36 #ifndef OPENMS_FILTERING_NOISEESTIMATION_SIGNALTONOISEESTIMATORMEDIAN_H 
   37 #define OPENMS_FILTERING_NOISEESTIMATION_SIGNALTONOISEESTIMATORMEDIAN_H 
   70   template <
typename Container = MSSpectrum<> >
 
   96       this->
setName(
"SignalToNoiseEstimatorMedian");
 
   98       defaults_.
setValue(
"max_intensity", -1, 
"maximal intensity considered for histogram construction. By default, it will be calculated automatically (see auto_mode)." \
 
   99                                               " Only provide this parameter if you know what you are doing (and change 'auto_mode' to '-1')!" \
 
  100                                               " All intensities EQUAL/ABOVE 'max_intensity' will be added to the LAST histogram bin." \
 
  101                                               " If you choose 'max_intensity' too small, the noise estimate might be too small as well. " \
 
  102                                               " If chosen too big, the bins become quite large (which you could counter by increasing 'bin_count', which increases runtime)." \
 
  103                                               " In general, the Median-S/N estimator is more robust to a manual max_intensity than the MeanIterative-S/N.", 
StringList::create(
"advanced"));
 
  106       defaults_.
setValue(
"auto_max_stdev_factor", 3.0, 
"parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev", 
StringList::create(
"advanced"));
 
  110       defaults_.
setValue(
"auto_max_percentile", 95, 
"parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile", 
StringList::create(
"advanced"));
 
  114       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", 
StringList::create(
"advanced"));
 
  124       defaults_.
setValue(
"min_required_elements", 10, 
"minimum number of elements required in a window (otherwise it is considered sparse)");
 
  146       if (&source == 
this) 
return *
this;
 
  172       double sparse_window_percent = 0;
 
  174       double histogram_oob_percent = 0;
 
  196                                         "auto_mode is on AUTOMAXBYPERCENT! auto_max_percentile is not in [0,100]. Use setAutoMaxPercentile(<value>) to change it!",
 
  200         std::vector<int> histogram_auto(100, 0);
 
  206         while (run != scan_last_)
 
  208           maxInt = std::max(maxInt, (*run).getIntensity());
 
  213         double bin_size = maxInt / 100;
 
  217         while (run != scan_last_)
 
  219           ++histogram_auto[(int) (((*run).getIntensity() - 1) / bin_size)];
 
  225         int elements_seen = 0;
 
  229         while (run != scan_last_ && elements_seen < elements_below_percentile)
 
  232           elements_seen += histogram_auto[i];
 
  246                                         "auto_mode is on MANUAL! max_intensity is <=0. Needs to be positive! Use setMaxIntensity(<value>) or enable auto_mode!",
 
  253         std::cerr << 
"TODO SignalToNoiseEstimatorMedian: the max_intensity_ value should be positive! " << 
max_intensity_ << std::endl;
 
  261       double window_half_size = 
win_len_ / 2;
 
  271         bin_value[bin] = (bin + 0.5) * bin_size;
 
  279       int element_inc_count = 0;
 
  282       int elements_in_window = 0;
 
  284       int window_count = 0;
 
  287       int element_in_window_half = 0;
 
  292       int windows_overall = 0;
 
  294       while (run != scan_last_)
 
  302       while (window_pos_center != scan_last_)
 
  306         while ((*window_pos_borderleft).getMZ() <  (*window_pos_center).getMZ() - window_half_size)
 
  308           to_bin = std::max(std::min<int>((
int)((*window_pos_borderleft).getIntensity() / bin_size), bin_count_minus_1), 0);
 
  310           --elements_in_window;
 
  311           ++window_pos_borderleft;
 
  315         while ((window_pos_borderright != scan_last_)
 
  316               && ((*window_pos_borderright).getMZ() <= (*window_pos_center).getMZ() + window_half_size))
 
  319           to_bin = std::max(std::min<int>((
int)((*window_pos_borderright).getIntensity() / bin_size), bin_count_minus_1), 0);
 
  321           ++elements_in_window;
 
  322           ++window_pos_borderright;
 
  328           ++sparse_window_percent;
 
  334           element_inc_count = 0;
 
  335           element_in_window_half = (elements_in_window + 1) / 2;
 
  336           while (median_bin < bin_count_minus_1 && element_inc_count < element_in_window_half)
 
  339             element_inc_count += histogram[median_bin];
 
  343           if (median_bin == bin_count_minus_1) {++histogram_oob_percent; }
 
  346           noise = std::max(1.0, bin_value[median_bin]);
 
  350         stn_estimates_[*window_pos_center] = (*window_pos_center).getIntensity() / noise;
 
  363       sparse_window_percent = sparse_window_percent * 100 / window_count;
 
  364       histogram_oob_percent = histogram_oob_percent * 100 / window_count;
 
  367       if (sparse_window_percent > 20)
 
  369         LOG_WARN << 
"WARNING in SignalToNoiseEstimatorMedian: " 
  370                  << sparse_window_percent
 
  371                  << 
"% of all windows were sparse. You should consider increasing 'win_len' or decreasing 'min_required_elements'" 
  376       if (histogram_oob_percent > 1)
 
  378         LOG_WARN << 
"WARNING in SignalToNoiseEstimatorMedian: " 
  379                  << histogram_oob_percent
 
  380                  << 
"% of all Signal-to-Noise estimates are too high, because the median was found in the rightmost histogram-bin. " 
  381                  << 
"You should consider increasing 'max_intensity' (and maybe 'bin_count' with it, to keep bin width reasonable)" 
  425 #endif //OPENMS_FILTERING_NOISEESTIMATION_DSIGNALTONOISEESTIMATORMEDIAN_H 
Real IntensityType
Intensity type. 
Definition: Peak2D.h:63
Param defaults_
Container for default parameters. This member should be filled in the constructor of derived classes!...
Definition: DefaultParamHandler.h:155
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:56
Param param_
Container for current parameters. 
Definition: DefaultParamHandler.h:148
SignalToNoiseEstimator & operator=(const SignalToNoiseEstimator &source)
Assignment operator. 
Definition: SignalToNoiseEstimator.h:93
Container::const_iterator PeakIterator
Definition: SignalToNoiseEstimator.h:66
GaussianEstimate estimate_(const PeakIterator &scan_first_, const PeakIterator &scan_last_) const 
calculate mean & stdev of intensities of a spectrum 
Definition: SignalToNoiseEstimator.h:176
#define LOG_WARN
Macro if a warning, a piece of information which should be read by the user, should be logged...
Definition: LogStream.h:451
bool is_result_valid_
flag: set to true if SignalToNoise estimates are calculated and none of the params were changed...
Definition: SignalToNoiseEstimator.h:216
void setMaxInt(const String &key, Int max)
Sets the maximum value for the integer or integer list parameter key. 
protected struct to store parameters my, sigma for a Gaussian distribution 
Definition: SignalToNoiseEstimator.h:168
void endProgress() const 
Ends the progress display. 
const DataValue & getValue(const String &key) const 
Returns a value of a parameter. 
PeakIterator::value_type PeakType
Definition: SignalToNoiseEstimator.h:67
static StringList create(const String &list, const char splitter= ',')
Returns a list that is created by splitting the given (comma-separated) string (String are not trimme...
Invalid value exception. 
Definition: Exception.h:336
void setMinInt(const String &key, Int min)
Sets the minimum value for the integer or integer list parameter key. 
This class represents the abstract base class of a signal to noise estimator. 
Definition: SignalToNoiseEstimator.h:58
std::map< PeakType, double, typename PeakType::PositionLess > stn_estimates_
stores the noise estimate for each peak 
Definition: SignalToNoiseEstimator.h:209
void startProgress(SignedSize begin, SignedSize end, const String &label) const 
Initializes the progress display. 
void setProgress(SignedSize value) const 
Sets the current progress. 
void setName(const String &name)
Mutable access to the name. 
void setMinFloat(const String &key, DoubleReal min)
Sets the minimum value for the floating point or floating point list parameter key. 
void defaultsToParam_()
Updates the parameters after the defaults have been set in the constructor. 
void setMaxFloat(const String &key, DoubleReal max)
Sets the maximum value for the floating point or floating point list parameter key.