XMassFile.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: Timo Sachsenberg $
// $Authors: Guillaume Belz $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/FORMAT/HANDLERS/AcqusHandler.h>
#include <OpenMS/FORMAT/HANDLERS/FidHandler.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/SYSTEM/File.h>
 
namespace OpenMS
{
  class OPENMS_DLLAPI XMassFile :
    public ProgressLogger
  {
public:
    XMassFile();
    ~XMassFile() override;
 
    void load(const String & filename, MSSpectrum & spectrum)
    {
      Internal::AcqusHandler acqus(filename.prefix(filename.length() - 3) + String("acqus"));
 
      Internal::FidHandler fid(filename);
      if (!fid)
      {
        if (!File::exists(filename))
        {
          throw Exception::FileNotFound(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, filename);
        }
        else if (!File::readable(filename))
        {
          throw Exception::FileNotReadable(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, filename);
        }
        else
        {
          throw Exception::IOException(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, filename);
        }
      }
 
      //  Delete old spectrum
      spectrum.clear(true);
 
      //temporary variables
      Peak1D p;
 
      while (spectrum.size() < acqus.getSize())
      {
        //fill peak
        p.setPosition((Peak1D::PositionType)acqus.getPosition(fid.getIndex()));
        p.setIntensity((Peak1D::IntensityType)fid.getIntensity());
        spectrum.push_back(p);
      }
      fid.close();
 
      // import metadata
      spectrum.setRT(0.0);
      spectrum.setMSLevel(1);
      spectrum.setName("Xmass analysis file " + acqus.getParam("$ID_raw"));
      spectrum.setType(SpectrumSettings::PROFILE);
      spectrum.setNativeID("spectrum=xsd:" + acqus.getParam("$ID_raw").remove('<').remove('>'));
      spectrum.setComment("no comment");
 
      InstrumentSettings instrument_settings;
      instrument_settings.setScanMode(InstrumentSettings::MASSSPECTRUM);
      instrument_settings.setZoomScan(false);
 
      if (acqus.getParam(".IONIZATION MODE") == "LD+")
      {
        instrument_settings.setPolarity(IonSource::Polarity::POSITIVE);
      }
      else if (acqus.getParam(".IONIZATION MODE") == "LD-")
      {
        instrument_settings.setPolarity(IonSource::Polarity::NEGATIVE);
      }
      else
      {
        instrument_settings.setPolarity(IonSource::Polarity::POLNULL);
      }
      spectrum.setInstrumentSettings(instrument_settings);
 
      AcquisitionInfo acquisition_info;
      acquisition_info.setMethodOfCombination("Sum of " + acqus.getParam("$NoSHOTS") + " raw spectrum");
      spectrum.setAcquisitionInfo(acquisition_info);
 
      SourceFile source_file;
      source_file.setNameOfFile("fid");
      source_file.setPathToFile(filename.prefix(filename.length() - 3));
      source_file.setFileSize(4.0 * acqus.getSize() / 1024 / 1024);   // 4 bytes / point
      source_file.setFileType("Xmass analysis file (fid)");
      spectrum.setSourceFile(source_file);
 
      DataProcessing data_processing;
      Software software;
      software.setName("FlexControl");
      String fc_ver = acqus.getParam("$FCVer");   // FlexControlVersion
      if (fc_ver.hasPrefix("<flexControl "))
      {
        fc_ver = fc_ver.suffix(' ');
      }
      if (fc_ver.hasSuffix(">"))
      {
        fc_ver = fc_ver.prefix('>');
      }
      software.setVersion(fc_ver);
      software.setMetaValue("Acquisition method", DataValue(acqus.getParam("$ACQMETH").remove('<').remove('>')));
      data_processing.setSoftware(software);
      std::set<DataProcessing::ProcessingAction> actions;
      actions.insert(DataProcessing::SMOOTHING);
      actions.insert(DataProcessing::BASELINE_REDUCTION);
      actions.insert(DataProcessing::CALIBRATION);
      data_processing.setProcessingActions(actions);
      data_processing.setCompletionTime(DateTime::now());
 
      std::vector< std::shared_ptr< DataProcessing> > data_processing_vector;
      data_processing_vector.push_back( std::shared_ptr< DataProcessing>(new DataProcessing(data_processing)) );
      spectrum.setDataProcessing(data_processing_vector);
    }
 
    void importExperimentalSettings(const String & filename, PeakMap & exp)
    {
      Internal::AcqusHandler acqus(filename.prefix(filename.length() - 3) + String("acqus"));
 
      ExperimentalSettings & experimental_settings = exp.getExperimentalSettings();
 
      Instrument & instrument = experimental_settings.getInstrument();
      instrument.setName(acqus.getParam("SPECTROMETER/DATASYSTEM"));
      instrument.setVendor(acqus.getParam("ORIGIN"));
      instrument.setModel(acqus.getParam("$InstrID").remove('<').remove('>'));
 
      std::vector<IonSource> & ionSourceList = instrument.getIonSources();
      ionSourceList.clear();
      ionSourceList.resize(1);
      if (acqus.getParam(".INLET") == "DIRECT")
      {
        ionSourceList[0].setInletType(IonSource::InletType::DIRECT);
      }
      else
      {
        ionSourceList[0].setInletType(IonSource::InletType::INLETNULL);
        ionSourceList[0].setIonizationMethod(IonSource::IonizationMethod::MALDI);
      }
      if (acqus.getParam(".IONIZATION MODE") == "LD+")
      {
        ionSourceList[0].setPolarity(IonSource::Polarity::POSITIVE);
      }
      else if (acqus.getParam(".IONIZATION MODE") == "LD-")
      {
        ionSourceList[0].setPolarity(IonSource::Polarity::NEGATIVE);
      }
      else
      {
        ionSourceList[0].setPolarity(IonSource::Polarity::POLNULL);
      }
      ionSourceList[0].setMetaValue("MALDI target reference", DataValue(acqus.getParam("$TgIDS").remove('<').remove('>')));
      ionSourceList[0].setOrder(0);
 
      std::vector<MassAnalyzer> & massAnalyzerList = instrument.getMassAnalyzers();
      massAnalyzerList.clear();
      massAnalyzerList.resize(1);
      if (acqus.getParam(".SPECTROMETER TYPE") == "TOF")
      {
        massAnalyzerList[0].setType(MassAnalyzer::TOF);
      }
      else
      {
        massAnalyzerList[0].setType(MassAnalyzer::ANALYZERNULL);
      }
 
      DateTime date;
      date.set(acqus.getParam("$AQ_DATE").remove('<').remove('>'));
      experimental_settings.setDateTime(date);
    }
 
    void store(const String & /*filename*/, const MSSpectrum & /*spectrum*/)
    {
      throw Exception::NotImplemented(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);
    }
 
  };
} // namespace OpenMS