DimMapper.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2021.
//
// 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: Chris Bielow $
// $Authors: Chris Bielow $
// --------------------------------------------------------------------------

#pragma once


#include <OpenMS/CONCEPT/Exception.h>
#include <OpenMS/CONCEPT/CommonEnums.h>
#include <OpenMS/DATASTRUCTURES/DPosition.h>
#include <OpenMS/DATASTRUCTURES/DRange.h>
#include <OpenMS/KERNEL/BaseFeature.h>
#include <OpenMS/KERNEL/MobilityPeak2D.h>
#include <OpenMS/KERNEL/Mobilogram.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/KERNEL/MSSpectrum.h>
#include <OpenMS/KERNEL/Peak1D.h>
#include <OpenMS/KERNEL/Peak2D.h>
#include <OpenMS/KERNEL/RangeManager.h>

#include <array>
#include <memory>


namespace OpenMS
{
  class OPENMS_DLLAPI DimBase
  {
  public:
    using ValueType = double;
    using ValueTypes = std::vector<ValueType>;

    DimBase() = delete;

    DimBase(DIM_UNIT unit) :
        unit_(unit) 
    {}

    DimBase& operator=(const DimBase& rhs) = default;

    virtual ~DimBase() noexcept = default;

    bool operator==(const DimBase& rhs) const
    {
      return unit_ == rhs.unit_;
    }

    virtual std::unique_ptr<DimBase> clone() const = 0;

    virtual ValueType map(const Peak1D& p) const = 0;
    virtual ValueType map(const Peak2D& p) const = 0;
    virtual ValueType map(const ChromatogramPeak& p) const = 0;
    virtual ValueType map(const MSExperiment::ConstAreaIterator& it) const = 0;
    virtual ValueType map(const MobilityPeak1D& p) const = 0;
    virtual ValueType map(const MobilityPeak2D& p) const = 0;

    virtual ValueType map(const MSSpectrum& spec, const Size index) const = 0;
    virtual ValueType map(const MSChromatogram& chrom, const Size index) const = 0;
    virtual ValueType map(const Mobilogram& mb, const Size index) const = 0;
    
    virtual ValueTypes map(const MSSpectrum& spec) const = 0;

    virtual ValueTypes map(const MSChromatogram& chrom) const = 0;

    virtual ValueType map(const BaseFeature& bf) const = 0;

    virtual ValueType map(const PeptideIdentification& pi) const = 0;

    virtual RangeBase map(const RangeAllType& rm) const = 0;

    virtual void setRange(const RangeBase& in, RangeAllType& out) const = 0;


    // from XY to a type

    virtual void fromXY(const ValueType in, Peak1D& p) const = 0;
    virtual void fromXY(const ValueType in, ChromatogramPeak& p) const = 0;
    virtual void fromXY(const ValueType in, MobilityPeak1D& p) const = 0;
    virtual void fromXY(const ValueType in, MobilityPeak2D& p) const = 0;

    std::string_view getDimName() const
    {
      return DIM_NAMES[(int)unit_];
    }

    std::string_view getDimNameShort() const
    {
      return DIM_NAMES_SHORT[(int)unit_];
    }

    DIM_UNIT getUnit() const
    {
      return unit_;
    }

    String formattedValue(const ValueType value) const;

    String formattedValue(ValueType value, const String& prefix) const;

    int valuePrecision() const;

  protected:
    DIM_UNIT unit_; 
  };



  class OPENMS_DLLAPI DimRT final : public DimBase
  {
  public:
    DimRT() : DimBase(DIM_UNIT::RT) {}

    std::unique_ptr<DimBase> clone() const override
    {
      return std::make_unique<DimRT>();
    }

    ValueType map(const Peak1D&) const override
    {
      throw Exception::InvalidRange(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);
    }
    ValueType map(const Peak2D& p) const override
    {
      return p.getRT();
    }
    ValueType map(const ChromatogramPeak& p) const override
    {
      return p.getRT();
    }
    ValueType map(const MSSpectrum& spec, const Size /*index*/) const override
    {
      return spec.getRT();
    }
    ValueType map(const MSChromatogram& chrom, const Size index) const override
    {
      return chrom[index].getRT();
    }
    ValueType map(const Mobilogram& mb, const Size /*index*/) const override
    {
      return mb.getRT();
    }

    ValueTypes map(const MSSpectrum&) const override
    {
      throw Exception::InvalidRange(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);
    }
    ValueTypes map(const MSChromatogram& chrom) const override
    {
      ValueTypes res;
      res.reserve(chrom.size());
      for (const auto& p : chrom)
      {
        res.push_back(p.getRT());
      }
      return res;
    }

    ValueType map(const MSExperiment::ConstAreaIterator& it) const override
    {
      return it.getRT();
    }
    ValueType map(const MobilityPeak1D&) const override
    {
      throw Exception::InvalidRange(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);
    }
    ValueType map(const MobilityPeak2D&) const override
    {
      throw Exception::InvalidRange(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);
    }

    ValueType map(const BaseFeature& bf) const override
    {
      return bf.getRT();
    }

    ValueType map(const PeptideIdentification& pi) const override
    {
      return pi.getRT();
    }

    RangeBase map(const RangeAllType& rm) const override
    {
      return rm.getRangeForDim(MSDim::RT);
    }

    void setRange(const RangeBase& in, RangeAllType& out) const override
    {
      out.RangeRT::operator=(in);
    }

    void fromXY(const ValueType, Peak1D&) const override
    {
      throw Exception::InvalidRange(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);
    }

    void fromXY(const ValueType in, ChromatogramPeak& p) const override
    {
      p.setRT(in);
    }
    void fromXY(const ValueType, MobilityPeak1D&) const override
    {
      throw Exception::InvalidRange(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);
    }
    void fromXY(const ValueType, MobilityPeak2D&) const override
    {
      throw Exception::InvalidRange(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);
    }
  };

  class OPENMS_DLLAPI DimMZ final : public DimBase
  {
  public:
    DimMZ() : DimBase(DIM_UNIT::MZ) {};
    
    std::unique_ptr<DimBase> clone() const override
    {
      return std::make_unique<DimMZ>();
    }
          
    ValueType map(const Peak1D& p) const override
    {
      return p.getMZ();
    }
    ValueType map(const Peak2D& p) const override
    {
      return p.getMZ();
    }
    ValueType map(const ChromatogramPeak&) const override
    {
      throw Exception::InvalidRange(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);
    }
    ValueType map(const MSExperiment::ConstAreaIterator& it) const override
    {
      return it->getMZ();
    }
    ValueType map(const MobilityPeak1D&) const override
    {
      throw Exception::InvalidRange(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);
    }
    ValueType map(const MobilityPeak2D& p) const override
    {
      return p.getMZ();
    }

    ValueType map(const MSSpectrum& spec, const Size index) const override
    {
      return spec[index].getMZ();
    }
    ValueType map(const MSChromatogram& chrom, const Size /*index*/) const override
    {
      return chrom.getPrecursor().getMZ();
    }
    ValueType map(const Mobilogram& /*mb*/, const Size /*index*/) const override
    {
      throw Exception::InvalidRange(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);
    }

    ValueTypes map(const MSSpectrum& spec) const override
    {
      ValueTypes res;
      res.reserve(spec.size());
      for (const auto& p : spec)
      {
        res.push_back(p.getMZ());
      }
      return res;
    }
    ValueTypes map(const MSChromatogram&) const override
    {
      throw Exception::InvalidRange(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);
    }  
    
    ValueType map(const BaseFeature& bf) const override
    {
      return bf.getMZ();
    }

    ValueType map(const PeptideIdentification& pi) const override
    {
      return pi.getMZ();
    }

    RangeBase map(const RangeAllType& rm) const override
    {
      return rm.getRangeForDim(MSDim::MZ);
    }

    void setRange(const RangeBase& in, RangeAllType& out) const override
    {
      out.RangeMZ::operator=(in);
    }

    void fromXY(const ValueType in, Peak1D& p) const override
    {
      p.setMZ(in);
    }

    void fromXY(const ValueType, ChromatogramPeak&) const override
    {
      throw Exception::InvalidRange(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);
    }

    void fromXY(const ValueType, MobilityPeak1D&) const override
    {
      throw Exception::InvalidRange(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);
    }
    void fromXY(const ValueType in, MobilityPeak2D& p) const override
    {
      p.setMZ(in);
    }
  };

  class OPENMS_DLLAPI DimINT final : public DimBase
  {
  public:
    DimINT() : DimBase(DIM_UNIT::INT) {};
    
    std::unique_ptr<DimBase> clone() const override
    {
      return std::make_unique<DimINT>();
    }
    
    ValueType map(const Peak1D& p) const override
    {
      return p.getIntensity();
    }
    ValueType map(const Peak2D& p) const override
    {
      return p.getIntensity();
    }
    ValueType map(const ChromatogramPeak& p) const override
    {
      return p.getIntensity();
    }
    ValueType map(const MSExperiment::ConstAreaIterator& it) const override
    {
      return it->getIntensity();
    }
    ValueType map(const MobilityPeak1D& p) const override
    {
      return p.getIntensity();
    }
    ValueType map(const MobilityPeak2D& p) const override
    {
      return p.getIntensity();
    }

    ValueType map(const MSSpectrum& spec, const Size index) const override
    {
      return spec[index].getIntensity();
    }
    ValueType map(const MSChromatogram& chrom, const Size index) const override
    {
      return chrom[index].getIntensity();
    }
    ValueType map(const Mobilogram& mb, const Size index) const override
    {
      return mb[index].getIntensity();
    }

    ValueTypes map(const MSSpectrum& spec) const override
    {
      ValueTypes res;
      res.reserve(spec.size());
      for (const auto& p : spec)
      {
        res.push_back(p.getIntensity());
      }
      return res;
    }

    ValueTypes map(const MSChromatogram& chrom) const override
    {
      ValueTypes res;
      res.reserve(chrom.size());
      for (const auto& p : chrom)
      {
        res.push_back(p.getIntensity());
      }
      return res;
    }

    ValueType map(const BaseFeature& bf) const override
    {
      return bf.getIntensity();
    }

    ValueType map(const PeptideIdentification&) const override
    {
      throw Exception::InvalidRange(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);
    }
    
    RangeBase map(const RangeAllType& rm) const override
    {
      return rm.getRangeForDim(MSDim::INT);
    }

    void setRange(const RangeBase& in, RangeAllType& out) const override
    {
      out.RangeIntensity::operator=(in);
    }

    void fromXY(const ValueType in, Peak1D& p) const override
    {
      p.setIntensity(in);
    }

    void fromXY(const ValueType in, ChromatogramPeak& p) const override
    {
      p.setIntensity(in);
    }
    void fromXY(const ValueType in, MobilityPeak1D& p) const override
    {
      p.setIntensity(in);
    }
    void fromXY(const ValueType in, MobilityPeak2D& p) const override
    {
      p.setIntensity(in);
    }
  };

  class OPENMS_DLLAPI DimIM final : public DimBase
  {
  public:
    DimIM(const DIM_UNIT im_unit) : DimBase(im_unit) {}

    std::unique_ptr<DimBase> clone() const override
    {
      return std::make_unique<DimIM>(*this);
    }

    ValueType map(const Peak1D&) const override
    {
      throw Exception::InvalidRange(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);
    }
    ValueType map(const Peak2D&) const override
    {
      throw Exception::InvalidRange(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);
    }
    ValueType map(const ChromatogramPeak&) const override
    {
      throw Exception::InvalidRange(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);
    }
    ValueTypes map(const MSSpectrum&) const override
    {
      throw Exception::InvalidRange(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);
    }
    ValueTypes map(const MSChromatogram&) const override
    {
      throw Exception::InvalidRange(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);
    }

    ValueType map(const MSExperiment::ConstAreaIterator& it) const override
    {
      return it.getDriftTime();
    }

    ValueType map(const MobilityPeak1D& p) const override
    {
      return p.getMobility();
    }
    ValueType map(const MobilityPeak2D& p) const override
    {
      return p.getMobility();
    }

    ValueType map(const MSSpectrum& spec, const Size /*index*/) const override
    {
      return spec.getDriftTime();
    }
    ValueType map(const MSChromatogram&, const Size) const override
    {
      throw Exception::InvalidRange(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);
    }
    ValueType map(const Mobilogram& mb, const Size index) const override
    {
      return mb[index].getMobility();
    }

    ValueType map(const BaseFeature&) const override
    {
      throw Exception::InvalidRange(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);
    }

    ValueType map(const PeptideIdentification&) const override
    {
      throw Exception::InvalidRange(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);
    }

    RangeBase map(const RangeAllType& rm) const override
    {
      return rm.getRangeForDim(MSDim::IM);
    }

    void setRange(const RangeBase& in, RangeAllType& out) const override
    {
      out.RangeMobility::operator=(in);
    }

    void fromXY(const ValueType, Peak1D&) const override
    {
      throw Exception::InvalidRange(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);
    }

    void fromXY(const ValueType, ChromatogramPeak&) const override
    {
      throw Exception::InvalidRange(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);
    }

    void fromXY(const ValueType in, MobilityPeak1D& p) const override
    {
      p.setMobility(in);
    }
    void fromXY(const ValueType in, MobilityPeak2D& p) const override
    {
      p.setMobility(in);
    }
  };
  
  enum class DIM
  {
    X = 0,  
    Y = 1,
    Z = 2
  };

  template<int N_DIM>
  class DimMapper
  {
  public:
    using Point = DPosition<N_DIM, DimBase::ValueType>;

    DimMapper() = delete;

    DimMapper(const DIM_UNIT (&units)[N_DIM])
      :dims_([&]() {
          std::array<std::unique_ptr<const DimBase>, N_DIM> dims_tmp;
          for (int i = 0; i < N_DIM; ++i)
          {
            dims_tmp[i] = create_(units[i]);
          }
          return dims_tmp;
      }()) // immediately evaluated lambda to enable 'dims_' to be const
    {
      static_assert(N_DIM >= 1); // at least one dimension (X)
      static_assert(N_DIM <= 3); // at most three (X, Y, Z)
    }

    DimMapper(const DimMapper& rhs) // cannot be defaulted due to unique_ptr
    {
      *this = rhs;
    };

    DimMapper& operator=(const DimMapper& rhs) // cannot be defaulted due to unique_ptr
    {
      for (int i = 0; i < N_DIM; ++i) dims_[i] = rhs.dims_[i]->clone(); 
      return *this;
    };

    bool operator==(const DimMapper& rhs) const
    {
      bool res {true};
      for (int i = 0; i < N_DIM; ++i)
      {
        res &= (*dims_[i] == *rhs.dims_[i]); 
      }
      return res;
    }
    
    bool operator!=(const DimMapper& rhs) const
    {
      return !operator==(rhs);
    }

    template <typename T>
    Point map(const T& data) const
    {
      Point pr;
      for (int i = 0; i < N_DIM; ++i) pr[i] = dims_[i]->map(data);
      return pr;
    }
    template<typename Container>
    Point map(const Container& data, const Size index) const
    {
      Point pr;
      for (int i = 0; i < N_DIM; ++i)
        pr[i] = dims_[i]->map(data, index);
      return pr;
    }

    template<typename ...Ranges>
    DRange<N_DIM> mapRange(const RangeManager<Ranges...>& ranges) const
    {
      DRange<N_DIM> res;
      RangeAllType all;
      all.assign(ranges);
      for (int i = 0; i < N_DIM; ++i)
      {
        RangeBase mm = dims_[i]->map(all);
        if (mm.isEmpty()) continue;
        res.setDimMinMax(i, {mm.getMin(), mm.getMax()});
      }
      return res;
    }

    template<typename... Ranges>
    void fromXY(const DRange<N_DIM>& in, RangeManager<Ranges...>& output) const
    {
      for (int i = 0; i < N_DIM; ++i)
      {
        if (in.isEmpty(i))
          dims_[i]->setRange(RangeBase(), output);
        else
          dims_[i]->setRange({in.minPosition()[i], in.maxPosition()[i]}, output);
      }
    }

    template<typename... Ranges>
    void fromXY(const Point& in, RangeManager<Ranges...>& output) const
    {
      for (int i = 0; i < N_DIM; ++i)
      {
        dims_[i]->setRange({in[i], in[i]}, output);
      }
    }

    template<typename T>
    void fromXY(const Point& in, T& out) const
    {
      for (int i = 0; i < N_DIM; ++i)
      {
        dims_[i]->fromXY(in[i], out);
      }
    }

    RangeAllType fromXY(const Point& in) const
    {
      RangeAllType output;
      for (int i = 0; i < N_DIM; ++i)
      {
        dims_[i]->setRange({in[i], in[i]}, output);
      }
      return output;
    }

    const DimBase& getDim(DIM d) const
    {
      assert((int)d <= N_DIM);
      return *dims_[(int)d];
    }

  protected:
    static std::unique_ptr<const DimBase> create_(DIM_UNIT u)
    {
      switch (u)
      {
        case DIM_UNIT::RT:
          return std::make_unique<DimRT>();
        case DIM_UNIT::MZ:
          return std::make_unique<DimMZ>();
        case DIM_UNIT::INT:
          return std::make_unique<DimINT>();
        case DIM_UNIT::FAIMS_CV:
        case DIM_UNIT::IM_MS:
        case DIM_UNIT::IM_VSSC:
          return std::make_unique<DimIM>(u);
        default:
          throw Exception::NotImplemented(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);
      }
    }

    std::array<std::unique_ptr<const DimBase>, N_DIM> dims_; 
  };


  template <int N_DIM>
  class Area
  {
  public:
    using AreaXYType = DRange<N_DIM>;

    Area() = delete;
    
    Area(const DimMapper<N_DIM>* const dims) 
      : mapper_(dims)
    {
    }

    Area(const Area& range) = default;

    Area& operator=(const Area& rhs)
    {
      // check that Dims are identical, otherwise this is very dangerous (the user probably only wanted to update the area, not change its mapping).
      if (mapper_ != rhs.mapper_ && *mapper_ != *rhs.mapper_)
      {
        throw Exception::Precondition(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "Assignment of Areas using different mappers!");
      }
      data_range_ = rhs.data_range_;
      visible_area_ = rhs.visible_area_;
      return *this;
    } 

    bool operator==(const Area& rhs) const
    {
      return data_range_ == rhs.data_range_
            && visible_area_ == rhs.visible_area_
            && (*mapper_ == *rhs.mapper_);
    }
    bool operator!=(const Area& rhs) const
    {
      return !operator==(rhs);
    }

    const Area& setArea(const RangeAllType& data)
    {
      data_range_ = data;
      // update axis view using dims
      visible_area_ = mapper_->mapRange(data);
      return *this;
    }

    const Area& setArea(const AreaXYType& data)
    {
      visible_area_ = data;
      // update range view from XY area using dims
      mapper_->fromXY(visible_area_, data_range_);
      return *this;
    }

    const AreaXYType& getAreaXY() const
    {
      return visible_area_;
    }

    const RangeAllType& getAreaUnit() const
    {
      return data_range_;
    }

    Area cloneWith(const AreaXYType& data) const
    {
      Area clone(*this);
      clone.setArea(data);
      return clone;
    }

    Area cloneWith(const RangeAllType& data) const
    {
      Area clone(*this);
      clone.setArea(data);
      return clone;
    }

    void pushInto(const RangeAllType& sandbox)
    {
      auto a = data_range_;
      a.pushInto(sandbox);
      setArea(a);
    }

    void clear()
    {
      setArea(RangeAllType());
    }

  private:
    /* two sides of the same coin... */
    RangeAllType data_range_;                     
    AreaXYType visible_area_ = AreaXYType::empty; 
    const DimMapper<N_DIM>* mapper_;
  };

} // namespace OpenMS