/usr/include/shogun/io/HDF5File.h is in libshogun-dev 3.2.0-7.3build4.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 | /*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 3 of the License, or
* (at your option) any later version.
*
* Written (W) 2010 Soeren Sonnenburg
* Copyright (C) 2010 Berlin Institute of Technology
*/
#ifndef __HDF5_FILE_H__
#define __HDF5_FILE_H__
#include <shogun/lib/config.h>
#ifdef HAVE_HDF5
#include <shogun/lib/common.h>
#include <shogun/io/SGIO.h>
#include <shogun/io/File.h>
#include <shogun/base/SGObject.h>
#include <hdf5.h>
namespace shogun
{
template <class ST> class SGString;
template <class ST> class SGSparseVector;
/** @brief A HDF5 File access class.
*
* This class allows reading and writing of vectors and matrices
* in the hierarchical file format version 5.
*
*/
#define IGNORE_IN_CLASSLIST
IGNORE_IN_CLASSLIST class CHDF5File : public CFile
{
public:
/** default constructor */
CHDF5File();
/** constructor
*
* @param fname filename to open
* @param rw mode, 'r' or 'w'
* @param name variable name (e.g. "x" or "/path/to/x")
*/
CHDF5File(char* fname, char rw='r', const char* name=NULL);
/** default destructor */
virtual ~CHDF5File();
/** @name Vector Access Functions
*
* Functions to access vectors of one of the several base data types.
* These functions are used when loading vectors from e.g. file
* and return the vector and its length len by reference
*/
//@{
virtual void get_vector(bool*& vector, int32_t& len);
virtual void get_vector(int8_t*& vector, int32_t& len);
virtual void get_vector(uint8_t*& vector, int32_t& len);
virtual void get_vector(char*& vector, int32_t& len);
virtual void get_vector(int32_t*& vector, int32_t& len);
virtual void get_vector(uint32_t*& vector, int32_t& len);
virtual void get_vector(float64_t*& vector, int32_t& len);
virtual void get_vector(float32_t*& vector, int32_t& len);
virtual void get_vector(floatmax_t*& vector, int32_t& len);
virtual void get_vector(int16_t*& vector, int32_t& len);
virtual void get_vector(uint16_t*& vector, int32_t& len);
virtual void get_vector(int64_t*& vector, int32_t& len);
virtual void get_vector(uint64_t*& vector, int32_t& len);
//@}
/** @name Matrix Access Functions
*
* Functions to access matrices of one of the several base data types.
* These functions are used when loading matrices from e.g. file
* and return the matrices and its dimensions num_feat and num_vec
* by reference
*/
//@{
virtual void get_matrix(
bool*& matrix, int32_t& num_feat, int32_t& num_vec);
virtual void get_matrix(
uint8_t*& matrix, int32_t& num_feat, int32_t& num_vec);
virtual void get_matrix(
char*& matrix, int32_t& num_feat, int32_t& num_vec);
virtual void get_matrix(
int32_t*& matrix, int32_t& num_feat, int32_t& num_vec);
virtual void get_matrix(
uint32_t*& matrix, int32_t& num_feat, int32_t& num_vec);
virtual void get_matrix(
int64_t*& matrix, int32_t& num_feat, int32_t& num_vec);
virtual void get_matrix(
uint64_t*& matrix, int32_t& num_feat, int32_t& num_vec);
virtual void get_matrix(
float32_t*& matrix, int32_t& num_feat, int32_t& num_vec);
virtual void get_matrix(
float64_t*& matrix, int32_t& num_feat, int32_t& num_vec);
virtual void get_matrix(
floatmax_t*& matrix, int32_t& num_feat, int32_t& num_vec);
virtual void get_matrix(
int16_t*& matrix, int32_t& num_feat, int32_t& num_vec);
virtual void get_matrix(
uint16_t*& matrix, int32_t& num_feat, int32_t& num_vec);
//@}
/** @name N-Dimensional Array Access Functions
*
* Functions to access n-dimensional arrays of one of the several base
* data types. These functions are used when loading n-dimensional arrays
* from e.g. file and return the them and its dimensions dims and num_dims
* by reference
*/
//@{
virtual void get_ndarray(
uint8_t*& array, int32_t*& dims, int32_t& num_dims);
virtual void get_ndarray(
char*& array, int32_t*& dims, int32_t& num_dims);
virtual void get_ndarray(
int32_t*& array, int32_t*& dims, int32_t& num_dims);
virtual void get_ndarray(
float32_t*& array, int32_t*& dims, int32_t& num_dims);
virtual void get_ndarray(
float64_t*& array, int32_t*& dims, int32_t& num_dims);
virtual void get_ndarray(
int16_t*& array, int32_t*& dims, int32_t& num_dims);
virtual void get_ndarray(
uint16_t*& array, int32_t*& dims, int32_t& num_dims);
//@}
/** @name Sparse Matrix Access Functions
*
* Functions to access sparse matrices of one of the several base data types.
* These functions are used when loading sparse matrices from e.g. file
* and return the sparse matrices and its dimensions num_feat and num_vec
* by reference
*/
//@{
virtual void get_sparse_matrix(
SGSparseVector<bool>*& matrix, int32_t& num_feat, int32_t& num_vec);
virtual void get_sparse_matrix(
SGSparseVector<int8_t>*& matrix, int32_t& num_feat, int32_t& num_vec);
virtual void get_sparse_matrix(
SGSparseVector<uint8_t>*& matrix, int32_t& num_feat, int32_t& num_vec);
virtual void get_sparse_matrix(
SGSparseVector<char>*& matrix, int32_t& num_feat, int32_t& num_vec);
virtual void get_sparse_matrix(
SGSparseVector<int32_t>*& matrix, int32_t& num_feat, int32_t& num_vec);
virtual void get_sparse_matrix(
SGSparseVector<uint32_t>*& matrix, int32_t& num_feat, int32_t& num_vec);
virtual void get_sparse_matrix(
SGSparseVector<int64_t>*& matrix, int32_t& num_feat, int32_t& num_vec);
virtual void get_sparse_matrix(
SGSparseVector<uint64_t>*& matrix, int32_t& num_feat, int32_t& num_vec);
virtual void get_sparse_matrix(
SGSparseVector<int16_t>*& matrix, int32_t& num_feat, int32_t& num_vec);
virtual void get_sparse_matrix(
SGSparseVector<uint16_t>*& matrix, int32_t& num_feat, int32_t& num_vec);
virtual void get_sparse_matrix(
SGSparseVector<float32_t>*& matrix, int32_t& num_feat, int32_t& num_vec);
virtual void get_sparse_matrix(
SGSparseVector<float64_t>*& matrix, int32_t& num_feat, int32_t& num_vec);
virtual void get_sparse_matrix(
SGSparseVector<floatmax_t>*& matrix, int32_t& num_feat, int32_t& num_vec);
//@}
/** @name String Access Functions
*
* Functions to access strings of one of the several base data types.
* These functions are used when loading variable length datatypes
* from e.g. file and return the strings and their number
* by reference
*/
//@{
virtual void get_string_list(
SGString<bool>*& strings, int32_t& num_str,
int32_t& max_string_len);
virtual void get_string_list(
SGString<int8_t>*& strings, int32_t& num_str,
int32_t& max_string_len);
virtual void get_string_list(
SGString<uint8_t>*& strings, int32_t& num_str,
int32_t& max_string_len);
virtual void get_string_list(
SGString<char>*& strings, int32_t& num_str,
int32_t& max_string_len);
virtual void get_string_list(
SGString<int32_t>*& strings, int32_t& num_str,
int32_t& max_string_len);
virtual void get_string_list(
SGString<uint32_t>*& strings, int32_t& num_str,
int32_t& max_string_len);
virtual void get_string_list(
SGString<int16_t>*& strings, int32_t& num_str,
int32_t& max_string_len);
virtual void get_string_list(
SGString<uint16_t>*& strings, int32_t& num_str,
int32_t& max_string_len);
virtual void get_string_list(
SGString<int64_t>*& strings, int32_t& num_str,
int32_t& max_string_len);
virtual void get_string_list(
SGString<uint64_t>*& strings, int32_t& num_str,
int32_t& max_string_len);
virtual void get_string_list(
SGString<float32_t>*& strings, int32_t& num_str,
int32_t& max_string_len);
virtual void get_string_list(
SGString<float64_t>*& strings, int32_t& num_str,
int32_t& max_string_len);
virtual void get_string_list(
SGString<floatmax_t>*& strings, int32_t& num_str,
int32_t& max_string_len);
//@}
/** @name Vector Access Functions
*
* Functions to access vectors of one of the several base data types.
* These functions are used when writing vectors of length len
* to e.g. a file
*/
//@{
virtual void set_vector(const bool* vector, int32_t len);
virtual void set_vector(const int8_t* vector, int32_t len);
virtual void set_vector(const uint8_t* vector, int32_t len);
virtual void set_vector(const char* vector, int32_t len);
virtual void set_vector(const int32_t* vector, int32_t len);
virtual void set_vector(const uint32_t* vector, int32_t len);
virtual void set_vector(const float32_t* vector, int32_t len);
virtual void set_vector(const float64_t* vector, int32_t len);
virtual void set_vector(const floatmax_t* vector, int32_t len);
virtual void set_vector(const int16_t* vector, int32_t len);
virtual void set_vector(const uint16_t* vector, int32_t len);
virtual void set_vector(const int64_t* vector, int32_t len);
virtual void set_vector(const uint64_t* vector, int32_t len);
//@}
/** @name Matrix Access Functions
*
* Functions to access matrices of one of the several base data types.
* These functions are used when writing matrices of num_feat rows and
* num_vec columns to e.g. a file
*/
//@{
virtual void set_matrix(
const bool* matrix, int32_t num_feat, int32_t num_vec);
virtual void set_matrix(
const int8_t* matrix, int32_t num_feat, int32_t num_vec);
virtual void set_matrix(
const uint8_t* matrix, int32_t num_feat, int32_t num_vec);
virtual void set_matrix(
const char* matrix, int32_t num_feat, int32_t num_vec);
virtual void set_matrix(
const int32_t* matrix, int32_t num_feat, int32_t num_vec);
virtual void set_matrix(
const uint32_t* matrix, int32_t num_feat, int32_t num_vec);
virtual void set_matrix(
const int64_t* matrix, int32_t num_feat, int32_t num_vec);
virtual void set_matrix(
const uint64_t* matrix, int32_t num_feat, int32_t num_vec);
virtual void set_matrix(
const float32_t* matrix, int32_t num_feat, int32_t num_vec);
virtual void set_matrix(
const float64_t* matrix, int32_t num_feat, int32_t num_vec);
virtual void set_matrix(
const floatmax_t* matrix, int32_t num_feat, int32_t num_vec);
virtual void set_matrix(
const int16_t* matrix, int32_t num_feat, int32_t num_vec);
virtual void set_matrix(
const uint16_t* matrix, int32_t num_feat, int32_t num_vec);
//@}
/** @name Sparse Matrix Access Functions
*
* Functions to access sparse matrices of one of the several base data types.
* These functions are used when writing sparse matrices of num_feat rows and
* num_vec columns to e.g. a file
*/
//@{
virtual void set_sparse_matrix(
const SGSparseVector<bool>* matrix, int32_t num_feat, int32_t num_vec);
virtual void set_sparse_matrix(
const SGSparseVector<int8_t>* matrix, int32_t num_feat, int32_t num_vec);
virtual void set_sparse_matrix(
const SGSparseVector<uint8_t>* matrix, int32_t num_feat, int32_t num_vec);
virtual void set_sparse_matrix(
const SGSparseVector<char>* matrix, int32_t num_feat, int32_t num_vec);
virtual void set_sparse_matrix(
const SGSparseVector<int32_t>* matrix, int32_t num_feat, int32_t num_vec);
virtual void set_sparse_matrix(
const SGSparseVector<uint32_t>* matrix, int32_t num_feat, int32_t num_vec);
virtual void set_sparse_matrix(
const SGSparseVector<int64_t>* matrix, int32_t num_feat, int32_t num_vec);
virtual void set_sparse_matrix(
const SGSparseVector<uint64_t>* matrix, int32_t num_feat, int32_t num_vec);
virtual void set_sparse_matrix(
const SGSparseVector<int16_t>* matrix, int32_t num_feat, int32_t num_vec);
virtual void set_sparse_matrix(
const SGSparseVector<uint16_t>* matrix, int32_t num_feat, int32_t num_vec);
virtual void set_sparse_matrix(
const SGSparseVector<float32_t>* matrix, int32_t num_feat, int32_t num_vec);
virtual void set_sparse_matrix(
const SGSparseVector<float64_t>* matrix, int32_t num_feat, int32_t num_vec);
virtual void set_sparse_matrix(
const SGSparseVector<floatmax_t>* matrix, int32_t num_feat, int32_t num_vec);
//@}
/** @name String Access Functions
*
* Functions to access strings of one of the several base data types.
* These functions are used when writing variable length datatypes
* like strings to a file. Here num_str denotes the number of strings
* and strings is a pointer to a string structure.
*/
//@{
virtual void set_string_list(
const SGString<bool>* strings, int32_t num_str);
virtual void set_string_list(
const SGString<int8_t>* strings, int32_t num_str);
virtual void set_string_list(
const SGString<uint8_t>* strings, int32_t num_str);
virtual void set_string_list(
const SGString<char>* strings, int32_t num_str);
virtual void set_string_list(
const SGString<int32_t>* strings, int32_t num_str);
virtual void set_string_list(
const SGString<uint32_t>* strings, int32_t num_str);
virtual void set_string_list(
const SGString<int16_t>* strings, int32_t num_str);
virtual void set_string_list(
const SGString<uint16_t>* strings, int32_t num_str);
virtual void set_string_list(
const SGString<int64_t>* strings, int32_t num_str);
virtual void set_string_list(
const SGString<uint64_t>* strings, int32_t num_str);
virtual void set_string_list(
const SGString<float32_t>* strings, int32_t num_str);
virtual void set_string_list(
const SGString<float64_t>* strings, int32_t num_str);
virtual void set_string_list(
const SGString<floatmax_t>* strings, int32_t num_str);
//@}
virtual void get_matrix(int8_t*&, int32_t&, int32_t&)
{
SG_NOTIMPLEMENTED
}
virtual void get_int8_sparsematrix(shogun::SGSparseVector<signed char>*&, int32_t&, int32_t&)
{
SG_NOTIMPLEMENTED
}
virtual void get_int8_string_list(shogun::SGString<signed char>*&, int32_t&, int32_t&)
{
SG_NOTIMPLEMENTED
}
virtual void set_int8_matrix(const int8_t*, int32_t, int32_t)
{
SG_NOTIMPLEMENTED
}
virtual void set_int8_sparsematrix(const shogun::SGSparseVector<signed char>*, int32_t, int32_t)
{
SG_NOTIMPLEMENTED
}
virtual void set_int8_string_list(const shogun::SGString<signed char>*, int32_t)
{
SG_NOTIMPLEMENTED
}
/** @return object name */
virtual const char* get_name() const { return "HDF5File"; }
protected:
/** determine the hdf5 type compatible to 'bool' */
void get_boolean_type();
/** determine the hdf5 type of class t_class that is
* compatible to datatype
*
* @param t_class hdf5 class
* @param datatype shogun file data type
*
* @return compatible hdf5 datatype or -1
*/
hid_t get_compatible_type(H5T_class_t t_class,
const TSGDataType* datatype);
/** get dimensionality of the data
*
* @param dataset hdf5 dataset
* @param dims dimensions (returned by reference)
* @param ndims (returned by reference)
* @param total_elements (returned by reference)
*/
void get_dims(hid_t dataset, int32_t*& dims, int32_t& ndims, int64_t& total_elements);
/** create a group hierarchy in the hdf5 file h5file according to name */
void create_group_hierarchy();
protected:
/** hdf5 file handle */
hid_t h5file;
/** hdf5 type closest to 'bool' */
hid_t boolean_type;
};
}
#endif // HAVE_HDF5
#endif //__HDF5_FILE_H__
|