79 template <
typename Container = MSSpectrum>
105 this->
setName(
"SignalToNoiseEstimatorMedian");
107 defaults_.
setValue(
"max_intensity", -1,
"maximal intensity considered for histogram construction. By default, it will be calculated automatically (see auto_mode)." \
108 " Only provide this parameter if you know what you are doing (and change 'auto_mode' to '-1')!" \
109 " All intensities EQUAL/ABOVE 'max_intensity' will be added to the LAST histogram bin." \
110 " If you choose 'max_intensity' too small, the noise estimate might be too small as well. " \
111 " If chosen too big, the bins become quite large (which you could counter by increasing 'bin_count', which increases runtime)." \
112 " In general, the Median-S/N estimator is more robust to a manual max_intensity than the MeanIterative-S/N.", ListUtils::create<String>(
"advanced"));
115 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"));
119 defaults_.
setValue(
"auto_max_percentile", 95,
"parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile", ListUtils::create<String>(
"advanced"));
123 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"));
133 defaults_.
setValue(
"min_required_elements", 10,
"minimum number of elements required in a window (otherwise it is considered sparse)");
136 defaults_.
setValue(
"noise_for_empty_window", std::pow(10.0, 20),
"noise value used for sparse windows", ListUtils::create<String>(
"advanced"));
138 defaults_.
setValue(
"write_log_messages",
"true",
"Write out log messages in case of sparse windows or median in rightmost histogram bin");
157 if (&source ==
this)
return *
this;
217 OPENMS_PRETTY_FUNCTION,
218 "auto_mode is on AUTOMAXBYPERCENT! auto_max_percentile is not in [0,100]. Use setAutoMaxPercentile(<value>) to change it!",
222 std::vector<int> histogram_auto(100, 0);
228 while (run != scan_last_)
230 maxInt = std::max(maxInt, (*run).getIntensity());
235 double bin_size = maxInt / 100;
239 while (run != scan_last_)
241 ++histogram_auto[(int) (((*run).getIntensity() - 1) / bin_size)];
247 int elements_seen = 0;
251 while (run != scan_last_ && elements_seen < elements_below_percentile)
254 elements_seen += histogram_auto[i];
267 OPENMS_PRETTY_FUNCTION,
268 "auto_mode is on MANUAL! max_intensity is <=0. Needs to be positive! Use setMaxIntensity(<value>) or enable auto_mode!",
275 std::cerr <<
"TODO SignalToNoiseEstimatorMedian: the max_intensity_ value should be positive! " <<
max_intensity_ << std::endl;
283 double window_half_size =
win_len_ / 2;
293 bin_value[bin] = (bin + 0.5) * bin_size;
301 int element_inc_count = 0;
304 int elements_in_window = 0;
306 int window_count = 0;
309 int element_in_window_half = 0;
314 int windows_overall = 0;
316 while (run != scan_last_)
324 while (window_pos_center != scan_last_)
328 while ((*window_pos_borderleft).getMZ() < (*window_pos_center).getMZ() - window_half_size)
330 to_bin = std::max(std::min<int>((
int)((*window_pos_borderleft).getIntensity() / bin_size), bin_count_minus_1), 0);
332 --elements_in_window;
333 ++window_pos_borderleft;
337 while ((window_pos_borderright != scan_last_)
338 && ((*window_pos_borderright).getMZ() <= (*window_pos_center).getMZ() + window_half_size))
341 to_bin = std::max(std::min<int>((
int)((*window_pos_borderright).getIntensity() / bin_size), bin_count_minus_1), 0);
343 ++elements_in_window;
344 ++window_pos_borderright;
356 element_inc_count = 0;
357 element_in_window_half = (elements_in_window + 1) / 2;
358 while (median_bin < bin_count_minus_1 && element_inc_count < element_in_window_half)
361 element_inc_count += histogram[median_bin];
368 noise = std::max(1.0, bin_value[median_bin]);
372 stn_estimates_[*window_pos_center] = (*window_pos_center).getIntensity() / noise;
391 LOG_WARN <<
"WARNING in SignalToNoiseEstimatorMedian: " 393 <<
"% of all windows were sparse. You should consider increasing 'win_len' or decreasing 'min_required_elements'" 400 LOG_WARN <<
"WARNING in SignalToNoiseEstimatorMedian: " 402 <<
"% of all Signal-to-Noise estimates are too high, because the median was found in the rightmost histogram-bin. " 403 <<
"You should consider increasing 'max_intensity' (and maybe 'bin_count' with it, to keep bin width reasonable)"
Param defaults_
Container for default parameters. This member should be filled in the constructor of derived classes!...
Definition: DefaultParamHandler.h:156
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:57
Param param_
Container for current parameters.
Definition: DefaultParamHandler.h:149
void endProgress() const
Ends the progress display.
SignalToNoiseEstimator & operator=(const SignalToNoiseEstimator &source)
Assignment operator.
Definition: SignalToNoiseEstimator.h:91
Container::const_iterator PeakIterator
Definition: SignalToNoiseEstimator.h:64
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
bool toBool() const
Conversion to bool.
#define LOG_WARN
Macro if a warning, a piece of information which should be read by the user, should be logged...
Definition: LogStream.h:450
bool is_result_valid_
flag: set to true if SignalToNoise estimates are calculated and none of the params were changed...
Definition: SignalToNoiseEstimator.h:214
void setMaxInt(const String &key, Int max)
Sets the maximum value for the integer or integer 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:174
protected struct to store parameters my, sigma for a Gaussian distribution
Definition: SignalToNoiseEstimator.h:166
const DataValue & getValue(const String &key) const
Returns a value of a parameter.
void setProgress(SignedSize value) const
Sets the current progress.
void setMaxFloat(const String &key, double max)
Sets the maximum value for the floating point or floating point list parameter key.
PeakIterator::value_type PeakType
Definition: SignalToNoiseEstimator.h:65
void setValidStrings(const String &key, const std::vector< String > &strings)
Sets the valid strings for the parameter key.
Invalid value exception.
Definition: Exception.h:335
void setMinInt(const String &key, Int min)
Sets the minimum value for the integer or integer list parameter key.
void startProgress(SignedSize begin, SignedSize end, const String &label) const
Initializes the progress display.
This class represents the abstract base class of a signal to noise estimator.
Definition: SignalToNoiseEstimator.h:56
std::map< PeakType, double, typename PeakType::PositionLess > stn_estimates_
stores the noise estimate for each peak
Definition: SignalToNoiseEstimator.h:207
void setName(const String &name)
Mutable access to the name.
void setMinFloat(const String &key, double 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.