subsitute vector<double> for map<PeakType, double> in SignalToNoiseEstimator

src/openms/include/OpenMS/ANALYSIS/OPENSWATH/DATAACCESS/MRMFeatureAccessOpenMS.h

@@ -206,12 +206,12 @@ namespace OpenMS
       if (std::fabs(prev->getMZ() - RT) < std::fabs(iter->getMZ() - RT) )
       {
         // prev is closer to the apex
-        return sn_.getSignalToNoise(*prev);
+        return sn_.getSignalToNoise((Size) distance(chromatogram_.begin(),prev));
       }
       else
       {
         // iter is closer to the apex
-        return sn_.getSignalToNoise(*iter);
+        return sn_.getSignalToNoise((Size) distance(chromatogram_.begin(),iter));
       }
     }
 

src/openms/include/OpenMS/FILTERING/NOISEESTIMATION/SignalToNoiseEstimator.h

@@ -70,21 +70,15 @@ namespace OpenMS
     /// Constructor
     inline SignalToNoiseEstimator() :
       DefaultParamHandler("SignalToNoiseEstimator"),
-      ProgressLogger(),
-      first_(),
-      last_(),
-      is_result_valid_(false)
+      ProgressLogger()
     {
     }
 
     /// Copy constructor
     inline SignalToNoiseEstimator(const SignalToNoiseEstimator & source) :
       DefaultParamHandler(source),
       ProgressLogger(source),
-      stn_estimates_(source.stn_estimates_),
-      first_(source.first_),
-      last_(source.last_),
-      is_result_valid_(source.is_result_valid_)
+      stn_estimates_(source.stn_estimates_)
     {}
 
     /// Assignment operator
@@ -95,56 +89,26 @@ namespace OpenMS
       DefaultParamHandler::operator=(source);
       ProgressLogger::operator=(source);
       stn_estimates_ = source.stn_estimates_;
-      first_ = source.first_;
-      last_  = source.last_;
       return *this;
     }
 
     /// Destructor
     ~SignalToNoiseEstimator() override
     {}
 
-
     /// Set the start and endpoint of the raw data interval, for which signal to noise ratios will be estimated immediately
-    virtual void init(const PeakIterator & it_begin, const PeakIterator & it_end)
-    {
-      first_ = it_begin;
-      last_ = it_end;
-      computeSTN_(first_, last_);
-      is_result_valid_ = true;
-    }
-
-    /// Set the start and endpoint of the raw data interval, for which signal to noise ratios will be estimated immediately
-    virtual void init(const Container & c)
-    {
-      init(c.begin(), c.end());
-    }
-
-    /// Return to signal/noise estimate for data point @p data_point
-    /// @note the first query to this function will take longer, as
-    ///       all SignalToNoise values are calculated
-    /// @note you will get a warning to stderr if more than 20% of the
-    ///       noise estimates used sparse windows
-    virtual double getSignalToNoise(const PeakIterator & data_point)
+    virtual void init(const Container& c)
     {
-      if (!is_result_valid_)
-      {
-        // recompute ...
-        init(first_, last_);
-      }
-
-      return stn_estimates_[*data_point];
+      computeSTN_(c);
     }
 
-    virtual double getSignalToNoise(const PeakType & data_point)
+    ///Return to signal/noise estimate for date point @p index
+    ///@note you will get a warning to stderr if more than 20% of the
+    ///      noise estimates used sparse windows
+    virtual double getSignalToNoise(const Size index)
     {
-      if (!is_result_valid_)
-      {
-        // recompute ...
-        init(first_, last_);
-      }
-
-      return stn_estimates_[data_point];
+      OPENMS_POSTCONDITION(index < stn_estimates_.size(),"SignalToNoiseEstimator estimates beyond container size was requested.");
+      return stn_estimates_[index];
     }
 
 protected:
@@ -154,7 +118,7 @@ namespace OpenMS
          *
          * @exception Throws Exception::InvalidValue
          */
-    virtual void computeSTN_(const PeakIterator & scan_first_, const PeakIterator & scan_last_) = 0;
+    virtual void computeSTN_(const Container& c) = 0;
 
 
 
@@ -204,14 +168,7 @@ namespace OpenMS
     //MEMBERS:
 
     /// stores the noise estimate for each peak
-    std::map<PeakType, double, typename PeakType::PositionLess> stn_estimates_;
-
-    /// points to the first raw data point in the interval
-    PeakIterator first_;
-    /// points to the right position next to the last raw data point in the interval
-    PeakIterator last_;
-    /// flag: set to true if SignalToNoise estimates are calculated and none of the params were changed. otherwise false.
-    mutable bool is_result_valid_;
+    std::vector<double> stn_estimates_;
   };
 
 } // namespace OpenMS

src/openms/include/OpenMS/FILTERING/NOISEESTIMATION/SignalToNoiseEstimatorMeanIterative.h

@@ -39,6 +39,7 @@
 #include <OpenMS/CONCEPT/Exception.h>
 #include <OpenMS/DATASTRUCTURES/ListUtils.h>
 #include <vector>
+#include <algorithm> //for std::max_element
 
 namespace OpenMS
 {
@@ -76,9 +77,6 @@ namespace OpenMS
     enum IntensityThresholdCalculation {MANUAL = -1, AUTOMAXBYSTDEV = 0, AUTOMAXBYPERCENT = 1};
 
     using SignalToNoiseEstimator<Container>::stn_estimates_;
-    using SignalToNoiseEstimator<Container>::first_;
-    using SignalToNoiseEstimator<Container>::last_;
-    using SignalToNoiseEstimator<Container>::is_result_valid_;
     using SignalToNoiseEstimator<Container>::defaults_;
     using SignalToNoiseEstimator<Container>::param_;
 
@@ -164,17 +162,22 @@ namespace OpenMS
 
 
     /** calculate StN values for all datapoints given, by using a sliding window approach
-                  @param scan_first_ first element in the scan
-                  @param scan_last_ last element in the scan (disregarded)
+                  @param c raw data
                   @exception Throws Exception::InvalidValue
            */
-    void computeSTN_(const PeakIterator & scan_first_, const PeakIterator & scan_last_) override
+    void computeSTN_(const Container& c) override
     {
+      //first element in the scan
+      PeakIterator scan_first_ = c.begin();
+      //last element in the scan
+      PeakIterator scan_last_ = c.end();
+
       // reset counter for sparse windows
       double sparse_window_percent = 0;
 
       // reset the results
       stn_estimates_.clear();
+      stn_estimates_.resize(c.size());
 
       // maximal range of histogram needs to be calculated first
       if (auto_mode_ == AUTOMAXBYSTDEV)
@@ -200,28 +203,21 @@ namespace OpenMS
         std::vector<int> histogram_auto(100, 0);
 
         // find maximum of current scan
-        int size = 0;
-        typename PeakType::IntensityType maxInt = 0;
-        PeakIterator run = scan_first_;
-        while (run != scan_last_)
-        {
-          maxInt = std::max(maxInt, (*run).getIntensity());
-          ++size;
-          ++run;
-        }
+        auto maxIt = std::max_element(c.begin(), c.end() ,[](const PeakType& a, const PeakType& b){ return a.getIntensity() > b.getIntensity();});
+        typename PeakType::IntensityType maxInt = maxIt->getIntensity();
 
         double bin_size = maxInt / 100;
 
         // fill histogram
-        run = scan_first_;
+        PeakIterator run = scan_first_;
         while (run != scan_last_)
         {
           ++histogram_auto[(int) (((*run).getIntensity() - 1) / bin_size)];
           ++run;
         }
 
         // add up element counts in histogram until ?th percentile is reached
-        int elements_below_percentile = (int) (auto_max_percentile_ * size / 100);
+        int elements_below_percentile = (int) (auto_max_percentile_ * c.size() / 100);
         int elements_seen = 0;
         int i = -1;
         run = scan_first_;
@@ -283,15 +279,8 @@ namespace OpenMS
 
       double noise;      // noise value of a datapoint
 
-      // determine how many elements we need to estimate (for progress estimation)
-      int windows_overall = 0;
-      PeakIterator run = scan_first_;
-      while (run != scan_last_)
-      {
-        ++windows_overall;
-        ++run;
-      }
-      SignalToNoiseEstimator<Container>::startProgress(0, windows_overall, "noise estimation of data");
+      ///start progress estimation
+      SignalToNoiseEstimator<Container>::startProgress(0, c.size(), "noise estimation of data");
 
       // MAIN LOOP
       while (window_pos_center != scan_last_)
@@ -370,7 +359,7 @@ namespace OpenMS
         }
 
         // store result
-        stn_estimates_[*window_pos_center] = (*window_pos_center).getIntensity() / noise;
+        stn_estimates_[window_count] = (*window_pos_center).getIntensity() / noise;
 
 
 
@@ -412,7 +401,7 @@ namespace OpenMS
       stdev_                 = (double)param_.getValue("stdev_mp");
       min_required_elements_ = param_.getValue("min_required_elements");
       noise_for_empty_window_ = (double)param_.getValue("noise_for_empty_window");
-      is_result_valid_ = false;
+      stn_estimates_.clear();
     }
 
     /// maximal intensity considered during binning (values above get discarded)

src/openms/include/OpenMS/FILTERING/NOISEESTIMATION/SignalToNoiseEstimatorMedian.h

@@ -41,6 +41,7 @@
 #include <OpenMS/CONCEPT/Exception.h>
 #include <OpenMS/DATASTRUCTURES/ListUtils.h>
 #include <vector>
+#include <algorithm> //for std::max_element
 
 namespace OpenMS
 {
@@ -87,9 +88,6 @@ namespace OpenMS
     enum IntensityThresholdCalculation {MANUAL = -1, AUTOMAXBYSTDEV = 0, AUTOMAXBYPERCENT = 1};
 
     using SignalToNoiseEstimator<Container>::stn_estimates_;
-    using SignalToNoiseEstimator<Container>::first_;
-    using SignalToNoiseEstimator<Container>::last_;
-    using SignalToNoiseEstimator<Container>::is_result_valid_;
     using SignalToNoiseEstimator<Container>::defaults_;
     using SignalToNoiseEstimator<Container>::param_;
 
@@ -184,19 +182,24 @@ namespace OpenMS
 
     /** Calculate signal-to-noise values for all data points given, by using a sliding window approach
 
-        @param scan_first_ first element in the scan
-        @param scan_last_ last element in the scan (disregarded)
+        @param c raw data
         @exception Throws Exception::InvalidValue
     */
-    void computeSTN_(const PeakIterator & scan_first_, const PeakIterator & scan_last_) override
+    void computeSTN_(const Container& c) override
     {
+      //first element in the scan
+      PeakIterator scan_first_ = c.begin();
+      //last element in the scan
+      PeakIterator scan_last_ = c.end();
+
       // reset counter for sparse windows
       sparse_window_percent_ = 0;
       // reset counter for histogram overflow
       histogram_oob_percent_ = 0;
 
       // reset the results
       stn_estimates_.clear();
+      stn_estimates_.resize(c.size());
 
       // maximal range of histogram needs to be calculated first
       if (auto_mode_ == AUTOMAXBYSTDEV)
@@ -222,28 +225,21 @@ namespace OpenMS
         std::vector<int> histogram_auto(100, 0);
 
         // find maximum of current scan
-        int size = 0;
-        typename PeakType::IntensityType maxInt = 0;
-        PeakIterator run = scan_first_;
-        while (run != scan_last_)
-        {
-          maxInt = std::max(maxInt, (*run).getIntensity());
-          ++size;
-          ++run;
-        }
+        auto maxIt = std::max_element(c.begin(), c.end() ,[](const PeakType& a, const PeakType& b){ return a.getIntensity() > b.getIntensity();});
+        typename PeakType::IntensityType maxInt = maxIt->getIntensity();
 
         double bin_size = maxInt / 100;
 
         // fill histogram
-        run = scan_first_;
+        PeakIterator run = scan_first_;
         while (run != scan_last_)
         {
           ++histogram_auto[(int) (((*run).getIntensity() - 1) / bin_size)];
           ++run;
         }
 
         // add up element counts in histogram until ?th percentile is reached
-        int elements_below_percentile = (int) (auto_max_percentile_ * size / 100);
+        int elements_below_percentile = (int) (auto_max_percentile_ * c.size() / 100);
         int elements_seen = 0;
         int i = -1;
         run = scan_first_;
@@ -310,15 +306,8 @@ namespace OpenMS
 
       double noise;    // noise value of a datapoint
 
-      // determine how many elements we need to estimate (for progress estimation)
-      int windows_overall = 0;
-      PeakIterator run = scan_first_;
-      while (run != scan_last_)
-      {
-        ++windows_overall;
-        ++run;
-      }
-      SignalToNoiseEstimator<Container>::startProgress(0, windows_overall, "noise estimation of data");
+      ///start progress estimation
+      SignalToNoiseEstimator<Container>::startProgress(0, c.size(), "noise estimation of data");
 
       // MAIN LOOP
       while (window_pos_center != scan_last_)
@@ -369,7 +358,7 @@ namespace OpenMS
         }
 
         // store result
-        stn_estimates_[*window_pos_center] = (*window_pos_center).getIntensity() / noise;
+        stn_estimates_[window_count] = (*window_pos_center).getIntensity() / noise;
 
 
         // advance the window center by one datapoint
@@ -418,7 +407,7 @@ namespace OpenMS
       min_required_elements_   = param_.getValue("min_required_elements");
       noise_for_empty_window_  = (double)param_.getValue("noise_for_empty_window");
       write_log_messages_      = (bool)param_.getValue("write_log_messages").toBool();
-      is_result_valid_         = false;
+      stn_estimates_.clear();
     }
 
     /// maximal intensity considered during binning (values above get discarded)

src/openms/include/OpenMS/TRANSFORMATIONS/RAW2PEAK/PeakPickerIterative.h

@@ -209,7 +209,7 @@ namespace OpenMS
         {
           if (signal_to_noise_ > 0.0)
           {
-            if (snt.getSignalToNoise(input[i - k]) < signal_to_noise_)
+            if (snt.getSignalToNoise(i - k) < signal_to_noise_)
             {
               break;
             }
@@ -229,7 +229,7 @@ namespace OpenMS
         {
           if (signal_to_noise_ > 0.0)
           {
-            if (snt.getSignalToNoise(input[i + k]) < signal_to_noise_)
+            if (snt.getSignalToNoise(i + k) < signal_to_noise_)
             {
               break;
             }

src/openms/source/ANALYSIS/OPENSWATH/PeakPickerMRM.cpp

@@ -198,7 +198,7 @@ namespace OpenMS
              //&& std::fabs(chromatogram[min_i-k].getMZ() - peak_raw_data.begin()->first) < spacing_difference*min_spacing
             && (chromatogram[min_i - k].getIntensity() < chromatogram[min_i - k + 1].getIntensity()
                || (peak_width_ > 0.0 && std::fabs(chromatogram[min_i - k].getRT() - central_peak_rt) < peak_width_))
-            && (signal_to_noise_ <= 0.0 || snt_.getSignalToNoise(chromatogram[min_i - k]) >= signal_to_noise_))
+            && (signal_to_noise_ <= 0.0 || snt_.getSignalToNoise(min_i - k) >= signal_to_noise_))
       {
         ++k;
       }
@@ -210,7 +210,7 @@ namespace OpenMS
              //&& std::fabs(chromatogram[min_i+k].getMZ() - peak_raw_data.rbegin()->first) < spacing_difference*min_spacing
             && (chromatogram[min_i + k].getIntensity() < chromatogram[min_i + k - 1].getIntensity()
                || (peak_width_ > 0.0 && std::fabs(chromatogram[min_i + k].getRT() - central_peak_rt) < peak_width_))
-            && (signal_to_noise_ <= 0.0 || snt_.getSignalToNoise(chromatogram[min_i + k]) >= signal_to_noise_) )
+            && (signal_to_noise_ <= 0.0 || snt_.getSignalToNoise(min_i + k) >= signal_to_noise_) )
       {
         ++k;
       }