FeatureOverlapFilter.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Julianus Pfeuffer $
// $Authors: Julianus Pfeuffer $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/KERNEL/FeatureMap.h>
#include <OpenMS/CONCEPT/Constants.h>
 
namespace OpenMS
{
  enum class FeatureOverlapMode
  {
    CONVEX_HULL,     
    TRACE_LEVEL,     
    CENTROID_BASED   
  };
 
  enum class MergeIntensityMode
  {
    SUM,  
    MAX   
  };
 
  struct CentroidTolerances
  {
    double rt_tolerance = 5.0;        
    double mz_tolerance = 0.05;       
    bool require_same_charge = true;  
    bool require_same_im = false;     
  };
 
  class OPENMS_DLLAPI FeatureOverlapFilter
  {
    public:
    
    using OverlapMode = FeatureOverlapMode;
    
    /*
        @brief Filter overlapping features using a spatial datastructure (quadtree). 
               Retains only the best feature in each cluster of overlapping features.
 
        @param FeatureComparator must implement the concept of a less comparator.
               If several features overlap, the feature that evaluates as "smallest" is considered the best (according to the passed comparator) and is kept.
               The other overlapping features are removed and FeatureOverlapCallback evaluated on them.
               Default: overall feature quality.
 
        @param FeatureOverlapCallback(best_in_cluster, f) is called if a feature f overlaps with a feature best_in_cluster.
               FeatureOverlapCallback provides a customization point to e.g.:
              - transfer information from the soon-to-be-removed feature f over to the best_in_cluster feature
              - gather overlap statistics
              - help in debugging
              - etc.
              in form of a callable.
              If the FeatureOverlapCallback returns false, the overlapping feature will be treated as not overlapping with best_in_cluster (and not removed).
              Default: function that just returns true.
 
        @ingroup Datareduction
    */
    static void filter(FeatureMap& fmap, 
      std::function<bool(const Feature&, const Feature&)> FeatureComparator = [](const Feature& left, const Feature& right){ return left.getOverallQuality() > right.getOverallQuality(); },
      std::function<bool(Feature&, Feature&)> FeatureOverlapCallback = [](Feature&, Feature&){ return true; },
      bool check_overlap_at_trace_level = true);
      
    /*
        @brief Filter overlapping features with configurable overlap detection mode.
               Extended version that allows choosing between different overlap detection strategies.
 
        @param fmap The feature map to filter
        @param FeatureComparator Comparator to determine the best feature in overlapping clusters
        @param FeatureOverlapCallback Callback function called when features overlap
        @param mode The overlap detection mode to use
        @param tolerances Tolerances for centroid-based overlap detection (only used when mode == CENTROID_BASED)
 
        @ingroup Datareduction
    */
    static void filter(FeatureMap& fmap,
      std::function<bool(const Feature&, const Feature&)> FeatureComparator,
      std::function<bool(Feature&, Feature&)> FeatureOverlapCallback,
      FeatureOverlapMode mode,
      const CentroidTolerances& tolerances = CentroidTolerances());
 
    static std::function<bool(Feature&, Feature&)> createFAIMSMergeCallback(
      MergeIntensityMode intensity_mode = MergeIntensityMode::SUM,
      bool write_meta_values = true);
 
    static void mergeOverlappingFeatures(FeatureMap& feature_map,
                                         double max_rt_diff = 5.0,
                                         double max_mz_diff = 0.05,
                                         bool require_same_charge = true,
                                         bool require_same_im = false,
                                         MergeIntensityMode intensity_mode = MergeIntensityMode::SUM,
                                         bool write_meta_values = true);
 
    static void mergeFAIMSFeatures(FeatureMap& feature_map,
                                   double max_rt_diff = 5.0,
                                   double max_mz_diff = 0.05);
  };
 
}