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MSNumpressCoder.h
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31 // $Maintainer: Hannes Roest $
32 // $Authors: Hannes Roest $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/CONCEPT/Exception.h>
38 #include <OpenMS/DATASTRUCTURES/String.h>
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
67 class OPENMS_DLLAPI MSNumpressCoder
68 {
69
70 public:
71
73 enum NumpressCompression {
74 NONE,
75 LINEAR,
76 PIC,
77 SLOF,
78 SIZE_OF_NUMPRESSCOMPRESSION
79 };
80 static const std::string NamesOfNumpressCompression[SIZE_OF_NUMPRESSCOMPRESSION];
81
87 struct OPENMS_DLLAPI NumpressConfig
88 {
97 double numpressFixedPoint;
107 double numpressErrorTolerance;
113 NumpressCompression np_compression;
122 bool estimate_fixed_point;
130 double linear_fp_mass_acc;
131
132 NumpressConfig () :
133 numpressFixedPoint(0.0),
134 numpressErrorTolerance(BinaryDataEncoder_default_numpressErrorTolerance),
135 np_compression(NONE),
136 estimate_fixed_point(true),
137 linear_fp_mass_acc(-1)
138 {
139 }
140
148 void setCompression(const std::string& compression)
149 {
150 const std::string* match = std::find(NamesOfNumpressCompression,
151 NamesOfNumpressCompression + SIZE_OF_NUMPRESSCOMPRESSION, compression);
152
153 if (match == NamesOfNumpressCompression + SIZE_OF_NUMPRESSCOMPRESSION) // == end()
154 {
155 throw Exception::InvalidParameter(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION,
156 "Value '" + compression + "' is not a valid Numpress compression scheme.");
157 }
158
159 np_compression = (NumpressCompression)std::distance(NamesOfNumpressCompression, match);
160 }
161
162 };
163
165 MSNumpressCoder() {}
166
168 virtual ~MSNumpressCoder() {}
169
188 void encodeNP(const std::vector<double> & in,
189 String & result,
190 bool zlib_compression,
191 const NumpressConfig & config);
192
194 void encodeNP(const std::vector<float> & in,
195 String & result,
196 bool zlib_compression,
197 const NumpressConfig & config);
198
217 void decodeNP(const String & in,
218 std::vector<double> & out,
219 bool zlib_compression,
220 const NumpressConfig & config);
221
240 void encodeNPRaw(const std::vector<double> & in,
241 String & result,
242 const NumpressConfig & config);
243
264 void decodeNPRaw(const std::string & in,
265 std::vector<double> & out,
266 const NumpressConfig & config);
267
268 private:
269
270 void decodeNPInternal_(const unsigned char* in, size_t in_size, std::vector<double>& out, const NumpressConfig & config);
271 };
272
273 } //namespace OpenMS
274
275
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::MSNumpressCoder::NumpressConfig::linear_fp_mass_acc
double linear_fp_mass_acc
Desired mass accuracy for *linear* encoding.
Definition: MSNumpressCoder.h:130
OpenMS::MSNumpressCoder::MSNumpressCoder
MSNumpressCoder()
default constructor
Definition: MSNumpressCoder.h:165
OpenMS::MSNumpressCoder::LINEAR
Linear (MS:1002312, MS-Numpress linear prediction compression)
Definition: MSNumpressCoder.h:75
OpenMS::MSNumpressCoder::NumpressConfig::estimate_fixed_point
bool estimate_fixed_point
Whether to estimate the fixed point used for encoding (highly recommended)
Definition: MSNumpressCoder.h:122
Exception.h
OpenMS::MSNumpressCoder::NONE
No compression is applied.
Definition: MSNumpressCoder.h:74
OpenMS::MSNumpressCoder::NumpressConfig::numpressErrorTolerance
double numpressErrorTolerance
Check error tolerance after encoding.
Definition: MSNumpressCoder.h:107
OpenMS::MSNumpressCoder::NumpressConfig::NumpressConfig
NumpressConfig()
Definition: MSNumpressCoder.h:132
OpenMS::MSNumpressCoder::NumpressConfig::setCompression
void setCompression(const std::string &compression)
Set compression using a string mapping to enum NumpressCompression.
Definition: MSNumpressCoder.h:148
OpenMS::BinaryDataEncoder_default_numpressErrorTolerance
const double BinaryDataEncoder_default_numpressErrorTolerance
Definition: MSNumpressCoder.h:45
OpenMS::MSNumpressCoder::~MSNumpressCoder
virtual ~MSNumpressCoder()
Destructor.
Definition: MSNumpressCoder.h:168
String.h
OpenMS::Exception::InvalidParameter
Exception indicating that an invalid parameter was handed over to an algorithm.
Definition: Exception.h:347
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::MSNumpressCoder
Class to encode and decode data encoded with MSNumpress.
Definition: MSNumpressCoder.h:67
OpenMS::MSNumpressCoder::NumpressCompression
NumpressCompression
Names of compression schemes.
Definition: MSNumpressCoder.h:73
OpenMS::MSNumpressCoder::NumpressConfig::np_compression
NumpressCompression np_compression
Which compression schema to use.
Definition: MSNumpressCoder.h:113
OpenMS::MSNumpressCoder::SLOF
Slof (MS:1002314, MS-Numpress short logged float compression)
Definition: MSNumpressCoder.h:77
seqan::find
bool find(TFinder &finder, const Pattern< TNeedle, FuzzyAC > &me, PatternAuxData< TNeedle > &dh)
Definition: AhoCorasickAmbiguous.h:884
OpenMS::MSNumpressCoder::NumpressConfig
Configuration class for MSNumpress.
Definition: MSNumpressCoder.h:87
OpenMS::MSNumpressCoder::PIC
Pic (MS:1002313, MS-Numpress positive integer compression)
Definition: MSNumpressCoder.h:76
OpenMS::MSNumpressCoder::NumpressConfig::numpressFixedPoint
double numpressFixedPoint
fixed point for numpress algorithms
Definition: MSNumpressCoder.h:97