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OpenMS
2.6.0
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Go to the documentation of this file.
80 template <
typename Container = MSSpectrum>
103 this->
setName(
"SignalToNoiseEstimatorMedian");
105 defaults_.
setValue(
"max_intensity", -1,
"maximal intensity considered for histogram construction. By default, it will be calculated automatically (see auto_mode)." \
106 " Only provide this parameter if you know what you are doing (and change 'auto_mode' to '-1')!" \
107 " All intensities EQUAL/ABOVE 'max_intensity' will be added to the LAST histogram bin." \
108 " If you choose 'max_intensity' too small, the noise estimate might be too small as well. " \
109 " If chosen too big, the bins become quite large (which you could counter by increasing 'bin_count', which increases runtime)." \
110 " In general, the Median-S/N estimator is more robust to a manual max_intensity than the MeanIterative-S/N.", ListUtils::create<String>(
"advanced"));
113 defaults_.
setValue(
"auto_max_stdev_factor", 3.0,
"parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev", ListUtils::create<String>(
"advanced"));
117 defaults_.
setValue(
"auto_max_percentile", 95,
"parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile", ListUtils::create<String>(
"advanced"));
121 defaults_.
setValue(
"auto_mode", 0,
"method to use to determine maximal intensity: -1 --> use 'max_intensity'; 0 --> 'auto_max_stdev_factor' method (default); 1 --> 'auto_max_percentile' method", ListUtils::create<String>(
"advanced"));
131 defaults_.
setValue(
"min_required_elements", 10,
"minimum number of elements required in a window (otherwise it is considered sparse)");
134 defaults_.
setValue(
"noise_for_empty_window", std::pow(10.0, 20),
"noise value used for sparse windows", ListUtils::create<String>(
"advanced"));
136 defaults_.
setValue(
"write_log_messages",
"true",
"Write out log messages in case of sparse windows or median in rightmost histogram bin");
155 if (&source ==
this)
return *
this;
220 OPENMS_PRETTY_FUNCTION,
221 "auto_mode is on AUTOMAXBYPERCENT! auto_max_percentile is not in [0,100]. Use setAutoMaxPercentile(<value>) to change it!",
225 std::vector<int> histogram_auto(100, 0);
228 auto maxIt = std::max_element(
c.begin(),
c.end() ,[](
const PeakType& a,
const PeakType& b){
return a.getIntensity() > b.getIntensity();});
231 double bin_size = maxInt / 100;
234 for(
const auto& peak :
c)
236 ++histogram_auto[(
int) ((peak.getIntensity() - 1) / bin_size)];
241 int elements_seen = 0;
245 while (run != scan_last_ && elements_seen < elements_below_percentile)
248 elements_seen += histogram_auto[i];
261 OPENMS_PRETTY_FUNCTION,
262 "auto_mode is on MANUAL! max_intensity is <=0. Needs to be positive! Use setMaxIntensity(<value>) or enable auto_mode!",
269 std::cerr <<
"TODO SignalToNoiseEstimatorMedian: the max_intensity_ value should be positive! " <<
max_intensity_ << std::endl;
277 double window_half_size =
win_len_ / 2;
287 bin_value[bin] = (bin + 0.5) * bin_size;
295 int element_inc_count = 0;
298 int elements_in_window = 0;
300 int window_count = 0;
303 int element_in_window_half = 0;
311 while (window_pos_center != scan_last_)
315 while ((*window_pos_borderleft).getMZ() < (*window_pos_center).getMZ() - window_half_size)
317 to_bin = std::max(std::min<int>((
int)((*window_pos_borderleft).getIntensity() / bin_size), bin_count_minus_1), 0);
319 --elements_in_window;
320 ++window_pos_borderleft;
324 while ((window_pos_borderright != scan_last_)
325 && ((*window_pos_borderright).getMZ() <= (*window_pos_center).getMZ() + window_half_size))
328 to_bin = std::max(std::min<int>((
int)((*window_pos_borderright).getIntensity() / bin_size), bin_count_minus_1), 0);
330 ++elements_in_window;
331 ++window_pos_borderright;
343 element_inc_count = 0;
344 element_in_window_half = (elements_in_window + 1) / 2;
345 while (median_bin < bin_count_minus_1 && element_inc_count < element_in_window_half)
348 element_inc_count += histogram[median_bin];
355 noise = std::max(1.0, bin_value[median_bin]);
359 stn_estimates_[window_count] = (*window_pos_center).getIntensity() / noise;
380 <<
"% of all windows were sparse. You should consider increasing 'win_len' or decreasing 'min_required_elements'"
389 <<
"% of all Signal-to-Noise estimates are too high, because the median was found in the rightmost histogram-bin. "
390 <<
"You should consider increasing 'max_intensity' (and maybe 'bin_count' with it, to keep bin width reasonable)"
void setProgress(SignedSize value) const
Sets the current progress.
void setMinFloat(const String &key, double min)
Sets the minimum value for the floating point or floating point list parameter key.
Invalid value exception.
Definition: Exception.h:335
void setValue(const String &key, const DataValue &value, const String &description="", const StringList &tags=StringList())
Sets a value.
A more convenient string class.
Definition: String.h:59
This class represents the abstract base class of a signal to noise estimator.
Definition: SignalToNoiseEstimator.h:56
std::vector< double > stn_estimates_
stores the noise estimate for each peak
Definition: SignalToNoiseEstimator.h:171
void setName(const String &name)
Mutable access to the name.
void setValidStrings(const String &key, const std::vector< String > &strings)
Sets the valid strings for the parameter key.
void setMaxInt(const String &key, Int max)
Sets the maximum value for the integer or integer list parameter key.
const DataValue & getValue(const String &key) const
Returns a value of a parameter.
void startProgress(SignedSize begin, SignedSize end, const String &label) const
Initializes the progress display.
#define OPENMS_LOG_WARN
Macro if a warning, a piece of information which should be read by the user, should be logged.
Definition: LogStream.h:460
void endProgress() const
Ends the progress display.
PeakIterator::value_type PeakType
Definition: SignalToNoiseEstimator.h:65
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
bool toBool() const
Conversion to bool.
SignalToNoiseEstimator & operator=(const SignalToNoiseEstimator &source)
Assignment operator.
Definition: SignalToNoiseEstimator.h:85
void setMinInt(const String &key, Int min)
Sets the minimum value for the integer or integer list parameter key.
void setMaxFloat(const String &key, double max)
Sets the maximum value for the floating point or floating point list parameter key.
GaussianEstimate estimate_(const PeakIterator &scan_first_, const PeakIterator &scan_last_) const
calculate mean & stdev of intensities of a spectrum
Definition: SignalToNoiseEstimator.h:138
Param defaults_
Container for default parameters. This member should be filled in the constructor of derived classes!
Definition: DefaultParamHandler.h:169
void defaultsToParam_()
Updates the parameters after the defaults have been set in the constructor.
Container::const_iterator PeakIterator
Definition: SignalToNoiseEstimator.h:64
protected struct to store parameters my, sigma for a Gaussian distribution
Definition: SignalToNoiseEstimator.h:130
Param param_
Container for current parameters.
Definition: DefaultParamHandler.h:162