BinnedSpectrum.h

Go to the documentation of this file.

// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2023.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
//  * Neither the name of any author or any participating institution
//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Timo Sachsenberg, Mathias Walzer $
// --------------------------------------------------------------------------
//
#pragma once
 
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/KERNEL/MSSpectrum.h>
#include <OpenMS/CONCEPT/Exception.h>
 
#include <cmath>
 
// forward decl
namespace Eigen
{
    template<typename _Scalar, int _Flags, typename _StorageIndex>
    class SparseVector;
}
 
namespace OpenMS
{
 
  class OPENMS_DLLAPI BinnedSpectrum
  {
    // smallest possible m/z value (needs to be >= 1)
    static constexpr const float MIN_MZ_ = 1.0;
 
public:
    // default bin width for low-resolution data (adapted from doi:10.1007/s13361-015-1179-x)
    static constexpr const float DEFAULT_BIN_WIDTH_LOWRES = 1.0005f;
 
    // default bin width for high-resolution data (adapted from doi:10.1007/s13361-015-1179-x)
    static constexpr const float DEFAULT_BIN_WIDTH_HIRES = 0.02f;
 
    static constexpr const float DEFAULT_BIN_OFFSET_HIRES = 0.0f;
 
    static constexpr const float DEFAULT_BIN_OFFSET_LOWRES = 0.4f;
 
    using SparseVectorType = Eigen::SparseVector<float, 0, int>;
 
    // static const SparseVectorType EmptySparseVector;
 
    // BinnedSpectrum() = delete;
    BinnedSpectrum() {};
 
    BinnedSpectrum(const PeakSpectrum& ps, float size, bool unit_ppm, UInt spread, float offset);
 
    BinnedSpectrum(const BinnedSpectrum&);
 
    virtual ~BinnedSpectrum();
 
    BinnedSpectrum& operator=(const BinnedSpectrum&);
 
    bool operator==(const BinnedSpectrum& rhs) const;
 
    bool operator!=(const BinnedSpectrum& rhs) const;
 
    float getBinIntensity(double mz);
 
    size_t getBinIndex(float mz) const;
 
    inline float getBinLowerMZ(size_t i) const
    {
      if (unit_ppm_)
      {
        // mz = MIN_MZ_ * (1.0 + bin_size_)^index for index
        return float(MIN_MZ_ * pow(1.0 + bin_size_ * 1e-6, i));
      }
      else 
      { 
        return ((static_cast<float>(i) - offset_) * bin_size_);
      }
    }
 
    inline float getBinSize() const { return bin_size_; }
 
    inline size_t getBinSpread() const { return bin_spread_; }
 
    const SparseVectorType* getBins() const;
 
    SparseVectorType* getBins();
 
    inline float getOffset() const { return offset_; }
 
    const std::vector<Precursor>& getPrecursors() const;
 
    std::vector<Precursor>& getPrecursors();
 
    //  returns true if bin size, unit and offset are equal, otherwise false
    static bool isCompatible(const BinnedSpectrum& a, const BinnedSpectrum& b);
 
private:
    UInt bin_spread_ {0};
 
    float bin_size_ {0};
 
    bool unit_ppm_ {false};
 
    float offset_ {0};
 
    SparseVectorType* bins_ {nullptr};
 
    void binSpectrum_(const PeakSpectrum& ps);
 
    std::vector<Precursor> precursors_;
  };
 
}