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MSNumpressCoder.h
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34 
35 #ifndef OPENMS_FORMAT_MSNUMPRESSCODER_H
36 #define OPENMS_FORMAT_MSNUMPRESSCODER_H
37 
38 #include <OpenMS/FORMAT/Base64.h>
39 
40 namespace OpenMS
41 {
42  const double BinaryDataEncoder_default_numpressErrorTolerance = .0001; // 1/100th of one percent
43 
53  class OPENMS_DLLAPI MSNumpressCoder
54  {
55 
56 public:
57 
58  enum NumpressCompression { NONE, LINEAR, PIC, SLOF };
59 
65  struct OPENMS_DLLAPI NumpressConfig
66  {
71 
73  numpressFixedPoint(0.0),
75  np_compression(NONE),
76  estimate_fixed_point(false)
77  {
78  }
79 
80  };
81 
84 
86  virtual ~MSNumpressCoder() {}
87 
106  void encodeNP(const std::vector<double> & in, String & result,
107  bool zlib_compression, const NumpressConfig & config)
108  {
109  result.clear();
110  encodeNP_(in, result, config);
111  if (result.empty())
112  {
113  return;
114  }
115 
116  // Encode in base64 and compress
117  std::vector<String> tmp;
118  tmp.push_back(result);
119  base64coder_.encodeStrings(tmp, result, zlib_compression, false);
120  }
121 
123  void encodeNP(const std::vector<float> & in, String & result,
124  bool zlib_compression, const NumpressConfig & config)
125  {
126  std::vector<double> dvector(in.begin(), in.end());
127  encodeNP(dvector, result, zlib_compression, config);
128  }
129 
148  void decodeNP(const String & in, std::vector<double> & out,
149  bool zlib_compression, const NumpressConfig & config)
150  {
151  QByteArray base64_uncompressed;
152  base64coder_.decodeSingleString(in, base64_uncompressed, zlib_compression);
153 
154  // Create a temporary string (*not* null-terminated) to hold the data
155  std::string tmpstring(base64_uncompressed.constData(), base64_uncompressed.size());
156  decodeNP_(tmpstring, out, config);
157 
158  // NOTE: it is possible (and likely faster) to call directly the const
159  // unsigned char * function but this would make it necessary to deal with
160  // reinterpret_cast ugliness here ...
161  //
162  // decodeNP_internal_(reinterpret_cast<const unsigned char*>(base64_uncompressed.constData()), base64_uncompressed.size(), out, config);
163  }
164 
165 private:
166 
173  void encodeNP_(const std::vector<double> & in, String & result, const NumpressConfig & config);
174 
184  void decodeNP_(const std::string & in, std::vector<double> & out, const NumpressConfig & config);
185 
186  void decodeNPInternal_(const unsigned char* in, size_t in_size, std::vector<double>& out, const NumpressConfig & config);
187 
189  };
190 
191 } //namespace OpenMS
192 
193 #endif /* OPENMS_FORMAT_MSNUMPRESSCODER_H */
Class to encode and decode data encoded with MSNumpress.
Definition: MSNumpressCoder.h:53
NumpressCompression np_compression
check error tolerance after encoding, guarantee abs(1.0-(encoded/decoded)) &lt;= this, 0=do not guarantee anything
Definition: MSNumpressCoder.h:69
MSNumpressCoder()
default constructor
Definition: MSNumpressCoder.h:83
A more convenient string class.
Definition: String.h:57
Class to encode and decode Base64.
Definition: Base64.h:64
const double BinaryDataEncoder_default_numpressErrorTolerance
Definition: MSNumpressCoder.h:42
Configuration class for MSNumpress.
Definition: MSNumpressCoder.h:65
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.
Definition: MSNumpressCoder.h:148
NumpressCompression
Definition: MSNumpressCoder.h:58
void encodeNP(const std::vector< float > &in, String &result, bool zlib_compression, const NumpressConfig &config)
encodeNP from a float (convert first to double)
Definition: MSNumpressCoder.h:123
NumpressConfig()
whether to estimate the fixed point or use the one proved with numpressFixedPoint ...
Definition: MSNumpressCoder.h:72
double numpressFixedPoint
Definition: MSNumpressCoder.h:67
Base64 base64coder_
Definition: MSNumpressCoder.h:188
bool estimate_fixed_point
which compression schema to use
Definition: MSNumpressCoder.h:70
virtual ~MSNumpressCoder()
Destructor.
Definition: MSNumpressCoder.h:86
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.
Definition: MSNumpressCoder.h:106
double numpressErrorTolerance
fixed point for numpress algorithms
Definition: MSNumpressCoder.h:68

OpenMS / TOPP release 2.0.0 Documentation generated on Wed Mar 30 2016 16:18:40 using doxygen 1.8.5