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>
 
  
 | 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 | |
| SignalToNoiseEstimatorMedian & | operator= (const SignalToNoiseEstimatorMedian &source) | 
|  Public Member Functions inherited from SignalToNoiseEstimator< Container > | |
| SignalToNoiseEstimator () | |
| Constructor.  More... | |
| SignalToNoiseEstimator (const SignalToNoiseEstimator &source) | |
| Copy constructor.  More... | |
| SignalToNoiseEstimator & | operator= (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 DefaultParamHandler & | operator= (const DefaultParamHandler &rhs) | 
| Assignment operator.  More... | |
| virtual bool | operator== (const DefaultParamHandler &rhs) const | 
| Equality operator.  More... | |
| void | setParameters (const Param ¶m) | 
| 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... | |
| 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< 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_ | 
| 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_ | 
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).
| Name | Type | Default | Restrictions | Description | 
|---|---|---|---|---|
| max_intensity | int | -1 | min: -1 | maximal 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 | float | 3 | min: 0 max: 999 | parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev | 
| auto_max_percentile | int | 95 | min: 0 max: 100 | parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile | 
| auto_mode | int | 0 | min: -1 max: 1 | method to use to determine maximal intensity: -1 --> use 'max_intensity'; 0 --> 'auto_max_stdev_factor' method (default); 1 --> 'auto_max_percentile' method | 
| win_len | float | 200 | min: 1 | window length in Thomson | 
| bin_count | int | 30 | min: 3 | number of bins for intensity values | 
| min_required_elements | int | 10 | min: 1 | minimum number of elements required in a window (otherwise it is considered sparse) | 
| noise_for_empty_window | float | 1e+20 | noise value used for sparse windows | 
| typedef SignalToNoiseEstimator<Container>::GaussianEstimate GaussianEstimate | 
| typedef SignalToNoiseEstimator<Container>::PeakIterator PeakIterator | 
| typedef SignalToNoiseEstimator<Container>::PeakType PeakType | 
| 
 | inline | 
default constructor
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 | inline | 
Copy Constructor.
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 | inlinevirtual | 
Destructor.
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 | inlineprotectedvirtual | 
calculate StN values for all datapoints given, by using a sliding window approach
| scan_first_ | first element in the scan | 
| scan_last_ | last element in the scan (disregarded) | 
| Throws | Exception::InvalidValue | 
Implements SignalToNoiseEstimator< Container >.
| 
 | inline | 
| 
 | 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().
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 | protected | 
parameter for initial automatic estimation of "max_intensity_" percentile or a stdev
Referenced by SignalToNoiseEstimatorMedian< OpenMS::OpenMS::MSSpectrum< PeakT > >::computeSTN_(), and SignalToNoiseEstimatorMedian< OpenMS::OpenMS::MSSpectrum< PeakT > >::updateMembers_().
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 | protected | 
parameter for initial automatic estimation of "max_intensity_": a stdev multiplier
Referenced by SignalToNoiseEstimatorMedian< OpenMS::OpenMS::MSSpectrum< PeakT > >::computeSTN_(), and SignalToNoiseEstimatorMedian< OpenMS::OpenMS::MSSpectrum< PeakT > >::updateMembers_().
| 
 | 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_().
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 | protected | 
number of bins in the histogram
Referenced by SignalToNoiseEstimatorMedian< OpenMS::OpenMS::MSSpectrum< PeakT > >::computeSTN_(), and SignalToNoiseEstimatorMedian< OpenMS::OpenMS::MSSpectrum< PeakT > >::updateMembers_().
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 | protected | 
maximal intensity considered during binning (values above get discarded)
Referenced by SignalToNoiseEstimatorMedian< OpenMS::OpenMS::MSSpectrum< PeakT > >::computeSTN_(), and SignalToNoiseEstimatorMedian< OpenMS::OpenMS::MSSpectrum< PeakT > >::updateMembers_().
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 | protected | 
minimal number of elements a window needs to cover to be used
Referenced by SignalToNoiseEstimatorMedian< OpenMS::OpenMS::MSSpectrum< PeakT > >::computeSTN_(), and SignalToNoiseEstimatorMedian< OpenMS::OpenMS::MSSpectrum< PeakT > >::updateMembers_().
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 | 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_().
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 | protected | 
range of data points which belong to a window in Thomson
Referenced by SignalToNoiseEstimatorMedian< OpenMS::OpenMS::MSSpectrum< PeakT > >::computeSTN_(), and SignalToNoiseEstimatorMedian< OpenMS::OpenMS::MSSpectrum< PeakT > >::updateMembers_().
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:30 using doxygen 1.8.5 |