BrukerTimsFile.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
 
#pragma once
 
#include <OpenMS/config.h>
 
#ifdef WITH_OPENTIMS
 
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/INTERFACES/IMSDataConsumer.h>
#include <OpenMS/OPENSWATHALGO/DATAACCESS/SwathMap.h>
#include <cstdint>
#include <string>
 
class TimsDataHandle;
 
namespace OpenMS
{
  class FullSwathFileConsumer;
 
  class OPENMS_DLLAPI BrukerTimsFile : public ProgressLogger
  {
  public:
    struct Config
    {
      double calibration_tolerance = 0.0;  
      bool calibrate = false;              
 
      float ms1_centroid_mz_ppm = 0.0f; 
      float ms1_centroid_im_pct = 0.0f;  
 
      int dia_ms2_n_neighbors = 0;  
      int dia_ms2_min_support = 1;  
      bool dia_ms2_centroid = false; 
 
      enum ExportMode { AUTO, SPECTRUM, FRAME };
      ExportMode export_mode = AUTO;       
 
      enum class TimsCalibrationStrategy { AUTO, BRUKER_SDK, RATIONAL, LINEAR };
      TimsCalibrationStrategy tims_calibration_strategy = TimsCalibrationStrategy::AUTO;
 
      enum class PressureCompensation { NONE, GLOBAL, PER_FRAME };
      PressureCompensation pressure_compensation = PressureCompensation::NONE;
 
      std::string bruker_sdk_path;
    };
 
    struct DIAStreamingMetadata
    {
      std::vector<OpenSwath::SwathMap> boundaries;  
      int nr_ms1_spectra = 0;                       
      std::vector<int> nr_ms2_spectra;              
    };
 
    DIAStreamingMetadata readDIAMetadata(const String& path, ExperimentalSettings& exp_settings);
    DIAStreamingMetadata readDIAMetadata(const String& path, ExperimentalSettings& exp_settings,
                                         const Config& config);
 
    void loadDIAStreaming(const String& path, FullSwathFileConsumer& consumer);
    void loadDIAStreaming(const String& path, FullSwathFileConsumer& consumer,
                          const Config& config);
 
    void load(const String& path, MSExperiment& exp);
    void load(const String& path, MSExperiment& exp, const Config& config);
 
    void transform(const String& path, Interfaces::IMSDataConsumer* consumer);
    void transform(const String& path, Interfaces::IMSDataConsumer* consumer, const Config& config);
 
  private:
    void loadDDA_(TimsDataHandle& handle, MSExperiment& exp, const Config& config);
 
    void loadDIA_(TimsDataHandle& handle, MSExperiment& exp, const Config& config);
 
    void loadFrames_(TimsDataHandle& handle, MSExperiment& exp, const Config& config);
 
    bool isDIA_(const String& tdf_path) const;
 
    void loadExperimentalSettings_(const String& path, ExperimentalSettings& settings);
  };
 
} // namespace OpenMS
 
#endif // WITH_OPENTIMS