#include <OpenMS/FILTERING/NOISEESTIMATION/SignalToNoiseEstimatorMeanIterative.h>
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).
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 Member Functions | |
SignalToNoiseEstimatorMeanIterative () | |
default constructor | |
SignalToNoiseEstimatorMeanIterative (const SignalToNoiseEstimatorMeanIterative &source) | |
Copy Constructor. | |
virtual | ~SignalToNoiseEstimatorMeanIterative () |
Destructor. | |
Assignment | |
SignalToNoiseEstimatorMeanIterative & | operator= (const SignalToNoiseEstimatorMeanIterative &source) |
Protected Member Functions | |
virtual void | computeSTN_ (const PeakIterator &scan_first_, const PeakIterator &scan_last_) throw (Exception::InvalidValue) |
void | updateMembers_ () |
overridden function from DefaultParamHandler to keep members up to date, when a parameter is changed | |
Protected Attributes | |
double | max_intensity_ |
maximal intensity considered during binning (values above get discarded) | |
double | auto_max_stdev_Factor_ |
parameter for initial automatic estimation of "max_intensity_": a stdev multiplier | |
double | auto_max_percentile_ |
parameter for initial automatic estimation of "max_intensity_" percentile or a stdev | |
int | auto_mode_ |
determines which method shall be used for estimating "max_intensity_". valid are MANUAL=-1, AUTOMAXBYSTDEV=0 or AUTOMAXBYPERCENT=1 | |
double | win_len_ |
range of data points which belong to a window in Thomson | |
int | bin_count_ |
number of bins in the histogram | |
double | stdev_ |
multiplier for the stdev of intensities | |
int | min_required_elements_ |
minimal number of elements a window needs to cover to be used | |
double | noise_for_empty_window_ |
typedef SignalToNoiseEstimator< Container >::PeakIterator PeakIterator |
Reimplemented from SignalToNoiseEstimator.
typedef SignalToNoiseEstimator< Container >::PeakType PeakType |
Reimplemented from SignalToNoiseEstimator.
typedef SignalToNoiseEstimator< Container >::GaussianEstimate GaussianEstimate |
SignalToNoiseEstimatorMeanIterative | ( | ) | [inline] |
default constructor
SignalToNoiseEstimatorMeanIterative | ( | const SignalToNoiseEstimatorMeanIterative< Container > & | source | ) | [inline] |
Copy Constructor.
virtual ~SignalToNoiseEstimatorMeanIterative | ( | ) | [inline, virtual] |
Destructor.
SignalToNoiseEstimatorMeanIterative& operator= | ( | const SignalToNoiseEstimatorMeanIterative< Container > & | source | ) | [inline] |
virtual void computeSTN_ | ( | const PeakIterator & | scan_first_, | |
const PeakIterator & | scan_last_ | |||
) | throw (Exception::InvalidValue) [inline, protected, virtual] |
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) |
void updateMembers_ | ( | ) | [inline, protected, virtual] |
overridden function from DefaultParamHandler to keep members up to date, when a parameter is changed
Reimplemented from DefaultParamHandler.
double max_intensity_ [protected] |
maximal intensity considered during binning (values above get discarded)
double auto_max_stdev_Factor_ [protected] |
parameter for initial automatic estimation of "max_intensity_": a stdev multiplier
double auto_max_percentile_ [protected] |
parameter for initial automatic estimation of "max_intensity_" percentile or a stdev
int auto_mode_ [protected] |
determines which method shall be used for estimating "max_intensity_". valid are MANUAL=-1, AUTOMAXBYSTDEV=0 or AUTOMAXBYPERCENT=1
double win_len_ [protected] |
range of data points which belong to a window in Thomson
int bin_count_ [protected] |
number of bins in the histogram
double stdev_ [protected] |
multiplier for the stdev of intensities
int min_required_elements_ [protected] |
minimal number of elements a window needs to cover to be used
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
Generated Tue Apr 1 15:36:44 2008 -- using doxygen 1.5.4 | OpenMS / TOPP 1.1 |