OpenMS  2.4.0
MSNumpressCoder.h
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31 // $Maintainer: Hannes Roest $
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34 
35 #pragma once
36 
39 
40 #include <string>
41 #include <vector>
42 
43 namespace OpenMS
44 {
45  const double BinaryDataEncoder_default_numpressErrorTolerance = .0001; // 1/100th of one percent
46 
56  class OPENMS_DLLAPI MSNumpressCoder
57  {
58 
59 public:
60 
61  enum NumpressCompression { NONE, LINEAR, PIC, SLOF, SIZE_OF_NUMPRESSCOMPRESSION };
63  static const std::string NamesOfNumpressCompression[SIZE_OF_NUMPRESSCOMPRESSION];
64 
70  struct OPENMS_DLLAPI NumpressConfig
71  {
77 
79  numpressFixedPoint(0.0),
81  np_compression(NONE),
82  estimate_fixed_point(false),
83  linear_fp_mass_acc(-1)
84  {
85  }
86 
94  void setCompression(const std::string& compression)
95  {
96  const std::string* match = std::find(NamesOfNumpressCompression, NamesOfNumpressCompression + SIZE_OF_NUMPRESSCOMPRESSION, compression);
97 
98  if (match == NamesOfNumpressCompression + SIZE_OF_NUMPRESSCOMPRESSION) // == end()
99  {
100  throw Exception::InvalidParameter(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "Value '" + compression + "' is not a valid Numpress compression scheme.");
101  }
102 
103  np_compression = (NumpressCompression)std::distance(NamesOfNumpressCompression, match);
104  }
105 
106  };
107 
110 
112  virtual ~MSNumpressCoder() {}
113 
132  void encodeNP(const std::vector<double> & in, String & result,
133  bool zlib_compression, const NumpressConfig & config);
134 
136  void encodeNP(const std::vector<float> & in, String & result,
137  bool zlib_compression, const NumpressConfig & config);
138 
157  void decodeNP(const String & in, std::vector<double> & out,
158  bool zlib_compression, const NumpressConfig & config);
159 
177  void encodeNPRaw(const std::vector<double> & in, String & result, const NumpressConfig & config);
178 
199  void decodeNPRaw(const std::string & in, std::vector<double> & out, const NumpressConfig & config);
200 
201 private:
202 
203  void decodeNPInternal_(const unsigned char* in, size_t in_size, std::vector<double>& out, const NumpressConfig & config);
204  };
205 
206 } //namespace OpenMS
207 
208 
Class to encode and decode data encoded with MSNumpress.
Definition: MSNumpressCoder.h:56
NumpressCompression np_compression
check error tolerance after encoding, guarantee abs(1.0-(encoded/decoded)) <= this, 0=do not guarantee anything
Definition: MSNumpressCoder.h:74
MSNumpressCoder()
default constructor
Definition: MSNumpressCoder.h:109
A more convenient string class.
Definition: String.h:57
const double BinaryDataEncoder_default_numpressErrorTolerance
Definition: MSNumpressCoder.h:45
void setCompression(const std::string &compression)
set compression using a string mapping to enum NumpressCompression.
Definition: MSNumpressCoder.h:94
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
Configuration class for MSNumpress.
Definition: MSNumpressCoder.h:70
bool find(TFinder &finder, const Pattern< TNeedle, FuzzyAC > &me, PatternAuxData< TNeedle > &dh)
Definition: AhoCorasickAmbiguous.h:884
NumpressCompression
Definition: MSNumpressCoder.h:61
double linear_fp_mass_acc
whether to estimate the fixed point or use the one proved with numpressFixedPoint ...
Definition: MSNumpressCoder.h:76
NumpressConfig()
desired mass accuracy for linear encoding (-1 no effect, use 0.0001 for 0.2 ppm accuracy @ 500 m/z) ...
Definition: MSNumpressCoder.h:78
double numpressFixedPoint
Definition: MSNumpressCoder.h:72
Exception indicating that an invalid parameter was handed over to an algorithm.
Definition: Exception.h:347
bool estimate_fixed_point
which compression schema to use
Definition: MSNumpressCoder.h:75
virtual ~MSNumpressCoder()
Destructor.
Definition: MSNumpressCoder.h:112
double numpressErrorTolerance
fixed point for numpress algorithms
Definition: MSNumpressCoder.h:73
Definition: MSNumpressCoder.h:61