BinnedSpectrum.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
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// $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 <Eigen/Sparse>

#include <cmath>

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 = 1.0005;

    // default bin width for high-resolution data (adapted from doi:10.1007/s13361-015-1179-x)
    static constexpr const float DEFAULT_BIN_WIDTH_HIRES = 0.02;

    static constexpr const float DEFAULT_BIN_OFFSET_HIRES = 0.0;

    static constexpr const float DEFAULT_BIN_OFFSET_LOWRES = 0.4;

    using SparseVectorType = Eigen::SparseVector<float>;

    using SparseVectorIndexType = Eigen::SparseVector<float>::Index;
 
    using SparseVectorIteratorType = Eigen::SparseVector<float>::InnerIterator;

    static const SparseVectorType EmptySparseVector;

    // BinnedSpectrum() = delete;
    BinnedSpectrum() {}

    BinnedSpectrum(const PeakSpectrum& ps, float size, bool unit_ppm, UInt spread, float offset);

    BinnedSpectrum(const BinnedSpectrum&) = default;

    virtual ~BinnedSpectrum();

    BinnedSpectrum& operator=(const BinnedSpectrum&) = default;

    bool operator==(const BinnedSpectrum& rhs) const;

    bool operator!=(const BinnedSpectrum& rhs) const;

    inline float getBinIntensity(double mz) { return bins_.coeffRef(getBinIndex(mz)); }

    inline SparseVectorIndexType getBinIndex(float mz) const 
    {
      if (unit_ppm_)
      {
        /*
         * By solving:    mz = MIN_MZ_ * (1.0 + bin_size_ * 1e-6)^index for index
         *     we get: index = floor(log(mz/MIN_MZ_)/log(1.0 + bin_size_ * 1e-6))
         * Note: for ppm we don't need to consider an offset_.
         */  
        return static_cast<SparseVectorIndexType>(floor(log(mz/MIN_MZ_)/log1p(bin_size_ * 1e-6)));
      }
      else 
      { // implemented as described in PMC4607604
        // Note: Consider a peak offset (important for low-resolution data, where most peak boundaries
        //       may fall on the mass peak apex. See publication for details.).
        return static_cast<SparseVectorIndexType>(floor(mz / bin_size_ + offset_)); 
      }
    }

    inline float getBinLowerMZ(size_t i) const
    {
      if (unit_ppm_)
      {
        // mz = MIN_MZ_ * (1.0 + bin_size_)^index for index
        return (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_;

    float bin_size_;

    bool unit_ppm_;

    float offset_;

    SparseVectorType bins_;

    void binSpectrum_(const PeakSpectrum& ps);

    std::vector<Precursor> precursors_;
  };

}