MSNumpressCoder.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2022.
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// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/CONCEPT/Exception.h>
#include <OpenMS/DATASTRUCTURES/String.h>

#include <algorithm>
#include <string>
#include <vector>

namespace OpenMS
{
  const double BinaryDataEncoder_default_numpressErrorTolerance = .0001; // 1/100th of one percent

  class OPENMS_DLLAPI MSNumpressCoder
  {

public:

    enum NumpressCompression {
      NONE, 
      LINEAR, 
      PIC, 
      SLOF, 
      SIZE_OF_NUMPRESSCOMPRESSION
    };
    static const std::string NamesOfNumpressCompression[SIZE_OF_NUMPRESSCOMPRESSION];

    struct OPENMS_DLLAPI NumpressConfig
    {
      double numpressFixedPoint;
      double numpressErrorTolerance;
      NumpressCompression np_compression;
      bool estimate_fixed_point;
      double linear_fp_mass_acc;

      NumpressConfig () :
        numpressFixedPoint(0.0),
        numpressErrorTolerance(BinaryDataEncoder_default_numpressErrorTolerance),
        np_compression(NONE),
        estimate_fixed_point(true),
        linear_fp_mass_acc(-1)
      {
      }

      void setCompression(const std::string& compression)
      {
        const std::string* match = std::find(NamesOfNumpressCompression,
                                             NamesOfNumpressCompression + SIZE_OF_NUMPRESSCOMPRESSION, compression);

        if (match == NamesOfNumpressCompression + SIZE_OF_NUMPRESSCOMPRESSION) // == end()
        {
          throw Exception::InvalidParameter(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION,
                                            "Value '" + compression + "' is not a valid Numpress compression scheme.");
        }

        np_compression = (NumpressCompression)std::distance(NamesOfNumpressCompression, match);
      }

    };

    MSNumpressCoder() {}

    virtual ~MSNumpressCoder() {}

    void encodeNP(const std::vector<double> & in,
                  String & result,
                  bool zlib_compression,
                  const NumpressConfig & config);

    void encodeNP(const std::vector<float> & in,
                  String & result,
                  bool zlib_compression,
                  const NumpressConfig & config);

    void decodeNP(const String & in,
                  std::vector<double> & out,
                  bool zlib_compression,
                  const NumpressConfig & config);

    void encodeNPRaw(const std::vector<double> & in,
                     String & result,
                     const NumpressConfig & config);

    void decodeNPRaw(const std::string & in,
                     std::vector<double> & out,
                     const NumpressConfig & config);

private:

    void decodeNPInternal_(const unsigned char* in, size_t in_size, std::vector<double>& out, const NumpressConfig & config);
  };

} //namespace OpenMS