OpenMS
MSNumpressCoder.h
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1 // Copyright (c) 2002-present, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
2 // SPDX-License-Identifier: BSD-3-Clause
3 //
4 // --------------------------------------------------------------------------
5 // $Maintainer: Hannes Roest $
6 // $Authors: Hannes Roest $
7 // --------------------------------------------------------------------------
8 
9 #pragma once
10 
13 
14 #include <algorithm>
15 #include <string>
16 #include <vector>
17 
18 namespace OpenMS
19 {
20  const double BinaryDataEncoder_default_numpressErrorTolerance = .0001; // 1/100th of one percent
21 
42  class OPENMS_DLLAPI MSNumpressCoder
43  {
44 
45 public:
46 
49  NONE,
51  PIC,
52  SLOF,
53  SIZE_OF_NUMPRESSCOMPRESSION
54  };
55  static const std::string NamesOfNumpressCompression[SIZE_OF_NUMPRESSCOMPRESSION];
56 
62  struct OPENMS_DLLAPI NumpressConfig
63  {
106 
108  numpressFixedPoint(0.0),
109  numpressErrorTolerance(BinaryDataEncoder_default_numpressErrorTolerance),
110  np_compression(NONE),
111  estimate_fixed_point(true),
112  linear_fp_mass_acc(-1)
113  {
114  }
115 
123  void setCompression(const std::string& compression)
124  {
125  const std::string* match = std::find(NamesOfNumpressCompression,
126  NamesOfNumpressCompression + SIZE_OF_NUMPRESSCOMPRESSION, compression);
127 
128  if (match == NamesOfNumpressCompression + SIZE_OF_NUMPRESSCOMPRESSION) // == end()
129  {
130  throw Exception::InvalidParameter(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION,
131  "Value '" + compression + "' is not a valid Numpress compression scheme.");
132  }
133 
134  np_compression = (NumpressCompression)std::distance(NamesOfNumpressCompression, match);
135  }
136 
137  };
138 
141 
143  virtual ~MSNumpressCoder() {}
144 
163  void encodeNP(const std::vector<double> & in,
164  String & result,
165  bool zlib_compression,
166  const NumpressConfig & config);
167 
169  void encodeNP(const std::vector<float> & in,
170  String & result,
171  bool zlib_compression,
172  const NumpressConfig & config);
173 
192  void decodeNP(const String & in,
193  std::vector<double> & out,
194  bool zlib_compression,
195  const NumpressConfig & config);
196 
215  void encodeNPRaw(const std::vector<double> & in,
216  String & result,
217  const NumpressConfig & config);
218 
239  void decodeNPRaw(const std::string & in,
240  std::vector<double> & out,
241  const NumpressConfig & config);
242 
243 private:
244 
245  void decodeNPInternal_(const unsigned char* in, size_t in_size, std::vector<double>& out, const NumpressConfig & config);
246  };
247 
248 } //namespace OpenMS
249 
250 
Exception indicating that an invalid parameter was handed over to an algorithm.
Definition: Exception.h:316
Class to encode and decode data encoded with MSNumpress.
Definition: MSNumpressCoder.h:43
void decodeNPInternal_(const unsigned char *in, size_t in_size, std::vector< double > &out, const NumpressConfig &config)
void encodeNP(const std::vector< float > &in, String &result, bool zlib_compression, const NumpressConfig &config)
encodeNP from a float (convert first to double)
virtual ~MSNumpressCoder()
Destructor.
Definition: MSNumpressCoder.h:143
void decodeNPRaw(const std::string &in, std::vector< double > &out, const NumpressConfig &config)
Decode the raw byte array "in" to the result vector "out".
MSNumpressCoder()
default constructor
Definition: MSNumpressCoder.h:140
NumpressCompression
Names of compression schemes.
Definition: MSNumpressCoder.h:48
@ PIC
Pic (MS:1002313, MS-Numpress positive integer compression)
Definition: MSNumpressCoder.h:51
@ SLOF
Slof (MS:1002314, MS-Numpress short logged float compression)
Definition: MSNumpressCoder.h:52
@ NONE
No compression is applied.
Definition: MSNumpressCoder.h:49
@ LINEAR
Linear (MS:1002312, MS-Numpress linear prediction compression)
Definition: MSNumpressCoder.h:50
void encodeNPRaw(const std::vector< double > &in, String &result, const NumpressConfig &config)
Encode the data vector "in" to a raw byte array.
void encodeNP(const std::vector< double > &in, String &result, bool zlib_compression, const NumpressConfig &config)
Encodes a vector of floating point numbers into a Base64 string using numpress.
void decodeNP(const String &in, std::vector< double > &out, bool zlib_compression, const NumpressConfig &config)
Decodes a Base64 string to a vector of floating point numbers using numpress.
A more convenient string class.
Definition: String.h:34
Main OpenMS namespace.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:19
const double BinaryDataEncoder_default_numpressErrorTolerance
Definition: MSNumpressCoder.h:20
Configuration class for MSNumpress.
Definition: MSNumpressCoder.h:63
double numpressErrorTolerance
Check error tolerance after encoding.
Definition: MSNumpressCoder.h:82
void setCompression(const std::string &compression)
Set compression using a string mapping to enum NumpressCompression.
Definition: MSNumpressCoder.h:123
double linear_fp_mass_acc
Desired mass accuracy for linear encoding.
Definition: MSNumpressCoder.h:105
NumpressCompression np_compression
Which compression schema to use.
Definition: MSNumpressCoder.h:88
NumpressConfig()
Definition: MSNumpressCoder.h:107
double numpressFixedPoint
fixed point for numpress algorithms
Definition: MSNumpressCoder.h:72
bool estimate_fixed_point
Whether to estimate the fixed point used for encoding (highly recommended)
Definition: MSNumpressCoder.h:97