ImzMLFile.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: Aditya Sarna, Patrick Boschmann $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/DATASTRUCTURES/StringUtils.h>
#include <OpenMS/FORMAT/HANDLERS/ImzMLHandlerHelper.h>
#include <OpenMS/FORMAT/OPTIONS/PeakFileOptions.h>
#include <OpenMS/FORMAT/XMLFile.h>
#include <OpenMS/INTERFACES/IMSDataConsumer.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/OpenMSConfig.h>
 
#include <iosfwd>
#include <string>
#include <vector>
 
namespace OpenMS
{
 
  class MSImagingExperiment;
  class MSImagingGeometry;
 
  class OPENMS_DLLAPI ImzMLFile :
    public Internal::XMLFile,
    public ProgressLogger
  {
  public:
 
    ImzMLFile();
    ~ImzMLFile() override = default;
 
    PeakFileOptions& getOptions();
    const PeakFileOptions& getOptions() const;
    void setOptions(const PeakFileOptions& options);
 
    void load(const std::string& filename, MSImagingExperiment& exp);
 
    static void buildImagingGeometry(const MSExperiment& exp, MSImagingGeometry& geom);
 
    static void buildImagingGeometry(const std::vector<ImzMLSpectrumIndex>& index,
                                     const ImzMLMeta& meta,
                                     MSImagingGeometry& geom);
 
    void load(const std::string& filename, Interfaces::IMSDataConsumer& consumer);
 
    void loadSpectraIndex(const std::string& filename,
                          ImzMLMeta& meta,
                          std::vector<ImzMLSpectrumIndex>& index,
                          MSExperiment& spectra,
                          const std::string& ibd_path = "");
 
    bool isValid(const std::string& filename, std::ostream& os);
 
    void store(const std::string& filename, const MSExperiment& exp) const;
 
    void store(const std::string& filename, const MSImagingExperiment& exp) const;
 
  private:
 
    void loadImpl_(const std::string& filename,
                   Interfaces::IMSDataConsumer* consumer,
                   MSExperiment& meta_exp,
                   ImzMLMeta* out_meta,
                   std::vector<ImzMLSpectrumIndex>* out_index,
                   bool index_only,
                   const std::string& ibd_path_override = "");
 
    static std::string inferIbdPath_(const std::string& imzml_path);
 
    PeakFileOptions options_;
  };
 
} // namespace OpenMS