MSNumpressCoder.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 2002-2021.
//
// 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: Hannes Roest $
// $Authors: Hannes Roest $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/CONCEPT/Exception.h>
#include <OpenMS/DATASTRUCTURES/String.h>
 
#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