| OpenMS 2.5.0

Classes | Public Member Functions | Protected Member Functions | Protected Attributes | 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 >:

## Classes

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

## Public Types

Type definitions
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

| SignalToNoiseEstimator ()
| Constructor. More...
| SignalToNoiseEstimator (const SignalToNoiseEstimator &source)
| Copy constructor. More...
SignalToNoiseEstimator & | operator= (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)
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 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...
Public Member Functions inherited from ProgressLogger
| ProgressLogger ()
| Constructor. More...
| ~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 () const
| Ends the progress display. More...
void | nextProgress () const
| increment progress by 1 (according to range begin-end) More...

## Protected Member Functions

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...
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...

## Protected Attributes

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< 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...
Protected Attributes inherited from ProgressLogger
LogType | type_
time_t | last_invoke_
ProgressLoggerImpl * | current_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::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]

SignalToNoiseEstimator | ( |  | ) |

inline

Constructor.

## ◆ SignalToNoiseEstimator() [2/2]

SignalToNoiseEstimator | ( | const SignalToNoiseEstimator< Container > & | source | ) |

inline

Copy constructor.

## ◆ ~SignalToNoiseEstimator()

~SignalToNoiseEstimator | ( |  | ) |

inline override

Destructor.

## Member Function Documentation

## ◆ computeSTN_()

virtual void computeSTN_ | ( | const PeakIterator & | scan_first_,
|  | const PeakIterator & | scan_last_
| ) |  |

protected pure virtual

computes the S/N values when init() is called

Exceptions

  Throws | Exception::InvalidValue

Implemented in SignalToNoiseEstimatorMedian< Container >, SignalToNoiseEstimatorMedian< OpenMS::MSChromatogram >, SignalToNoiseEstimatorMedian< ContainerT >, and SignalToNoiseEstimatorMeanIterative< Container >.

Referenced by SignalToNoiseEstimator< ContainerT >::init().

## ◆ estimate_()

GaussianEstimate estimate_ | ( | const PeakIterator & | scan_first_,
|  | const PeakIterator & | scan_last_
| ) |  | const

inline protected

calculate mean & stdev of intensities of a spectrum

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

## ◆ getSignalToNoise() [1/2]

virtual double getSignalToNoise | ( | const PeakIterator & | data_point | ) |

inline virtual

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 | ) |

inline virtual

## ◆ init() [1/2]

virtual void init | ( | const PeakIterator & | it_begin,
|  | const PeakIterator & | it_end
| ) |  |

inline virtual

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().

## ◆ init() [2/2]

virtual void init | ( | const Container & | c | ) |

inline virtual

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

## ◆ operator=()

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

inline

Assignment operator.

## Member Data Documentation

## ◆ first_

PeakIterator first_

protected

points to the first raw data point in the interval

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

## ◆ is_result_valid_

bool is_result_valid_

mutable protected

flag: set to true if SignalToNoise estimates are calculated and none of the params were changed. otherwise false.

Referenced by SignalToNoiseEstimator< ContainerT >::getSignalToNoise(), SignalToNoiseEstimator< ContainerT >::init(), SignalToNoiseEstimatorMeanIterative< Container >::updateMembers_(), and SignalToNoiseEstimatorMedian< ContainerT >::updateMembers_().

## ◆ 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

stores the noise estimate for each peak

Referenced by SignalToNoiseEstimatorMeanIterative< Container >::computeSTN_(), SignalToNoiseEstimatorMedian< ContainerT >::computeSTN_(), SignalToNoiseEstimator< ContainerT >::getSignalToNoise(), and SignalToNoiseEstimator< ContainerT >::operator=().