OnDiscImzMLExperiment.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/OpenMSConfig.h>
#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/KERNEL/MSSpectrum.h>
#include <OpenMS/FORMAT/HANDLERS/ImzMLHandlerHelper.h>
#include <OpenMS/DATASTRUCTURES/StringUtils.h>
 
#include <cstddef>
#include <cstdint>
#include <memory>
#include <string>
 
namespace OpenMS
{
 
  class MSImagingGeometry; // OpenMS/IMAGING/MSImagingGeometry.h — included in the .cpp
  class IonImage;          // OpenMS/IMAGING/IonImage.h — included in the .cpp
  class ExperimentalSettings; // OpenMS/METADATA/ExperimentalSettings.h — included in the .cpp
 
  class OPENMS_DLLAPI OnDiscImzMLExperiment
  {
  public:
 
    OnDiscImzMLExperiment();
    ~OnDiscImzMLExperiment();           // needs Impl complete — defined in .cpp
 
    OnDiscImzMLExperiment(const OnDiscImzMLExperiment&)            = delete;
    OnDiscImzMLExperiment& operator=(const OnDiscImzMLExperiment&) = delete;
 
    OnDiscImzMLExperiment(OnDiscImzMLExperiment&&);
    OnDiscImzMLExperiment& operator=(OnDiscImzMLExperiment&&);
 
    // ------------------------------------------------------------------
    // Open
    // ------------------------------------------------------------------
 
    void open(const std::string& imzml_path, const std::string& ibd_path = "", bool skip_metadata = false);
 
    void close() noexcept;
 
    // ------------------------------------------------------------------
    // State
    // ------------------------------------------------------------------
 
    bool        isOpen()       const noexcept;
    std::size_t getNrSpectra() const noexcept;
    std::size_t size()         const noexcept { return getNrSpectra(); }
 
    // ------------------------------------------------------------------
    // Index access — no IBD read, O(1)
    // ------------------------------------------------------------------
 
    const ImzMLSpectrumIndex& getIndex(std::size_t i) const;
 
    // ------------------------------------------------------------------
    // On-demand spectrum decode — one fseek + fread per call
    // ------------------------------------------------------------------
 
    MSSpectrum getSpectrum(std::size_t i) const;
 
    MSSpectrum operator[](std::size_t i) const { return getSpectrum(i); }
 
    MSSpectrum getSpectrumAtCoord(uint32_t x, uint32_t y, uint32_t z = 1) const;
 
    // ------------------------------------------------------------------
    // Ion image extraction — lazy decode, no full dataset in memory
    // ------------------------------------------------------------------
 
    IonImage extractIonImage(double mz, double tolerance_ppm) const;
 
    IonImage extractIonImage(double mz, double tolerance_ppm, Size region_id) const;
 
    // ------------------------------------------------------------------
    // Dataset-level metadata
    // ------------------------------------------------------------------
 
    const ImzMLMeta& getImzMLMeta() const noexcept;
 
    const ExperimentalSettings& getExperimentalSettings() const;
 
    const MSImagingGeometry& getGeometry() const;
 
    MSImagingGeometry& getGeometry();
 
    uint32_t gridWidth()  const noexcept;
 
    uint32_t gridHeight() const noexcept;
 
  private:
 
    struct Impl;
    std::unique_ptr<Impl> pimpl_;
  };
 
} // namespace OpenMS