MSImagingExperiment.h

Go to the documentation of this file.

// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Timo Sachsenberg, Patrick Boschmann $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/IMAGING/IonImage.h>
#include <OpenMS/IMAGING/MSImagingGeometry.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/KERNEL/MSSpectrum.h>
 
namespace OpenMS
{
class OPENMS_DLLAPI MSImagingExperiment final
{
public:
  MSImagingExperiment() = default;
 
  explicit MSImagingExperiment(MSExperiment exp);
 
  MSImagingExperiment& operator=(MSExperiment exp);
 
  MSExperiment& getMSExperiment();
 
  const MSExperiment& getMSExperiment() const;
 
  void setMSExperiment(MSExperiment exp);
 
  MSImagingGeometry& getGeometry();
 
  const MSImagingGeometry& getGeometry() const;
 
  void setGeometry(MSImagingGeometry geom);
 
  Size getNumberOfPixels() const;
 
  Size getNumberOfSpectra() const;
 
  bool hasPixel(UInt x, UInt y) const;
 
  MSSpectrum& getSpectrum(UInt x, UInt y);
 
  const MSSpectrum& getSpectrum(UInt x, UInt y) const;
 
  IonImage extractIonImage(double mz, double tolerance_ppm) const;
 
  IonImage extractIonImage(double mz, double tolerance_ppm, Size region_id) const;
  void validate() const;
 
  std::vector<Size> getRegionSpectrumIndices(Size region_id) const;
 
 
private:
  MSExperiment experiment_;
  MSImagingGeometry geometry_;
  void extractIntoImage_(IonImage& image,
                         double mz_lo,
                         double mz_hi,
                         const std::vector<MSImagingGeometry::Pixel>& pixels,
                         const std::vector<Size>& pixel_indices) const;
};
 
} // namespace OpenMS