Test

AUTHORS

@@ -120,4 +120,5 @@ the authors tag in the respective file header.
  - Witold Wolski
  - Xiao Liang
  - Yasset Perez-Riverol
- - Peter Jones
+ - Peter Jones
+ - Anjali Gajurel

src/openms/include/OpenMS/IONMOBILITY/IMTypes.h

@@ -40,12 +40,18 @@ namespace OpenMS
   OPENMS_DLLAPI const std::string& toString(const DriftTimeUnit value);
 
   /// Different ways to represent ion mobility data in a spectrum
+  /// Note: 
+  /// 1. MIXED is only used for MSExperiment, not for MSSpectrum
+  /// 2. UNKNOWN should be used if the format is not yet determined. 
+  /// FileHandler or e.g. IM peak picker should ideally set the format a known value.
   enum class IMFormat
   {
     NONE,            ///< no ion mobility
     CONCATENATED,    ///< ion mobility frame is stacked in a single spectrum (i.e. has an IM float data array)
     MULTIPLE_SPECTRA,///< ion mobility is recorded as multiple spectra per frame (i.e. has one IM annotation per spectrum)
     MIXED,           ///< an MSExperiment contains both CONCATENATED and MULTIPLE_SPECTRA
+    CENTROIDED,      ///< ion mobility of peaks after centroiding in IM dimension. Ion mobility is annotated in a single float data array (i.e., each peak might have a different IM value in the data array); identical to CONCATENATED in terms of data layout.
+    UNKNOWN,         ///< ion mobility format not yet determined. 
     SIZE_OF_IMFORMAT
   };
   /// Names of IMFormat

src/openms/include/OpenMS/METADATA/MetaInfoInterface.h

@@ -36,7 +36,7 @@ namespace OpenMS
 public:
 
     /// Constructor
-    MetaInfoInterface();
+    MetaInfoInterface() = default;
     /// Copy constructor
     MetaInfoInterface(const MetaInfoInterface& rhs);
     /// Move constructor
@@ -107,8 +107,8 @@ namespace OpenMS
     /// Creates the MetaInfo object if it does not exist
     inline void createIfNotExists_();
 
-    /// Pointer to the MetaInfo object (0 by default)
-    MetaInfo* meta_;
+    /// Pointer to the MetaInfo object
+    MetaInfo* meta_ = nullptr;
   };
 
 } // namespace OpenMS

src/openms/include/OpenMS/METADATA/SpectrumSettings.h

@@ -3,7 +3,7 @@
 //
 // --------------------------------------------------------------------------
 // $Maintainer: Timo Sachsenberg $
-// $Authors: Marc Sturm $
+// $Authors: Marc Sturm, Timo Sachsenberg $
 // --------------------------------------------------------------------------
 
 #pragma once
@@ -16,6 +16,7 @@
 #include <OpenMS/METADATA/Product.h>
 #include <OpenMS/METADATA/PeptideIdentification.h>
 #include <OpenMS/METADATA/DataProcessing.h>
+#include <OpenMS/IONMOBILITY/IMTypes.h>
 
 #include <map>
 #include <vector>
@@ -52,13 +53,13 @@ namespace OpenMS
     static const std::string NamesOfSpectrumType[SIZE_OF_SPECTRUMTYPE];
 
     /// Constructor
-    SpectrumSettings();
+    SpectrumSettings() = default;
     /// Copy constructor
     SpectrumSettings(const SpectrumSettings &) = default;
     /// Move constructor
-    SpectrumSettings(SpectrumSettings&&) = default;
+    SpectrumSettings(SpectrumSettings&&) noexcept = default;
     /// Destructor
-    ~SpectrumSettings();
+    ~SpectrumSettings() noexcept = default;
 
     // Assignment operator
     SpectrumSettings & operator=(const SpectrumSettings &) = default;
@@ -78,6 +79,16 @@ namespace OpenMS
     ///sets the spectrum type
     void setType(SpectrumType type);
 
+    /// @brief sets the IMFormat of the spectrum
+    /// @param im_type
+    void setIMFormat(const IMFormat& im_type);
+
+    /// @brief returns the IMFormat of the spectrum if set. Otherwise UNKNOWN (default). 
+    /// 
+    /// Note: If UNKNOWN, use IMFormat::determineIMFormat to determine the IMFormat based on the data.
+    /// @return IMFormat of the spectrum
+    IMFormat getIMFormat() const;
+
     /// returns the native identifier for the spectrum, used by the acquisition software.
     const String & getNativeID() const;
     /// sets the native identifier for the spectrum, used by the acquisition software.
@@ -141,7 +152,8 @@ namespace OpenMS
 
 protected:
 
-    SpectrumType type_;
+    SpectrumType type_ = UNKNOWN;
+    IMFormat im_type_ = IMFormat::UNKNOWN;
     String native_id_;
     String comment_;
     InstrumentSettings instrument_settings_;

src/openms/include/OpenMS/PROCESSING/CENTROIDING/PeakPickerIM.h

@@ -0,0 +1,71 @@
+// Copyright (c) 2002-present, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
+// SPDX-License-Identifier: BSD-3-Clause
+//
+// --------------------------------------------------------------------------
+// $Author: Timo Sachsenberg, Mohammed Alhigaylan $
+// $Maintainer: Timo Sachsenberg $
+// -------------------------------------------------------------------------------------------------------------------------------------------
+
+#pragma once
+
+#include <OpenMS/KERNEL/MSSpectrum.h>
+#include <OpenMS/DATASTRUCTURES/Param.h>
+
+namespace OpenMS
+{
+  /**
+    @brief Peak picking algorithm for ion mobility data
+
+  @ingroup PeakPicking
+      */
+  class OPENMS_DLLAPI PeakPickerIM
+  {
+  public:
+    /// Default constructor initializing parameters with default values.
+    PeakPickerIM();
+
+    /// Destructor.
+    virtual ~PeakPickerIM();
+
+    /// Picks ion mobility traces from the given spectrum.
+    void pickIMTraces(MSSpectrum& spectrum);
+
+    /// Sets the parameters for peak picking.
+    void setParameters(const Param& param);
+
+    /// Gets the current parameters.
+    Param getParameters() const;
+
+  protected:
+    /// Updates internal member variables when parameters are changed.
+    void updateMembers_();
+
+    /// Returns the default parameters.
+    Param getDefaultParameters() const;
+
+    /// Stores the parameters for peak picking.
+    Param parameters_;
+
+  private:
+    /// determine sampling rate for linear resampler
+    double computeOptimalSamplingRate(const std::vector<MSSpectrum>& spectra);
+
+    /// Sum up the intensity of data points with nearly identical float values
+    MSSpectrum SumFrame(const MSSpectrum& spectrum, double ppm_tolerance = 0.01);
+
+    /// Compute lower and upper m/z bounds based on ppm
+    std::pair<double, double> ppmBounds(double mz, double ppm);
+
+    /// Extract ion mobility traces as MSSpectra from the raw TimsTOF frame
+    /// Ion mobility is temporarily written in place of m/z inside Peak1D object.
+    /// raw m/z values are allocated to float data arrays with the label 'raw_mz'
+    std::vector<MSSpectrum> extractIonMobilityTraces(
+      const MSSpectrum& picked_spectrum,
+      const MSSpectrum& raw_spectrum);
+
+    /// compute m/z and ion mobility centers for picked traces. Returns centroided spectrum.
+    MSSpectrum ComputeCenters(const std::vector<MSSpectrum>& mobilogram_traces,
+                              const std::vector<MSSpectrum>& picked_traces);
+  };
+
+} // namespace OpenMS

src/openms/include/OpenMS/PROCESSING/CENTROIDING/sources.cmake

@@ -5,6 +5,7 @@ set(directory include/OpenMS/PROCESSING/CENTROIDING)
 set(sources_list_h
 PeakPickerHiRes.h
 PeakPickerIterative.h
+PeakPickerIM.h
 )
 
 ### add path to the filenames

src/openms/source/IONMOBILITY/IMTypes.cpp

@@ -16,7 +16,7 @@ namespace OpenMS
 {
 
   const std::string NamesOfDriftTimeUnit[] = {"<NONE>", "ms", "1/K0", "FAIMS_CV"};
-  const std::string NamesOfIMFormat[] = {"none", "concatenated", "multiple_spectra", "mixed"};
+  const std::string NamesOfIMFormat[] = {"none", "concatenated", "multiple_spectra", "mixed", "centroided", "unknown"};
 
 
  DriftTimeUnit toDriftTimeUnit(const std::string& dtu_string)
@@ -73,33 +73,45 @@ namespace OpenMS
     if (occs.empty())
     {
       return IMFormat::NONE;
-    }
-    if (occs.size() == 1 && (occs.find(IMFormat::CONCATENATED) != occs.end() || occs.find(IMFormat::MULTIPLE_SPECTRA) != occs.end()))
+    }    
+
+    if (occs.size() == 1) 
     {
-      return *occs.begin();
+      auto format = *occs.begin();
+      if (format != IMFormat::CONCATENATED
+          && format != IMFormat::MULTIPLE_SPECTRA
+          && format != IMFormat::CENTROIDED)
+      {
+        throw Exception::InvalidValue(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "subfunction returned invalid value(s)", "Number of different values: " + String(occs.size()));
+      }
+      return format;
     }
-    if (occs.size() == 2 && occs.find(IMFormat::CONCATENATED) != occs.end() && occs.find(IMFormat::MULTIPLE_SPECTRA) != occs.end())
+    else    
     {
       return IMFormat::MIXED;
-    }
-
-    throw Exception::InvalidValue(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "subfunction returned invalid value(s)", "Number of different values: " + String(occs.size()));
+    }    
   }
 
   IMFormat IMTypes::determineIMFormat(const MSSpectrum& spec)
   {
-    bool has_float_data = spec.containsIMData(); // cache value; query is 'expensive'
-    bool has_drift_time = spec.getDriftTime() != DRIFTTIME_NOT_SET;
-    if (has_float_data && has_drift_time)
+    // First check if format is already set and not UNKNOWN
+    IMFormat current_format = spec.getIMFormat();
+    if (current_format != IMFormat::UNKNOWN)
     {
-      const auto& fda = spec.getFloatDataArrays()[spec.getIMData().first];
-      String array_val = fda.empty() ? "[empty]" : String(fda[0]);
-      throw Exception::InvalidValue(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "MSSpectrum contains both an float-data-array and a single drift time. At most one is allowed per spectrum!", String("Array: ") + array_val + ", ... <> Spec: " + spec.getDriftTime());
+      return current_format;
     }
 
+    // If format is UNKNOWN, determine it
+    bool has_float_data = spec.containsIMData(); // cache value; query is 'expensive'
+    bool has_drift_time = spec.getDriftTime() != DRIFTTIME_NOT_SET;
+
     if (has_float_data)
     {
-      return IMFormat::CONCATENATED;
+      if (has_drift_time)
+      {
+        OPENMS_LOG_DEBUG << "both drift time and IM data array found in spectrum " << spec.getNativeID() << "\n. Support for both is experimental." << std::endl;
+      }
+      return IMFormat::CONCATENATED; // TODO: or CENTROIDED. for now assume that no picking was done (otherwise we would have annotated it)
     }
     else if (has_drift_time)
     {

src/openms/source/METADATA/MetaInfoInterface.cpp

@@ -14,12 +14,6 @@ using namespace std;
 
 namespace OpenMS
 {
-
-  MetaInfoInterface::MetaInfoInterface() :
-    meta_(nullptr)
-  {
-  }
-
   /// Copy constructor
   MetaInfoInterface::MetaInfoInterface(const MetaInfoInterface& rhs) :
     meta_(nullptr)

src/openms/source/METADATA/SpectrumSettings.cpp

@@ -9,7 +9,6 @@
 #include <OpenMS/METADATA/SpectrumSettings.h>
 
 #include <OpenMS/CONCEPT/Helpers.h>
-#include <boost/iterator/indirect_iterator.hpp> // for equality
 
 using namespace std;
 
@@ -18,23 +17,6 @@ namespace OpenMS
 
   const std::string SpectrumSettings::NamesOfSpectrumType[] = {"Unknown", "Centroid", "Profile"};
 
-  SpectrumSettings::SpectrumSettings() :
-    MetaInfoInterface(),
-    type_(UNKNOWN),
-    native_id_(),
-    comment_(),
-    instrument_settings_(),
-    source_file_(),
-    acquisition_info_(),
-    precursors_(),
-    products_(),
-    identification_(),
-    data_processing_()
-  {
-  }
-
-  SpectrumSettings::~SpectrumSettings() = default;
-
   bool SpectrumSettings::operator==(const SpectrumSettings & rhs) const
   {
     return MetaInfoInterface::operator==(rhs) &&
@@ -94,6 +76,20 @@ namespace OpenMS
     type_ = type;
   }
 
+  void SpectrumSettings::setIMFormat(const IMFormat& im_type)
+  {
+    if (im_type == IMFormat::MIXED)
+    {
+      throw Exception::InvalidValue(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "Single spectrum can't have MIXED ion mobility format.", "SIZE_OF_IMFORMAT");
+    }
+    im_type_ = im_type;
+  }
+
+  IMFormat SpectrumSettings::getIMFormat() const
+  {
+    return im_type_;
+  }
+
   const String & SpectrumSettings::getComment() const
   {
     return comment_;