Pmsb 23 mass trace detection #144

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open

cbielow wants to merge 40 commits into cbielow:develop from Austernpilz:pmsb_23_MassTraceDetection

AUTHORS

-Original file line number
+Diff line change
@@ Expand Up / @@ -73,6 +73,7 @@ the authors tag in the respective file header. @@
      - Marc Sturm
      - Markus Mueller
      - Martin Langwisch
+     - Manuel Zschäbitz
      - Mateusz Łącki
      - Mathias Walzer
      - Matthew The
@@ Expand Down Expand Up / @@ -102,6 +103,7 @@ the authors tag in the respective file header. @@
      - Till Englert
      - Tom Lukas Lankenau
      - Tom Waschischeck
+     - Tristan Aretz
      - Uwe Schmitt
      - Valentin Noske
      - Vincent Musch
@@ Expand Down @@

src/openms/include/OpenMS/FILTERING/DATAREDUCTION/MassTraceDetection.h

-Original file line number
+Diff line change
@@ Expand Up / @@ -29,11 +29,12 @@ @@
     //
     // --------------------------------------------------------------------------
     // $Maintainer: Timo Sachsenberg $
-    // $Authors: Erhan Kenar, Holger Franken $
+    // $Authors: Erhan Kenar, Holger Franken, Tristan Aretz, Manuel Zschaebitz $
     // --------------------------------------------------------------------------
     #pragma once
+    #include <boost/dynamic_bitset.hpp>
     #include <OpenMS/CONCEPT/ProgressLogger.h>
     #include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
     #include <OpenMS/KERNEL/MassTrace.h>
@@ Expand Down Expand Up / @@ -84,7 +85,12 @@ namespace OpenMS @@
             */
             /// Allows the iterative computation of the intensity-weighted mean of a mass trace's centroid m/z.
-            void updateIterativeWeightedMeanMZ(const double &, const double &, double &, double &, double &);
+            void updateIterativeWeightedMeanMZ(const double added_mz,
+                                               const double added_int,
+                                               double& centroid_mz,
+                                               double& prev_counter,
+                                               double& prev_denom
+                                              );
             /** @name Main computation methods
             */
@@ Expand All / @@ -97,27 +103,82 @@ namespace OpenMS @@
             /** @name Private methods and members
             */
         protected:
             void updateMembers_() override;
         private:
             struct Apex
             {
-              Apex(double intensity, Size scan_idx, Size peak_idx);
-              double intensity;
-              Size scan_idx;
-              Size peak_idx;
+              Apex(PeakMap& map, const Size scan_idx, const Size peak_idx);
+              // Default constructors
+              Apex() = default;
+              Apex(const Apex& other) = default;
+              Apex(Apex&& other) = default;
+              // Move assignment operator
+              Apex& operator=(Apex&& other) = default;
+              std::reference_wrapper<PeakMap> map_;
+              Size scan_idx_;
+              Size peak_idx_;
+              ///get's the corresponding values
+              double getMZ() const;
+              double getRT() const;
+              double getIntensity() const;
             };
+            struct NextIndex
+            {
+              /// C'tor: init with number of threads in parallel region
+              NextIndex(const std::vector<Apex>& data, const Size total_peak_count, const std::vector<Size>& spec_offsets, const double mass_error_ppm);
+              /// Get the next free apex index which is not in the neighbourhood of a currently processing apex (in another thread)
+              /// (Internally adds the apex's m/z to a blacklist which prevents other threads from obtaining an apex nearby)
+              /// This function blocks until the next free apex is not conflicting anymore - i.e. another thread called setApexAsProcessed()
+              Size getNextFreeIndex();
+              /// If an apex was processed call this function to remove the apex from the blacklist and increase the current_apex_
+              /// ... doesn't create a feature
+              void setApexAsProcessed();
+              /// ... does create a feature
+              void setApexAsProcessed(const std::vector<std::pair<Size, Size> >& gathered_idx);
+              bool isConflictingApex(const Apex a) const;
+              bool isVisited(const Size scan_idx, const Size peak_idx) const;
+              void setNumberOfThreads(const Size thread_num);
+              /// reference for usage
+              const std::vector<Apex>& data_;
+              const std::vector<Size>& spec_offsets_;
+              /// own datastructure
+              std::vector<bool> peak_visited_;
+              Size current_Apex_;
+              std::vector<double> lock_list_;
+              double mass_error_ppm_;
+            };
+            /// internal check for FWHM meta data
+            bool checkFWHMMetaData_(const PeakMap& work_exp);
             /// The internal run method
-            void run_(const std::vector<Apex>& chrom_apices,
+            void run_(std::vector<Apex>& chrom_apices,
                       const Size peak_count,
                       const PeakMap & work_exp,
                       const std::vector<Size>& spec_offsets,
                       std::vector<MassTrace> & found_masstraces,
                       const Size max_traces = 0);
+            // Find Offset for Peak
+            static double findOffset_(const double centroid_mz, const double mass_error_ppm_);
             // parameter stuff
             double mass_error_ppm_;
             double mass_error_da_;
@@ Expand All / @@ -133,4 +194,4 @@ namespace OpenMS @@
             bool reestimate_mt_sd_;
         };
-    }
+    }

src/openms/include/OpenMS/KERNEL/MassTrace.h

-Original file line number
+Diff line change
@@ Expand Up / @@ -88,6 +88,15 @@ namespace OpenMS @@
         /// Detailed constructor for vector
         MassTrace(const std::vector<PeakType>& trace_peaks);
+        /// Constructor for typr T with move iterator
+        template <typename InputIterator>
+        MassTrace(InputIterator begin, InputIterator end) :
+                  trace_peaks_(std::make_move_iterator(begin), std::make_move_iterator(end)),
+                  label_(),
+                  smoothed_intensities_()
+        {
+        }
         /// Destructor
         ~MassTrace() = default;
@@ Expand Down @@

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Pmsb 23 mass trace detection #144

Uh oh!

Diff view

Diff view

There are no files selected for viewing

Uh oh!

Pmsb 23 mass trace detection #144

Are you sure you want to change the base?

Uh oh!

Pmsb 23 mass trace detection #144

Uh oh!

Uh oh!

Diff view

Diff view

There are no files selected for viewing

Uh oh!