the median of the intensities of the current window. If the number of elements in the current window is not sufficient (param: MinReqElements), 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 (params: AutoMaxIntensity, auto_mode) by two different methods or can be set directly by the user (param: max_intensity). If the (estimated) max_intensity value is too low and the median is found to be in the last (&highest) bin, a warning to std:err will be given. In this case you should increase max_intensity (and optionally the bin_count).

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.
If more than 1 percent of median estimations had to rely on the last(=rightmost) bin (which gives an unreliable result), a warning is issued to stderr.
Parameters of this class are:

NameTypeDefaultRestrictionsDescription
max_intensity int-1 min: -1maximal intensity considered for histogram construction. By default, it will be calculated automatically (see auto_mode). Only provide this parameter if you know what you are doing (and change 'auto_mode' to '-1')! All intensities EQUAL/ABOVE 'max_intensity' will be added to the LAST histogram bin. If you choose 'max_intensity' too small, the noise estimate might be too small as well. If chosen too big, the bins become quite large (which you could counter by increasing 'bin_count', which increases runtime). In general, the Median-S/N estimator is more robust to a manual max_intensity than the MeanIterative-S/N.
auto_max_stdev_factor float3 min: 0 max: 999parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev
auto_max_percentile int95 min: 0 max: 100parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile
auto_mode int0 min: -1 max: 1method to use to determine maximal intensity: -1 --> use 'max_intensity'; 0 --> 'auto_max_stdev_factor' method (default); 1 --> 'auto_max_percentile' method
win_len float200 min: 1window length in Thomson
bin_count int30 min: 3number of bins for intensity values
min_required_elements int10 min: 1minimum number of elements required in a window (otherwise it is considered sparse)
noise_for_empty_window float1e+20  noise value used for sparse windows

Note:

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

default constructor

SignalToNoiseEstimatorMedian ( const SignalToNoiseEstimatorMedian< Container > &  source)
inline

Copy Constructor.

virtual ~SignalToNoiseEstimatorMedian ( )
inlinevirtual

Destructor.

Member Function Documentation

void computeSTN_ ( const PeakIterator scan_first_,
const PeakIterator scan_last_ 
)
inlineprotectedvirtual

calculate StN values for all datapoints given, by using a sliding window approach

Parameters
scan_first_first element in the scan
scan_last_last element in the scan (disregarded)
Exceptions
ThrowsException::InvalidValue

Implements SignalToNoiseEstimator< Container >.

SignalToNoiseEstimatorMedian& operator= ( const SignalToNoiseEstimatorMedian< Container > &  source)
inline
void updateMembers_ ( )
inlineprotectedvirtual

overridden function from DefaultParamHandler to keep members up to date, when a parameter is changed

Reimplemented from DefaultParamHandler.

Referenced by SignalToNoiseEstimatorMedian< OpenMS::OpenMS::MSSpectrum< PeakT > >::SignalToNoiseEstimatorMedian().

Member Data Documentation

double auto_max_percentile_
protected
double auto_max_stdev_Factor_
protected
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 SignalToNoiseEstimatorMedian< OpenMS::OpenMS::MSSpectrum< PeakT > >::computeSTN_(), and SignalToNoiseEstimatorMedian< OpenMS::OpenMS::MSSpectrum< PeakT > >::updateMembers_().

int bin_count_
protected
double max_intensity_
protected
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 SignalToNoiseEstimatorMedian< OpenMS::OpenMS::MSSpectrum< PeakT > >::computeSTN_(), and SignalToNoiseEstimatorMedian< OpenMS::OpenMS::MSSpectrum< PeakT > >::updateMembers_().

double win_len_
protected

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:30 using doxygen 1.8.5