OpenMS  3.0.0
MSNumpressCoder.h
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34 
35 #pragma once
36 
39 
40 #include <algorithm>
41 #include <string>
42 #include <vector>
43 
44 namespace OpenMS
45 {
46  const double BinaryDataEncoder_default_numpressErrorTolerance = .0001; // 1/100th of one percent
47 
68  class OPENMS_DLLAPI MSNumpressCoder
69  {
70 
71 public:
72 
75  NONE,
77  PIC,
78  SLOF,
79  SIZE_OF_NUMPRESSCOMPRESSION
80  };
81  static const std::string NamesOfNumpressCompression[SIZE_OF_NUMPRESSCOMPRESSION];
82 
88  struct OPENMS_DLLAPI NumpressConfig
89  {
132 
134  numpressFixedPoint(0.0),
135  numpressErrorTolerance(BinaryDataEncoder_default_numpressErrorTolerance),
136  np_compression(NONE),
137  estimate_fixed_point(true),
138  linear_fp_mass_acc(-1)
139  {
140  }
141 
149  void setCompression(const std::string& compression)
150  {
151  const std::string* match = std::find(NamesOfNumpressCompression,
152  NamesOfNumpressCompression + SIZE_OF_NUMPRESSCOMPRESSION, compression);
153 
154  if (match == NamesOfNumpressCompression + SIZE_OF_NUMPRESSCOMPRESSION) // == end()
155  {
156  throw Exception::InvalidParameter(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION,
157  "Value '" + compression + "' is not a valid Numpress compression scheme.");
158  }
159 
160  np_compression = (NumpressCompression)std::distance(NamesOfNumpressCompression, match);
161  }
162 
163  };
164 
167 
169  virtual ~MSNumpressCoder() {}
170 
189  void encodeNP(const std::vector<double> & in,
190  String & result,
191  bool zlib_compression,
192  const NumpressConfig & config);
193 
195  void encodeNP(const std::vector<float> & in,
196  String & result,
197  bool zlib_compression,
198  const NumpressConfig & config);
199 
218  void decodeNP(const String & in,
219  std::vector<double> & out,
220  bool zlib_compression,
221  const NumpressConfig & config);
222 
241  void encodeNPRaw(const std::vector<double> & in,
242  String & result,
243  const NumpressConfig & config);
244 
265  void decodeNPRaw(const std::string & in,
266  std::vector<double> & out,
267  const NumpressConfig & config);
268 
269 private:
270 
271  void decodeNPInternal_(const unsigned char* in, size_t in_size, std::vector<double>& out, const NumpressConfig & config);
272  };
273 
274 } //namespace OpenMS
275 
276 
OpenMS::MSNumpressCoder::NumpressConfig::numpressFixedPoint
double numpressFixedPoint
fixed point for numpress algorithms
Definition: MSNumpressCoder.h:98
OpenMS::MSNumpressCoder::NumpressConfig::linear_fp_mass_acc
double linear_fp_mass_acc
Desired mass accuracy for *linear* encoding.
Definition: MSNumpressCoder.h:131
OpenMS::MSNumpressCoder::NumpressConfig::setCompression
void setCompression(const std::string &compression)
Set compression using a string mapping to enum NumpressCompression.
Definition: MSNumpressCoder.h:149
OpenMS::MSNumpressCoder
Class to encode and decode data encoded with MSNumpress.
Definition: MSNumpressCoder.h:68
OpenMS::DriftTimeUnit::NONE
No unit.
OpenMS::MSNumpressCoder::NumpressConfig::estimate_fixed_point
bool estimate_fixed_point
Whether to estimate the fixed point used for encoding (highly recommended)
Definition: MSNumpressCoder.h:123
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::MSNumpressCoder::NONE
No compression is applied.
Definition: MSNumpressCoder.h:75
OpenMS::MSNumpressCoder::NumpressConfig::numpressErrorTolerance
double numpressErrorTolerance
Check error tolerance after encoding.
Definition: MSNumpressCoder.h:108
OpenMS::Exception::InvalidParameter
Exception indicating that an invalid parameter was handed over to an algorithm.
Definition: Exception.h:339
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
Exception.h
OpenMS::MSNumpressCoder::MSNumpressCoder
MSNumpressCoder()
default constructor
Definition: MSNumpressCoder.h:166
OpenMS::MSNumpressCoder::~MSNumpressCoder
virtual ~MSNumpressCoder()
Destructor.
Definition: MSNumpressCoder.h:169
OpenMS::MSNumpressCoder::NumpressConfig::NumpressConfig
NumpressConfig()
Definition: MSNumpressCoder.h:133
OpenMS::MSNumpressCoder::SLOF
Slof (MS:1002314, MS-Numpress short logged float compression)
Definition: MSNumpressCoder.h:78
OpenMS::MSNumpressCoder::NumpressConfig
Configuration class for MSNumpress.
Definition: MSNumpressCoder.h:88
String.h
OpenMS::MSNumpressCoder::NumpressConfig::np_compression
NumpressCompression np_compression
Which compression schema to use.
Definition: MSNumpressCoder.h:114
OpenMS::MSNumpressCoder::NumpressCompression
NumpressCompression
Names of compression schemes.
Definition: MSNumpressCoder.h:74
OpenMS::MSNumpressCoder::LINEAR
Linear (MS:1002312, MS-Numpress linear prediction compression)
Definition: MSNumpressCoder.h:76
OpenMS::BinaryDataEncoder_default_numpressErrorTolerance
const double BinaryDataEncoder_default_numpressErrorTolerance
Definition: MSNumpressCoder.h:46
OpenMS::MSNumpressCoder::PIC
Pic (MS:1002313, MS-Numpress positive integer compression)
Definition: MSNumpressCoder.h:77