SHOGUN v0.9.0
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00001 /* 00002 * This program is free software; you can redistribute it and/or modify 00003 * it under the terms of the GNU General Public License as published by 00004 * the Free Software Foundation; either version 3 of the License, or 00005 * (at your option) any later version. 00006 * 00007 * Written (W) 2010 Soeren Sonnenburg 00008 * Copyright (C) 2010 Berlin Institute of Technology 00009 */ 00010 #ifndef __HDF5_FILE_H__ 00011 #define __HDF5_FILE_H__ 00012 00013 #include <shogun/lib/config.h> 00014 00015 #ifdef HAVE_HDF5 00016 #include <shogun/lib/common.h> 00017 #include <shogun/lib/io.h> 00018 #include <shogun/lib/File.h> 00019 #include <shogun/base/SGObject.h> 00020 #include <hdf5.h> 00021 00022 00023 namespace shogun 00024 { 00025 template <class ST> struct TString; 00026 template <class ST> struct TSparse; 00027 00034 #define IGNORE_IN_CLASSLIST 00035 IGNORE_IN_CLASSLIST class CHDF5File : public CFile 00036 { 00037 public: 00039 CHDF5File(void); 00040 00047 CHDF5File(char* fname, char rw='r', const char* name=NULL); 00048 00050 virtual ~CHDF5File(); 00051 00059 virtual void get_bool_vector(bool*& vector, int32_t& len); 00060 virtual void get_byte_vector(uint8_t*& vector, int32_t& len); 00061 virtual void get_char_vector(char*& vector, int32_t& len); 00062 virtual void get_int_vector(int32_t*& vector, int32_t& len); 00063 virtual void get_real_vector(float64_t*& vector, int32_t& len); 00064 virtual void get_shortreal_vector(float32_t*& vector, int32_t& len); 00065 virtual void get_short_vector(int16_t*& vector, int32_t& len); 00066 virtual void get_word_vector(uint16_t*& vector, int32_t& len); 00068 00077 virtual void get_bool_matrix( 00078 bool*& matrix, int32_t& num_feat, int32_t& num_vec); 00079 virtual void get_byte_matrix( 00080 uint8_t*& matrix, int32_t& num_feat, int32_t& num_vec); 00081 virtual void get_char_matrix( 00082 char*& matrix, int32_t& num_feat, int32_t& num_vec); 00083 virtual void get_int_matrix( 00084 int32_t*& matrix, int32_t& num_feat, int32_t& num_vec); 00085 virtual void get_uint_matrix( 00086 uint32_t*& matrix, int32_t& num_feat, int32_t& num_vec); 00087 virtual void get_long_matrix( 00088 int64_t*& matrix, int32_t& num_feat, int32_t& num_vec); 00089 virtual void get_ulong_matrix( 00090 uint64_t*& matrix, int32_t& num_feat, int32_t& num_vec); 00091 virtual void get_shortreal_matrix( 00092 float32_t*& matrix, int32_t& num_feat, int32_t& num_vec); 00093 virtual void get_real_matrix( 00094 float64_t*& matrix, int32_t& num_feat, int32_t& num_vec); 00095 virtual void get_longreal_matrix( 00096 floatmax_t*& matrix, int32_t& num_feat, int32_t& num_vec); 00097 virtual void get_short_matrix( 00098 int16_t*& matrix, int32_t& num_feat, int32_t& num_vec); 00099 virtual void get_word_matrix( 00100 uint16_t*& matrix, int32_t& num_feat, int32_t& num_vec); 00102 00111 virtual void get_byte_ndarray( 00112 uint8_t*& array, int32_t*& dims, int32_t& num_dims); 00113 virtual void get_char_ndarray( 00114 char*& array, int32_t*& dims, int32_t& num_dims); 00115 virtual void get_int_ndarray( 00116 int32_t*& array, int32_t*& dims, int32_t& num_dims); 00117 virtual void get_shortreal_ndarray( 00118 float32_t*& array, int32_t*& dims, int32_t& num_dims); 00119 virtual void get_real_ndarray( 00120 float64_t*& array, int32_t*& dims, int32_t& num_dims); 00121 virtual void get_short_ndarray( 00122 int16_t*& array, int32_t*& dims, int32_t& num_dims); 00123 virtual void get_word_ndarray( 00124 uint16_t*& array, int32_t*& dims, int32_t& num_dims); 00126 00135 virtual void get_bool_sparsematrix( 00136 TSparse<bool>*& matrix, int32_t& num_feat, int32_t& num_vec); 00137 virtual void get_byte_sparsematrix( 00138 TSparse<uint8_t>*& matrix, int32_t& num_feat, int32_t& num_vec); 00139 virtual void get_char_sparsematrix( 00140 TSparse<char>*& matrix, int32_t& num_feat, int32_t& num_vec); 00141 virtual void get_int_sparsematrix( 00142 TSparse<int32_t>*& matrix, int32_t& num_feat, int32_t& num_vec); 00143 virtual void get_uint_sparsematrix( 00144 TSparse<uint32_t>*& matrix, int32_t& num_feat, int32_t& num_vec); 00145 virtual void get_long_sparsematrix( 00146 TSparse<int64_t>*& matrix, int32_t& num_feat, int32_t& num_vec); 00147 virtual void get_ulong_sparsematrix( 00148 TSparse<uint64_t>*& matrix, int32_t& num_feat, int32_t& num_vec); 00149 virtual void get_short_sparsematrix( 00150 TSparse<int16_t>*& matrix, int32_t& num_feat, int32_t& num_vec); 00151 virtual void get_word_sparsematrix( 00152 TSparse<uint16_t>*& matrix, int32_t& num_feat, int32_t& num_vec); 00153 virtual void get_shortreal_sparsematrix( 00154 TSparse<float32_t>*& matrix, int32_t& num_feat, int32_t& num_vec); 00155 virtual void get_real_sparsematrix( 00156 TSparse<float64_t>*& matrix, int32_t& num_feat, int32_t& num_vec); 00157 virtual void get_longreal_sparsematrix( 00158 TSparse<floatmax_t>*& matrix, int32_t& num_feat, int32_t& num_vec); 00160 00161 00170 virtual void get_bool_string_list( 00171 TString<bool>*& strings, int32_t& num_str, 00172 int32_t& max_string_len); 00173 virtual void get_byte_string_list( 00174 TString<uint8_t>*& strings, int32_t& num_str, 00175 int32_t& max_string_len); 00176 virtual void get_char_string_list( 00177 TString<char>*& strings, int32_t& num_str, 00178 int32_t& max_string_len); 00179 virtual void get_int_string_list( 00180 TString<int32_t>*& strings, int32_t& num_str, 00181 int32_t& max_string_len); 00182 virtual void get_uint_string_list( 00183 TString<uint32_t>*& strings, int32_t& num_str, 00184 int32_t& max_string_len); 00185 virtual void get_short_string_list( 00186 TString<int16_t>*& strings, int32_t& num_str, 00187 int32_t& max_string_len); 00188 virtual void get_word_string_list( 00189 TString<uint16_t>*& strings, int32_t& num_str, 00190 int32_t& max_string_len); 00191 virtual void get_long_string_list( 00192 TString<int64_t>*& strings, int32_t& num_str, 00193 int32_t& max_string_len); 00194 virtual void get_ulong_string_list( 00195 TString<uint64_t>*& strings, int32_t& num_str, 00196 int32_t& max_string_len); 00197 virtual void get_shortreal_string_list( 00198 TString<float32_t>*& strings, int32_t& num_str, 00199 int32_t& max_string_len); 00200 virtual void get_real_string_list( 00201 TString<float64_t>*& strings, int32_t& num_str, 00202 int32_t& max_string_len); 00203 virtual void get_longreal_string_list( 00204 TString<floatmax_t>*& strings, int32_t& num_str, 00205 int32_t& max_string_len); 00207 00215 virtual void set_bool_vector(const bool* vector, int32_t len); 00216 virtual void set_byte_vector(const uint8_t* vector, int32_t len); 00217 virtual void set_char_vector(const char* vector, int32_t len); 00218 virtual void set_int_vector(const int32_t* vector, int32_t len); 00219 virtual void set_shortreal_vector( const float32_t* vector, int32_t len); 00220 virtual void set_real_vector(const float64_t* vector, int32_t len); 00221 virtual void set_short_vector(const int16_t* vector, int32_t len); 00222 virtual void set_word_vector(const uint16_t* vector, int32_t len); 00224 00225 00233 virtual void set_bool_matrix( 00234 const bool* matrix, int32_t num_feat, int32_t num_vec); 00235 virtual void set_byte_matrix( 00236 const uint8_t* matrix, int32_t num_feat, int32_t num_vec); 00237 virtual void set_char_matrix( 00238 const char* matrix, int32_t num_feat, int32_t num_vec); 00239 virtual void set_int_matrix( 00240 const int32_t* matrix, int32_t num_feat, int32_t num_vec); 00241 virtual void set_uint_matrix( 00242 const uint32_t* matrix, int32_t num_feat, int32_t num_vec); 00243 virtual void set_long_matrix( 00244 const int64_t* matrix, int32_t num_feat, int32_t num_vec); 00245 virtual void set_ulong_matrix( 00246 const uint64_t* matrix, int32_t num_feat, int32_t num_vec); 00247 virtual void set_shortreal_matrix( 00248 const float32_t* matrix, int32_t num_feat, int32_t num_vec); 00249 virtual void set_real_matrix( 00250 const float64_t* matrix, int32_t num_feat, int32_t num_vec); 00251 virtual void set_longreal_matrix( 00252 const floatmax_t* matrix, int32_t num_feat, int32_t num_vec); 00253 virtual void set_short_matrix( 00254 const int16_t* matrix, int32_t num_feat, int32_t num_vec); 00255 virtual void set_word_matrix( 00256 const uint16_t* matrix, int32_t num_feat, int32_t num_vec); 00258 00266 virtual void set_bool_sparsematrix( 00267 const TSparse<bool>* matrix, int32_t num_feat, int32_t num_vec); 00268 virtual void set_byte_sparsematrix( 00269 const TSparse<uint8_t>* matrix, int32_t num_feat, int32_t num_vec); 00270 virtual void set_char_sparsematrix( 00271 const TSparse<char>* matrix, int32_t num_feat, int32_t num_vec); 00272 virtual void set_int_sparsematrix( 00273 const TSparse<int32_t>* matrix, int32_t num_feat, int32_t num_vec); 00274 virtual void set_uint_sparsematrix( 00275 const TSparse<uint32_t>* matrix, int32_t num_feat, int32_t num_vec); 00276 virtual void set_long_sparsematrix( 00277 const TSparse<int64_t>* matrix, int32_t num_feat, int32_t num_vec); 00278 virtual void set_ulong_sparsematrix( 00279 const TSparse<uint64_t>* matrix, int32_t num_feat, int32_t num_vec); 00280 virtual void set_short_sparsematrix( 00281 const TSparse<int16_t>* matrix, int32_t num_feat, int32_t num_vec); 00282 virtual void set_word_sparsematrix( 00283 const TSparse<uint16_t>* matrix, int32_t num_feat, int32_t num_vec); 00284 virtual void set_shortreal_sparsematrix( 00285 const TSparse<float32_t>* matrix, int32_t num_feat, int32_t num_vec); 00286 virtual void set_real_sparsematrix( 00287 const TSparse<float64_t>* matrix, int32_t num_feat, int32_t num_vec); 00288 virtual void set_longreal_sparsematrix( 00289 const TSparse<floatmax_t>* matrix, int32_t num_feat, int32_t num_vec); 00291 00292 00301 virtual void set_bool_string_list( 00302 const TString<bool>* strings, int32_t num_str); 00303 virtual void set_byte_string_list( 00304 const TString<uint8_t>* strings, int32_t num_str); 00305 virtual void set_char_string_list( 00306 const TString<char>* strings, int32_t num_str); 00307 virtual void set_int_string_list( 00308 const TString<int32_t>* strings, int32_t num_str); 00309 virtual void set_uint_string_list( 00310 const TString<uint32_t>* strings, int32_t num_str); 00311 virtual void set_short_string_list( 00312 const TString<int16_t>* strings, int32_t num_str); 00313 virtual void set_word_string_list( 00314 const TString<uint16_t>* strings, int32_t num_str); 00315 virtual void set_long_string_list( 00316 const TString<int64_t>* strings, int32_t num_str); 00317 virtual void set_ulong_string_list( 00318 const TString<uint64_t>* strings, int32_t num_str); 00319 virtual void set_shortreal_string_list( 00320 const TString<float32_t>* strings, int32_t num_str); 00321 virtual void set_real_string_list( 00322 const TString<float64_t>* strings, int32_t num_str); 00323 virtual void set_longreal_string_list( 00324 const TString<floatmax_t>* strings, int32_t num_str); 00326 00327 virtual void get_int8_matrix(int8_t*&, int32_t&, int32_t&) 00328 { 00329 SG_NOTIMPLEMENTED; 00330 } 00331 virtual void get_int8_sparsematrix(shogun::TSparse<signed char>*&, int32_t&, int32_t&) 00332 { 00333 SG_NOTIMPLEMENTED; 00334 } 00335 virtual void get_int8_string_list(shogun::TString<signed char>*&, int32_t&, int32_t&) 00336 { 00337 SG_NOTIMPLEMENTED; 00338 } 00339 virtual void set_int8_matrix(const int8_t*, int32_t, int32_t) 00340 { 00341 SG_NOTIMPLEMENTED; 00342 } 00343 virtual void set_int8_sparsematrix(const shogun::TSparse<signed char>*, int32_t, int32_t) 00344 { 00345 SG_NOTIMPLEMENTED; 00346 } 00347 virtual void set_int8_string_list(const shogun::TString<signed char>*, int32_t) 00348 { 00349 SG_NOTIMPLEMENTED; 00350 } 00351 00352 00354 inline virtual const char* get_name() const { return "HDF5File"; } 00355 00356 protected: 00358 void get_boolean_type(); 00359 00368 hid_t get_compatible_type(H5T_class_t t_class, 00369 const TSGDataType* datatype); 00370 00378 void get_dims(hid_t dataset, int32_t*& dims, int32_t& ndims, int64_t& total_elements); 00379 00381 void create_group_hierarchy(); 00382 00383 protected: 00385 hid_t h5file; 00387 hid_t boolean_type; 00388 }; 00389 } 00390 #endif // HAVE_HDF5 00391 #endif //__HDF5_FILE_H__ 00392